Enum: CoordinationGeometry

Coordination geometry of metal centers in protein structures

URI: valuesets:CoordinationGeometry

Permissible Values

Value	Meaning	Description
LINEAR	None	Linear coordination geometry (2 ligands at 180°)
TRIGONAL_PLANAR	None	Trigonal planar coordination geometry (3 ligands, 120° angles)
TRIGONAL_PYRAMIDAL	None	Trigonal pyramidal coordination geometry
T_SHAPED	None	T-shaped coordination geometry
TETRAHEDRAL	NCIT:C103215	Tetrahedral coordination geometry (4 ligands, 109
SQUARE_PLANAR	None	Square planar coordination geometry (4 ligands in plane)
TRIGONAL_BIPYRAMIDAL	None	Trigonal bipyramidal coordination geometry (5 ligands)
SQUARE_PYRAMIDAL	None	Square pyramidal coordination geometry (5 ligands)
PENTAGONAL_PLANAR	None	Pentagonal planar coordination geometry (5 ligands in plane)
OCTAHEDRAL	None	Octahedral coordination geometry (6 ligands)
TRIGONAL_PRISMATIC	None	Trigonal prismatic coordination geometry (6 ligands)
PENTAGONAL_BIPYRAMIDAL	None	Pentagonal bipyramidal coordination geometry (7 ligands)
HEXAGONAL_BIPYRAMIDAL	None	Hexagonal bipyramidal coordination geometry (8 ligands)
SQUARE_ANTIPRISMATIC	None	Square antiprismatic coordination geometry (8 ligands)
DODECAHEDRAL	None	Dodecahedral coordination geometry (8 ligands)
CUBIC	None	Cubic coordination geometry (8 ligands)
BENT	None	Bent or angular coordination geometry
SEE_SAW	None	See-saw coordination geometry (4 ligands)

Slots

Name	Description
coordination_geometry	Geometry of metal coordination in protein structures

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: CoordinationGeometry
description: Coordination geometry of metal centers in protein structures
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  LINEAR:
    text: LINEAR
    description: Linear coordination geometry (2 ligands at 180°)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '2'
  TRIGONAL_PLANAR:
    text: TRIGONAL_PLANAR
    description: Trigonal planar coordination geometry (3 ligands, 120° angles)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '3'
  TRIGONAL_PYRAMIDAL:
    text: TRIGONAL_PYRAMIDAL
    description: Trigonal pyramidal coordination geometry
    annotations:
      coordination_number:
        tag: coordination_number
        value: '3'
  T_SHAPED:
    text: T_SHAPED
    description: T-shaped coordination geometry
    annotations:
      coordination_number:
        tag: coordination_number
        value: '3'
  TETRAHEDRAL:
    text: TETRAHEDRAL
    description: Tetrahedral coordination geometry (4 ligands, 109.5° angles)
    meaning: NCIT:C103215
    annotations:
      coordination_number:
        tag: coordination_number
        value: '4'
    title: tetrahedral molecular geometry
  SQUARE_PLANAR:
    text: SQUARE_PLANAR
    description: Square planar coordination geometry (4 ligands in plane)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '4'
      ncit_variants:
        tag: ncit_variants
        value: NCIT:C103211, NCIT:C103212, NCIT:C103213, NCIT:C103214
    title: square planar molecular geometry
  TRIGONAL_BIPYRAMIDAL:
    text: TRIGONAL_BIPYRAMIDAL
    description: Trigonal bipyramidal coordination geometry (5 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '5'
  SQUARE_PYRAMIDAL:
    text: SQUARE_PYRAMIDAL
    description: Square pyramidal coordination geometry (5 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '5'
  PENTAGONAL_PLANAR:
    text: PENTAGONAL_PLANAR
    description: Pentagonal planar coordination geometry (5 ligands in plane)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '5'
  OCTAHEDRAL:
    text: OCTAHEDRAL
    description: Octahedral coordination geometry (6 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '6'
      ncit_variants:
        tag: ncit_variants
        value: NCIT:C103216, NCIT:C103217, NCIT:C103218
    title: octahedral molecular geometry
  TRIGONAL_PRISMATIC:
    text: TRIGONAL_PRISMATIC
    description: Trigonal prismatic coordination geometry (6 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '6'
  PENTAGONAL_BIPYRAMIDAL:
    text: PENTAGONAL_BIPYRAMIDAL
    description: Pentagonal bipyramidal coordination geometry (7 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '7'
  HEXAGONAL_BIPYRAMIDAL:
    text: HEXAGONAL_BIPYRAMIDAL
    description: Hexagonal bipyramidal coordination geometry (8 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '8'
  SQUARE_ANTIPRISMATIC:
    text: SQUARE_ANTIPRISMATIC
    description: Square antiprismatic coordination geometry (8 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '8'
  DODECAHEDRAL:
    text: DODECAHEDRAL
    description: Dodecahedral coordination geometry (8 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '8'
  CUBIC:
    text: CUBIC
    description: Cubic coordination geometry (8 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '8'
  BENT:
    text: BENT
    description: Bent or angular coordination geometry
    annotations:
      coordination_number:
        tag: coordination_number
        value: '2'
  SEE_SAW:
    text: SEE_SAW
    description: See-saw coordination geometry (4 ligands)
    annotations:
      coordination_number:
        tag: coordination_number
        value: '4'