# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 06:19:01 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1C(=O)C[C@@H](C1=O)[P](O)(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 KVM  KVM  '[(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]phosphonic acid'  ligand  16  12  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KVM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 KVM  OAH  O  OP    -1  -0.881   2.4237  -1.3042   0.1203
 KVM  PAG  P  P      0   1.206   1.5296  -0.0995   0.4038
 KVM  OAI  O  O      0  -0.877   0.6340  -0.2426   1.6355
 KVM  OAJ  O  OP    -1  -0.873   2.2111   1.2539   0.2508
 KVM  CAF  C  CR15   0  -0.677   0.2361  -0.1727  -1.0105
 KVM  CAE  C  CH2    0  -0.581  -0.5444  -1.4786  -0.8753
 KVM  CAB  C  CR5    0   0.527  -1.7180  -1.1152  -0.0130
 KVM  OAA  O  O      0  -0.446  -2.4770  -1.8287   0.5999
 KVM  NAC  N  NR5    0  -0.223  -1.8271   0.2492  -0.1033
 KVM  OAD  O  OH1    0  -0.550  -2.8410   0.9317   0.4688
 KVM  CAK  C  CR5    0   0.529  -0.7610   0.8818  -0.7342
 KVM  OAL  O  O      0  -0.447  -0.7271   2.0753  -0.9274
 KVM  H3   H  HCR5   0   0.261   0.7191  -0.0360  -1.9778
 KVM  H4   H  HCH2   0   0.283  -0.9366  -1.8243  -1.8374
 KVM  H5   H  HCH2   0   0.268   0.0308  -2.2947  -0.4419
 KVM  H6   H  HOH1   0   0.480  -2.5420   1.1840   1.3547

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 KVM  OAI  PAG  deloc   1.530  0.020  1.530
 KVM  CAF  CAE  single  1.527  0.020  1.527
 KVM  CAF  PAG  single  1.918  0.020  1.918
 KVM  CAF  CAK  single  1.477  0.020  1.477
 KVM  CAE  CAB  single  1.501  0.020  1.501
 KVM  PAG  OAJ  deloc   1.523  0.020  1.523
 KVM  PAG  OAH  deloc   1.527  0.020  1.527
 KVM  OAL  CAK  double  1.210  0.020  1.210
 KVM  CAK  NAC  single  1.391  0.020  1.391
 KVM  CAB  NAC  single  1.372  0.020  1.372
 KVM  CAB  OAA  double  1.209  0.020  1.209
 KVM  NAC  OAD  single  1.349  0.020  1.349
 KVM  CAF  H3   single  0.970  0.020  1.090
 KVM  CAE  H4   single  0.970  0.020  1.090
 KVM  CAE  H5   single  0.970  0.020  1.090
 KVM  OAD  H6   single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 KVM  CAF  PAG  OAJ  105.17  3.000
 KVM  OAJ  PAG  OAI  115.21  3.000
 KVM  CAF  PAG  OAI  101.26  3.000
 KVM  OAJ  PAG  OAH  114.86  3.000
 KVM  CAF  PAG  OAH  103.17  3.000
 KVM  OAI  PAG  OAH  114.75  3.000
 KVM  H3   CAF  CAK  112.06  3.000
 KVM  H3   CAF  CAE  114.35  3.000
 KVM  CAK  CAF  CAE  104.41  3.000
 KVM  H3   CAF  PAG  110.53  3.000
 KVM  CAK  CAF  PAG  106.86  3.000
 KVM  CAE  CAF  PAG  108.17  3.000
 KVM  H5   CAE  H4   107.61  3.000
 KVM  H5   CAE  CAB  111.46  3.000
 KVM  H4   CAE  CAB  107.52  3.000
 KVM  H5   CAE  CAF  113.98  3.000
 KVM  H4   CAE  CAF  112.03  3.000
 KVM  CAB  CAE  CAF  104.09  3.000
 KVM  NAC  CAB  OAA  124.79  3.000
 KVM  OAA  CAB  CAE  129.75  3.000
 KVM  NAC  CAB  CAE  105.38  3.000
 KVM  CAK  NAC  OAD  122.55  3.000
 KVM  OAD  NAC  CAB  122.34  3.000
 KVM  CAK  NAC  CAB  114.91  3.000
 KVM  H6   OAD  NAC  106.72  3.000
 KVM  OAL  CAK  NAC  122.87  3.000
 KVM  NAC  CAK  CAF  106.11  3.000
 KVM  OAL  CAK  CAF  130.96  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 KVM  CONST_01  CAK  NAC  CAB  CAE    0.00   0.0  0
 KVM  CONST_02  OAD  NAC  CAB  CAE  180.00   0.0  0
 KVM  CONST_03  CAK  NAC  CAB  OAA  180.00   0.0  0
 KVM  CONST_04  OAD  NAC  CAB  OAA    0.00   0.0  0
 KVM  Var_01    NAC  CAB  CAE  CAF   19.75  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KVM  chir_01  CAF  CAE  PAG  CAK  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KVM  plan-1  CAF  0.020
 KVM  plan-1  NAC  0.020
 KVM  plan-1  CAK  0.020
 KVM  plan-1  OAL  0.020
 KVM  plan-2  CAE  0.020
 KVM  plan-2  CAB  0.020
 KVM  plan-2  OAA  0.020
 KVM  plan-2  NAC  0.020
 KVM  plan-2  OAD  0.020
 KVM  plan-2  CAK  0.020

