# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:42:48 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-{[5-(naphthalen-1-ylmethyl)-4-oxo-4H-1lambda~4~,3-thiazol-2-yl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1NC2=NC(=O)C(=[SH]2)Cc3cccc4ccccc34
#
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
 3RY  3RY  '2-{[5-(naphthalen-1-ylmethyl)-4-oxo-4H-1lambda~4~,3-thiazol-2-yl]amino}benzoic acid'  ligand  42  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3RY
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
 3RY  O8   O  OC    -1  -0.542   4.6166   2.5098  -1.8151
 3RY  C7   C  C      0   0.493   3.7789   1.7781  -1.2844
 3RY  O1   O  O      0  -0.612   2.5843   2.1116  -1.0192
 3RY  C5   C  CR6    0  -0.229   4.1973   0.3636  -0.9133
 3RY  C4   C  CR6    0   0.362   3.3195  -0.5570  -0.3045
 3RY  C3   C  CR16   0  -0.307   3.7568  -1.8426   0.0146
 3RY  C2   C  CR16   0  -0.253   5.0628  -2.2142  -0.2640
 3RY  C1   C  CR16   0  -0.257   5.9404  -1.3214  -0.8628
 3RY  C6   C  CR16   0  -0.286   5.4987  -0.0464  -1.1802
 3RY  N11  N  NH1    0  -0.769   2.0279  -0.0991  -0.0507
 3RY  C13  C  CR5    0   0.374   1.0205  -0.7602   0.4882
 3RY  N14  N  N      0  -0.472   0.8570  -1.9611   0.8478
 3RY  C15  C  CR5    0   0.483  -0.4164  -2.2231   1.4373
 3RY  S17  S  S3     0   0.167  -0.4820   0.2815   0.8519
 3RY  O18  O  O      0  -0.513  -0.7197  -3.3742   1.7410
 3RY  C16  C  CR5    0  -0.407  -1.2362  -1.0765   1.5701
 3RY  C19  C  CH2    0  -0.576  -2.7176  -1.1188   1.7946
 3RY  C21  C  CR6    0   0.105  -3.5087  -0.8072   0.5480
 3RY  C22  C  CR16   0  -0.323  -3.8332  -1.8214  -0.3191
 3RY  C23  C  CR16   0  -0.243  -4.5077  -1.5727  -1.5291
 3RY  C24  C  CR16   0  -0.337  -4.8535  -0.2954  -1.8739
 3RY  C25  C  CR66   0   0.117  -4.5405   0.7829  -1.0157
 3RY  C26  C  CR66   0   0.075  -3.8682   0.5303   0.2130
 3RY  C39  C  CR16   0  -0.312  -4.8819   2.1133  -1.3590
 3RY  C38  C  CR16   0  -0.260  -4.5766   3.1549  -0.5280
 3RY  C37  C  CR16   0  -0.253  -3.9184   2.9098   0.6943
 3RY  C36  C  CR16   0  -0.335  -3.5750   1.6347   1.0529
 3RY  H2   H  HCR6   0   0.284   3.0793  -2.5453   0.4756
 3RY  H3   H  HCR6   0   0.260   5.3907  -3.2137  -0.0088
 3RY  H4   H  HCR6   0   0.253   6.9587  -1.6146  -1.0811
 3RY  H5   H  HCR6   0   0.255   6.1757   0.6558  -1.6479
 3RY  H6   H  HNH1   0   0.446   1.9603   0.9183  -0.3894
 3RY  H7   H  HCH2   0   0.276  -2.9418  -2.1394   2.1093
 3RY  H8   H  HCH2   0   0.257  -3.0340  -0.4861   2.6277
 3RY  H9   H  HCR6   0   0.247  -3.5557  -2.8386  -0.0684
 3RY  H10  H  HCR6   0   0.255  -4.7500  -2.3998  -2.1840
 3RY  H11  H  HCR6   0   0.252  -5.3712  -0.0944  -2.8043
 3RY  H12  H  HCR6   0   0.254  -5.3910   2.2955  -2.2981
 3RY  H13  H  HCR6   0   0.258  -4.8395   4.1676  -0.8040
 3RY  H14  H  HCR6   0   0.258  -3.6846   3.7366   1.3523
 3RY  H15  H  HCR6   0   0.252  -3.0844   1.4748   2.0047
 3RY  H16  H  HSH1   0   0.303   0.1456   0.9821   1.8337

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
 3RY  O1   C7   deloc     1.268  0.020  1.268
 3RY  O8   C7   deloc     1.232  0.020  1.232
 3RY  C7   C5   single    1.521  0.020  1.521
 3RY  C23  C24  aromatic  1.367  0.020  1.367
 3RY  C23  C22  aromatic  1.407  0.020  1.407
 3RY  C24  C25  aromatic  1.413  0.020  1.413
 3RY  S17  C13  single    1.864  0.020  1.864
 3RY  S17  C16  double    1.711  0.020  1.711
 3RY  C5   C6   aromatic  1.390  0.020  1.390
 3RY  C5   C4   aromatic  1.410  0.020  1.410
 3RY  N11  C13  single    1.320  0.020  1.320
 3RY  N11  C4   single    1.394  0.020  1.394
 3RY  C22  C21  aromatic  1.373  0.020  1.373
 3RY  C6   C1   aromatic  1.386  0.020  1.386
 3RY  C13  N14  double    1.264  0.020  1.264
 3RY  C4   C3   aromatic  1.395  0.020  1.395
 3RY  C25  C39  aromatic  1.416  0.020  1.416
 3RY  C25  C26  aromatic  1.423  0.020  1.423
 3RY  C21  C26  aromatic  1.425  0.020  1.425
 3RY  C21  C19  single    1.509  0.020  1.509
 3RY  C16  C19  single    1.499  0.020  1.499
 3RY  C16  C15  single    1.416  0.020  1.416
 3RY  C39  C38  aromatic  1.367  0.020  1.367
 3RY  N14  C15  single    1.427  0.020  1.427
 3RY  C1   C2   aromatic  1.388  0.020  1.388
 3RY  C26  C36  aromatic  1.418  0.020  1.418
 3RY  C3   C2   aromatic  1.386  0.020  1.386
 3RY  C15  O18  double    1.229  0.020  1.229
 3RY  C38  C37  aromatic  1.410  0.020  1.410
 3RY  C36  C37  aromatic  1.368  0.020  1.368
 3RY  C3   H2   single    0.930  0.020  1.080
 3RY  C2   H3   single    0.930  0.020  1.080
 3RY  C1   H4   single    0.930  0.020  1.080
 3RY  C6   H5   single    0.930  0.020  1.080
 3RY  N11  H6   single    0.860  0.020  1.020
 3RY  C19  H7   single    0.970  0.020  1.090
 3RY  C19  H8   single    0.970  0.020  1.090
 3RY  C22  H9   single    0.930  0.020  1.080
 3RY  C23  H10  single    0.930  0.020  1.080
 3RY  C24  H11  single    0.930  0.020  1.080
 3RY  C39  H12  single    0.930  0.020  1.080
 3RY  C38  H13  single    0.930  0.020  1.080
 3RY  C37  H14  single    0.930  0.020  1.080
 3RY  C36  H15  single    0.930  0.020  1.080
 3RY  S17  H16  single    1.200  0.020  1.300

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
 3RY  C5   C7   O1   116.91  3.000
 3RY  C5   C7   O8   118.05  3.000
 3RY  O1   C7   O8   125.04  3.000
 3RY  C6   C5   C4   118.23  3.000
 3RY  C4   C5   C7   122.77  3.000
 3RY  C6   C5   C7   119.00  3.000
 3RY  N11  C4   C3   123.48  3.000
 3RY  C3   C4   C5   120.35  3.000
 3RY  N11  C4   C5   116.17  3.000
 3RY  H2   C3   C2   120.17  3.000
 3RY  H2   C3   C4   120.06  3.000
 3RY  C2   C3   C4   119.77  3.000
 3RY  H3   C2   C1   120.27  3.000
 3RY  H3   C2   C3   119.06  3.000
 3RY  C1   C2   C3   120.67  3.000
 3RY  H4   C1   C6   120.20  3.000
 3RY  H4   C1   C2   120.53  3.000
 3RY  C6   C1   C2   119.28  3.000
 3RY  H5   C6   C1   119.78  3.000
 3RY  H5   C6   C5   118.51  3.000
 3RY  C1   C6   C5   121.70  3.000
 3RY  H6   N11  C13  123.71  3.000
 3RY  H6   N11  C4   108.18  3.000
 3RY  C13  N11  C4   128.11  3.000
 3RY  S17  C13  N14  111.78  3.000
 3RY  N14  C13  N11  133.68  3.000
 3RY  S17  C13  N11  114.51  3.000
 3RY  C15  N14  C13  114.03  3.000
 3RY  C16  C15  O18  126.34  3.000
 3RY  O18  C15  N14  119.63  3.000
 3RY  C16  C15  N14  114.00  3.000
 3RY  H16  S17  C16  108.02  3.000
 3RY  H16  S17  C13   93.25  3.000
 3RY  C16  S17  C13   89.64  3.000
 3RY  C19  C16  S17  121.39  3.000
 3RY  C19  C16  C15  124.30  3.000
 3RY  S17  C16  C15  110.37  3.000
 3RY  H8   C19  H7   105.19  3.000
 3RY  H8   C19  C21  111.00  3.000
 3RY  H7   C19  C21  108.89  3.000
 3RY  H8   C19  C16  112.58  3.000
 3RY  H7   C19  C16  105.82  3.000
 3RY  C21  C19  C16  112.87  3.000
 3RY  C26  C21  C22  119.03  3.000
 3RY  C26  C21  C19  121.35  3.000
 3RY  C22  C21  C19  119.54  3.000
 3RY  H9   C22  C23  119.17  3.000
 3RY  H9   C22  C21  119.12  3.000
 3RY  C23  C22  C21  121.70  3.000
 3RY  H10  C23  C24  120.31  3.000
 3RY  H10  C23  C22  119.49  3.000
 3RY  C24  C23  C22  120.20  3.000
 3RY  H11  C24  C25  119.06  3.000
 3RY  H11  C24  C23  120.71  3.000
 3RY  C25  C24  C23  120.24  3.000
 3RY  C39  C25  C26  119.35  3.000
 3RY  C26  C25  C24  119.57  3.000
 3RY  C39  C25  C24  121.08  3.000
 3RY  C36  C26  C25  118.08  3.000
 3RY  C36  C26  C21  122.66  3.000
 3RY  C25  C26  C21  119.26  3.000
 3RY  H12  C39  C38  120.24  3.000
 3RY  H12  C39  C25  118.79  3.000
 3RY  C38  C39  C25  120.98  3.000
 3RY  H13  C38  C37  119.82  3.000
 3RY  H13  C38  C39  120.25  3.000
 3RY  C37  C38  C39  119.93  3.000
 3RY  H14  C37  C36  119.89  3.000
 3RY  H14  C37  C38  119.68  3.000
 3RY  C36  C37  C38  120.43  3.000
 3RY  H15  C36  C37  118.80  3.000
 3RY  H15  C36  C26  119.95  3.000
 3RY  C37  C36  C26  121.24  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
 3RY  CONST_01  C2   C1   C6   C5      0.00   0.0  0
 3RY  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 3RY  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 3RY  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 3RY  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 3RY  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 3RY  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 3RY  CONST_08  C24  C25  C26  C21     0.00   0.0  0
 3RY  CONST_09  C39  C25  C26  C21   180.00   0.0  0
 3RY  CONST_10  C37  C36  C26  C21   180.00   0.0  0
 3RY  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 3RY  CONST_12  C25  C26  C21  C22     0.00   0.0  0
 3RY  CONST_13  C36  C26  C21  C22   180.00   0.0  0
 3RY  CONST_14  C39  C25  C24  C23   180.00   0.0  0
 3RY  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 3RY  CONST_16  C26  C21  C22  C23     0.00   0.0  0
 3RY  CONST_17  C38  C39  C25  C24   180.00   0.0  0
 3RY  CONST_18  C36  C26  C25  C24   180.00   0.0  0
 3RY  CONST_19  C37  C38  C39  C25     0.00   0.0  0
 3RY  CONST_20  C37  C36  C26  C25     0.00   0.0  0
 3RY  CONST_21  C38  C39  C25  C26     0.00   0.0  0
 3RY  CONST_22  C38  C37  C36  C26     0.00   0.0  0
 3RY  CONST_23  C36  C26  C25  C39     0.00   0.0  0
 3RY  CONST_24  C36  C37  C38  C39     0.00   0.0  0
 3RY  CONST_25  S17  C13  N14  C15     0.00   0.0  0
 3RY  CONST_26  C1   C6   C5   C7    180.00   0.0  0
 3RY  CONST_27  C3   C4   C5   C7    180.00   0.0  0
 3RY  CONST_28  N11  C4   C3   C2    180.00   0.0  0
 3RY  CONST_29  N11  C4   C5   C6    180.00   0.0  0
 3RY  CONST_30  C23  C22  C21  C19   180.00   0.0  0
 3RY  CONST_31  C25  C26  C21  C19   180.00   0.0  0
 3RY  CONST_32  C36  C26  C21  C19     0.00   0.0  0
 3RY  CONST_33  C13  N11  C4   C5    180.00   0.0  0
 3RY  CONST_34  S17  C13  N11  C4    180.00   0.0  0
 3RY  CONST_35  N14  C13  N11  C4      0.00   0.0  0
 3RY  CONST_36  C13  N11  C4   C3      0.00   0.0  0
 3RY  CONST_37  C15  N14  C13  N11   180.00   0.0  0
 3RY  CONST_38  H4   C1   C6   C5    180.00   0.0  0
 3RY  CONST_39  H2   C3   C4   C5    180.00   0.0  0
 3RY  CONST_40  H5   C6   C5   C4    180.00   0.0  0
 3RY  CONST_41  H3   C2   C3   C4    180.00   0.0  0
 3RY  CONST_42  H10  C23  C22  C21   180.00   0.0  0
 3RY  CONST_43  H15  C36  C26  C21     0.00   0.0  0
 3RY  CONST_44  H11  C24  C23  C22   180.00   0.0  0
 3RY  CONST_45  H9   C22  C23  C24   180.00   0.0  0
 3RY  CONST_46  H12  C39  C25  C24     0.00   0.0  0
 3RY  CONST_47  H13  C38  C39  C25   180.00   0.0  0
 3RY  CONST_48  H14  C37  C36  C26   180.00   0.0  0
 3RY  CONST_49  H6   N11  C4   C5      0.00   0.0  0
 3RY  Var_01    C21  C19  C16  C15  -103.24  30.0  3
 3RY  Var_02    C22  C21  C19  C16    87.73  30.0  3
 3RY  Var_03    C6   C5   C7   O8      0.20  30.0  2

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
 3RY  plan-1  C7   0.020
 3RY  plan-1  C5   0.020
 3RY  plan-1  C4   0.020
 3RY  plan-1  C3   0.020
 3RY  plan-1  C2   0.020
 3RY  plan-1  C1   0.020
 3RY  plan-1  C6   0.020
 3RY  plan-1  N11  0.020
 3RY  plan-1  H2   0.020
 3RY  plan-1  H3   0.020
 3RY  plan-1  H4   0.020
 3RY  plan-1  H5   0.020
 3RY  plan-2  C19  0.020
 3RY  plan-2  C21  0.020
 3RY  plan-2  C22  0.020
 3RY  plan-2  C23  0.020
 3RY  plan-2  C24  0.020
 3RY  plan-2  C25  0.020
 3RY  plan-2  C26  0.020
 3RY  plan-2  C39  0.020
 3RY  plan-2  C38  0.020
 3RY  plan-2  C37  0.020
 3RY  plan-2  C36  0.020
 3RY  plan-2  H9   0.020
 3RY  plan-2  H10  0.020
 3RY  plan-2  H11  0.020
 3RY  plan-2  H12  0.020
 3RY  plan-2  H13  0.020
 3RY  plan-2  H14  0.020
 3RY  plan-2  H15  0.020
 3RY  plan-3  C4   0.020
 3RY  plan-3  N11  0.020
 3RY  plan-3  C13  0.020
 3RY  plan-3  N14  0.020
 3RY  plan-3  C15  0.020
 3RY  plan-3  S17  0.020
 3RY  plan-3  O18  0.020
 3RY  plan-3  C16  0.020
 3RY  plan-3  C19  0.020
 3RY  plan-3  H6   0.020
 3RY  plan-3  H16  0.020
 3RY  plan-4  O8   0.020
 3RY  plan-4  C7   0.020
 3RY  plan-4  O1   0.020
 3RY  plan-4  C5   0.020

