# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 03:43:58 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 3-[(4-chlorophenyl)carbamoyl]naphthalen-2-yl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1cc2ccccc2cc1C(=O)Nc3ccc(Cl)cc3
#
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
 N3P  N3P  '3-[(4-chlorophenyl)carbamoyl]naphthalen-2-yl dihydrogen phosphate'  ligand  38  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N3P
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
 N3P  CAF   C   CR16  0  -0.250   0.3662   -0.9458   0.1793
 N3P  CAG   C   CR16  0  -0.256  -0.3254   -1.9649   0.8687
 N3P  CAH   C   CR16  0  -0.201   5.9025  -10.2959  -0.0801
 N3P  CAI   C   CR16  0  -0.201   7.6442   -8.8826   0.7833
 N3P  CAJ   C   CR16  0  -0.313   5.0632   -9.1989  -0.2148
 N3P  CAK   C   CR16  0  -0.348   6.8102   -7.7890   0.6456
 N3P  CAL   C   CR16  0  -0.312   1.5251   -1.2231  -0.4927
 N3P  CAM   C   CR16  0  -0.306   0.1571   -3.2445   0.8723
 N3P  CAN   C   CR16  0  -0.392   3.2396   -2.8539  -1.1945
 N3P  CAO   C   CR16  0  -0.336   1.8714   -4.8728   0.1617
 N3P  CAS   C   CR6   0  -0.057   7.1840  -10.1378   0.4166
 N3P  CAT   C   CR6   0   0.385   5.5121   -7.9291   0.1485
 N3P  CAU   C   CR6   0   0.372   3.7233   -4.1305  -1.1728
 N3P  CAV   C   CR6   0  -0.144   3.0465   -5.1621  -0.4802
 N3P  CAW   C   CR66  0   0.129   2.0489   -2.5365  -0.5039
 N3P  CAX   C   CR66  0   0.125   1.3534   -3.5605   0.1871
 N3P  NAP   N   NH1   0  -0.738   4.7473   -6.7627   0.0579
 N3P  OAA   O   O     0  -0.443   2.8285   -7.4710  -0.9483
 N3P  OAB   O   O     0  -0.678   6.4660   -2.4108  -1.9529
 N3P  OAC   O   OH1   0  -0.744   6.4757   -4.1383  -0.0188
 N3P  OAD   O   OH1   0  -0.711   7.1444   -4.9178  -2.3335
 N3P  OAQ   O   O2    0  -0.609   4.8466   -4.4849  -1.8848
 N3P  PAY   P   P     0   1.454   6.2879   -3.8233  -1.5751
 N3P  HAF   H   HCR6  0   0.265  -0.0261    0.0625   0.1855
 N3P  HAG   H   HCR6  0   0.265  -1.2408   -1.7279   1.3942
 N3P  HAH   H   HCR6  0   0.283   5.5412  -11.2750  -0.3637
 N3P  HAI   H   HCR6  0   0.284   8.6449   -8.7499   1.1713
 N3P  HAJ   H   HCR6  0   0.291   4.0683   -9.3533  -0.5972
 N3P  HAK   H   HCR6  0   0.275   7.1809   -6.8110   0.9269
 N3P  HAL   H   HCR6  0   0.263   2.0533   -0.4406  -1.0232
 N3P  HAM   H   HCR6  0   0.263  -0.3695   -4.0295   1.4010
 N3P  HAN   H   HCR6  0   0.285   3.7484   -2.0817  -1.7576
 N3P  HAO   H   HCR6  0   0.274   1.3345   -5.6578   0.6806
 N3P  HNAP  H   HNH1  0   0.425   5.1792   -5.9433   0.4608
 N3P  HOAC  H   HOH1  0   0.511   6.6563   -3.3665   0.5352
 N3P  HOAD  H   HOH1  0   0.511   8.0128   -4.6095  -2.6269
 N3P  CAR   C   C     0   0.510   3.5264   -6.5829  -0.4970
 N3P  CLA   CL  CL    0  -0.132   8.2203  -11.5170   0.5844

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
 N3P  CAF  CAG   aromatic  1.411  0.020  1.411
 N3P  CAF  CAL   aromatic  1.368  0.020  1.368
 N3P  CAF  HAF   single    0.930  0.020  1.080
 N3P  CAG  CAM   aromatic  1.368  0.020  1.368
 N3P  CAG  HAG   single    0.930  0.020  1.080
 N3P  CAH  CAJ   aromatic  1.388  0.020  1.388
 N3P  CAH  CAS   aromatic  1.383  0.020  1.383
 N3P  CAH  HAH   single    0.930  0.020  1.080
 N3P  CAI  CAK   aromatic  1.382  0.020  1.382
 N3P  CAI  CAS   aromatic  1.386  0.020  1.386
 N3P  CAI  HAI   single    0.930  0.020  1.080
 N3P  CAJ  CAT   aromatic  1.395  0.020  1.395
 N3P  CAJ  HAJ   single    0.930  0.020  1.080
 N3P  CAK  CAT   aromatic  1.397  0.020  1.397
 N3P  CAK  HAK   single    0.930  0.020  1.080
 N3P  CAL  CAW   aromatic  1.414  0.020  1.414
 N3P  CAL  HAL   single    0.930  0.020  1.080
 N3P  CAM  CAX   aromatic  1.414  0.020  1.414
 N3P  CAM  HAM   single    0.930  0.020  1.080
 N3P  CAN  CAW   aromatic  1.413  0.020  1.413
 N3P  CAN  CAU   aromatic  1.365  0.020  1.365
 N3P  CAN  HAN   single    0.930  0.020  1.080
 N3P  CAO  CAX   aromatic  1.411  0.020  1.411
 N3P  CAO  CAV   aromatic  1.370  0.020  1.370
 N3P  CAO  HAO   single    0.930  0.020  1.080
 N3P  CAR  OAA   double    1.216  0.020  1.216
 N3P  CAR  CAV   single    1.500  0.020  1.500
 N3P  CAR  NAP   single    1.353  0.020  1.353
 N3P  CAS  CLA   single    1.733  0.020  1.733
 N3P  CAT  NAP   single    1.398  0.020  1.398
 N3P  CAU  CAV   aromatic  1.415  0.020  1.415
 N3P  CAU  OAQ   single    1.376  0.020  1.376
 N3P  CAW  CAX   aromatic  1.418  0.020  1.418
 N3P  NAP  HNAP  single    0.860  0.020  1.020
 N3P  OAB  PAY   double    1.473  0.020  1.473
 N3P  OAC  PAY   single    1.599  0.020  1.599
 N3P  OAC  HOAC  single    0.850  0.020  0.980
 N3P  OAD  PAY   single    1.583  0.020  1.583
 N3P  OAD  HOAD  single    0.850  0.020  0.980
 N3P  OAQ  PAY   single    1.616  0.020  1.616

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
 N3P  HAF   CAF  CAL  119.93  3.000
 N3P  HAF   CAF  CAG  119.50  3.000
 N3P  CAL   CAF  CAG  120.57  3.000
 N3P  HAG   CAG  CAM  120.15  3.000
 N3P  HAG   CAG  CAF  119.58  3.000
 N3P  CAM   CAG  CAF  120.27  3.000
 N3P  HAH   CAH  CAS  120.47  3.000
 N3P  HAH   CAH  CAJ  119.22  3.000
 N3P  CAS   CAH  CAJ  120.31  3.000
 N3P  HAI   CAI  CAS  120.88  3.000
 N3P  HAI   CAI  CAK  119.80  3.000
 N3P  CAS   CAI  CAK  119.32  3.000
 N3P  HAJ   CAJ  CAT  121.35  3.000
 N3P  HAJ   CAJ  CAH  118.67  3.000
 N3P  CAT   CAJ  CAH  119.98  3.000
 N3P  HAK   CAK  CAT  120.07  3.000
 N3P  HAK   CAK  CAI  118.82  3.000
 N3P  CAT   CAK  CAI  121.12  3.000
 N3P  HAL   CAL  CAW  119.12  3.000
 N3P  HAL   CAL  CAF  120.49  3.000
 N3P  CAW   CAL  CAF  120.40  3.000
 N3P  HAM   CAM  CAX  119.06  3.000
 N3P  HAM   CAM  CAG  120.53  3.000
 N3P  CAX   CAM  CAG  120.41  3.000
 N3P  HAN   CAN  CAW  119.35  3.000
 N3P  HAN   CAN  CAU  120.57  3.000
 N3P  CAW   CAN  CAU  120.06  3.000
 N3P  HAO   CAO  CAX  118.90  3.000
 N3P  HAO   CAO  CAV  119.77  3.000
 N3P  CAX   CAO  CAV  121.32  3.000
 N3P  CLA   CAS  CAI  119.76  3.000
 N3P  CLA   CAS  CAH  119.84  3.000
 N3P  CAI   CAS  CAH  120.40  3.000
 N3P  NAP   CAT  CAK  116.60  3.000
 N3P  NAP   CAT  CAJ  124.52  3.000
 N3P  CAK   CAT  CAJ  118.88  3.000
 N3P  OAQ   CAU  CAV  117.12  3.000
 N3P  OAQ   CAU  CAN  121.45  3.000
 N3P  CAV   CAU  CAN  121.33  3.000
 N3P  CAU   CAV  CAR  122.16  3.000
 N3P  CAU   CAV  CAO  119.06  3.000
 N3P  CAR   CAV  CAO  118.67  3.000
 N3P  CAX   CAW  CAN  119.31  3.000
 N3P  CAX   CAW  CAL  119.03  3.000
 N3P  CAN   CAW  CAL  121.65  3.000
 N3P  CAW   CAX  CAO  118.87  3.000
 N3P  CAW   CAX  CAM  119.32  3.000
 N3P  CAO   CAX  CAM  121.81  3.000
 N3P  HNAP  NAP  CAT  114.66  3.000
 N3P  HNAP  NAP  CAR  116.20  3.000
 N3P  CAT   NAP  CAR  129.14  3.000
 N3P  HOAC  OAC  PAY  114.98  3.000
 N3P  HOAD  OAD  PAY  114.25  3.000
 N3P  PAY   OAQ  CAU  121.56  3.000
 N3P  OAQ   PAY  OAD   96.18  3.000
 N3P  OAQ   PAY  OAC  102.16  3.000
 N3P  OAD   PAY  OAC  105.46  3.000
 N3P  OAQ   PAY  OAB  116.83  3.000
 N3P  OAD   PAY  OAB  118.34  3.000
 N3P  OAC   PAY  OAB  115.11  3.000
 N3P  OAA   CAR  NAP  124.95  3.000
 N3P  NAP   CAR  CAV  114.21  3.000
 N3P  OAA   CAR  CAV  120.82  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
 N3P  CONST_01  CAX   CAM  CAG  CAF    0.00   0.0  0
 N3P  CONST_02  CAN   CAW  CAL  CAF  180.00   0.0  0
 N3P  CONST_03  CAX   CAW  CAL  CAF    0.00   0.0  0
 N3P  CONST_04  CAW   CAL  CAF  CAG    0.00   0.0  0
 N3P  CONST_05  CAO   CAX  CAM  CAG  180.00   0.0  0
 N3P  CONST_06  CAW   CAX  CAM  CAG    0.00   0.0  0
 N3P  CONST_07  CAK   CAT  CAJ  CAH    0.00   0.0  0
 N3P  CONST_08  CAK   CAI  CAS  CAH    0.00   0.0  0
 N3P  CONST_09  CAJ   CAT  CAK  CAI    0.00   0.0  0
 N3P  CONST_10  CAJ   CAH  CAS  CAI    0.00   0.0  0
 N3P  CONST_11  CAM   CAG  CAF  CAL    0.00   0.0  0
 N3P  CONST_12  CAU   CAN  CAW  CAL  180.00   0.0  0
 N3P  CONST_13  CAM   CAX  CAW  CAL    0.00   0.0  0
 N3P  CONST_14  CAO   CAX  CAW  CAL  180.00   0.0  0
 N3P  CONST_15  CAV   CAO  CAX  CAM  180.00   0.0  0
 N3P  CONST_16  CAN   CAW  CAX  CAM  180.00   0.0  0
 N3P  CONST_17  CAO   CAX  CAW  CAN    0.00   0.0  0
 N3P  CONST_18  CAO   CAV  CAU  CAN    0.00   0.0  0
 N3P  CONST_19  CAT   CAJ  CAH  CAS    0.00   0.0  0
 N3P  CONST_20  CAT   CAK  CAI  CAS    0.00   0.0  0
 N3P  CONST_21  CAX   CAW  CAN  CAU    0.00   0.0  0
 N3P  CONST_22  CAX   CAO  CAV  CAU    0.00   0.0  0
 N3P  CONST_23  CAW   CAX  CAO  CAV    0.00   0.0  0
 N3P  CONST_24  CAW   CAN  CAU  CAV    0.00   0.0  0
 N3P  CONST_25  NAP   CAT  CAJ  CAH  180.00   0.0  0
 N3P  CONST_26  NAP   CAT  CAK  CAI  180.00   0.0  0
 N3P  CONST_27  CLA   CAS  CAH  CAJ  180.00   0.0  0
 N3P  CONST_28  CLA   CAS  CAI  CAK  180.00   0.0  0
 N3P  CONST_29  CAR   CAV  CAU  CAN  180.00   0.0  0
 N3P  CONST_30  OAQ   CAU  CAV  CAO  180.00   0.0  0
 N3P  CONST_31  CAX   CAO  CAV  CAR  180.00   0.0  0
 N3P  CONST_32  OAQ   CAU  CAN  CAW  180.00   0.0  0
 N3P  CONST_33  HAM   CAM  CAG  CAF  180.00   0.0  0
 N3P  CONST_34  HAL   CAL  CAF  CAG  180.00   0.0  0
 N3P  CONST_35  HAI   CAI  CAS  CAH  180.00   0.0  0
 N3P  CONST_36  HAH   CAH  CAS  CAI  180.00   0.0  0
 N3P  CONST_37  HAK   CAK  CAT  CAJ  180.00   0.0  0
 N3P  CONST_38  HAJ   CAJ  CAT  CAK  180.00   0.0  0
 N3P  CONST_39  HAG   CAG  CAF  CAL  180.00   0.0  0
 N3P  CONST_40  HAN   CAN  CAW  CAL    0.00   0.0  0
 N3P  CONST_41  HAF   CAF  CAG  CAM  180.00   0.0  0
 N3P  CONST_42  HAO   CAO  CAX  CAM    0.00   0.0  0
 N3P  CONST_43  CAV   CAR  NAP  CAT  180.00   0.0  0
 N3P  CONST_44  CAR   NAP  CAT  CAJ    0.00   0.0  0
 N3P  CONST_45  CAR   NAP  CAT  CAK  180.00   0.0  0
 N3P  CONST_46  HNAP  NAP  CAT  CAJ  180.00   0.0  0
 N3P  CONST_47  OAA   CAR  NAP  CAT    0.00   0.0  0
 N3P  Var_01    OAA   CAR  CAV  CAO   57.04  30.0  2
 N3P  Var_02    OAB   PAY  OAQ  CAU  -70.66  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
 N3P  plan-1  CAH   0.020
 N3P  plan-1  CAI   0.020
 N3P  plan-1  CAJ   0.020
 N3P  plan-1  CAK   0.020
 N3P  plan-1  CAS   0.020
 N3P  plan-1  CAT   0.020
 N3P  plan-1  NAP   0.020
 N3P  plan-1  HAH   0.020
 N3P  plan-1  HAI   0.020
 N3P  plan-1  HAJ   0.020
 N3P  plan-1  HAK   0.020
 N3P  plan-1  CLA   0.020
 N3P  plan-2  CAF   0.020
 N3P  plan-2  CAG   0.020
 N3P  plan-2  CAL   0.020
 N3P  plan-2  CAM   0.020
 N3P  plan-2  CAN   0.020
 N3P  plan-2  CAO   0.020
 N3P  plan-2  CAU   0.020
 N3P  plan-2  CAV   0.020
 N3P  plan-2  CAW   0.020
 N3P  plan-2  CAX   0.020
 N3P  plan-2  OAQ   0.020
 N3P  plan-2  HAF   0.020
 N3P  plan-2  HAG   0.020
 N3P  plan-2  HAL   0.020
 N3P  plan-2  HAM   0.020
 N3P  plan-2  HAN   0.020
 N3P  plan-2  HAO   0.020
 N3P  plan-2  CAR   0.020
 N3P  plan-3  CAT   0.020
 N3P  plan-3  CAV   0.020
 N3P  plan-3  NAP   0.020
 N3P  plan-3  OAA   0.020
 N3P  plan-3  HNAP  0.020
 N3P  plan-3  CAR   0.020

