# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:26:39 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-(4-methylphenyl)-8-oxidanyl-3H-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)C2=Nc3c(O)cccc3C(=O)N2
#
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
 VT3  VT3  2-(4-methylphenyl)-8-oxidanyl-3H-quinazolin-4-one  ligand  31  19  .  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_VT3
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
 VT3  CAD   C  CR16  0  -0.256  -2.3318  -1.1337  -0.3445
 VT3  CAC   C  CR16  0  -0.282  -3.7013  -1.3246  -0.3123
 VT3  CAB   C  CR6   0   0.098  -4.5670  -0.2918   0.0486
 VT3  CAA   C  CH3   0  -0.721  -6.0520  -0.4958   0.0530
 VT3  CAG   C  CR16  0  -0.281  -4.0109   0.9402   0.3833
 VT3  CAF   C  CR16  0  -0.284  -2.6407   1.1431   0.3446
 VT3  CAE   C  CR6   0   0.002  -1.7831   0.1081  -0.0243
 VT3  CAH   C  CR6   0   0.480  -0.3218   0.2804  -0.0704
 VT3  NAI   N  N     0  -0.449   0.4492  -0.7362   0.0898
 VT3  CAJ   C  CR66  0   0.184   1.8024  -0.5352   0.0360
 VT3  CAO   C  CR6   0   0.280   2.6541  -1.6520   0.1993
 VT3  OAP   O  OH1   0  -0.608   2.0683  -2.8431   0.3889
 VT3  CAN   C  CR16  0  -0.375   4.0244  -1.4752   0.1570
 VT3  CAM   C  CR16  0  -0.253   4.5777  -0.2083  -0.0439
 VT3  CAL   C  CR16  0  -0.312   3.7677   0.8931  -0.2051
 VT3  CAK   C  CR66  0  -0.088   2.3816   0.7258  -0.1644
 VT3  CAQ   C  CR6   0   0.538   1.4937   1.8687  -0.3466
 VT3  OAR   O  O     0  -0.452   1.8527   3.0156  -0.5437
 VT3  NAS   N  NR16  0  -0.724   0.1585   1.5404  -0.2927
 VT3  HAD   H  HCR6  0   0.260  -1.6789  -1.9490  -0.6257
 VT3  HAC   H  HCR6  0   0.256  -4.1055  -2.2945  -0.5755
 VT3  HAA1  H  HCH3  0   0.248  -6.3139  -1.5261   0.2908
 VT3  HAA2  H  HCH3  0   0.248  -6.5434   0.1564   0.7740
 VT3  HAA3  H  HCH3  0   0.255  -6.4747  -0.2717  -0.9287
 VT3  HAG   H  HCR6  0   0.257  -4.6550   1.7565   0.6864
 VT3  HAF   H  HCR6  0   0.260  -2.2567   2.1120   0.6392
 VT3  HAS   H  HNR6  0   0.430  -0.4929   2.2948  -0.4676
 VT3  HAP   H  HOH1  0   0.479   2.7377  -3.5290   0.4943
 VT3  HAN   H  HCR6  0   0.281   4.6799  -2.3297   0.2820
 VT3  HAM   H  HCR6  0   0.268   5.6537  -0.1024  -0.0711
 VT3  HAL   H  HCR6  0   0.263   4.1906   1.8753  -0.3641

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
 VT3  CAD  CAC   aromatic  1.383  0.020  1.383
 VT3  CAD  CAE   aromatic  1.395  0.020  1.395
 VT3  CAC  CAB   aromatic  1.395  0.020  1.395
 VT3  CAB  CAA   single    1.499  0.020  1.499
 VT3  CAB  CAG   aromatic  1.393  0.020  1.393
 VT3  CAG  CAF   aromatic  1.386  0.020  1.386
 VT3  CAF  CAE   aromatic  1.394  0.020  1.394
 VT3  CAE  CAH   single    1.472  0.020  1.472
 VT3  CAH  NAI   double    1.286  0.020  1.286
 VT3  CAH  NAS   single    1.367  0.020  1.367
 VT3  NAI  CAJ   single    1.369  0.020  1.369
 VT3  CAJ  CAO   aromatic  1.414  0.020  1.414
 VT3  CAJ  CAK   aromatic  1.402  0.020  1.402
 VT3  CAO  OAP   single    1.341  0.020  1.341
 VT3  CAO  CAN   aromatic  1.382  0.020  1.382
 VT3  CAN  CAM   aromatic  1.397  0.020  1.397
 VT3  CAM  CAL   aromatic  1.377  0.020  1.377
 VT3  CAL  CAK   aromatic  1.397  0.020  1.397
 VT3  CAK  CAQ   single    1.459  0.020  1.459
 VT3  CAQ  OAR   double    1.218  0.020  1.218
 VT3  CAQ  NAS   single    1.376  0.020  1.376
 VT3  CAD  HAD   single    0.930  0.020  1.080
 VT3  CAC  HAC   single    0.930  0.020  1.080
 VT3  CAA  HAA1  single    0.970  0.020  1.090
 VT3  CAA  HAA2  single    0.970  0.020  1.090
 VT3  CAA  HAA3  single    0.970  0.020  1.090
 VT3  CAG  HAG   single    0.930  0.020  1.080
 VT3  CAF  HAF   single    0.930  0.020  1.080
 VT3  NAS  HAS   single    0.860  0.020  1.020
 VT3  OAP  HAP   single    0.850  0.020  0.980
 VT3  CAN  HAN   single    0.930  0.020  1.080
 VT3  CAM  HAM   single    0.930  0.020  1.080
 VT3  CAL  HAL   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
 VT3  HAD   CAD  CAE   119.55  3.000
 VT3  HAD   CAD  CAC   119.98  3.000
 VT3  CAE   CAD  CAC   120.47  3.000
 VT3  HAC   CAC  CAB   119.61  3.000
 VT3  HAC   CAC  CAD   119.17  3.000
 VT3  CAB   CAC  CAD   121.22  3.000
 VT3  CAG   CAB  CAA   121.02  3.000
 VT3  CAG   CAB  CAC   117.99  3.000
 VT3  CAA   CAB  CAC   120.98  3.000
 VT3  HAA3  CAA  HAA2  107.31  3.000
 VT3  HAA3  CAA  HAA1  107.29  3.000
 VT3  HAA2  CAA  HAA1  108.26  3.000
 VT3  HAA3  CAA  CAB   110.66  3.000
 VT3  HAA2  CAA  CAB   111.56  3.000
 VT3  HAA1  CAA  CAB   111.57  3.000
 VT3  HAG   CAG  CAF   119.05  3.000
 VT3  HAG   CAG  CAB   119.77  3.000
 VT3  CAF   CAG  CAB   121.18  3.000
 VT3  HAF   CAF  CAE   121.21  3.000
 VT3  HAF   CAF  CAG   118.29  3.000
 VT3  CAE   CAF  CAG   120.47  3.000
 VT3  CAH   CAE  CAF   122.15  3.000
 VT3  CAH   CAE  CAD   119.18  3.000
 VT3  CAF   CAE  CAD   118.67  3.000
 VT3  NAS   CAH  NAI   122.57  3.000
 VT3  NAS   CAH  CAE   117.51  3.000
 VT3  NAI   CAH  CAE   119.92  3.000
 VT3  CAJ   NAI  CAH   118.14  3.000
 VT3  CAK   CAJ  CAO   118.55  3.000
 VT3  CAK   CAJ  NAI   123.09  3.000
 VT3  CAO   CAJ  NAI   118.35  3.000
 VT3  CAN   CAO  OAP   123.44  3.000
 VT3  CAN   CAO  CAJ   119.51  3.000
 VT3  OAP   CAO  CAJ   117.05  3.000
 VT3  HAP   OAP  CAO   110.12  3.000
 VT3  HAN   CAN  CAM   119.46  3.000
 VT3  HAN   CAN  CAO   119.67  3.000
 VT3  CAM   CAN  CAO   120.86  3.000
 VT3  HAM   CAM  CAL   120.27  3.000
 VT3  HAM   CAM  CAN   119.11  3.000
 VT3  CAL   CAM  CAN   120.62  3.000
 VT3  HAL   CAL  CAK   120.09  3.000
 VT3  HAL   CAL  CAM   120.93  3.000
 VT3  CAK   CAL  CAM   118.99  3.000
 VT3  CAQ   CAK  CAL   120.43  3.000
 VT3  CAQ   CAK  CAJ   118.10  3.000
 VT3  CAL   CAK  CAJ   121.46  3.000
 VT3  NAS   CAQ  OAR   121.14  3.000
 VT3  NAS   CAQ  CAK   113.51  3.000
 VT3  OAR   CAQ  CAK   125.35  3.000
 VT3  HAS   NAS  CAQ   116.10  3.000
 VT3  HAS   NAS  CAH   119.29  3.000
 VT3  CAQ   NAS  CAH   124.57  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
 VT3  CONST_01  CAG   CAB  CAC  CAD    0.00   0.0  0
 VT3  CONST_02  CAG   CAF  CAE  CAD    0.00   0.0  0
 VT3  CONST_03  CAF   CAE  CAD  CAC    0.00   0.0  0
 VT3  CONST_04  CAF   CAG  CAB  CAC    0.00   0.0  0
 VT3  CONST_05  CAE   CAD  CAC  CAB    0.00   0.0  0
 VT3  CONST_06  CAE   CAF  CAG  CAB    0.00   0.0  0
 VT3  CONST_07  CAM   CAN  CAO  CAJ    0.00   0.0  0
 VT3  CONST_08  CAM   CAL  CAK  CAJ    0.00   0.0  0
 VT3  CONST_09  CAL   CAK  CAJ  CAO    0.00   0.0  0
 VT3  CONST_10  CAL   CAM  CAN  CAO    0.00   0.0  0
 VT3  CONST_11  CAK   CAJ  CAO  CAN    0.00   0.0  0
 VT3  CONST_12  CAK   CAL  CAM  CAN    0.00   0.0  0
 VT3  CONST_13  CAH   CAE  CAD  CAC  180.00   0.0  0
 VT3  CONST_14  CAH   CAE  CAF  CAG  180.00   0.0  0
 VT3  CONST_15  CAJ   NAI  CAH  CAE  180.00   0.0  0
 VT3  CONST_16  CAQ   NAS  CAH  CAE  180.00   0.0  0
 VT3  CONST_17  CAK   CAQ  NAS  CAH    0.00   0.0  0
 VT3  CONST_18  CAQ   NAS  CAH  NAI    0.00   0.0  0
 VT3  CONST_19  NAS   CAH  NAI  CAJ    0.00   0.0  0
 VT3  CONST_20  CAA   CAB  CAC  CAD  180.00   0.0  0
 VT3  CONST_21  CAF   CAG  CAB  CAA  180.00   0.0  0
 VT3  CONST_22  OAP   CAO  CAJ  NAI    0.00   0.0  0
 VT3  CONST_23  CAK   CAJ  CAO  OAP  180.00   0.0  0
 VT3  CONST_24  CAM   CAN  CAO  OAP  180.00   0.0  0
 VT3  CONST_25  OAR   CAQ  NAS  CAH  180.00   0.0  0
 VT3  CONST_26  HAF   CAF  CAE  CAD  180.00   0.0  0
 VT3  CONST_27  HAG   CAG  CAB  CAC  180.00   0.0  0
 VT3  CONST_28  HAD   CAD  CAC  CAB  180.00   0.0  0
 VT3  CONST_29  HAC   CAC  CAB  CAG  180.00   0.0  0
 VT3  CONST_30  HAN   CAN  CAO  CAJ  180.00   0.0  0
 VT3  CONST_31  HAL   CAL  CAK  CAJ  180.00   0.0  0
 VT3  CONST_32  HAM   CAM  CAN  CAO  180.00   0.0  0
 VT3  CONST_33  HAS   NAS  CAH  CAE    0.00   0.0  0
 VT3  Var_01    NAI   CAH  CAE  CAD  -25.60  30.0  2
 VT3  Var_02    HAA1  CAA  CAB  CAC   30.96  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
 VT3  plan-1  CAD  0.020
 VT3  plan-1  CAC  0.020
 VT3  plan-1  CAB  0.020
 VT3  plan-1  CAA  0.020
 VT3  plan-1  CAG  0.020
 VT3  plan-1  CAF  0.020
 VT3  plan-1  CAE  0.020
 VT3  plan-1  CAH  0.020
 VT3  plan-1  HAD  0.020
 VT3  plan-1  HAC  0.020
 VT3  plan-1  HAG  0.020
 VT3  plan-1  HAF  0.020
 VT3  plan-2  CAE  0.020
 VT3  plan-2  CAH  0.020
 VT3  plan-2  NAI  0.020
 VT3  plan-2  CAJ  0.020
 VT3  plan-2  CAO  0.020
 VT3  plan-2  OAP  0.020
 VT3  plan-2  CAN  0.020
 VT3  plan-2  CAM  0.020
 VT3  plan-2  CAL  0.020
 VT3  plan-2  CAK  0.020
 VT3  plan-2  CAQ  0.020
 VT3  plan-2  OAR  0.020
 VT3  plan-2  NAS  0.020
 VT3  plan-2  HAS  0.020
 VT3  plan-2  HAN  0.020
 VT3  plan-2  HAM  0.020
 VT3  plan-2  HAL  0.020

