PDBx:geom_hbondType

Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the contents of the ATOM,
CELL and SYMMETRY data.

    Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
                Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
<PDBx:geom_hbondCategory>
   <PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6">
      <PDBx:angle_DHA>169.6</PDBx:angle_DHA>
      <PDBx:dist_DA>2.801</PDBx:dist_DA>
      <PDBx:dist_DH>0.888</PDBx:dist_DH>
      <PDBx:dist_HA>1.921</PDBx:dist_HA>
      <PDBx:publ_flag>yes</PDBx:publ_flag>
   </PDBx:geom_hbond>
   <PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2">
      <PDBx:angle_DHA>153.5</PDBx:angle_DHA>
      <PDBx:dist_DA>2.793</PDBx:dist_DA>
      <PDBx:dist_DH>0.917</PDBx:dist_DH>
      <PDBx:dist_HA>1.923</PDBx:dist_HA>
      <PDBx:publ_flag>yes</PDBx:publ_flag>
   </PDBx:geom_hbond>
   <PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1">
      <PDBx:angle_DHA>179.7</PDBx:angle_DHA>
      <PDBx:dist_DA>2.842</PDBx:dist_DA>
      <PDBx:dist_DH>0.894</PDBx:dist_DH>
      <PDBx:dist_HA>1.886</PDBx:dist_HA>
      <PDBx:publ_flag>yes</PDBx:publ_flag>
   </PDBx:geom_hbond>
</PDBx:geom_hbondCategory>

Complex Type Information

Model

Children: PDBx:geom_hbond

Used By

Source

<xsd:complexType name="geom_hbondType">
  <xsd:annotation>
    <xsd:documentation xml:lang="en">Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. <PDBx:geom_hbondCategory> <PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6"> <PDBx:angle_DHA>169.6</PDBx:angle_DHA> <PDBx:dist_DA>2.801</PDBx:dist_DA> <PDBx:dist_DH>0.888</PDBx:dist_DH> <PDBx:dist_HA>1.921</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2"> <PDBx:angle_DHA>153.5</PDBx:angle_DHA> <PDBx:dist_DA>2.793</PDBx:dist_DA> <PDBx:dist_DH>0.917</PDBx:dist_DH> <PDBx:dist_HA>1.923</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1"> <PDBx:angle_DHA>179.7</PDBx:angle_DHA> <PDBx:dist_DA>2.842</PDBx:dist_DA> <PDBx:dist_DH>0.894</PDBx:dist_DH> <PDBx:dist_HA>1.886</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> </PDBx:geom_hbondCategory></xsd:documentation>
  </xsd:annotation>
  <xsd:sequence>
    <xsd:element name="geom_hbond" minOccurs="0" maxOccurs="unbounded">
      <xsd:complexType>
        <xsd:all>
          <xsd:element name="angle_DHA" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond.</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:decimal">
                <xsd:minInclusive value="0.0"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
          <xsd:element name="angle_DHA_esd" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The standard uncertainty (estimated standard deviation) of attribute angle_DHA in category geom_hbond.</xsd:documentation>
            </xsd:annotation>
            <xsd:complexType>
              <xsd:simpleContent>
                <xsd:extension base="xsd:decimal">
                  <xsd:attribute fixed="angstroms" name="units" type="xsd:string" use="optional"/>
                </xsd:extension>
              </xsd:simpleContent>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="atom_site_auth_asym_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_asym_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_asym_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_atom_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_atom_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_atom_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_comp_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_comp_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_comp_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_seq_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_seq_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_auth_seq_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_alt_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_alt_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_alt_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_asym_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_asym_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_asym_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_atom_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_atom_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_atom_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_comp_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_comp_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_comp_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:string">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_seq_id_A" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:integer">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_seq_id_D" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:integer">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="atom_site_label_seq_id_H" minOccurs="0" maxOccurs="1" nillable="true" type="xsd:integer">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category.</xsd:documentation>
            </xsd:annotation>
          </xsd:element>
          <xsd:element name="dist_DA" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond.</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:decimal">
                <xsd:minInclusive value="0.0"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
          <xsd:element name="dist_DA_esd" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DA in category geom_hbond.</xsd:documentation>
            </xsd:annotation>
            <xsd:complexType>
              <xsd:simpleContent>
                <xsd:extension base="xsd:decimal">
                  <xsd:attribute fixed="angstroms" name="units" type="xsd:string" use="optional"/>
                </xsd:extension>
              </xsd:simpleContent>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="dist_DH" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond.</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:decimal">
                <xsd:minInclusive value="0.0"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
          <xsd:element name="dist_DH_esd" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DH in category geom_hbond.</xsd:documentation>
            </xsd:annotation>
            <xsd:complexType>
              <xsd:simpleContent>
                <xsd:extension base="xsd:decimal">
                  <xsd:attribute fixed="angstroms" name="units" type="xsd:string" use="optional"/>
                </xsd:extension>
              </xsd:simpleContent>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="dist_HA" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond.</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:decimal">
                <xsd:minInclusive value="0.0"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
          <xsd:element name="dist_HA_esd" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_HA in category geom_hbond.</xsd:documentation>
            </xsd:annotation>
            <xsd:complexType>
              <xsd:simpleContent>
                <xsd:extension base="xsd:decimal">
                  <xsd:attribute fixed="angstroms" name="units" type="xsd:string" use="optional"/>
                </xsd:extension>
              </xsd:simpleContent>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="publ_flag" minOccurs="0" maxOccurs="1" nillable="true">
            <xsd:annotation>
              <xsd:documentation xml:lang="en">This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry.</xsd:documentation>
            </xsd:annotation>
            <xsd:simpleType>
              <xsd:restriction base="xsd:string">
                <xsd:enumeration value="no"/>
                <xsd:enumeration value="n"/>
                <xsd:enumeration value="yes"/>
                <xsd:enumeration value="y"/>
              </xsd:restriction>
            </xsd:simpleType>
          </xsd:element>
        </xsd:all>
        <xsd:attribute name="atom_site_id_A" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category.</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="atom_site_id_D" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category.</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="atom_site_id_H" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category.</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="site_symmetry_A" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The symmetry code of the acceptor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="site_symmetry_D" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The symmetry code of the donor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
        <xsd:attribute name="site_symmetry_H" use="required" type="xsd:string">
          <xsd:annotation>
            <xsd:documentation xml:lang="en">The symmetry code of the hydrogen-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645</xsd:documentation>
          </xsd:annotation>
        </xsd:attribute>
      </xsd:complexType>
    </xsd:element>
  </xsd:sequence>
</xsd:complexType>