# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:06:36 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2',5'-dideoxy-5'-{[(4-nitrophenyl)carbamoyl]amino}-3,4-dihydrothymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2C[C@H](O)[C@@H](CNC(=O)Nc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O
#
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
 WMJ  WMJ  2',5'-dideoxy-5'-{[(4-nitrophenyl)carbamoyl]amino}-3,4-dihydrothymidine  ligand  48  29  .  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_WMJ
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
 WMJ  OAD   O  O      0  -0.639   5.4123   0.1082   2.2776
 WMJ  CAX   C  CR6    0   0.731   4.9956   0.7190   1.3145
 WMJ  NAQ   N  NR16   0  -0.593   5.3915   2.0026   1.0439
 WMJ  CAW   C  CR6    0   0.498   4.9965   2.8175  -0.0016
 WMJ  OAC   O  O      0  -0.558   5.4405   3.9452  -0.1093
 WMJ  CAT   C  CR6    0  -0.082   4.0396   2.2094  -0.9065
 WMJ  CAA   C  CH3    0  -0.734   3.5355   3.0047  -2.0650
 WMJ  CAL   C  CR16   0  -0.032   3.6478   0.9510  -0.6502
 WMJ  NBC   N  NR6    0  -0.437   4.1048   0.1998   0.4026
 WMJ  CBA   C  CR15   0   0.225   3.5758  -1.1425   0.5975
 WMJ  OAR   O  O      0  -0.533   2.1756  -1.0680   0.7556
 WMJ  CAN   C  CH2    0  -0.530   3.8317  -2.0895  -0.5674
 WMJ  CAY   C  CR15   0  -0.004   2.6063  -2.9945  -0.5056
 WMJ  OAE   O  OH1    0  -0.679   2.2486  -3.6157  -1.7070
 WMJ  CAZ   C  CR15   0  -0.005   1.5202  -2.0047  -0.0903
 WMJ  CAM   C  CH2    0  -0.261   0.3692  -2.6478   0.6594
 WMJ  NAO   N  NH1    0  -0.666  -0.6232  -1.7049   1.1118
 WMJ  CAS   C  C      0   0.757  -1.6582  -1.3177   0.3364
 WMJ  OAB   O  O      0  -0.550  -1.8529  -1.7501  -0.7872
 WMJ  NAP   N  NH1    0  -0.727  -2.4819  -0.3926   0.9513
 WMJ  CAU   C  CR6    0   0.306  -3.6484   0.1676   0.4797
 WMJ  CAI   C  CR16   0  -0.306  -4.3440   1.0044   1.3672
 WMJ  CAK   C  CR16   0  -0.337  -5.5240   1.6104   1.0047
 WMJ  CAH   C  CR16   0  -0.222  -4.1772  -0.0351  -0.8029
 WMJ  CAJ   C  CR16   0  -0.313  -5.3680   0.5648  -1.1614
 WMJ  CAV   C  CR6    0   0.317  -6.0398   1.3856  -0.2666
 WMJ  NBB   N  N      1   0.318  -7.2788   2.0121  -0.6585
 WMJ  OAG   O  O     -1  -0.402  -7.8454   2.7135   0.1500
 WMJ  OAF   O  O      0  -0.338  -7.6954   1.8081  -1.7771
 WMJ  HAQ   H  HNR6   0   0.432   6.0523   2.3972   1.7017
 WMJ  HAA1  H  HCH3   0   0.280   4.3552   3.3346  -2.7044
 WMJ  HAA2  H  HCH3   0   0.280   2.8526   2.4153  -2.6745
 WMJ  HAA3  H  HCH3   0   0.233   3.0050   3.8987  -1.7345
 WMJ  HAL   H  HCR6   0   0.305   2.9284   0.4615  -1.2922
 WMJ  HBA   H  HCR5   0   0.328   4.0294  -1.5197   1.5131
 WMJ  HAN1  H  HCH2   0   0.248   3.8472  -1.5623  -1.5254
 WMJ  HAN2  H  HCH2   0   0.282   4.7781  -2.6173  -0.4575
 WMJ  HAZ   H  HCR5   0   0.237   1.1390  -1.4937  -0.9854
 WMJ  HAY   H  HCR5   0   0.269   2.7436  -3.7324   0.2983
 WMJ  HAE   H  HOH1   0   0.445   2.8613  -4.3383  -1.8704
 WMJ  HAM1  H  HCH2   0   0.293  -0.0999  -3.3924   0.0163
 WMJ  HAM2  H  HCH2   0   0.247   0.7531  -3.1734   1.5356
 WMJ  HAO   H  HNH1   0   0.396  -0.4667  -1.2690   2.0053
 WMJ  HAP   H  HNH1   0   0.361  -2.2484  -0.1365   1.8990
 WMJ  HAI   H  HCR6   0   0.294  -3.9510   1.1765   2.3615
 WMJ  HAH   H  HCR6   0   0.296  -3.6763  -0.6660  -1.5164
 WMJ  HAK   H  HCR6   0   0.286  -6.0307   2.2492   1.7129
 WMJ  HAJ   H  HCR6   0   0.284  -5.7607   0.3877  -2.1522

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
 WMJ  OAD  CAX   double    1.214  0.020  1.214
 WMJ  CAX  NAQ   single    1.370  0.020  1.370
 WMJ  CAX  NBC   single    1.376  0.020  1.376
 WMJ  NAQ  CAW   single    1.383  0.020  1.383
 WMJ  CAW  OAC   double    1.217  0.020  1.217
 WMJ  CAW  CAT   single    1.451  0.020  1.451
 WMJ  CAT  CAA   single    1.493  0.020  1.493
 WMJ  CAT  CAL   double    1.343  0.020  1.343
 WMJ  CAL  NBC   single    1.372  0.020  1.372
 WMJ  NBC  CBA   single    1.456  0.020  1.456
 WMJ  CBA  OAR   single    1.411  0.020  1.411
 WMJ  CBA  CAN   single    1.523  0.020  1.523
 WMJ  OAR  CAZ   single    1.422  0.020  1.422
 WMJ  CAN  CAY   single    1.525  0.020  1.525
 WMJ  CAY  OAE   single    1.399  0.020  1.399
 WMJ  CAY  CAZ   single    1.527  0.020  1.527
 WMJ  CAZ  CAM   single    1.517  0.020  1.517
 WMJ  CAM  NAO   single    1.442  0.020  1.442
 WMJ  NAO  CAS   single    1.350  0.020  1.350
 WMJ  CAS  OAB   double    1.220  0.020  1.220
 WMJ  CAS  NAP   single    1.383  0.020  1.383
 WMJ  NAP  CAU   single    1.377  0.020  1.377
 WMJ  CAU  CAI   aromatic  1.404  0.020  1.404
 WMJ  CAU  CAH   aromatic  1.402  0.020  1.402
 WMJ  CAI  CAK   aromatic  1.375  0.020  1.375
 WMJ  CAK  CAV   aromatic  1.390  0.020  1.390
 WMJ  CAH  CAJ   aromatic  1.381  0.020  1.381
 WMJ  CAJ  CAV   aromatic  1.388  0.020  1.388
 WMJ  CAV  NBB   single    1.443  0.020  1.443
 WMJ  NBB  OAG   single    1.211  0.020  1.211
 WMJ  NBB  OAF   double    1.211  0.020  1.211
 WMJ  NAQ  HAQ   single    0.860  0.020  1.020
 WMJ  CAA  HAA1  single    0.970  0.020  1.090
 WMJ  CAA  HAA2  single    0.970  0.020  1.090
 WMJ  CAA  HAA3  single    0.970  0.020  1.090
 WMJ  CAL  HAL   single    0.930  0.020  1.080
 WMJ  CBA  HBA   single    0.970  0.020  1.090
 WMJ  CAN  HAN1  single    0.970  0.020  1.090
 WMJ  CAN  HAN2  single    0.970  0.020  1.090
 WMJ  CAZ  HAZ   single    0.970  0.020  1.090
 WMJ  CAY  HAY   single    0.970  0.020  1.090
 WMJ  OAE  HAE   single    0.850  0.020  0.980
 WMJ  CAM  HAM1  single    0.970  0.020  1.090
 WMJ  CAM  HAM2  single    0.970  0.020  1.090
 WMJ  NAO  HAO   single    0.860  0.020  1.020
 WMJ  NAP  HAP   single    0.860  0.020  1.020
 WMJ  CAI  HAI   single    0.930  0.020  1.080
 WMJ  CAH  HAH   single    0.930  0.020  1.080
 WMJ  CAK  HAK   single    0.930  0.020  1.080
 WMJ  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
 WMJ  NBC   CAX  NAQ   114.17  3.000
 WMJ  NBC   CAX  OAD   123.91  3.000
 WMJ  NAQ   CAX  OAD   121.92  3.000
 WMJ  HAQ   NAQ  CAW   116.61  3.000
 WMJ  HAQ   NAQ  CAX   115.17  3.000
 WMJ  CAW   NAQ  CAX   128.22  3.000
 WMJ  CAT   CAW  OAC   125.03  3.000
 WMJ  CAT   CAW  NAQ   114.39  3.000
 WMJ  OAC   CAW  NAQ   120.58  3.000
 WMJ  CAL   CAT  CAA   123.29  3.000
 WMJ  CAL   CAT  CAW   117.80  3.000
 WMJ  CAA   CAT  CAW   118.91  3.000
 WMJ  HAA3  CAA  HAA2  107.95  3.000
 WMJ  HAA3  CAA  HAA1  107.17  3.000
 WMJ  HAA2  CAA  HAA1  107.87  3.000
 WMJ  HAA3  CAA  CAT   111.45  3.000
 WMJ  HAA2  CAA  CAT   110.97  3.000
 WMJ  HAA1  CAA  CAT   111.24  3.000
 WMJ  HAL   CAL  NBC   115.43  3.000
 WMJ  HAL   CAL  CAT   120.34  3.000
 WMJ  NBC   CAL  CAT   124.23  3.000
 WMJ  CBA   NBC  CAL   119.12  3.000
 WMJ  CBA   NBC  CAX   119.62  3.000
 WMJ  CAL   NBC  CAX   121.16  3.000
 WMJ  HBA   CBA  CAN   110.95  3.000
 WMJ  HBA   CBA  OAR   109.71  3.000
 WMJ  CAN   CBA  OAR   106.58  3.000
 WMJ  HBA   CBA  NBC   106.29  3.000
 WMJ  CAN   CBA  NBC   114.20  3.000
 WMJ  OAR   CBA  NBC   109.08  3.000
 WMJ  CAZ   OAR  CBA   110.85  3.000
 WMJ  HAN2  CAN  HAN1  108.04  3.000
 WMJ  HAN2  CAN  CAY   114.00  3.000
 WMJ  HAN1  CAN  CAY   109.45  3.000
 WMJ  HAN2  CAN  CBA   111.73  3.000
 WMJ  HAN1  CAN  CBA   111.88  3.000
 WMJ  CAY   CAN  CBA   101.72  3.000
 WMJ  HAY   CAY  CAZ   108.95  3.000
 WMJ  HAY   CAY  OAE   111.20  3.000
 WMJ  CAZ   CAY  OAE   109.85  3.000
 WMJ  HAY   CAY  CAN   109.12  3.000
 WMJ  CAZ   CAY  CAN   101.42  3.000
 WMJ  OAE   CAY  CAN   115.75  3.000
 WMJ  HAE   OAE  CAY   108.46  3.000
 WMJ  HAZ   CAZ  CAM   109.67  3.000
 WMJ  HAZ   CAZ  CAY   109.06  3.000
 WMJ  CAM   CAZ  CAY   113.54  3.000
 WMJ  HAZ   CAZ  OAR   109.76  3.000
 WMJ  CAM   CAZ  OAR   109.57  3.000
 WMJ  CAY   CAZ  OAR   105.12  3.000
 WMJ  HAM2  CAM  HAM1  107.22  3.000
 WMJ  HAM2  CAM  NAO   107.77  3.000
 WMJ  HAM1  CAM  NAO   109.61  3.000
 WMJ  HAM2  CAM  CAZ   109.52  3.000
 WMJ  HAM1  CAM  CAZ   108.94  3.000
 WMJ  NAO   CAM  CAZ   113.59  3.000
 WMJ  HAO   NAO  CAS   120.33  3.000
 WMJ  HAO   NAO  CAM   117.05  3.000
 WMJ  CAS   NAO  CAM   122.35  3.000
 WMJ  NAP   CAS  OAB   123.49  3.000
 WMJ  NAP   CAS  NAO   113.15  3.000
 WMJ  OAB   CAS  NAO   123.36  3.000
 WMJ  HAP   NAP  CAU   114.48  3.000
 WMJ  HAP   NAP  CAS   116.72  3.000
 WMJ  CAU   NAP  CAS   128.63  3.000
 WMJ  CAH   CAU  CAI   118.52  3.000
 WMJ  CAH   CAU  NAP   125.02  3.000
 WMJ  CAI   CAU  NAP   116.45  3.000
 WMJ  HAI   CAI  CAK   118.91  3.000
 WMJ  HAI   CAI  CAU   119.69  3.000
 WMJ  CAK   CAI  CAU   121.40  3.000
 WMJ  HAK   CAK  CAV   121.41  3.000
 WMJ  HAK   CAK  CAI   119.36  3.000
 WMJ  CAV   CAK  CAI   119.22  3.000
 WMJ  HAH   CAH  CAJ   118.95  3.000
 WMJ  HAH   CAH  CAU   121.05  3.000
 WMJ  CAJ   CAH  CAU   120.00  3.000
 WMJ  HAJ   CAJ  CAV   120.82  3.000
 WMJ  HAJ   CAJ  CAH   118.71  3.000
 WMJ  CAV   CAJ  CAH   120.47  3.000
 WMJ  NBB   CAV  CAJ   119.83  3.000
 WMJ  NBB   CAV  CAK   119.79  3.000
 WMJ  CAJ   CAV  CAK   120.37  3.000
 WMJ  OAF   NBB  OAG   123.59  3.000
 WMJ  OAF   NBB  CAV   118.24  3.000
 WMJ  OAG   NBB  CAV   118.16  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
 WMJ  CONST_01  CAV   CAK  CAI  CAU    0.00   0.0  0
 WMJ  CONST_02  CAV   CAJ  CAH  CAU    0.00   0.0  0
 WMJ  CONST_03  CAJ   CAH  CAU  CAI    0.00   0.0  0
 WMJ  CONST_04  CAJ   CAV  CAK  CAI    0.00   0.0  0
 WMJ  CONST_05  CAH   CAU  CAI  CAK    0.00   0.0  0
 WMJ  CONST_06  CAH   CAJ  CAV  CAK    0.00   0.0  0
 WMJ  CONST_07  CAL   NBC  CAX  NAQ    0.00   0.0  0
 WMJ  CONST_08  CBA   NBC  CAX  NAQ  180.00   0.0  0
 WMJ  CONST_09  NBC   CAX  NAQ  CAW    0.00   0.0  0
 WMJ  CONST_10  CAK   CAI  CAU  NAP  180.00   0.0  0
 WMJ  CONST_11  CAJ   CAH  CAU  NAP  180.00   0.0  0
 WMJ  CONST_12  NBB   CAV  CAK  CAI  180.00   0.0  0
 WMJ  CONST_13  NBB   CAV  CAJ  CAH  180.00   0.0  0
 WMJ  CONST_14  CAW   NAQ  CAX  OAD  180.00   0.0  0
 WMJ  CONST_15  CAL   NBC  CAX  OAD  180.00   0.0  0
 WMJ  CONST_16  CBA   NBC  CAX  OAD    0.00   0.0  0
 WMJ  CONST_17  HAK   CAK  CAI  CAU  180.00   0.0  0
 WMJ  CONST_18  HAJ   CAJ  CAH  CAU  180.00   0.0  0
 WMJ  CONST_19  HAH   CAH  CAU  CAI  180.00   0.0  0
 WMJ  CONST_20  HAI   CAI  CAU  CAH  180.00   0.0  0
 WMJ  CONST_21  HAQ   NAQ  CAX  NBC  180.00   0.0  0
 WMJ  CONST_22  CAI   CAU  NAP  CAS  180.00   0.0  0
 WMJ  CONST_23  CAH   CAU  NAP  CAS    0.00   0.0  0
 WMJ  CONST_24  OAG   NBB  CAV  CAK    0.00   0.0  0
 WMJ  CONST_25  OAF   NBB  CAV  CAK  180.00   0.0  0
 WMJ  CONST_26  OAG   NBB  CAV  CAJ  180.00   0.0  0
 WMJ  CONST_27  OAF   NBB  CAV  CAJ    0.00   0.0  0
 WMJ  CONST_28  HAP   NAP  CAU  CAI    0.00   0.0  0
 WMJ  CONST_29  CAU   NAP  CAS  OAB    0.00   0.0  0
 WMJ  CONST_30  CAU   NAP  CAS  NAO  180.00   0.0  0
 WMJ  CONST_31  OAB   CAS  NAO  CAM    0.00   0.0  0
 WMJ  CONST_32  NAP   CAS  NAO  CAM  180.00   0.0  0
 WMJ  CONST_33  HAO   NAO  CAS  OAB  180.00   0.0  0
 WMJ  Var_01    HAA1  CAA  CAT  CAW   58.03  30.0  3
 WMJ  Var_02    CAS   NAO  CAM  CAZ   87.19  30.0  3

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
 WMJ  chir_01  CBA  NBC  OAR  CAN  negativ
 WMJ  chir_02  CAY  OAE  CAZ  CAN  positiv
 WMJ  chir_03  CAZ  OAR  CAY  CAM  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
 WMJ  plan-1  OAD  0.020
 WMJ  plan-1  CAX  0.020
 WMJ  plan-1  NAQ  0.020
 WMJ  plan-1  CAW  0.020
 WMJ  plan-1  OAC  0.020
 WMJ  plan-1  CAT  0.020
 WMJ  plan-1  CAA  0.020
 WMJ  plan-1  CAL  0.020
 WMJ  plan-1  NBC  0.020
 WMJ  plan-1  CBA  0.020
 WMJ  plan-1  HAQ  0.020
 WMJ  plan-1  HAL  0.020
 WMJ  plan-2  NAP  0.020
 WMJ  plan-2  CAU  0.020
 WMJ  plan-2  CAI  0.020
 WMJ  plan-2  CAK  0.020
 WMJ  plan-2  CAH  0.020
 WMJ  plan-2  CAJ  0.020
 WMJ  plan-2  CAV  0.020
 WMJ  plan-2  NBB  0.020
 WMJ  plan-2  HAI  0.020
 WMJ  plan-2  HAH  0.020
 WMJ  plan-2  HAK  0.020
 WMJ  plan-2  HAJ  0.020
 WMJ  plan-3  CAM  0.020
 WMJ  plan-3  NAO  0.020
 WMJ  plan-3  CAS  0.020
 WMJ  plan-3  OAB  0.020
 WMJ  plan-3  NAP  0.020
 WMJ  plan-3  CAU  0.020
 WMJ  plan-3  HAO  0.020
 WMJ  plan-3  HAP  0.020
 WMJ  plan-4  CAV  0.020
 WMJ  plan-4  NBB  0.020
 WMJ  plan-4  OAG  0.020
 WMJ  plan-4  OAF  0.020

