# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:48:08 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-methylsulfanyl-butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](CCSC)NCc1c(O)c(C)ncc1CO[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
 G03  G03  'methyl (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-methylsulfanyl-butanoate'  ligand  48  25  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G03
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
 G03  OAU  O  OH1   0  -0.748  -32.3664   9.1473  -22.0749
 G03  PAT  P  P     0   1.484  -32.5315   9.6084  -23.5932
 G03  OAV  O  O     0  -0.696  -33.8775  10.0051  -24.0428
 G03  OAW  O  OH1   0  -0.744  -31.8551   8.3869  -24.3723
 G03  OAS  O  O2    0  -0.584  -31.5221  10.8384  -23.6734
 G03  CAR  C  CH2   0  -0.300  -30.1248  10.7451  -23.3501
 G03  CAQ  C  CR6   0  -0.011  -29.6028  12.1310  -23.1358
 G03  CAX  C  CR16  0  -0.152  -28.6359  12.6303  -23.9910
 G03  NAY  N  N     0  -0.409  -28.1188  13.8483  -23.8834
 G03  CAB  C  CR6   0   0.133  -28.5448  14.6469  -22.9184
 G03  CAA  C  CH3   0  -0.721  -27.9594  16.0214  -22.8194
 G03  CAC  C  CR6   0   0.257  -29.5326  14.2370  -22.0057
 G03  OAD  O  OH1   0  -0.645  -29.9266  15.1128  -21.0734
 G03  CAE  C  CR6   0   0.038  -30.0717  12.9526  -22.1054
 G03  CAF  C  CH2   0  -0.329  -31.1699  12.5003  -21.1761
 G03  N    N  NH1   0  -0.668  -31.0568  13.1122  -19.8539
 G03  CA   C  CH1   0  -0.164  -32.2879  13.0541  -19.0765
 G03  C    C  C     0   0.592  -32.1025  13.9199  -17.8463
 G03  O    O  O     0  -0.444  -31.0652  14.0055  -17.2388
 G03  OAN  O  O2    0  -0.444  -33.2162  14.5426  -17.5057
 G03  CAO  C  CH3   0  -0.428  -33.1887  15.3494  -16.3246
 G03  CB   C  CH2   0  -0.464  -32.6880  11.6290  -18.6634
 G03  CG   C  CH2   0  -0.568  -34.0694  11.4960  -18.0372
 G03  SD   S  S2    0  -0.035  -35.4383  12.0375  -19.0976
 G03  CE   C  CH3   0  -0.774  -35.4051  10.7571  -20.3730
 G03  H1   H  HOH1  0   0.504  -32.9236   8.4026  -21.8106
 G03  H2   H  HOH1  0   0.500  -32.0379   8.3751  -25.3217
 G03  H3   H  HCH2  0   0.259  -29.9776  10.1294  -22.4590
 G03  H4   H  HCH2  0   0.275  -29.5914  10.2675  -24.1738
 G03  H5   H  HCR6  0   0.255  -28.2580  12.0131  -24.8001
 G03  H6   H  HCH3  0   0.245  -27.2039  16.1608  -23.5897
 G03  H7   H  HCH3  0   0.246  -28.7212  16.7934  -22.9436
 G03  H8   H  HCH3  0   0.246  -27.4942  16.1899  -21.8465
 G03  H9   H  HOH1  0   0.473  -30.4516  14.5890  -20.4020
 G03  H10  H  HCH2  0   0.275  -32.1306  12.8052  -21.6019
 G03  H11  H  HCH1  0   0.281  -33.0850  13.4815  -19.6902
 G03  H12  H  HCH3  0   0.255  -34.1909  15.7521  -16.2172
 G03  H13  H  HCH3  0   0.243  -32.9388  14.7572  -15.4450
 G03  H14  H  HCH3  0   0.244  -32.4775  16.1686  -16.4244
 G03  H15  H  HCH2  0   0.262  -32.6355  10.9857  -19.5442
 G03  H16  H  HCH2  0   0.260  -31.9495  11.2343  -17.9584
 G03  H17  H  HCH2  0   0.283  -34.2398  10.4555  -17.7558
 G03  H18  H  HCH2  0   0.281  -34.1567  12.0857  -17.1240
 G03  H19  H  HCH3  0   0.279  -36.2931  10.8909  -20.9881
 G03  H20  H  HCH3  0   0.254  -34.5316  10.8327  -21.0177
 G03  H21  H  HCH3  0   0.263  -35.4407   9.7639  -19.9266
 G03  H22  H  HCH2  0   0.258  -31.1904  11.4113  -21.1116
 G03  H23  H  HNH1  0   0.382  -30.2965  12.6777  -19.3408

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
 G03  OAV  PAT  double    1.474  0.020  1.474
 G03  NAY  CAX  aromatic  1.328  0.020  1.328
 G03  NAY  CAB  aromatic  1.323  0.020  1.323
 G03  CAX  CAQ  aromatic  1.384  0.020  1.384
 G03  OAS  PAT  single    1.593  0.020  1.593
 G03  OAS  CAR  single    1.437  0.020  1.437
 G03  CAA  CAB  single    1.497  0.020  1.497
 G03  OAW  PAT  single    1.599  0.020  1.599
 G03  CAB  CAC  aromatic  1.406  0.020  1.406
 G03  PAT  OAU  single    1.595  0.020  1.595
 G03  CAQ  CAR  single    1.496  0.020  1.496
 G03  CAQ  CAE  aromatic  1.399  0.020  1.399
 G03  CAC  CAE  aromatic  1.397  0.020  1.397
 G03  CAC  OAD  single    1.338  0.020  1.338
 G03  CAE  CAF  single    1.508  0.020  1.508
 G03  CAF  N    single    1.461  0.020  1.461
 G03  CE   SD   single    1.808  0.020  1.808
 G03  N    CA   single    1.457  0.020  1.457
 G03  CB   CA   single    1.537  0.020  1.537
 G03  CB   CG   single    1.523  0.020  1.523
 G03  SD   CG   single    1.814  0.020  1.814
 G03  CA   C    single    1.516  0.020  1.516
 G03  C    O    double    1.205  0.020  1.205
 G03  C    OAN  single    1.321  0.020  1.321
 G03  OAN  CAO  single    1.431  0.020  1.431
 G03  OAU  H1   single    0.850  0.020  0.980
 G03  OAW  H2   single    0.850  0.020  0.980
 G03  CAR  H3   single    0.970  0.020  1.090
 G03  CAR  H4   single    0.970  0.020  1.090
 G03  CAX  H5   single    0.930  0.020  1.080
 G03  CAA  H6   single    0.970  0.020  1.090
 G03  CAA  H7   single    0.970  0.020  1.090
 G03  CAA  H8   single    0.970  0.020  1.090
 G03  OAD  H9   single    0.850  0.020  0.980
 G03  CAF  H10  single    0.970  0.020  1.090
 G03  CA   H11  single    0.970  0.020  1.090
 G03  CAO  H12  single    0.970  0.020  1.090
 G03  CAO  H13  single    0.970  0.020  1.090
 G03  CAO  H14  single    0.970  0.020  1.090
 G03  CB   H15  single    0.970  0.020  1.090
 G03  CB   H16  single    0.970  0.020  1.090
 G03  CG   H17  single    0.970  0.020  1.090
 G03  CG   H18  single    0.970  0.020  1.090
 G03  CE   H19  single    0.970  0.020  1.090
 G03  CE   H20  single    0.970  0.020  1.090
 G03  CE   H21  single    0.970  0.020  1.090
 G03  CAF  H22  single    0.970  0.020  1.090
 G03  N    H23  single    0.890  0.020  1.040

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
 G03  H1   OAU  PAT  115.03  3.000
 G03  OAS  PAT  OAW  107.30  3.000
 G03  OAW  PAT  OAV  116.32  3.000
 G03  OAS  PAT  OAV  110.82  3.000
 G03  OAW  PAT  OAU  101.49  3.000
 G03  OAS  PAT  OAU  101.86  3.000
 G03  OAV  PAT  OAU  117.56  3.000
 G03  H2   OAW  PAT  114.07  3.000
 G03  CAR  OAS  PAT  123.67  3.000
 G03  H4   CAR  H3   107.64  3.000
 G03  H4   CAR  CAQ  110.05  3.000
 G03  H3   CAR  CAQ  110.98  3.000
 G03  H4   CAR  OAS  109.50  3.000
 G03  H3   CAR  OAS  110.54  3.000
 G03  CAQ  CAR  OAS  108.13  3.000
 G03  CAE  CAQ  CAX  118.52  3.000
 G03  CAE  CAQ  CAR  122.18  3.000
 G03  CAX  CAQ  CAR  119.30  3.000
 G03  H5   CAX  NAY  116.52  3.000
 G03  H5   CAX  CAQ  119.91  3.000
 G03  NAY  CAX  CAQ  123.57  3.000
 G03  CAB  NAY  CAX  119.18  3.000
 G03  CAC  CAB  CAA  119.96  3.000
 G03  CAC  CAB  NAY  121.58  3.000
 G03  CAA  CAB  NAY  118.46  3.000
 G03  H8   CAA  H7   106.84  3.000
 G03  H8   CAA  H6   108.39  3.000
 G03  H7   CAA  H6   108.27  3.000
 G03  H8   CAA  CAB  111.55  3.000
 G03  H7   CAA  CAB  111.64  3.000
 G03  H6   CAA  CAB  110.01  3.000
 G03  CAE  CAC  OAD  122.54  3.000
 G03  OAD  CAC  CAB  117.92  3.000
 G03  CAE  CAC  CAB  119.54  3.000
 G03  H9   OAD  CAC  106.22  3.000
 G03  CAF  CAE  CAC  120.86  3.000
 G03  CAF  CAE  CAQ  121.46  3.000
 G03  CAC  CAE  CAQ  117.61  3.000
 G03  H22  CAF  H10  106.53  3.000
 G03  H22  CAF  N    111.47  3.000
 G03  H10  CAF  N    107.66  3.000
 G03  H22  CAF  CAE  110.45  3.000
 G03  H10  CAF  CAE  108.42  3.000
 G03  N    CAF  CAE  112.07  3.000
 G03  H23  N    CA   110.25  3.000
 G03  H23  N    CAF  109.64  3.000
 G03  CA   N    CAF  113.62  3.000
 G03  H11  CA   CB   108.88  3.000
 G03  H11  CA   C    108.76  3.000
 G03  CB   CA   C    110.08  3.000
 G03  H11  CA   N    107.52  3.000
 G03  C    CA   N    107.87  3.000
 G03  CB   CA   N    113.60  3.000
 G03  OAN  C    O    124.22  3.000
 G03  OAN  C    CA   112.05  3.000
 G03  O    C    CA   123.71  3.000
 G03  CAO  OAN  C    117.56  3.000
 G03  H14  CAO  H13  109.45  3.000
 G03  H14  CAO  H12  109.44  3.000
 G03  H13  CAO  H12  109.48  3.000
 G03  H14  CAO  OAN  111.16  3.000
 G03  H13  CAO  OAN  111.38  3.000
 G03  H12  CAO  OAN  105.85  3.000
 G03  H16  CB   H15  105.94  3.000
 G03  H16  CB   CG   108.41  3.000
 G03  H15  CB   CG   108.90  3.000
 G03  H16  CB   CA   109.38  3.000
 G03  H15  CB   CA   108.48  3.000
 G03  CG   CB   CA   115.32  3.000
 G03  H18  CG   H17  106.69  3.000
 G03  H18  CG   SD   105.52  3.000
 G03  H17  CG   SD   108.51  3.000
 G03  H18  CG   CB   111.71  3.000
 G03  H17  CG   CB   109.33  3.000
 G03  SD   CG   CB   114.71  3.000
 G03  CE   SD   CG   100.78  3.000
 G03  H21  CE   H20  109.40  3.000
 G03  H21  CE   H19  108.48  3.000
 G03  H20  CE   H19  108.15  3.000
 G03  H21  CE   SD   110.86  3.000
 G03  H20  CE   SD   112.55  3.000
 G03  H19  CE   SD   107.26  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
 G03  CONST_01  CAB  NAY  CAX  CAQ     0.00   0.0  0
 G03  CONST_02  CAB  CAC  CAE  CAQ     0.00   0.0  0
 G03  CONST_03  CAC  CAB  NAY  CAX     0.00   0.0  0
 G03  CONST_04  CAC  CAE  CAQ  CAX     0.00   0.0  0
 G03  CONST_05  CAE  CAQ  CAX  NAY     0.00   0.0  0
 G03  CONST_06  CAE  CAC  CAB  NAY     0.00   0.0  0
 G03  CONST_07  NAY  CAX  CAQ  CAR   180.00   0.0  0
 G03  CONST_08  CAC  CAE  CAQ  CAR   180.00   0.0  0
 G03  CONST_09  OAD  CAC  CAE  CAQ   180.00   0.0  0
 G03  CONST_10  CAA  CAB  NAY  CAX   180.00   0.0  0
 G03  CONST_11  CAF  CAE  CAQ  CAX   180.00   0.0  0
 G03  CONST_12  OAD  CAC  CAB  NAY   180.00   0.0  0
 G03  CONST_13  CAF  CAE  CAC  CAB   180.00   0.0  0
 G03  CONST_14  CAE  CAC  CAB  CAA   180.00   0.0  0
 G03  CONST_15  H5   CAX  NAY  CAB   180.00   0.0  0
 G03  Var_01    CAX  CAQ  CAR  OAS  -116.09  30.0  1
 G03  Var_02    N    CAF  CAE  CAQ   150.86  30.0  2
 G03  Var_03    H6   CAA  CAB  NAY    -1.50  30.0  2
 G03  Var_04    CAQ  CAR  OAS  PAT  -163.00  30.0  3
 G03  Var_05    CA   N    CAF  CAE   161.54  30.0  3
 G03  Var_06    SD   CG   CB   CA     59.54  30.0  3
 G03  Var_07    H12  CAO  OAN  C    -179.13  30.0  3
 G03  Var_08    H19  CE   SD   CG    171.18  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
 G03  chir_01  CA  N  CB  C  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
 G03  plan-1  CAR  0.020
 G03  plan-1  CAQ  0.020
 G03  plan-1  CAX  0.020
 G03  plan-1  NAY  0.020
 G03  plan-1  CAB  0.020
 G03  plan-1  CAA  0.020
 G03  plan-1  CAC  0.020
 G03  plan-1  OAD  0.020
 G03  plan-1  CAE  0.020
 G03  plan-1  CAF  0.020
 G03  plan-1  H5   0.020
 G03  plan-2  CA   0.020
 G03  plan-2  C    0.020
 G03  plan-2  O    0.020
 G03  plan-2  OAN  0.020

