# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 06:52:03 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-{[(8-phenylnaphthalen-2-yl)carbonyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(NC(=O)c2ccc3cccc(c4ccccc4)c3c2)cc1
#
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
 JYH  JYH  '4-{[(8-phenylnaphthalen-2-yl)carbonyl]amino}benzoic acid'  ligand  45  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JYH
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
 JYH  CAJ  C  CR16  0  -0.348   3.9902   1.4884   0.5688
 JYH  CAM  C  CR16  0  -0.241   5.3390   1.2115   0.6010
 JYH  CAW  C  CR6   0  -0.098   5.8268  -0.0012   0.1143
 JYH  CAT  C  C     0   0.528   7.2818  -0.2543   0.1684
 JYH  OAC  O  OH1   0  -0.596   7.6229  -1.4437  -0.3113
 JYH  OAA  O  O     0  -0.444   8.0874   0.5358   0.6033
 JYH  CAN  C  CR16  0  -0.249   4.9195  -0.9216  -0.4040
 JYH  CAK  C  CR16  0  -0.300   3.5609  -0.6558  -0.4416
 JYH  CAV  C  CR6   0   0.398   3.0795   0.5617   0.0470
 JYH  NAS  N  NH1   0  -0.768   1.7425   0.9432   0.0480
 JYH  CAU  C  C     0   0.545   0.6460   0.2442  -0.3564
 JYH  OAB  O  O     0  -0.450   0.6865  -0.9106  -0.7392
 JYH  CAX  C  CR6   0  -0.040  -0.6417   0.9974  -0.2838
 JYH  CAR  C  CR16  0  -0.371  -1.7996   0.2654  -0.1853
 JYH  CBB  C  CR66  0   0.134  -3.0650   0.8876  -0.1165
 JYH  CAO  C  CR16  0  -0.303  -0.7099   2.4095  -0.3400
 JYH  CAQ  C  CR16  0  -0.299  -1.9182   3.0402  -0.2697
 JYH  CBA  C  CR66  0   0.117  -3.1204   2.3072  -0.1431
 JYH  CAP  C  CR16  0  -0.325  -4.3674   2.9617  -0.0353
 JYH  CAG  C  CR16  0  -0.237  -5.5149   2.2334   0.1051
 JYH  CAL  C  CR16  0  -0.312  -5.4665   0.8261   0.1250
 JYH  CAZ  C  CR6   0   0.072  -4.2789   0.1464   0.0050
 JYH  CAY  C  CR6   0   0.023  -4.2873  -1.3340   0.0095
 JYH  CAH  C  CR16  0  -0.293  -4.8083  -2.0268   1.1012
 JYH  CAE  C  CR16  0  -0.241  -4.8507  -3.4144   1.1040
 JYH  CAD  C  CR16  0  -0.262  -4.3760  -4.1289   0.0125
 JYH  CAF  C  CR16  0  -0.241  -3.8603  -3.4474  -1.0826
 JYH  CAI  C  CR16  0  -0.296  -3.8156  -2.0608  -1.0841
 JYH  H1   H  HCR6  0   0.280   3.6333   2.4375   0.9501
 JYH  H2   H  HCR6  0   0.269   6.0179   1.9485   1.0083
 JYH  H3   H  HOH1  0   0.487   8.5827  -1.5600  -0.2528
 JYH  H4   H  HCR6  0   0.271   5.2588  -1.8721  -0.7917
 JYH  H5   H  HCR6  0   0.289   2.8949  -1.3975  -0.8484
 JYH  H6   H  HNH1  0   0.429   1.5728   1.8505   0.4538
 JYH  H7   H  HCR6  0   0.265  -1.7353  -0.8129  -0.1399
 JYH  H8   H  HCR6  0   0.264   0.1821   3.0106  -0.4626
 JYH  H9   H  HCR6  0   0.266  -1.9674   4.1210  -0.3133
 JYH  H10  H  HCR6  0   0.262  -4.3994   4.0438  -0.0602
 JYH  H11  H  HCR6  0   0.265  -6.4710   2.7324   0.1929
 JYH  H12  H  HCR6  0   0.260  -6.3901   0.2685   0.2175
 JYH  H13  H  HCR6  0   0.255  -5.1744  -1.4767   1.9592
 JYH  H14  H  HCR6  0   0.259  -5.2532  -3.9359   1.9626
 JYH  H15  H  HCR6  0   0.258  -4.4089  -5.2106   0.0140
 JYH  H16  H  HCR6  0   0.259  -3.4947  -3.9950  -1.9414
 JYH  H17  H  HCR6  0   0.261  -3.4232  -1.5397  -1.9488

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
 JYH  OAA  CAT  double    1.209  0.020  1.209
 JYH  CAT  OAC  single    1.327  0.020  1.327
 JYH  CAT  CAW  single    1.478  0.020  1.478
 JYH  CAM  CAW  aromatic  1.395  0.020  1.395
 JYH  CAM  CAJ  aromatic  1.377  0.020  1.377
 JYH  CAW  CAN  aromatic  1.393  0.020  1.393
 JYH  CAJ  CAV  aromatic  1.400  0.020  1.400
 JYH  CAD  CAF  aromatic  1.389  0.020  1.389
 JYH  CAD  CAE  aromatic  1.388  0.020  1.388
 JYH  CAF  CAI  aromatic  1.387  0.020  1.387
 JYH  OAB  CAU  double    1.217  0.020  1.217
 JYH  CAN  CAK  aromatic  1.385  0.020  1.385
 JYH  CAE  CAH  aromatic  1.388  0.020  1.388
 JYH  CAV  CAK  aromatic  1.397  0.020  1.397
 JYH  CAV  NAS  single    1.390  0.020  1.390
 JYH  CAI  CAY  aromatic  1.395  0.020  1.395
 JYH  CAU  NAS  single    1.362  0.020  1.362
 JYH  CAU  CAX  single    1.494  0.020  1.494
 JYH  CAH  CAY  aromatic  1.394  0.020  1.394
 JYH  CAY  CAZ  single    1.480  0.020  1.480
 JYH  CAR  CAX  aromatic  1.373  0.020  1.373
 JYH  CAR  CBB  aromatic  1.412  0.020  1.412
 JYH  CAX  CAO  aromatic  1.415  0.020  1.415
 JYH  CAZ  CBB  aromatic  1.427  0.020  1.427
 JYH  CAZ  CAL  aromatic  1.374  0.020  1.374
 JYH  CBB  CBA  aromatic  1.421  0.020  1.421
 JYH  CAO  CAQ  aromatic  1.365  0.020  1.365
 JYH  CAL  CAG  aromatic  1.408  0.020  1.408
 JYH  CBA  CAQ  aromatic  1.414  0.020  1.414
 JYH  CBA  CAP  aromatic  1.412  0.020  1.412
 JYH  CAG  CAP  aromatic  1.366  0.020  1.366
 JYH  CAJ  H1   single    0.930  0.020  1.080
 JYH  CAM  H2   single    0.930  0.020  1.080
 JYH  OAC  H3   single    0.850  0.020  0.980
 JYH  CAN  H4   single    0.930  0.020  1.080
 JYH  CAK  H5   single    0.930  0.020  1.080
 JYH  NAS  H6   single    0.860  0.020  1.020
 JYH  CAR  H7   single    0.930  0.020  1.080
 JYH  CAO  H8   single    0.930  0.020  1.080
 JYH  CAQ  H9   single    0.930  0.020  1.080
 JYH  CAP  H10  single    0.930  0.020  1.080
 JYH  CAG  H11  single    0.930  0.020  1.080
 JYH  CAL  H12  single    0.930  0.020  1.080
 JYH  CAH  H13  single    0.930  0.020  1.080
 JYH  CAE  H14  single    0.930  0.020  1.080
 JYH  CAD  H15  single    0.930  0.020  1.080
 JYH  CAF  H16  single    0.930  0.020  1.080
 JYH  CAI  H17  single    0.930  0.020  1.080

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
 JYH  H1   CAJ  CAV  119.78  3.000
 JYH  H1   CAJ  CAM  119.38  3.000
 JYH  CAV  CAJ  CAM  120.84  3.000
 JYH  H2   CAM  CAW  120.29  3.000
 JYH  H2   CAM  CAJ  119.11  3.000
 JYH  CAW  CAM  CAJ  120.61  3.000
 JYH  CAN  CAW  CAT  122.81  3.000
 JYH  CAN  CAW  CAM  118.47  3.000
 JYH  CAT  CAW  CAM  118.72  3.000
 JYH  OAA  CAT  OAC  122.98  3.000
 JYH  OAC  CAT  CAW  113.16  3.000
 JYH  OAA  CAT  CAW  123.85  3.000
 JYH  H3   OAC  CAT  109.91  3.000
 JYH  H4   CAN  CAK  117.83  3.000
 JYH  H4   CAN  CAW  120.67  3.000
 JYH  CAK  CAN  CAW  121.50  3.000
 JYH  H5   CAK  CAV  121.28  3.000
 JYH  H5   CAK  CAN  119.00  3.000
 JYH  CAV  CAK  CAN  119.72  3.000
 JYH  NAS  CAV  CAK  124.79  3.000
 JYH  NAS  CAV  CAJ  116.33  3.000
 JYH  CAK  CAV  CAJ  118.87  3.000
 JYH  H6   NAS  CAU  116.48  3.000
 JYH  H6   NAS  CAV  114.14  3.000
 JYH  CAU  NAS  CAV  129.29  3.000
 JYH  CAX  CAU  OAB  121.50  3.000
 JYH  CAX  CAU  NAS  114.89  3.000
 JYH  OAB  CAU  NAS  123.61  3.000
 JYH  CAO  CAX  CAR  119.62  3.000
 JYH  CAO  CAX  CAU  122.88  3.000
 JYH  CAR  CAX  CAU  117.49  3.000
 JYH  H7   CAR  CBB  119.39  3.000
 JYH  H7   CAR  CAX  118.98  3.000
 JYH  CBB  CAR  CAX  121.62  3.000
 JYH  CAZ  CBB  CBA  119.16  3.000
 JYH  CBA  CBB  CAR  118.31  3.000
 JYH  CAZ  CBB  CAR  122.51  3.000
 JYH  H8   CAO  CAQ  118.60  3.000
 JYH  H8   CAO  CAX  121.26  3.000
 JYH  CAQ  CAO  CAX  120.12  3.000
 JYH  H9   CAQ  CBA  118.85  3.000
 JYH  H9   CAQ  CAO  119.96  3.000
 JYH  CBA  CAQ  CAO  121.19  3.000
 JYH  CAP  CBA  CAQ  121.15  3.000
 JYH  CAP  CBA  CBB  119.73  3.000
 JYH  CAQ  CBA  CBB  119.12  3.000
 JYH  H10  CAP  CAG  120.67  3.000
 JYH  H10  CAP  CBA  119.17  3.000
 JYH  CAG  CAP  CBA  120.15  3.000
 JYH  H11  CAG  CAL  119.35  3.000
 JYH  H11  CAG  CAP  120.31  3.000
 JYH  CAL  CAG  CAP  120.35  3.000
 JYH  H12  CAL  CAZ  119.35  3.000
 JYH  H12  CAL  CAG  119.11  3.000
 JYH  CAZ  CAL  CAG  121.53  3.000
 JYH  CAY  CAZ  CAL  119.32  3.000
 JYH  CAL  CAZ  CBB  119.06  3.000
 JYH  CAY  CAZ  CBB  121.62  3.000
 JYH  CAI  CAY  CAH  118.77  3.000
 JYH  CAH  CAY  CAZ  120.10  3.000
 JYH  CAI  CAY  CAZ  121.10  3.000
 JYH  H13  CAH  CAE  119.73  3.000
 JYH  H13  CAH  CAY  119.63  3.000
 JYH  CAE  CAH  CAY  120.64  3.000
 JYH  H14  CAE  CAD  120.19  3.000
 JYH  H14  CAE  CAH  119.64  3.000
 JYH  CAD  CAE  CAH  120.17  3.000
 JYH  H15  CAD  CAF  120.18  3.000
 JYH  H15  CAD  CAE  120.20  3.000
 JYH  CAF  CAD  CAE  119.62  3.000
 JYH  H16  CAF  CAI  119.61  3.000
 JYH  H16  CAF  CAD  120.18  3.000
 JYH  CAI  CAF  CAD  120.21  3.000
 JYH  H17  CAI  CAF  119.56  3.000
 JYH  H17  CAI  CAY  119.84  3.000
 JYH  CAF  CAI  CAY  120.59  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
 JYH  CONST_01  CAN  CAW  CAM  CAJ     0.00   0.0  0
 JYH  CONST_02  CAN  CAK  CAV  CAJ     0.00   0.0  0
 JYH  CONST_03  CAK  CAN  CAW  CAM     0.00   0.0  0
 JYH  CONST_04  CAK  CAV  CAJ  CAM     0.00   0.0  0
 JYH  CONST_05  CAV  CAJ  CAM  CAW     0.00   0.0  0
 JYH  CONST_06  CAV  CAK  CAN  CAW     0.00   0.0  0
 JYH  CONST_07  CAZ  CBB  CAR  CAX   180.00   0.0  0
 JYH  CONST_08  CBA  CBB  CAR  CAX     0.00   0.0  0
 JYH  CONST_09  CBA  CAQ  CAO  CAX     0.00   0.0  0
 JYH  CONST_10  CAQ  CAO  CAX  CAR     0.00   0.0  0
 JYH  CONST_11  CAY  CAZ  CBB  CAR     0.00   0.0  0
 JYH  CONST_12  CAL  CAZ  CBB  CAR   180.00   0.0  0
 JYH  CONST_13  CAQ  CBA  CBB  CAR     0.00   0.0  0
 JYH  CONST_14  CAP  CBA  CBB  CAR   180.00   0.0  0
 JYH  CONST_15  CAO  CAX  CAR  CBB     0.00   0.0  0
 JYH  CONST_18  CAG  CAL  CAZ  CBB     0.00   0.0  0
 JYH  CONST_19  CAO  CAQ  CBA  CBB     0.00   0.0  0
 JYH  CONST_20  CAG  CAP  CBA  CBB     0.00   0.0  0
 JYH  CONST_21  CAP  CBA  CAQ  CAO   180.00   0.0  0
 JYH  CONST_22  CAZ  CBB  CBA  CAQ   180.00   0.0  0
 JYH  CONST_23  CAG  CAP  CBA  CAQ   180.00   0.0  0
 JYH  CONST_24  CAY  CAZ  CBB  CBA   180.00   0.0  0
 JYH  CONST_25  CAL  CAZ  CBB  CBA     0.00   0.0  0
 JYH  CONST_26  CAL  CAG  CAP  CBA     0.00   0.0  0
 JYH  CONST_27  CAZ  CBB  CBA  CAP     0.00   0.0  0
 JYH  CONST_28  CAZ  CAL  CAG  CAP     0.00   0.0  0
 JYH  CONST_29  CAY  CAZ  CAL  CAG   180.00   0.0  0
 JYH  CONST_32  CAF  CAI  CAY  CAZ   180.00   0.0  0
 JYH  CONST_33  CAE  CAH  CAY  CAZ   180.00   0.0  0
 JYH  CONST_34  CAD  CAF  CAI  CAY     0.00   0.0  0
 JYH  CONST_35  CAD  CAE  CAH  CAY     0.00   0.0  0
 JYH  CONST_36  CAF  CAD  CAE  CAH     0.00   0.0  0
 JYH  CONST_37  CAF  CAI  CAY  CAH     0.00   0.0  0
 JYH  CONST_38  CAI  CAF  CAD  CAE     0.00   0.0  0
 JYH  CONST_39  CAI  CAY  CAH  CAE     0.00   0.0  0
 JYH  CONST_40  CAT  CAW  CAM  CAJ   180.00   0.0  0
 JYH  CONST_41  NAS  CAV  CAJ  CAM   180.00   0.0  0
 JYH  CONST_42  CAK  CAN  CAW  CAT   180.00   0.0  0
 JYH  CONST_43  NAS  CAV  CAK  CAN   180.00   0.0  0
 JYH  CONST_44  CBB  CAR  CAX  CAU   180.00   0.0  0
 JYH  CONST_45  CAQ  CAO  CAX  CAU   180.00   0.0  0
 JYH  CONST_46  H5   CAK  CAV  CAJ   180.00   0.0  0
 JYH  CONST_47  H4   CAN  CAW  CAM   180.00   0.0  0
 JYH  CONST_48  H1   CAJ  CAM  CAW   180.00   0.0  0
 JYH  CONST_49  H2   CAM  CAW  CAN   180.00   0.0  0
 JYH  CONST_50  H9   CAQ  CAO  CAX   180.00   0.0  0
 JYH  CONST_51  H8   CAO  CAX  CAR   180.00   0.0  0
 JYH  CONST_52  H12  CAL  CAZ  CBB   180.00   0.0  0
 JYH  CONST_53  H10  CAP  CBA  CBB   180.00   0.0  0
 JYH  CONST_54  H7   CAR  CAX  CAO   180.00   0.0  0
 JYH  CONST_55  H11  CAG  CAP  CBA   180.00   0.0  0
 JYH  CONST_56  H17  CAI  CAY  CAZ     0.00   0.0  0
 JYH  CONST_57  H13  CAH  CAY  CAZ     0.00   0.0  0
 JYH  CONST_58  H16  CAF  CAI  CAY   180.00   0.0  0
 JYH  CONST_59  H14  CAE  CAH  CAY   180.00   0.0  0
 JYH  CONST_60  H15  CAD  CAE  CAH   180.00   0.0  0
 JYH  CONST_61  CAX  CAU  NAS  CAV   180.00   0.0  0
 JYH  CONST_62  CAU  NAS  CAV  CAJ   180.00   0.0  0
 JYH  CONST_63  CAU  NAS  CAV  CAK     0.00   0.0  0
 JYH  CONST_64  H6   NAS  CAV  CAJ     0.00   0.0  0
 JYH  CONST_65  OAB  CAU  NAS  CAV     0.00   0.0  0
 JYH  CONST_66  H3   OAC  CAT  CAW   180.00   0.0  0
 JYH  Var_01    OAA  CAT  CAW  CAM    -0.59  30.0  3
 JYH  Var_02    CAR  CAX  CAU  NAS  -156.30  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
 JYH  plan-1  CAJ  0.020
 JYH  plan-1  CAM  0.020
 JYH  plan-1  CAW  0.020
 JYH  plan-1  CAT  0.020
 JYH  plan-1  CAN  0.020
 JYH  plan-1  CAK  0.020
 JYH  plan-1  CAV  0.020
 JYH  plan-1  NAS  0.020
 JYH  plan-1  H1   0.020
 JYH  plan-1  H2   0.020
 JYH  plan-1  H4   0.020
 JYH  plan-1  H5   0.020
 JYH  plan-2  CAZ  0.020
 JYH  plan-2  CAY  0.020
 JYH  plan-2  CAH  0.020
 JYH  plan-2  CAE  0.020
 JYH  plan-2  CAD  0.020
 JYH  plan-2  CAF  0.020
 JYH  plan-2  CAI  0.020
 JYH  plan-2  H13  0.020
 JYH  plan-2  H14  0.020
 JYH  plan-2  H15  0.020
 JYH  plan-2  H16  0.020
 JYH  plan-2  H17  0.020
 JYH  plan-3  CAU  0.020
 JYH  plan-3  CAX  0.020
 JYH  plan-3  CAR  0.020
 JYH  plan-3  CBB  0.020
 JYH  plan-3  CAO  0.020
 JYH  plan-3  CAQ  0.020
 JYH  plan-3  CBA  0.020
 JYH  plan-3  CAP  0.020
 JYH  plan-3  CAG  0.020
 JYH  plan-3  CAL  0.020
 JYH  plan-3  CAZ  0.020
 JYH  plan-3  CAY  0.020
 JYH  plan-3  H7   0.020
 JYH  plan-3  H8   0.020
 JYH  plan-3  H9   0.020
 JYH  plan-3  H10  0.020
 JYH  plan-3  H11  0.020
 JYH  plan-3  H12  0.020
 JYH  plan-4  CAV  0.020
 JYH  plan-4  NAS  0.020
 JYH  plan-4  CAU  0.020
 JYH  plan-4  OAB  0.020
 JYH  plan-4  CAX  0.020
 JYH  plan-4  H6   0.020
 JYH  plan-5  CAW  0.020
 JYH  plan-5  CAT  0.020
 JYH  plan-5  OAC  0.020
 JYH  plan-5  OAA  0.020
 JYH  plan-5  H3   0.020

