# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 14:25:39 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: ({4-chloro-6-[(2,3-dimethylphenyl)amino]pyrimidin-2-yl}sulfanyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Nc2cc(Cl)nc(SCC(O)=O)n2)c1C
#
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
 WY1  WY1  '({4-chloro-6-[(2,3-dimethylphenyl)amino]pyrimidin-2-yl}sulfanyl)acetic acid'  ligand  35  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WY1
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
 WY1  CAB   C   CH3   0  -0.752   4.3715   1.0480   1.2124
 WY1  CAR   C   CR6   0   0.020   4.0309  -0.0793   0.2798
 WY1  CAP   C   CR6   0   0.066   4.8666  -1.2007   0.1704
 WY1  CAA   C   CH3   0  -0.744   6.1302  -1.3038   0.9766
 WY1  CAG   C   CR16  0  -0.304   4.5131  -2.2367  -0.6874
 WY1  CAF   C   CR16  0  -0.265   3.3561  -2.1720  -1.4508
 WY1  CAH   C   CR16  0  -0.277   2.5431  -1.0566  -1.3769
 WY1  CAT   C   CR6   0   0.289   2.8808  -0.0176  -0.5142
 WY1  NAM   N   NH1   0  -0.770   2.0897   1.1499  -0.4682
 WY1  C4    C   CR6   0   0.556   0.7526   1.2116  -0.3263
 WY1  N3    N   N     0  -0.463   0.0642   0.0886  -0.1398
 WY1  C5    C   CR16  0  -0.384   0.1007   2.4636  -0.3634
 WY1  C6    C   CR6   0   0.209  -1.2560   2.4197  -0.2017
 WY1  CL6   CL  CL    0  -0.089  -2.1587   3.8919  -0.2268
 WY1  N1    N   N     0  -0.429  -1.9610   1.3128  -0.0263
 WY1  C2    C   CR6   0   0.249  -1.2449   0.2022  -0.0073
 WY1  SAN   S   S2    0   0.081  -2.0468  -1.3396   0.2170
 WY1  CAJ   C   CH2   0  -0.680  -3.7712  -0.8177   0.3524
 WY1  CAO   C   C     0   0.567  -4.6106  -2.0464   0.5782
 WY1  OAC   O   O     0  -0.430  -4.1718  -3.1658   0.6419
 WY1  OAD   O   OH1   0  -0.582  -5.8896  -1.7349   0.6949
 WY1  HAB1  H   HCH3  0   0.255   4.9539   1.8240   0.7084
 WY1  HAB2  H   HCH3  0   0.249   3.4781   1.5243   1.6142
 WY1  HAB3  H   HCH3  0   0.258   4.9644   0.7067   2.0586
 WY1  HAA1  H   HCH3  0   0.248   5.9204  -1.4138   2.0429
 WY1  HAA2  H   HCH3  0   0.251   6.7169  -2.1678   0.6687
 WY1  HAA3  H   HCH3  0   0.246   6.7578  -0.4185   0.8668
 WY1  HAG   H   HCR6  0   0.247   5.1580  -3.1041  -0.7620
 WY1  HAF   H   HCR6  0   0.254   3.0993  -2.9835  -2.1193
 WY1  HAH   H   HCR6  0   0.261   1.6578  -0.9855  -1.9927
 WY1  HAM   H   HNH1  0   0.419   2.5731   2.0325  -0.5338
 WY1  H5    H   HCR6  0   0.304   0.6401   3.3874  -0.5130
 WY1  HAJ1  H   HCH2  0   0.326  -3.9007  -0.1196   1.1804
 WY1  HAJ2  H   HCH2  0   0.327  -4.0953  -0.3102  -0.5573
 WY1  HAD   H   HOH1  0   0.489  -6.4197  -2.5332   0.8424

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
 WY1  CAB  CAR   single    1.502  0.020  1.502
 WY1  CAR  CAP   aromatic  1.403  0.020  1.403
 WY1  CAR  CAT   aromatic  1.399  0.020  1.399
 WY1  CAP  CAA   single    1.502  0.020  1.502
 WY1  CAP  CAG   aromatic  1.391  0.020  1.391
 WY1  CAG  CAF   aromatic  1.388  0.020  1.388
 WY1  CAF  CAH   aromatic  1.382  0.020  1.382
 WY1  CAH  CAT   aromatic  1.392  0.020  1.392
 WY1  CAT  NAM   single    1.411  0.020  1.411
 WY1  NAM  C4    single    1.346  0.020  1.346
 WY1  C4   N3    aromatic  1.330  0.020  1.330
 WY1  C4   C5    aromatic  1.412  0.020  1.412
 WY1  N3   C2    aromatic  1.321  0.020  1.321
 WY1  C5   C6    aromatic  1.367  0.020  1.367
 WY1  C6   CL6   single    1.727  0.020  1.727
 WY1  C6   N1    aromatic  1.324  0.020  1.324
 WY1  N1   C2    aromatic  1.322  0.020  1.322
 WY1  C2   SAN   single    1.752  0.020  1.752
 WY1  SAN  CAJ   single    1.807  0.020  1.807
 WY1  CAJ  CAO   single    1.505  0.020  1.505
 WY1  CAO  OAC   double    1.204  0.020  1.204
 WY1  CAO  OAD   single    1.322  0.020  1.322
 WY1  CAB  HAB1  single    0.970  0.020  1.090
 WY1  CAB  HAB2  single    0.970  0.020  1.090
 WY1  CAB  HAB3  single    0.970  0.020  1.090
 WY1  CAA  HAA1  single    0.970  0.020  1.090
 WY1  CAA  HAA2  single    0.970  0.020  1.090
 WY1  CAA  HAA3  single    0.970  0.020  1.090
 WY1  CAG  HAG   single    0.930  0.020  1.080
 WY1  CAF  HAF   single    0.930  0.020  1.080
 WY1  CAH  HAH   single    0.930  0.020  1.080
 WY1  NAM  HAM   single    0.860  0.020  1.020
 WY1  C5   H5    single    0.930  0.020  1.080
 WY1  CAJ  HAJ1  single    0.970  0.020  1.090
 WY1  CAJ  HAJ2  single    0.970  0.020  1.090
 WY1  OAD  HAD   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
 WY1  HAB3  CAB  HAB2  107.29  3.000
 WY1  HAB3  CAB  HAB1  106.91  3.000
 WY1  HAB2  CAB  HAB1  107.26  3.000
 WY1  HAB3  CAB  CAR   111.77  3.000
 WY1  HAB2  CAB  CAR   111.79  3.000
 WY1  HAB1  CAB  CAR   111.55  3.000
 WY1  CAT   CAR  CAP   118.73  3.000
 WY1  CAT   CAR  CAB   120.38  3.000
 WY1  CAP   CAR  CAB   120.88  3.000
 WY1  CAG   CAP  CAA   119.58  3.000
 WY1  CAG   CAP  CAR   119.49  3.000
 WY1  CAA   CAP  CAR   120.93  3.000
 WY1  HAA3  CAA  HAA2  107.79  3.000
 WY1  HAA3  CAA  HAA1  106.89  3.000
 WY1  HAA2  CAA  HAA1  107.44  3.000
 WY1  HAA3  CAA  CAP   111.97  3.000
 WY1  HAA2  CAA  CAP   110.85  3.000
 WY1  HAA1  CAA  CAP   111.67  3.000
 WY1  HAG   CAG  CAF   119.72  3.000
 WY1  HAG   CAG  CAP   119.18  3.000
 WY1  CAF   CAG  CAP   121.10  3.000
 WY1  HAF   CAF  CAH   119.90  3.000
 WY1  HAF   CAF  CAG   120.18  3.000
 WY1  CAH   CAF  CAG   119.91  3.000
 WY1  HAH   CAH  CAT   120.18  3.000
 WY1  HAH   CAH  CAF   120.29  3.000
 WY1  CAT   CAH  CAF   119.52  3.000
 WY1  NAM   CAT  CAH   120.12  3.000
 WY1  NAM   CAT  CAR   118.62  3.000
 WY1  CAH   CAT  CAR   121.22  3.000
 WY1  HAM   NAM  C4    116.29  3.000
 WY1  HAM   NAM  CAT   116.96  3.000
 WY1  C4    NAM  CAT   126.75  3.000
 WY1  C5    C4   N3    120.88  3.000
 WY1  C5    C4   NAM   119.77  3.000
 WY1  N3    C4   NAM   119.35  3.000
 WY1  C2    N3   C4    117.02  3.000
 WY1  H5    C5   C6    122.65  3.000
 WY1  H5    C5   C4    122.10  3.000
 WY1  C6    C5   C4    115.25  3.000
 WY1  N1    C6   CL6   115.86  3.000
 WY1  N1    C6   C5    124.82  3.000
 WY1  CL6   C6   C5    119.32  3.000
 WY1  C2    N1   C6    114.57  3.000
 WY1  SAN   C2   N1    119.55  3.000
 WY1  SAN   C2   N3    113.00  3.000
 WY1  N1    C2   N3    127.44  3.000
 WY1  CAJ   SAN  C2    101.08  3.000
 WY1  HAJ2  CAJ  HAJ1  107.45  3.000
 WY1  HAJ2  CAJ  CAO   109.83  3.000
 WY1  HAJ1  CAJ  CAO   110.03  3.000
 WY1  HAJ2  CAJ  SAN   110.82  3.000
 WY1  HAJ1  CAJ  SAN   110.80  3.000
 WY1  CAO   CAJ  SAN   107.92  3.000
 WY1  OAD   CAO  OAC   124.55  3.000
 WY1  OAD   CAO  CAJ   111.13  3.000
 WY1  OAC   CAO  CAJ   124.31  3.000
 WY1  HAD   OAD  CAO   110.39  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
 WY1  CONST_01  CAF   CAG  CAP  CAR     0.00   0.0  0
 WY1  CONST_02  CAF   CAH  CAT  CAR     0.00   0.0  0
 WY1  CONST_03  CAH   CAT  CAR  CAP     0.00   0.0  0
 WY1  CONST_04  CAH   CAF  CAG  CAP     0.00   0.0  0
 WY1  CONST_05  CAT   CAR  CAP  CAG     0.00   0.0  0
 WY1  CONST_06  CAT   CAH  CAF  CAG     0.00   0.0  0
 WY1  CONST_07  N1    C2   N3   C4      0.00   0.0  0
 WY1  CONST_08  N1    C6   C5   C4      0.00   0.0  0
 WY1  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 WY1  CONST_10  C6    N1   C2   N3      0.00   0.0  0
 WY1  CONST_11  C2    N3   C4   C5      0.00   0.0  0
 WY1  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 WY1  CONST_13  CAG   CAP  CAR  CAB   180.00   0.0  0
 WY1  CONST_14  CAH   CAT  CAR  CAB   180.00   0.0  0
 WY1  CONST_15  NAM   CAT  CAR  CAP   180.00   0.0  0
 WY1  CONST_16  CAT   CAR  CAP  CAA   180.00   0.0  0
 WY1  CONST_17  CAF   CAG  CAP  CAA   180.00   0.0  0
 WY1  CONST_18  NAM   CAT  CAH  CAF   180.00   0.0  0
 WY1  CONST_19  C2    N3   C4   NAM   180.00   0.0  0
 WY1  CONST_20  C6    C5   C4   NAM   180.00   0.0  0
 WY1  CONST_21  SAN   C2   N3   C4    180.00   0.0  0
 WY1  CONST_22  CL6   C6   C5   C4    180.00   0.0  0
 WY1  CONST_23  SAN   C2   N1   C6    180.00   0.0  0
 WY1  CONST_24  C2    N1   C6   CL6   180.00   0.0  0
 WY1  CONST_25  HAG   CAG  CAP  CAR   180.00   0.0  0
 WY1  CONST_26  HAH   CAH  CAT  CAR   180.00   0.0  0
 WY1  CONST_27  HAF   CAF  CAG  CAP   180.00   0.0  0
 WY1  CONST_28  H5    C5   C4   N3    180.00   0.0  0
 WY1  CONST_29  HAD   OAD  CAO  CAJ   180.00   0.0  0
 WY1  Var_01    C4    NAM  CAT  CAR  -132.18  30.0  2
 WY1  Var_02    N3    C4   NAM  CAT     3.67  30.0  2
 WY1  Var_03    HAA1  CAA  CAP  CAR    67.90  30.0  2
 WY1  Var_04    HAB1  CAB  CAR  CAP    91.83  30.0  2
 WY1  Var_05    CAO   CAJ  SAN  C2   -178.98  30.0  3
 WY1  Var_06    OAC   CAO  CAJ  SAN    -0.47  30.0  3

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
 WY1  plan-1  CAB  0.020
 WY1  plan-1  CAR  0.020
 WY1  plan-1  CAP  0.020
 WY1  plan-1  CAA  0.020
 WY1  plan-1  CAG  0.020
 WY1  plan-1  CAF  0.020
 WY1  plan-1  CAH  0.020
 WY1  plan-1  CAT  0.020
 WY1  plan-1  NAM  0.020
 WY1  plan-1  HAG  0.020
 WY1  plan-1  HAF  0.020
 WY1  plan-1  HAH  0.020
 WY1  plan-2  NAM  0.020
 WY1  plan-2  C4   0.020
 WY1  plan-2  N3   0.020
 WY1  plan-2  C5   0.020
 WY1  plan-2  C6   0.020
 WY1  plan-2  CL6  0.020
 WY1  plan-2  N1   0.020
 WY1  plan-2  C2   0.020
 WY1  plan-2  SAN  0.020
 WY1  plan-2  H5   0.020
 WY1  plan-3  CAJ  0.020
 WY1  plan-3  CAO  0.020
 WY1  plan-3  OAC  0.020
 WY1  plan-3  OAD  0.020
 WY1  plan-3  HAD  0.020

