# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 20:58:26 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[(3S)-5-(4-iodophenoxy)-3-methylpentyl]-3-(pyridin-4-yl)imidazolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CCOc1ccc(I)cc1)CCN2CCN(C2=O)c3ccncc3
#
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
 VR2  VR2  1-[(3S)-5-(4-iodophenoxy)-3-methylpentyl]-3-(pyridin-4-yl)imidazolidin-2-one  ligand  50  26  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VR2
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
 VR2  CAJ   C  CR16  0  -0.340  -3.7025   0.8959  -1.7115
 VR2  CAH   C  CR16  0  -0.208  -5.0551   1.1359  -1.5560
 VR2  CAU   C  CR6   0  -0.248  -5.7106   0.6692  -0.4222
 VR2  IAC   I  I     0   0.039  -7.7686   1.0313  -0.1812
 VR2  CAI   C  CR16  0  -0.208  -5.0153  -0.0319   0.5474
 VR2  CAK   C  CR16  0  -0.375  -3.6550  -0.2738   0.3918
 VR2  CAV   C  CR6   0   0.394  -2.9888   0.1879  -0.7413
 VR2  OAS   O  O2    0  -0.472  -1.6816   0.0012  -0.9823
 VR2  CAL   C  CH2   0  -0.178  -0.9007  -0.7157  -0.0353
 VR2  CAM   C  CH2   0  -0.446   0.5182  -0.7859  -0.5621
 VR2  CAX   C  CH1   0  -0.244   1.4767  -1.4932   0.4008
 VR2  CAA   C  CH3   0  -0.673   1.1781  -2.9885   0.5018
 VR2  CAN   C  CH2   0  -0.426   2.9209  -1.2355  -0.0339
 VR2  CAO   C  CH2   0  -0.295   3.9564  -1.7332   0.9710
 VR2  NAY   N  NR5   0  -0.508   5.3184  -1.4823   0.5606
 VR2  CAT   C  CR5   0   0.752   5.8926  -0.2629   0.6615
 VR2  OAB   O  O     0  -0.503   5.4435   0.6934   1.2652
 VR2  CAP   C  CH2   0  -0.290   6.0067  -2.3329  -0.3826
 VR2  CAQ   C  CH2   0  -0.320   7.3738  -1.6642  -0.4821
 VR2  NAZ   N  NR5   0  -0.627   7.0969  -0.3076  -0.0327
 VR2  CAW   C  CR6   0   0.464   8.0424   0.6935  -0.1026
 VR2  CAF   C  CR16  0  -0.379   7.7787   2.0380   0.1922
 VR2  CAD   C  CR16  0  -0.073   8.7987   2.9607   0.0548
 VR2  NAR   N  N     0  -0.421  10.0353   2.6764  -0.3436
 VR2  CAE   C  CR16  0  -0.070  10.2777   1.4019  -0.6242
 VR2  CAG   C  CR16  0  -0.417   9.3418   0.3884  -0.5241
 VR2  HAJ   H  HCR6  0   0.273  -3.1900   1.2597  -2.5931
 VR2  HAH   H  HCR6  0   0.279  -5.5844   1.6845  -2.3233
 VR2  HAI   H  HCR6  0   0.281  -5.5113  -0.4021   1.4343
 VR2  HAK   H  HCR6  0   0.289  -3.1414  -0.8253   1.1669
 VR2  HAL1  H  HCH2  0   0.224  -0.9169  -0.2026   0.9337
 VR2  HAL2  H  HCH2  0   0.226  -1.3204  -1.7161   0.1128
 VR2  HAM1  H  HCH2  0   0.230   0.5266  -1.2976  -1.5298
 VR2  HAM2  H  HCH2  0   0.239   0.8726   0.2340  -0.7380
 VR2  HAX   H  HCH1  0   0.221   1.3427  -1.0488   1.3955
 VR2  HAA1  H  HCH3  0   0.237   1.7939  -3.4751   1.2584
 VR2  HAA2  H  HCH3  0   0.236   0.1404  -3.1818   0.7738
 VR2  HAA3  H  HCH3  0   0.220   1.3694  -3.4860  -0.4521
 VR2  HAN1  H  HCH2  0   0.224   3.0930  -1.7037  -1.0091
 VR2  HAN2  H  HCH2  0   0.236   3.0653  -0.1606  -0.1738
 VR2  HAO1  H  HCH2  0   0.251   3.7909  -1.2617   1.9415
 VR2  HAO2  H  HCH2  0   0.253   3.8655  -2.8087   1.1284
 VR2  HAP1  H  HCH2  0   0.266   6.0796  -3.3561  -0.0162
 VR2  HAP2  H  HCH2  0   0.252   5.4978  -2.3530  -1.3507
 VR2  HAQ1  H  HCH2  0   0.266   8.1055  -2.1470   0.1707
 VR2  HAQ2  H  HCH2  0   0.275   7.7593  -1.6725  -1.5002
 VR2  HAF   H  HCR6  0   0.285   6.8074   2.3733   0.5131
 VR2  HAG   H  HCR6  0   0.286   9.6424  -0.6196  -0.7699
 VR2  HAD   H  HCR6  0   0.261   8.5916   4.0017   0.2793
 VR2  HAE   H  HCR6  0   0.263  11.2829   1.1573  -0.9505

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
 VR2  CAJ  CAH   aromatic  1.383  0.020  1.383
 VR2  CAJ  CAV   aromatic  1.397  0.020  1.397
 VR2  CAH  CAU   aromatic  1.390  0.020  1.390
 VR2  CAU  IAC   single    2.104  0.020  2.104
 VR2  CAU  CAI   aromatic  1.384  0.020  1.384
 VR2  CAI  CAK   aromatic  1.390  0.020  1.390
 VR2  CAK  CAV   aromatic  1.393  0.020  1.393
 VR2  CAV  OAS   single    1.342  0.020  1.342
 VR2  OAS  CAL   single    1.421  0.020  1.421
 VR2  CAL  CAM   single    1.515  0.020  1.515
 VR2  CAM  CAX   single    1.532  0.020  1.532
 VR2  CAX  CAA   single    1.528  0.020  1.528
 VR2  CAX  CAN   single    1.530  0.020  1.530
 VR2  CAN  CAO   single    1.526  0.020  1.526
 VR2  CAO  NAY   single    1.444  0.020  1.444
 VR2  NAY  CAT   single    1.352  0.020  1.352
 VR2  NAY  CAP   single    1.445  0.020  1.445
 VR2  CAT  OAB   double    1.217  0.020  1.217
 VR2  CAT  NAZ   single    1.391  0.020  1.391
 VR2  CAP  CAQ   single    1.525  0.020  1.525
 VR2  CAQ  NAZ   single    1.456  0.020  1.456
 VR2  NAZ  CAW   single    1.379  0.020  1.379
 VR2  CAW  CAF   aromatic  1.401  0.020  1.401
 VR2  CAW  CAG   aromatic  1.400  0.020  1.400
 VR2  CAF  CAD   aromatic  1.382  0.020  1.382
 VR2  CAD  NAR   aromatic  1.330  0.020  1.330
 VR2  NAR  CAE   aromatic  1.327  0.020  1.327
 VR2  CAE  CAG   aromatic  1.383  0.020  1.383
 VR2  CAJ  HAJ   single    0.930  0.020  1.080
 VR2  CAH  HAH   single    0.930  0.020  1.080
 VR2  CAI  HAI   single    0.930  0.020  1.080
 VR2  CAK  HAK   single    0.930  0.020  1.080
 VR2  CAL  HAL1  single    0.970  0.020  1.090
 VR2  CAL  HAL2  single    0.970  0.020  1.090
 VR2  CAM  HAM1  single    0.970  0.020  1.090
 VR2  CAM  HAM2  single    0.970  0.020  1.090
 VR2  CAX  HAX   single    0.970  0.020  1.090
 VR2  CAA  HAA1  single    0.970  0.020  1.090
 VR2  CAA  HAA2  single    0.970  0.020  1.090
 VR2  CAA  HAA3  single    0.970  0.020  1.090
 VR2  CAN  HAN1  single    0.970  0.020  1.090
 VR2  CAN  HAN2  single    0.970  0.020  1.090
 VR2  CAO  HAO1  single    0.970  0.020  1.090
 VR2  CAO  HAO2  single    0.970  0.020  1.090
 VR2  CAP  HAP1  single    0.970  0.020  1.090
 VR2  CAP  HAP2  single    0.970  0.020  1.090
 VR2  CAQ  HAQ1  single    0.970  0.020  1.090
 VR2  CAQ  HAQ2  single    0.970  0.020  1.090
 VR2  CAF  HAF   single    0.930  0.020  1.080
 VR2  CAG  HAG   single    0.930  0.020  1.080
 VR2  CAD  HAD   single    0.930  0.020  1.080
 VR2  CAE  HAE   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
 VR2  HAJ   CAJ  CAV   119.60  3.000
 VR2  HAJ   CAJ  CAH   119.76  3.000
 VR2  CAV   CAJ  CAH   120.64  3.000
 VR2  HAH   CAH  CAU   121.20  3.000
 VR2  HAH   CAH  CAJ   119.15  3.000
 VR2  CAU   CAH  CAJ   119.65  3.000
 VR2  CAI   CAU  IAC   119.90  3.000
 VR2  CAI   CAU  CAH   120.31  3.000
 VR2  IAC   CAU  CAH   119.79  3.000
 VR2  HAI   CAI  CAK   118.74  3.000
 VR2  HAI   CAI  CAU   121.17  3.000
 VR2  CAK   CAI  CAU   120.08  3.000
 VR2  HAK   CAK  CAV   121.67  3.000
 VR2  HAK   CAK  CAI   118.25  3.000
 VR2  CAV   CAK  CAI   120.08  3.000
 VR2  OAS   CAV  CAK   124.45  3.000
 VR2  OAS   CAV  CAJ   116.31  3.000
 VR2  CAK   CAV  CAJ   119.24  3.000
 VR2  CAL   OAS  CAV   119.05  3.000
 VR2  HAL2  CAL  HAL1  107.59  3.000
 VR2  HAL2  CAL  CAM   111.32  3.000
 VR2  HAL1  CAL  CAM   110.05  3.000
 VR2  HAL2  CAL  OAS   109.89  3.000
 VR2  HAL1  CAL  OAS   110.16  3.000
 VR2  CAM   CAL  OAS   107.83  3.000
 VR2  HAM2  CAM  HAM1  106.93  3.000
 VR2  HAM2  CAM  CAX   109.20  3.000
 VR2  HAM1  CAM  CAX   109.58  3.000
 VR2  HAM2  CAM  CAL   108.42  3.000
 VR2  HAM1  CAM  CAL   109.65  3.000
 VR2  CAX   CAM  CAL   112.88  3.000
 VR2  HAX   CAX  CAN   107.72  3.000
 VR2  HAX   CAX  CAA   108.20  3.000
 VR2  CAN   CAX  CAA   111.59  3.000
 VR2  HAX   CAX  CAM   107.84  3.000
 VR2  CAN   CAX  CAM   109.53  3.000
 VR2  CAA   CAX  CAM   111.79  3.000
 VR2  HAA3  CAA  HAA2  107.68  3.000
 VR2  HAA3  CAA  HAA1  107.68  3.000
 VR2  HAA2  CAA  HAA1  106.59  3.000
 VR2  HAA3  CAA  CAX   110.70  3.000
 VR2  HAA2  CAA  CAX   112.09  3.000
 VR2  HAA1  CAA  CAX   111.86  3.000
 VR2  HAN2  CAN  HAN1  106.59  3.000
 VR2  HAN2  CAN  CAO   108.37  3.000
 VR2  HAN1  CAN  CAO   109.89  3.000
 VR2  HAN2  CAN  CAX   109.06  3.000
 VR2  HAN1  CAN  CAX   109.22  3.000
 VR2  CAO   CAN  CAX   113.48  3.000
 VR2  HAO2  CAO  HAO1  106.55  3.000
 VR2  HAO2  CAO  NAY   106.91  3.000
 VR2  HAO1  CAO  NAY   108.70  3.000
 VR2  HAO2  CAO  CAN   111.10  3.000
 VR2  HAO1  CAO  CAN   109.97  3.000
 VR2  NAY   CAO  CAN   113.33  3.000
 VR2  CAP   NAY  CAT   112.18  3.000
 VR2  CAP   NAY  CAO   122.18  3.000
 VR2  CAT   NAY  CAO   122.42  3.000
 VR2  NAZ   CAT  OAB   126.34  3.000
 VR2  NAZ   CAT  NAY   107.56  3.000
 VR2  OAB   CAT  NAY   126.10  3.000
 VR2  HAP2  CAP  HAP1  108.14  3.000
 VR2  HAP2  CAP  CAQ   111.55  3.000
 VR2  HAP1  CAP  CAQ   111.95  3.000
 VR2  HAP2  CAP  NAY   111.53  3.000
 VR2  HAP1  CAP  NAY   111.43  3.000
 VR2  CAQ   CAP  NAY   102.22  3.000
 VR2  HAQ2  CAQ  HAQ1  108.55  3.000
 VR2  HAQ2  CAQ  NAZ   111.30  3.000
 VR2  HAQ1  CAQ  NAZ   110.77  3.000
 VR2  HAQ2  CAQ  CAP   112.03  3.000
 VR2  HAQ1  CAQ  CAP   111.56  3.000
 VR2  NAZ   CAQ  CAP   102.59  3.000
 VR2  CAW   NAZ  CAQ   122.05  3.000
 VR2  CAW   NAZ  CAT   126.57  3.000
 VR2  CAQ   NAZ  CAT   110.41  3.000
 VR2  CAG   CAW  CAF   116.56  3.000
 VR2  CAG   CAW  NAZ   119.58  3.000
 VR2  CAF   CAW  NAZ   123.84  3.000
 VR2  HAF   CAF  CAD   119.18  3.000
 VR2  HAF   CAF  CAW   122.09  3.000
 VR2  CAD   CAF  CAW   118.73  3.000
 VR2  HAD   CAD  NAR   116.40  3.000
 VR2  HAD   CAD  CAF   118.63  3.000
 VR2  NAR   CAD  CAF   124.97  3.000
 VR2  CAE   NAR  CAD   116.00  3.000
 VR2  HAE   CAE  CAG   118.92  3.000
 VR2  HAE   CAE  NAR   116.70  3.000
 VR2  CAG   CAE  NAR   124.38  3.000
 VR2  HAG   CAG  CAE   118.62  3.000
 VR2  HAG   CAG  CAW   122.02  3.000
 VR2  CAE   CAG  CAW   119.36  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
 VR2  CONST_01  CAI   CAU  CAH  CAJ     0.00   0.0  0
 VR2  CONST_02  CAI   CAK  CAV  CAJ     0.00   0.0  0
 VR2  CONST_03  CAK   CAV  CAJ  CAH     0.00   0.0  0
 VR2  CONST_04  CAK   CAI  CAU  CAH     0.00   0.0  0
 VR2  CONST_05  CAV   CAJ  CAH  CAU     0.00   0.0  0
 VR2  CONST_06  CAV   CAK  CAI  CAU     0.00   0.0  0
 VR2  CONST_07  NAR   CAD  CAF  CAW     0.00   0.0  0
 VR2  CONST_08  NAR   CAE  CAG  CAW     0.00   0.0  0
 VR2  CONST_09  CAE   CAG  CAW  CAF     0.00   0.0  0
 VR2  CONST_10  CAE   NAR  CAD  CAF     0.00   0.0  0
 VR2  CONST_11  CAG   CAW  CAF  CAD     0.00   0.0  0
 VR2  CONST_12  CAG   CAE  NAR  CAD     0.00   0.0  0
 VR2  CONST_13  CAD   CAF  CAW  NAZ   180.00   0.0  0
 VR2  CONST_14  CAE   CAG  CAW  NAZ   180.00   0.0  0
 VR2  CONST_15  CAQ   NAZ  CAT  NAY     0.00   0.0  0
 VR2  CONST_16  CAW   NAZ  CAT  NAY   180.00   0.0  0
 VR2  CONST_20  NAZ   CAT  NAY  CAP     0.00   0.0  0
 VR2  CONST_21  CAW   NAZ  CAQ  CAP   180.00   0.0  0
 VR2  CONST_22  IAC   CAU  CAH  CAJ   180.00   0.0  0
 VR2  CONST_23  OAS   CAV  CAJ  CAH   180.00   0.0  0
 VR2  CONST_24  CAK   CAI  CAU  IAC   180.00   0.0  0
 VR2  CONST_25  OAS   CAV  CAK  CAI   180.00   0.0  0
 VR2  CONST_26  NAZ   CAT  NAY  CAO   180.00   0.0  0
 VR2  CONST_27  CAQ   CAP  NAY  CAO   180.00   0.0  0
 VR2  CONST_28  CAP   NAY  CAT  OAB   180.00   0.0  0
 VR2  CONST_29  CAQ   NAZ  CAT  OAB   180.00   0.0  0
 VR2  CONST_30  CAW   NAZ  CAT  OAB     0.00   0.0  0
 VR2  CONST_31  HAK   CAK  CAV  CAJ   180.00   0.0  0
 VR2  CONST_32  HAI   CAI  CAU  CAH   180.00   0.0  0
 VR2  CONST_33  HAJ   CAJ  CAH  CAU   180.00   0.0  0
 VR2  CONST_34  HAH   CAH  CAU  CAI   180.00   0.0  0
 VR2  CONST_35  HAF   CAF  CAW  NAZ     0.00   0.0  0
 VR2  CONST_36  HAG   CAG  CAW  NAZ     0.00   0.0  0
 VR2  CONST_37  HAD   CAD  CAF  CAW   180.00   0.0  0
 VR2  CONST_38  HAE   CAE  CAG  CAW   180.00   0.0  0
 VR2  CONST_39  OAB   CAT  NAY  CAO     0.00   0.0  0
 VR2  Var_01    CAF   CAW  NAZ  CAT   -19.06  30.0  2
 VR2  Var_02    HAQ1  CAQ  CAP  NAY    97.04  30.0  1
 VR2  Var_03    HAP1  CAP  NAY  CAT   139.56  30.0  1
 VR2  Var_04    CAT   NAY  CAO  CAN    77.40  30.0  3
 VR2  Var_05    CAM   CAL  OAS  CAV   179.50  30.0  3
 VR2  Var_06    NAY   CAO  CAN  CAX  -179.71  30.0  3
 VR2  Var_07    CAX   CAM  CAL  OAS   177.80  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
 VR2  chir_01  CAX  CAM  CAA  CAN  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
 VR2  plan-1  CAJ  0.020
 VR2  plan-1  CAH  0.020
 VR2  plan-1  CAU  0.020
 VR2  plan-1  IAC  0.020
 VR2  plan-1  CAI  0.020
 VR2  plan-1  CAK  0.020
 VR2  plan-1  CAV  0.020
 VR2  plan-1  OAS  0.020
 VR2  plan-1  HAJ  0.020
 VR2  plan-1  HAH  0.020
 VR2  plan-1  HAI  0.020
 VR2  plan-1  HAK  0.020
 VR2  plan-2  NAZ  0.020
 VR2  plan-2  CAW  0.020
 VR2  plan-2  CAF  0.020
 VR2  plan-2  CAD  0.020
 VR2  plan-2  NAR  0.020
 VR2  plan-2  CAE  0.020
 VR2  plan-2  CAG  0.020
 VR2  plan-2  HAF  0.020
 VR2  plan-2  HAG  0.020
 VR2  plan-2  HAD  0.020
 VR2  plan-2  HAE  0.020
 VR2  plan-3  CAO  0.020
 VR2  plan-3  NAY  0.020
 VR2  plan-3  CAT  0.020
 VR2  plan-3  OAB  0.020
 VR2  plan-3  CAP  0.020
 VR2  plan-3  CAQ  0.020
 VR2  plan-3  NAZ  0.020
 VR2  plan-3  CAW  0.020

