# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:01:06 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: O-[(S)-hydroxy(methoxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P@@](O)(=O)OC[C@H](N)C(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
 OMH  OMH  O-[(S)-hydroxy(methoxy)phosphoryl]-L-serine  L-peptide  20  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_OMH
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
 OMH  O     O  O      0  -0.608  61.5019  -36.7341  11.3228
 OMH  C     C  C      0   0.392  60.2690  -36.8940  11.2375
 OMH  CA    C  CH1    0  -0.243  59.7578  -38.1965  10.5767
 OMH  N     N  NH2    0  -0.799  58.8101  -38.9462  11.3989
 OMH  CB    C  CH2    0  -0.131  59.0534  -37.8797   9.2663
 OMH  OG    O  O2     0  -0.629  59.8980  -37.0856   8.4568
 OMH  P     P  P      0   1.348  59.2321  -36.3243   7.1580
 OMH  O3    O  OP    -1  -0.790  58.2573  -35.2902   7.6254
 OMH  O2    O  O      0  -0.804  58.8384  -37.3454   6.1338
 OMH  O1    O  O2     0  -0.607  60.5772  -35.5174   6.6894
 OMH  C31   C  CH3    0  -0.396  61.6431  -36.2156   6.0791
 OMH  OXT   O  OC    -1  -0.617  59.3820  -36.1103  11.6402
 OMH  HA    H  HCH1   0   0.201  60.6071  -38.8539  10.3657
 OMH  H     H  HNH2   0   0.340  59.2943  -39.3187  12.2064
 OMH  H2    H  HNH2   0   0.326  58.1384  -38.2850  11.7737
 OMH  HB    H  HCH2   0   0.200  58.7899  -38.8146   8.7580
 OMH  HBA   H  HCH2   0   0.183  58.1159  -37.3545   9.4889
 OMH  H31   H  HCH3   0   0.207  61.3273  -36.7508   5.1806
 OMH  H31A  H  HCH3   0   0.222  62.4007  -35.4856   5.7941
 OMH  H31B  H  HCH3   0   0.205  62.1083  -36.9356   6.7582

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
 OMH  C    O     deloc   1.231  0.020  1.231
 OMH  C    OXT   deloc   1.250  0.020  1.250
 OMH  CA   C     single  1.525  0.021  1.525
 OMH  CA   N     single  1.458  0.019  1.458
 OMH  CB   CA    single  1.530  0.020  1.530
 OMH  OG   CB    single  1.414  0.020  1.414
 OMH  P    OG    single  1.646  0.020  1.646
 OMH  P    O3    deloc   1.496  0.020  1.496
 OMH  O2   P     deloc   1.499  0.020  1.499
 OMH  O1   P     single  1.637  0.020  1.637
 OMH  C31  O1    single  1.413  0.020  1.413
 OMH  CA   HA    single  0.970  0.020  0.970
 OMH  N    H     single  0.860  0.020  0.860
 OMH  N    H2    single  0.890  0.020  1.040
 OMH  CB   HB    single  0.970  0.020  1.090
 OMH  CB   HBA   single  0.970  0.020  1.090
 OMH  C31  H31   single  0.970  0.020  1.090
 OMH  C31  H31A  single  0.970  0.020  1.090
 OMH  C31  H31B  single  0.970  0.020  1.090

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
 OMH  OXT   C    CA    115.51  3.000
 OMH  CA    C    O     120.80  1.700
 OMH  OXT   C    O     126.83  3.000
 OMH  HA    CA   CB    109.00  3.000
 OMH  HA    CA   N     110.00  3.000
 OMH  CB    CA   N     110.50  1.700
 OMH  HA    CA   C     109.00  3.000
 OMH  CB    CA   C     110.10  1.900
 OMH  N     CA   C     111.00  2.800
 OMH  H2    N    H     105.18  3.000
 OMH  H2    N    CA    107.63  3.000
 OMH  H     N    CA    114.00  3.000
 OMH  HBA   CB   HB    107.26  3.000
 OMH  HBA   CB   OG    110.95  3.000
 OMH  HB    CB   OG    110.92  3.000
 OMH  HBA   CB   CA    108.70  3.000
 OMH  HB    CB   CA    109.46  3.000
 OMH  OG    CB   CA    109.49  3.000
 OMH  P     OG   CB    118.03  3.000
 OMH  O1    P    O2    110.86  3.000
 OMH  O1    P    O3    106.51  3.000
 OMH  O2    P    O3    120.88  3.000
 OMH  O1    P    OG     96.97  3.000
 OMH  O2    P    OG    109.29  3.000
 OMH  O3    P    OG    109.68  3.000
 OMH  C31   O1   P     120.00  3.000
 OMH  H31B  C31  H31A  107.92  3.000
 OMH  H31B  C31  H31   108.12  3.000
 OMH  H31A  C31  H31   108.30  3.000
 OMH  H31B  C31  O1    112.21  3.000
 OMH  H31A  C31  O1    107.84  3.000
 OMH  H31   C31  O1    112.29  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
 OMH  Var_01  O3   P    OG  CB  66.00  30.0  1
 OMH  Var_02  HB   CB   OG  P   73.34  30.0  3
 OMH  Var_03  H31  C31  O1  P   57.27  30.0  3

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
 OMH  chir_01  CA  C  N  CB  negativ

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
 OMH  plan-1  O    0.020
 OMH  plan-1  C    0.020
 OMH  plan-1  CA   0.020
 OMH  plan-1  OXT  0.020

