# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:19:55 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: O-[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[P@](O)(=O)OC[C@H](O)CO)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
 GSE  GSE  O-[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]-L-serine  ligand  30  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GSE
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
 GSE  C1    C  CH2   0  -0.186  -0.6677  -0.3267  -2.7060
 GSE  O11   O  O2    0  -0.576  -0.3369   0.0717  -1.3709
 GSE  O12   O  O2    0  -0.581  -0.3680   0.2648   1.0030
 GSE  C2    C  CH1   0  -0.042   0.4643   0.1022  -3.6243
 GSE  C3    C  CH2   0  -0.165   0.1583  -0.3492  -5.0440
 GSE  O31   O  OH1   0  -0.666   1.2728  -0.0713  -5.8543
 GSE  P     P  P     0   1.470  -1.0554  -0.6203  -0.1307
 GSE  O14   O  OH1   0  -0.743  -2.6010  -0.2202  -0.1851
 GSE  O13   O  O     0  -0.704  -0.9274  -2.0837  -0.0061
 GSE  O21   O  OH1   0  -0.654   0.7207   1.4811  -3.5371
 GSE  C11   C  CH2   0  -0.164  -0.5095  -0.0712   2.3867
 GSE  C12   C  CH1   0  -0.259   0.6902   0.5469   3.1155
 GSE  N     N  NH2   0  -0.778   1.9796   0.1012   2.6530
 GSE  C13   C  C     0   0.546   0.5603   0.2800   4.6045
 GSE  O16   O  OH1   0  -0.592  -0.5474   0.8146   5.1020
 GSE  O15   O  O     0  -0.427   1.3525  -0.3459   5.2575
 GSE  H11   H  HCH2  0   0.243  -0.8017  -1.4100  -2.7662
 GSE  H12A  H  HCH2  0   0.242  -1.6079   0.1480  -3.0044
 GSE  H2    H  HCH1  0   0.243   1.3810  -0.3959  -3.2915
 GSE  H31   H  HCH2  0   0.204  -0.0794  -1.4208  -5.0316
 GSE  H32   H  HCH2  0   0.200  -0.7434   0.1703  -5.3995
 GSE  HO1   H  HOH1  0   0.457   1.0543  -0.3206  -6.7565
 GSE  HO4   H  HOH1  0   0.497  -2.7924   0.7259  -0.2413
 GSE  HO2   H  HOH1  0   0.446  -0.0428   1.9606  -3.8782
 GSE  H111  H  HCH2  0   0.246  -0.5075  -1.1569   2.5209
 GSE  H112  H  HCH2  0   0.254  -1.4554   0.3250   2.7577
 GSE  H12   H  HCH1  0   0.293   0.6344   1.6334   2.9816
 GSE  HN1   H  HNH2  0   0.349   2.0586  -0.9059   2.7274
 GSE  HN2   H  HNH2  0   0.360   2.0858   0.3278   1.6733
 GSE  HO6   H  HOH1  0   0.486  -0.6223   0.6121   6.0470

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
 GSE  C1   O11   single  1.432  0.020  1.432
 GSE  C1   C2    single  1.519  0.020  1.519
 GSE  C1   H11   single  0.970  0.020  1.090
 GSE  C1   H12A  single  0.970  0.020  1.090
 GSE  O11  P     single  1.592  0.020  1.592
 GSE  O12  P     single  1.594  0.020  1.594
 GSE  O12  C11   single  1.431  0.020  1.431
 GSE  C2   C3    single  1.521  0.020  1.521
 GSE  C2   O21   single  1.405  0.020  1.405
 GSE  C2   H2    single  0.970  0.020  1.090
 GSE  C3   O31   single  1.406  0.020  1.406
 GSE  C3   H31   single  0.970  0.020  1.090
 GSE  C3   H32   single  0.970  0.020  1.090
 GSE  O31  HO1   single  0.850  0.020  0.980
 GSE  P    O14   single  1.598  0.020  1.598
 GSE  P    O13   double  1.474  0.020  1.474
 GSE  O14  HO4   single  0.850  0.020  0.980
 GSE  O21  HO2   single  0.850  0.020  0.980
 GSE  C11  C12   single  1.534  0.020  1.534
 GSE  C11  H111  single  0.970  0.020  1.090
 GSE  C11  H112  single  0.970  0.020  1.090
 GSE  C12  N     single  1.440  0.020  1.440
 GSE  C12  C13   single  1.518  0.020  1.518
 GSE  C12  H12   single  0.970  0.020  1.090
 GSE  N    HN1   single  0.890  0.020  1.040
 GSE  N    HN2   single  0.890  0.020  1.040
 GSE  C13  O16   single  1.327  0.020  1.327
 GSE  C13  O15   double  1.202  0.020  1.202
 GSE  O16  HO6   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
 GSE  H12A  C1   H11   108.02  3.000
 GSE  H12A  C1   C2    110.66  3.000
 GSE  H11   C1   C2    109.74  3.000
 GSE  H12A  C1   O11   109.38  3.000
 GSE  H11   C1   O11   110.82  3.000
 GSE  C2    C1   O11   108.23  3.000
 GSE  P     O11  C1    120.08  3.000
 GSE  C11   O12  P     120.98  3.000
 GSE  H2    C2   O21   105.95  3.000
 GSE  H2    C2   C3    108.48  3.000
 GSE  O21   C2   C3    112.70  3.000
 GSE  H2    C2   C1    108.16  3.000
 GSE  O21   C2   C1    112.05  3.000
 GSE  C3    C2   C1    109.30  3.000
 GSE  H32   C3   H31   106.69  3.000
 GSE  H32   C3   O31   111.74  3.000
 GSE  H31   C3   O31   111.79  3.000
 GSE  H32   C3   C2    109.06  3.000
 GSE  H31   C3   C2    108.83  3.000
 GSE  O31   C3   C2    108.66  3.000
 GSE  HO1   O31  C3    108.03  3.000
 GSE  O13   P    O14   109.60  3.000
 GSE  O13   P    O12   116.97  3.000
 GSE  O14   P    O12   107.60  3.000
 GSE  O13   P    O11   117.27  3.000
 GSE  O14   P    O11   107.54  3.000
 GSE  O12   P    O11    96.78  3.000
 GSE  HO4   O14  P     116.01  3.000
 GSE  HO2   O21  C2    108.76  3.000
 GSE  H112  C11  H111  108.69  3.000
 GSE  H112  C11  C12   111.74  3.000
 GSE  H111  C11  C12   109.90  3.000
 GSE  H112  C11  O12   109.23  3.000
 GSE  H111  C11  O12   110.58  3.000
 GSE  C12   C11  O12   106.71  3.000
 GSE  H12   C12  C13   106.84  3.000
 GSE  H12   C12  N     108.25  3.000
 GSE  C13   C12  N     109.70  3.000
 GSE  H12   C12  C11   107.55  3.000
 GSE  C13   C12  C11   109.16  3.000
 GSE  N     C12  C11   115.01  3.000
 GSE  HN2   N    HN1   106.61  3.000
 GSE  HN2   N    C12   109.62  3.000
 GSE  HN1   N    C12   110.73  3.000
 GSE  O15   C13  O16   123.80  3.000
 GSE  O15   C13  C12   124.59  3.000
 GSE  O16   C13  C12   111.61  3.000
 GSE  HO6   O16  C13   110.23  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
 GSE  CONST_01  HO6  O16  C13  C12   180.00   0.0  0
 GSE  Var_01    O12  P    O11  C1   -176.83  30.0  3
 GSE  Var_02    C12  C11  O12  P     156.14  30.0  3
 GSE  Var_03    H11  C1   O11  P     -39.81  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
 GSE  chir_01  C2   C1   C3   O21  negativ
 GSE  chir_03  C12  N    C11  C13  negativ
 GSE  chir_04  P    O12  O14  O13  both

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
 GSE  plan-1  C12  0.020
 GSE  plan-1  C13  0.020
 GSE  plan-1  O16  0.020
 GSE  plan-1  O15  0.020
 GSE  plan-1  HO6  0.020

