# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 19:56:52 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (7R)-7-(5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazin-2-yl)-6-formyl-2,7-dihydro-1,4-thiazepine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=NC=C(C=O)[C@@H](SC1)c2cn3CCOCc3n2
#
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
 WY4  WY4  '(7R)-7-(5,6-dihydro-8H-imidazo[2,1-c][1,4]oxazin-2-yl)-6-formyl-2,7-dihydro-1,4-thiazepine-3-carboxylic acid'  ligand  34  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WY4
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
 WY4  S1    S  S2    0   0.084  -1.3681   3.5195   1.4986
 WY4  C2    C  CH2   0  -0.653  -1.1153   3.1316   3.2549
 WY4  C3    C  C     0   0.181   0.3235   2.8675   3.5678
 WY4  N4    N  N     0  -0.307   0.8927   1.7563   3.3500
 WY4  C5    C  C1    0  -0.125   0.2450   0.7786   2.6401
 WY4  C6    C  C     0   0.042  -0.2853   0.9742   1.4154
 WY4  C7    C  C1    0   0.131  -0.8657  -0.1920   0.7595
 WY4  O8    O  O     0  -0.402  -1.3888  -0.1810  -0.3338
 WY4  C31   C  C     0   0.543   1.1361   3.9876   4.1541
 WY4  O32   O  O     0  -0.418   0.6748   5.0843   4.3362
 WY4  O33   O  OH1   0  -0.577   2.3660   3.6267   4.4550
 WY4  C61   C  CH1   0  -0.649  -0.2669   2.3015   0.6996
 WY4  C62   C  CR5   0   0.237   1.1124   2.8467   0.4672
 WY4  N63   N  N     0  -0.474   1.6917   3.8065   1.2456
 WY4  C64   C  CR56  0   0.420   2.8814   4.0014   0.7380
 WY4  N65   N  N     0  -0.446   3.0979   3.2234  -0.3402
 WY4  C66   C  CR15  0  -0.123   1.9717   2.4716  -0.5289
 WY4  C67   C  C     0  -0.238   3.9196   4.9739   1.1957
 WY4  O68   O  O     0  -0.477   5.1721   4.6762   0.6268
 WY4  C69   C  C     0  -0.219   5.0863   4.5000  -0.7711
 WY4  C70   C  C     0  -0.290   4.3331   3.2233  -1.1003
 WY4  HC21  H  HCH2  0   0.308  -1.7100   2.2576   3.5239
 WY4  HC22  H  HCH2  0   0.318  -1.5007   3.9862   3.8078
 WY4  HC5   H  H     0   0.299   0.2661  -0.2140   3.0808
 WY4  HC7   H  H     0   0.200  -0.8051  -1.1230   1.3500
 WY4  H61   H  HCH1  0   0.326  -0.7285   2.1427  -0.2784
 WY4  H66   H  HCR5  0   0.290   1.8821   1.7555  -1.3291
 WY4  H671  H  H     0   0.241   3.6049   5.9959   0.9414
 WY4  H672  H  H     0   0.260   4.0252   4.9256   2.2803
 WY4  H691  H  H     0   0.264   6.1019   4.4361  -1.1599
 WY4  H692  H  H     0   0.230   4.5959   5.3604  -1.2449
 WY4  H701  H  H     0   0.270   4.1086   3.1812  -2.1656
 WY4  H702  H  H     0   0.266   4.9231   2.3426  -0.8408
 WY4  HO1   H  HOH1  0   0.490   2.8424   4.3754   4.8440

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
 WY4  S1   C2    single    1.816  0.020  1.816
 WY4  S1   C61   single    1.826  0.020  1.826
 WY4  C2   C3    single    1.496  0.020  1.496
 WY4  C2   HC21  single    0.970  0.020  1.090
 WY4  C2   HC22  single    0.970  0.020  1.090
 WY4  C3   N4    double    1.267  0.020  1.267
 WY4  C3   C31   single    1.503  0.020  1.503
 WY4  N4   C5    single    1.371  0.020  1.371
 WY4  C5   C6    double    1.349  0.020  1.349
 WY4  C5   HC5   single    0.930  0.020  1.080
 WY4  C6   C7    single    1.458  0.020  1.458
 WY4  C6   C61   single    1.508  0.020  1.508
 WY4  C7   O8    double    1.212  0.020  1.212
 WY4  C7   HC7   single    0.930  0.020  1.080
 WY4  C31  O32   double    1.204  0.020  1.204
 WY4  C31  O33   single    1.317  0.020  1.317
 WY4  C61  C62   single    1.501  0.020  1.501
 WY4  C61  H61   single    0.970  0.020  1.090
 WY4  C62  N63   aromatic  1.365  0.020  1.365
 WY4  C62  C66   aromatic  1.368  0.020  1.368
 WY4  N63  C64   aromatic  1.308  0.020  1.308
 WY4  C64  N65   aromatic  1.347  0.020  1.347
 WY4  C64  C67   single    1.494  0.020  1.494
 WY4  N65  C66   aromatic  1.367  0.020  1.367
 WY4  N65  C70   single    1.450  0.020  1.450
 WY4  C66  H66   single    0.930  0.020  1.080
 WY4  C67  O68   single    1.407  0.020  1.407
 WY4  C67  H671  single    0.970  0.020  1.090
 WY4  C67  H672  single    0.970  0.020  1.090
 WY4  O68  C69   single    1.412  0.020  1.412
 WY4  C69  C70   single    1.518  0.020  1.518
 WY4  C69  H691  single    0.970  0.020  1.090
 WY4  C69  H692  single    0.970  0.020  1.090
 WY4  C70  H701  single    0.970  0.020  1.090
 WY4  C70  H702  single    0.970  0.020  1.090
 WY4  HO1  O33   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
 WY4  C61   S1   C2    101.34  3.000
 WY4  HC22  C2   HC21  108.11  3.000
 WY4  HC22  C2   C3    111.90  3.000
 WY4  HC21  C2   C3    109.35  3.000
 WY4  HC22  C2   S1    105.91  3.000
 WY4  HC21  C2   S1    109.49  3.000
 WY4  C3    C2   S1    111.95  3.000
 WY4  C31   C3   N4    118.53  3.000
 WY4  C31   C3   C2    118.04  3.000
 WY4  N4    C3   C2    123.42  3.000
 WY4  C5    N4   C3    120.14  3.000
 WY4  HC5   C5   C6    120.56  3.000
 WY4  HC5   C5   N4    115.63  3.000
 WY4  C6    C5   N4    123.54  3.000
 WY4  C61   C6   C7    119.68  3.000
 WY4  C61   C6   C5    123.62  3.000
 WY4  C7    C6   C5    116.67  3.000
 WY4  HC7   C7   O8    120.91  3.000
 WY4  HC7   C7   C6    114.32  3.000
 WY4  O8    C7   C6    124.76  3.000
 WY4  O33   C31  O32   124.98  3.000
 WY4  O33   C31  C3    112.96  3.000
 WY4  O32   C31  C3    122.06  3.000
 WY4  HO1   O33  C31   109.83  3.000
 WY4  H61   C61  C62   107.59  3.000
 WY4  H61   C61  C6    106.96  3.000
 WY4  C62   C61  C6    113.85  3.000
 WY4  H61   C61  S1    103.51  3.000
 WY4  C62   C61  S1    112.31  3.000
 WY4  C6    C61  S1    111.84  3.000
 WY4  C66   C62  N63   109.97  3.000
 WY4  C66   C62  C61   126.18  3.000
 WY4  N63   C62  C61   123.85  3.000
 WY4  C64   N63  C62   105.63  3.000
 WY4  C67   C64  N65   120.62  3.000
 WY4  C67   C64  N63   127.59  3.000
 WY4  N65   C64  N63   111.76  3.000
 WY4  C70   N65  C66   128.99  3.000
 WY4  C70   N65  C64   123.80  3.000
 WY4  C66   N65  C64   107.20  3.000
 WY4  H66   C66  N65   122.44  3.000
 WY4  H66   C66  C62   132.12  3.000
 WY4  N65   C66  C62   105.44  3.000
 WY4  H672  C67  H671  107.39  3.000
 WY4  H672  C67  O68   107.84  3.000
 WY4  H671  C67  O68   110.97  3.000
 WY4  H672  C67  C64   110.06  3.000
 WY4  H671  C67  C64   109.60  3.000
 WY4  O68   C67  C64   110.91  3.000
 WY4  C69   O68  C67   111.87  3.000
 WY4  H692  C69  H691  107.96  3.000
 WY4  H692  C69  C70   110.11  3.000
 WY4  H691  C69  C70   109.62  3.000
 WY4  H692  C69  O68   110.90  3.000
 WY4  H691  C69  O68   107.70  3.000
 WY4  C70   C69  O68   110.48  3.000
 WY4  H702  C70  H701  108.22  3.000
 WY4  H702  C70  C69   111.03  3.000
 WY4  H701  C70  C69   110.28  3.000
 WY4  H702  C70  N65   109.63  3.000
 WY4  H701  C70  N65   109.69  3.000
 WY4  C69   C70  N65   107.98  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
 WY4  CONST_01  N65  C64  N63  C62    0.00   0.0  0
 WY4  CONST_02  C64  N65  C66  C62    0.00   0.0  0
 WY4  CONST_03  N65  C66  C62  N63    0.00   0.0  0
 WY4  CONST_04  C66  N65  C64  N63    0.00   0.0  0
 WY4  CONST_05  C66  C62  N63  C64    0.00   0.0  0
 WY4  CONST_06  C64  N63  C62  C61  180.00   0.0  0
 WY4  CONST_07  N65  C66  C62  C61  180.00   0.0  0
 WY4  CONST_08  H66  C66  C62  C61    0.00   0.0  0
 WY4  CONST_09  HO1  O33  C31  C3   180.00   0.0  0
 WY4  Var_01    O68  C67  C64  N63  165.61  30.0  1
 WY4  Var_02    C69  C70  N65  C64  -18.11  30.0  1
 WY4  Var_03    O68  C69  C70  N65   49.79  30.0  1
 WY4  Var_04    C70  C69  O68  C67  -69.37  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
 WY4  chir_01  C61  S1  C6  C62  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
 WY4  plan-1  C3   0.020
 WY4  plan-1  C31  0.020
 WY4  plan-1  O32  0.020
 WY4  plan-1  O33  0.020
 WY4  plan-1  HO1  0.020
 WY4  plan-2  C61  0.020
 WY4  plan-2  C62  0.020
 WY4  plan-2  N63  0.020
 WY4  plan-2  C64  0.020
 WY4  plan-2  N65  0.020
 WY4  plan-2  C66  0.020
 WY4  plan-2  C67  0.020
 WY4  plan-2  C70  0.020
 WY4  plan-2  H66  0.020
 WY4  plan-3  C6   0.020
 WY4  plan-3  C7   0.020
 WY4  plan-3  O8   0.020
 WY4  plan-3  HC7  0.020

