# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:20:01 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-(naphthalen-2-ylamino)-2-oxoethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)[C@H](C(=O)Nc1ccc2ccccc2c1)c3csc4ccc(Cl)cc34
#
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
 DRX  DRX  '[(1S)-1-(5-chloro-1-benzothiophen-3-yl)-2-(naphthalen-2-ylamino)-2-oxoethyl]phosphonic acid'  ligand  41  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DRX
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
 DRX  CAO   C   CR56   0   0.151   9.0557   -6.5277  -0.2299
 DRX  CAP   C   CR16   0  -0.314   8.6722   -7.8736  -0.2078
 DRX  CAQ   C   CR6    0  -0.034   9.5005   -8.7902   0.4010
 DRX  CLR   CL  CL     0  -0.135   9.0344  -10.4634   0.4301
 DRX  CBB   C   CR16   0  -0.238  10.7096   -8.4217   0.9990
 DRX  CBA   C   CR16   0  -0.282  11.0984   -7.0971   0.9865
 DRX  CAZ   C   CR56   0  -0.210  10.2724   -6.1602   0.3728
 DRX  SBC   S   S2     0   0.194  10.5411   -4.4572   0.2352
 DRX  CAY   C   CR15   0  -0.559   9.0547   -4.2594  -0.6288
 DRX  CAN   C   CR5    0   0.324   8.3602   -5.4070  -0.8110
 DRX  CAM   C   CH1    0  -0.830   7.0502   -5.5033  -1.5064
 DRX  PAD   P   P      0   1.229   7.0878   -4.7535  -3.2617
 DRX  OAB   O   OP    -1  -0.861   5.6753   -5.1360  -3.7784
 DRX  OAE   O   O      0  -0.858   7.2789   -3.2557  -3.0552
 DRX  OAC   O   OP    -1  -0.857   8.2123   -5.4819  -3.9775
 DRX  CAL   C   C      0   0.553   5.9225   -4.9236  -0.6794
 DRX  OAX   O   O      0  -0.483   6.0733   -4.4625   0.4414
 DRX  NAK   N   NH1    0  -0.786   4.7312   -4.9773  -1.3341
 DRX  CAW   C   CR6    0   0.397   3.4888   -4.5524  -0.8913
 DRX  CAV   C   CR16   0  -0.454   2.5310   -4.2643  -1.8416
 DRX  CAU   C   CR66   0   0.148   1.2230   -3.8836  -1.4814
 DRX  CAT   C   CR16   0  -0.323   0.2331   -3.5867  -2.4510
 DRX  CAS   C   CR16   0  -0.258  -1.0292   -3.2199  -2.0714
 DRX  CAF   C   CR16   0  -0.269  -1.3698   -3.1300  -0.7043
 DRX  CAG   C   CR16   0  -0.308  -0.4334   -3.4086   0.2543
 DRX  CAH   C   CR66   0   0.090   0.8790   -3.7892  -0.1082
 DRX  CAI   C   CR16   0  -0.306   1.8740   -4.0904   0.8492
 DRX  CAJ   C   CR16   0  -0.315   3.1377   -4.4595   0.4830
 DRX  HAP   H   HCR6   0   0.273   7.7409   -8.1897  -0.6596
 DRX  HBB   H   HCR6   0   0.279  11.3365   -9.1678   1.4676
 DRX  HBA   H   HCR6   0   0.275  12.0326   -6.8026   1.4463
 DRX  HAY   H   HCR5   0   0.284   8.7704   -3.2824  -0.9881
 DRX  HAM   H   HCH1   0   0.271   6.8058   -6.5575  -1.6766
 DRX  HNAK  H   HNH1   0   0.431   4.8592   -5.1191  -2.3699
 DRX  HAV   H   HCR6   0   0.252   2.7861   -4.3324  -2.8938
 DRX  HAT   H   HCR6   0   0.250   0.4901   -3.6541  -3.5015
 DRX  HAS   H   HCR6   0   0.254  -1.7755   -2.9967  -2.8231
 DRX  HAF   H   HCR6   0   0.253  -2.3723   -2.8396  -0.4186
 DRX  HAG   H   HCR6   0   0.251  -0.6884   -3.3403   1.3055
 DRX  HAI   H   HCR6   0   0.253   1.6227   -4.0308   1.9018
 DRX  HAJ   H   HCR6   0   0.268   3.8655   -4.6886   1.2446

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
 DRX  CAO  CAN   aromatic  1.441  0.020  1.441
 DRX  CAO  CAZ   aromatic  1.407  0.020  1.407
 DRX  CAO  CAP   aromatic  1.400  0.020  1.400
 DRX  CAP  CAQ   aromatic  1.377  0.020  1.377
 DRX  CAP  HAP   single    0.930  0.020  1.080
 DRX  CAQ  CBB   aromatic  1.398  0.020  1.398
 DRX  CAQ  CLR   single    1.737  0.020  1.737
 DRX  CBB  CBA   aromatic  1.381  0.020  1.381
 DRX  CBB  HBB   single    0.930  0.020  1.080
 DRX  CBA  CAZ   aromatic  1.392  0.020  1.392
 DRX  CBA  HBA   single    0.930  0.020  1.080
 DRX  CAZ  SBC   aromatic  1.730  0.020  1.730
 DRX  SBC  CAY   aromatic  1.731  0.020  1.731
 DRX  CAY  CAN   aromatic  1.354  0.020  1.354
 DRX  CAY  HAY   single    0.930  0.020  1.080
 DRX  CAN  CAM   single    1.486  0.020  1.486
 DRX  CAM  CAL   single    1.514  0.020  1.514
 DRX  CAM  PAD   single    1.909  0.020  1.909
 DRX  CAM  HAM   single    0.970  0.020  1.090
 DRX  PAD  OAE   deloc     1.524  0.020  1.524
 DRX  PAD  OAB   deloc     1.552  0.020  1.552
 DRX  PAD  OAC   deloc     1.519  0.020  1.519
 DRX  CAL  OAX   double    1.221  0.020  1.221
 DRX  CAL  NAK   single    1.360  0.020  1.360
 DRX  NAK  CAW   single    1.386  0.020  1.386
 DRX  NAK  HNAK  single    0.860  0.020  1.020
 DRX  CAW  CAJ   aromatic  1.421  0.020  1.421
 DRX  CAW  CAV   aromatic  1.380  0.020  1.380
 DRX  CAV  CAU   aromatic  1.409  0.020  1.409
 DRX  CAV  HAV   single    0.930  0.020  1.080
 DRX  CAU  CAH   aromatic  1.419  0.020  1.419
 DRX  CAU  CAT   aromatic  1.417  0.020  1.417
 DRX  CAT  CAS   aromatic  1.368  0.020  1.368
 DRX  CAT  HAT   single    0.930  0.020  1.080
 DRX  CAS  CAF   aromatic  1.412  0.020  1.412
 DRX  CAS  HAS   single    0.930  0.020  1.080
 DRX  CAF  CAG   aromatic  1.369  0.020  1.369
 DRX  CAF  HAF   single    0.930  0.020  1.080
 DRX  CAG  CAH   aromatic  1.414  0.020  1.414
 DRX  CAG  HAG   single    0.930  0.020  1.080
 DRX  CAH  CAI   aromatic  1.413  0.020  1.413
 DRX  CAI  CAJ   aromatic  1.367  0.020  1.367
 DRX  CAI  HAI   single    0.930  0.020  1.080
 DRX  CAJ  HAJ   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
 DRX  CAN   CAO  CAZ  112.77  3.000
 DRX  CAZ   CAO  CAP  118.78  3.000
 DRX  CAN   CAO  CAP  128.45  3.000
 DRX  HAP   CAP  CAQ  120.51  3.000
 DRX  HAP   CAP  CAO  120.67  3.000
 DRX  CAQ   CAP  CAO  118.83  3.000
 DRX  CBB   CAQ  CLR  118.60  3.000
 DRX  CLR   CAQ  CAP  119.15  3.000
 DRX  CBB   CAQ  CAP  122.26  3.000
 DRX  HBB   CBB  CBA  120.18  3.000
 DRX  HBB   CBB  CAQ  120.32  3.000
 DRX  CBA   CBB  CAQ  119.50  3.000
 DRX  HBA   CBA  CAZ  121.11  3.000
 DRX  HBA   CBA  CBB  120.03  3.000
 DRX  CAZ   CBA  CBB  118.87  3.000
 DRX  SBC   CAZ  CBA  127.29  3.000
 DRX  SBC   CAZ  CAO  110.95  3.000
 DRX  CBA   CAZ  CAO  121.76  3.000
 DRX  CAY   SBC  CAZ   91.08  3.000
 DRX  HAY   CAY  CAN  125.99  3.000
 DRX  HAY   CAY  SBC  119.73  3.000
 DRX  CAN   CAY  SBC  114.27  3.000
 DRX  CAM   CAN  CAY  124.75  3.000
 DRX  CAM   CAN  CAO  124.31  3.000
 DRX  CAY   CAN  CAO  110.94  3.000
 DRX  HAM   CAM  CAL  106.69  3.000
 DRX  HAM   CAM  PAD  103.86  3.000
 DRX  CAL   CAM  PAD  111.50  3.000
 DRX  HAM   CAM  CAN  109.37  3.000
 DRX  PAD   CAM  CAN  112.80  3.000
 DRX  CAL   CAM  CAN  112.10  3.000
 DRX  OAC   PAD  OAE  116.25  3.000
 DRX  OAC   PAD  OAB  113.50  3.000
 DRX  OAE   PAD  OAB  113.67  3.000
 DRX  OAC   PAD  CAM  105.04  3.000
 DRX  OAB   PAD  CAM  101.04  3.000
 DRX  OAE   PAD  CAM  105.30  3.000
 DRX  NAK   CAL  OAX  124.38  3.000
 DRX  NAK   CAL  CAM  111.98  3.000
 DRX  OAX   CAL  CAM  123.64  3.000
 DRX  HNAK  NAK  CAW  117.68  3.000
 DRX  HNAK  NAK  CAL  111.85  3.000
 DRX  CAW   NAK  CAL  128.26  3.000
 DRX  CAJ   CAW  CAV  118.74  3.000
 DRX  CAV   CAW  NAK  117.80  3.000
 DRX  CAJ   CAW  NAK  123.40  3.000
 DRX  HAV   CAV  CAU  118.90  3.000
 DRX  HAV   CAV  CAW  119.45  3.000
 DRX  CAU   CAV  CAW  121.65  3.000
 DRX  CAH   CAU  CAT  118.62  3.000
 DRX  CAT   CAU  CAV  122.01  3.000
 DRX  CAH   CAU  CAV  119.37  3.000
 DRX  HAT   CAT  CAS  120.29  3.000
 DRX  HAT   CAT  CAU  118.99  3.000
 DRX  CAS   CAT  CAU  120.72  3.000
 DRX  HAS   CAS  CAF  119.54  3.000
 DRX  HAS   CAS  CAT  119.91  3.000
 DRX  CAF   CAS  CAT  120.55  3.000
 DRX  HAF   CAF  CAG  120.24  3.000
 DRX  HAF   CAF  CAS  119.75  3.000
 DRX  CAG   CAF  CAS  120.01  3.000
 DRX  HAG   CAG  CAH  118.95  3.000
 DRX  HAG   CAG  CAF  120.36  3.000
 DRX  CAH   CAG  CAF  120.69  3.000
 DRX  CAI   CAH  CAG  122.49  3.000
 DRX  CAI   CAH  CAU  118.09  3.000
 DRX  CAG   CAH  CAU  119.42  3.000
 DRX  HAI   CAI  CAJ  119.31  3.000
 DRX  HAI   CAI  CAH  118.88  3.000
 DRX  CAJ   CAI  CAH  121.81  3.000
 DRX  HAJ   CAJ  CAI  119.49  3.000
 DRX  HAJ   CAJ  CAW  120.16  3.000
 DRX  CAI   CAJ  CAW  120.35  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
 DRX  CONST_01  SBC   CAY  CAN  CAO    0.00  0.0  0
 DRX  CONST_02  CBB   CBA  CAZ  CAO    0.00  0.0  0
 DRX  CONST_03  CAY   SBC  CAZ  CAO    0.00  0.0  0
 DRX  CONST_04  CBB   CAQ  CAP  CAO    0.00  0.0  0
 DRX  CONST_05  CAY   CAN  CAO  CAP  180.00  0.0  0
 DRX  CONST_06  CBA   CAZ  CAO  CAP    0.00  0.0  0
 DRX  CONST_07  SBC   CAZ  CAO  CAP  180.00  0.0  0
 DRX  CONST_08  CBA   CBB  CAQ  CAP    0.00  0.0  0
 DRX  CONST_09  CAN   CAO  CAP  CAQ  180.00  0.0  0
 DRX  CONST_10  CAZ   CAO  CAP  CAQ    0.00  0.0  0
 DRX  CONST_11  CAZ   CBA  CBB  CAQ    0.00  0.0  0
 DRX  CONST_12  SBC   CAZ  CBA  CBB  180.00  0.0  0
 DRX  CONST_13  CAN   CAO  CAZ  CBA  180.00  0.0  0
 DRX  CONST_14  CAY   SBC  CAZ  CBA  180.00  0.0  0
 DRX  CONST_15  CAY   CAN  CAO  CAZ    0.00  0.0  0
 DRX  CONST_16  CAN   CAY  SBC  CAZ    0.00  0.0  0
 DRX  CONST_17  CAN   CAO  CAZ  SBC    0.00  0.0  0
 DRX  CONST_18  CAH   CAI  CAJ  CAW    0.00  0.0  0
 DRX  CONST_19  CAH   CAU  CAV  CAW    0.00  0.0  0
 DRX  CONST_20  CAT   CAU  CAV  CAW  180.00  0.0  0
 DRX  CONST_21  CAI   CAJ  CAW  CAV    0.00  0.0  0
 DRX  CONST_22  CAG   CAH  CAU  CAV  180.00  0.0  0
 DRX  CONST_23  CAI   CAH  CAU  CAV    0.00  0.0  0
 DRX  CONST_24  CAS   CAT  CAU  CAV  180.00  0.0  0
 DRX  CONST_25  CAJ   CAW  CAV  CAU    0.00  0.0  0
 DRX  CONST_26  CAF   CAG  CAH  CAU    0.00  0.0  0
 DRX  CONST_27  CAJ   CAI  CAH  CAU    0.00  0.0  0
 DRX  CONST_28  CAF   CAS  CAT  CAU    0.00  0.0  0
 DRX  CONST_29  CAG   CAH  CAU  CAT    0.00  0.0  0
 DRX  CONST_30  CAI   CAH  CAU  CAT  180.00  0.0  0
 DRX  CONST_31  CAG   CAF  CAS  CAT    0.00  0.0  0
 DRX  CONST_32  CAH   CAU  CAT  CAS    0.00  0.0  0
 DRX  CONST_33  CAH   CAG  CAF  CAS    0.00  0.0  0
 DRX  CONST_34  CAI   CAH  CAG  CAF  180.00  0.0  0
 DRX  CONST_35  CAJ   CAI  CAH  CAG  180.00  0.0  0
 DRX  CONST_36  CLR   CAQ  CAP  CAO  180.00  0.0  0
 DRX  CONST_37  CAM   CAN  CAO  CAP    0.00  0.0  0
 DRX  CONST_38  CBA   CBB  CAQ  CLR  180.00  0.0  0
 DRX  CONST_39  CAM   CAN  CAO  CAZ  180.00  0.0  0
 DRX  CONST_40  CAM   CAN  CAY  SBC  180.00  0.0  0
 DRX  CONST_41  CAI   CAJ  CAW  NAK  180.00  0.0  0
 DRX  CONST_42  CAU   CAV  CAW  NAK  180.00  0.0  0
 DRX  CONST_43  HAY   CAY  CAN  CAO  180.00  0.0  0
 DRX  CONST_44  HBA   CBA  CAZ  CAO  180.00  0.0  0
 DRX  CONST_45  HBB   CBB  CAQ  CAP  180.00  0.0  0
 DRX  CONST_46  HAP   CAP  CAQ  CBB  180.00  0.0  0
 DRX  CONST_47  HAI   CAI  CAJ  CAW  180.00  0.0  0
 DRX  CONST_48  HAJ   CAJ  CAW  CAV  180.00  0.0  0
 DRX  CONST_49  HAT   CAT  CAU  CAV    0.00  0.0  0
 DRX  CONST_50  HAG   CAG  CAH  CAU  180.00  0.0  0
 DRX  CONST_51  HAS   CAS  CAT  CAU  180.00  0.0  0
 DRX  CONST_52  HAV   CAV  CAU  CAT    0.00  0.0  0
 DRX  CONST_53  HAF   CAF  CAS  CAT  180.00  0.0  0
 DRX  CONST_56  HNAK  NAK  CAW  CAV    0.00  0.0  0
 DRX  CONST_57  CAW   NAK  CAL  CAM  180.00  0.0  0
 DRX  CONST_58  CAW   NAK  CAL  OAX    0.00  0.0  0

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
 DRX  chir_01  CAM  CAN  CAL  PAD  negativ

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
 DRX  plan-1  CAO   0.020
 DRX  plan-1  CAP   0.020
 DRX  plan-1  CAQ   0.020
 DRX  plan-1  CLR   0.020
 DRX  plan-1  CBB   0.020
 DRX  plan-1  CBA   0.020
 DRX  plan-1  CAZ   0.020
 DRX  plan-1  SBC   0.020
 DRX  plan-1  CAY   0.020
 DRX  plan-1  CAN   0.020
 DRX  plan-1  CAM   0.020
 DRX  plan-1  HAP   0.020
 DRX  plan-1  HBB   0.020
 DRX  plan-1  HBA   0.020
 DRX  plan-1  HAY   0.020
 DRX  plan-2  NAK   0.020
 DRX  plan-2  CAW   0.020
 DRX  plan-2  CAV   0.020
 DRX  plan-2  CAU   0.020
 DRX  plan-2  CAT   0.020
 DRX  plan-2  CAS   0.020
 DRX  plan-2  CAF   0.020
 DRX  plan-2  CAG   0.020
 DRX  plan-2  CAH   0.020
 DRX  plan-2  CAI   0.020
 DRX  plan-2  CAJ   0.020
 DRX  plan-2  HAV   0.020
 DRX  plan-2  HAT   0.020
 DRX  plan-2  HAS   0.020
 DRX  plan-2  HAF   0.020
 DRX  plan-2  HAG   0.020
 DRX  plan-2  HAI   0.020
 DRX  plan-2  HAJ   0.020
 DRX  plan-3  CAM   0.020
 DRX  plan-3  CAL   0.020
 DRX  plan-3  OAX   0.020
 DRX  plan-3  NAK   0.020
 DRX  plan-3  CAW   0.020
 DRX  plan-3  HNAK  0.020

