# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Nov 14 07:48:11 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-chloro-3-(2-methoxyphenyl)-2-[(9H-purin-6-ylsulfanyl)methyl]quinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1N2C(=O)c3c(Cl)cccc3N=C2CSc4ncnc5[nH]cnc45
#
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
 039  039  "2-((9H-PURIN-6-YLTHIO)METHYL)-5-CHLORO-3-(2-METHOXYPHENYL)QUINAZOLIN-4(3H)-ONE"  ligand  46  31  .  2022-11-14  2022-11-14
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_039
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
 039  CAU   C   CH3   0  -0.439  -1.1782   2.8991  -2.9506
 039  OAT   O   O2    0  -0.460  -1.3159   2.1349  -1.7649
 039  CAP   C   CR6   0   0.405  -1.1297   2.7411  -0.5860
 039  CAQ   C   CR16  0  -0.392  -0.8276   4.0890  -0.4141
 039  CAR   C   CR16  0  -0.229  -0.6460   4.5976   0.8660
 039  CAJ   C   CR16  0  -0.288  -0.7584   3.7862   1.9843
 039  CAI   C   CR16  0  -0.236  -1.0609   2.4422   1.8162
 039  CAH   C   CR6   0   0.154  -1.2375   1.9272   0.5463
 039  NAG   N   NR6   0  -0.637  -1.5382   0.5437   0.3645
 039  CAF   C   CR6   0   0.572  -2.8891   0.1999   0.2736
 039  OAB   O   OC    0  -0.422  -3.7315   1.0636   0.3673
 039  CAE   C   CR66  0  -0.013  -3.1341  -1.2283   0.0740
 039  CAD   C   CR6   0  -0.091  -4.4182  -1.7933  -0.0151
 039  CL    CL  CL    0  -0.096  -5.8586  -0.8509   0.1185
 039  CAC   C   CR16  0  -0.220  -4.5837  -3.1487  -0.2109
 039  CAK   C   CR16  0  -0.247  -3.4688  -3.9774  -0.3228
 039  CAL   C   CR16  0  -0.307  -2.1990  -3.4564  -0.2407
 039  CAM   C   CR66  0   0.257  -2.0218  -2.0840  -0.0430
 039  NAN   N   N     0  -0.482  -0.7326  -1.6180   0.0250
 039  CAO   C   CR6   0   0.530  -0.5311  -0.3694   0.2139
 039  CAS   C   CH2   0  -0.677   0.8718   0.1480   0.2774
 039  S6    S   S2    0   0.119   2.0098  -1.2368   0.0166
 039  C6    C   CR6   0   0.043   3.5255  -0.3743   0.0951
 039  C5    C   CR56  0   0.117   4.7172  -1.0827  -0.0481
 039  N7    N   N     0  -0.440   5.0051  -2.4043  -0.2492
 039  C8    C   CR15  0   0.121   6.3064  -2.4409  -0.3033
 039  N9    N   NR15  0  -0.642   6.8915  -1.2224  -0.1502
 039  C4    C   CR56  0   0.481   5.8876  -0.3232   0.0173
 039  N3    N   N     0  -0.418   5.9535   0.9876   0.2033
 039  C2    C   CR16  0   0.045   4.7615   1.5417   0.3272
 039  N1    N   N     0  -0.433   3.5724   0.9355   0.2829
 039  HAU1  H   HCH3  0   0.235  -0.1768   3.3250  -3.0427
 039  HAU2  H   HCH3  0   0.265  -1.3475   2.2137  -3.7766
 039  HAU3  H   HCH3  0   0.235  -1.9149   3.7039  -3.0014
 039  HAQ   H   HCR6  0   0.290  -0.7324   4.7512  -1.2634
 039  HAR   H   HCR6  0   0.269  -0.4138   5.6481   0.9820
 039  HAJ   H   HCR6  0   0.263  -0.6141   4.1909   2.9762
 039  HAI   H   HCR6  0   0.275  -1.1568   1.7842   2.6709
 039  HAC   H   HCR6  0   0.290  -5.5785  -3.5664  -0.2777
 039  HAK   H   HCR6  0   0.282  -3.6129  -5.0386  -0.4740
 039  HAL   H   HCR6  0   0.276  -1.3248  -4.0869  -0.3265
 039  HAS1  H   HCH2  0   0.322   1.0386   0.9072  -0.4872
 039  HAS2  H   HCH2  0   0.326   1.0758   0.6117   1.2432
 039  H8    H   HCR5  0   0.299   6.8984  -3.3306  -0.4542
 039  H9    H   HNR5  0   0.433   7.8825  -1.0318  -0.1607
 039  H2    H   HCR6  0   0.265   4.7372   2.6138   0.4830

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
 039  CAU  OAT   single    1.417  0.020  1.399
 039  CAU  HAU1  single    0.970  0.020  1.090
 039  CAU  HAU2  single    0.970  0.020  1.090
 039  CAU  HAU3  single    0.970  0.020  1.090
 039  OAT  CAP   single    1.339  0.020  1.401
 039  CAP  CAQ   aromatic  1.392  0.020  1.385
 039  CAP  CAH   aromatic  1.399  0.020  1.385
 039  CAQ  CAR   aromatic  1.389  0.020  1.385
 039  CAQ  HAQ   single    0.930  0.020  1.080
 039  CAR  CAJ   aromatic  1.386  0.020  1.385
 039  CAR  HAR   single    0.930  0.020  1.080
 039  CAJ  CAI   aromatic  1.388  0.020  1.385
 039  CAJ  HAJ   single    0.930  0.020  1.080
 039  CAI  CAH   aromatic  1.382  0.020  1.385
 039  CAI  HAI   single    0.930  0.020  1.080
 039  CAH  NAG   single    1.427  0.020  1.320
 039  NAG  CAF   aromatic  1.397  0.020  1.326
 039  NAG  CAO   aromatic  1.368  0.020  1.360
 039  CAF  OAB   double    1.210  0.020  1.185
 039  CAF  CAE   aromatic  1.463  0.020  1.376
 039  CAE  CAD   aromatic  1.406  0.020  1.413
 039  CAE  CAM   aromatic  1.408  0.020  1.350
 039  CAD  CL    single    1.726  0.020  1.786
 039  CAD  CAC   aromatic  1.379  0.020  1.383
 039  CAC  CAK   aromatic  1.394  0.020  1.380
 039  CAC  HAC   single    0.930  0.020  1.080
 039  CAK  CAL   aromatic  1.375  0.020  1.383
 039  CAK  HAK   single    0.930  0.020  1.080
 039  CAL  CAM   aromatic  1.398  0.020  1.414
 039  CAL  HAL   single    0.930  0.020  1.080
 039  CAM  NAN   aromatic  1.372  0.020  1.342
 039  NAN  CAO   aromatic  1.279  0.020  1.356
 039  CAO  CAS   single    1.497  0.020  1.525
 039  CAS  S6    single    1.811  0.020  1.816
 039  CAS  HAS1  single    0.970  0.020  1.090
 039  CAS  HAS2  single    0.970  0.020  1.090
 039  S6   C6    single    1.746  0.020  1.816
 039  C6   C5    aromatic  1.394  0.020  1.378
 039  C6   N1    aromatic  1.324  0.020  1.323
 039  C5   N7    aromatic  1.367  0.020  1.340
 039  C5   C4    aromatic  1.397  0.020  1.335
 039  N7   C8    aromatic  1.303  0.020  1.336
 039  C8   N9    aromatic  1.360  0.020  1.335
 039  C8   H8    single    0.930  0.020  1.080
 039  N9   C4    aromatic  1.358  0.020  1.340
 039  N9   H9    single    0.860  0.020  1.020
 039  C4   N3    aromatic  1.326  0.020  1.345
 039  N3   C2    aromatic  1.320  0.020  1.352
 039  C2   N1    aromatic  1.335  0.020  1.353
 039  C2   H2    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
 039  HAU3  CAU  HAU2  108.92  3.000
 039  HAU3  CAU  HAU1  109.10  3.000
 039  HAU2  CAU  HAU1  108.95  3.000
 039  HAU3  CAU  OAT   111.76  3.000
 039  HAU2  CAU  OAT   106.31  3.000
 039  HAU1  CAU  OAT   111.71  3.000
 039  CAP   OAT  CAU   118.63  3.000
 039  CAH   CAP  CAQ   118.70  3.000
 039  CAH   CAP  OAT   116.02  3.000
 039  CAQ   CAP  OAT   125.27  3.000
 039  HAQ   CAQ  CAR   119.21  3.000
 039  HAQ   CAQ  CAP   121.01  3.000
 039  CAR   CAQ  CAP   119.78  3.000
 039  HAR   CAR  CAJ   119.94  3.000
 039  HAR   CAR  CAQ   118.83  3.000
 039  CAJ   CAR  CAQ   121.22  3.000
 039  HAJ   CAJ  CAI   120.18  3.000
 039  HAJ   CAJ  CAR   120.69  3.000
 039  CAI   CAJ  CAR   119.13  3.000
 039  HAI   CAI  CAH   119.18  3.000
 039  HAI   CAI  CAJ   120.81  3.000
 039  CAH   CAI  CAJ   120.01  3.000
 039  NAG   CAH  CAI   120.35  3.000
 039  NAG   CAH  CAP   118.50  3.000
 039  CAI   CAH  CAP   121.15  3.000
 039  CAO   NAG  CAF   122.72  3.000
 039  CAO   NAG  CAH   120.40  3.000
 039  CAF   NAG  CAH   116.77  3.000
 039  CAE   CAF  OAB   126.22  3.000
 039  CAE   CAF  NAG   114.27  3.000
 039  OAB   CAF  NAG   119.51  3.000
 039  CAM   CAE  CAD   118.17  3.000
 039  CAM   CAE  CAF   118.19  3.000
 039  CAD   CAE  CAF   123.64  3.000
 039  CAC   CAD  CL    116.56  3.000
 039  CAC   CAD  CAE   120.90  3.000
 039  CL    CAD  CAE   122.54  3.000
 039  HAC   CAC  CAK   120.10  3.000
 039  HAC   CAC  CAD   119.93  3.000
 039  CAK   CAC  CAD   119.98  3.000
 039  HAK   CAK  CAL   120.21  3.000
 039  HAK   CAK  CAC   119.22  3.000
 039  CAL   CAK  CAC   120.58  3.000
 039  HAL   CAL  CAM   118.76  3.000
 039  HAL   CAL  CAK   121.40  3.000
 039  CAM   CAL  CAK   119.84  3.000
 039  NAN   CAM  CAL   117.35  3.000
 039  NAN   CAM  CAE   122.11  3.000
 039  CAL   CAM  CAE   120.54  3.000
 039  CAO   NAN  CAM   119.13  3.000
 039  CAS   CAO  NAN   119.44  3.000
 039  CAS   CAO  NAG   117.05  3.000
 039  NAN   CAO  NAG   123.51  3.000
 039  HAS2  CAS  HAS1  107.23  3.000
 039  HAS2  CAS  S6    109.58  3.000
 039  HAS1  CAS  S6    109.59  3.000
 039  HAS2  CAS  CAO   111.10  3.000
 039  HAS1  CAS  CAO   110.75  3.000
 039  S6    CAS  CAO   108.58  3.000
 039  C6    S6   CAS    99.29  3.000
 039  N1    C6   C5    119.15  3.000
 039  N1    C6   S6    121.73  3.000
 039  C5    C6   S6    119.12  3.000
 039  C4    C5   N7    110.85  3.000
 039  C4    C5   C6    115.80  3.000
 039  N7    C5   C6    133.35  3.000
 039  C8    N7   C5    104.10  3.000
 039  H8    C8   N9    121.21  3.000
 039  H8    C8   N7    125.22  3.000
 039  N9    C8   N7    113.56  3.000
 039  H9    N9   C4    127.02  3.000
 039  H9    N9   C8    126.18  3.000
 039  C4    N9   C8    106.80  3.000
 039  N3    C4   N9    129.44  3.000
 039  N3    C4   C5    125.87  3.000
 039  N9    C4   C5    104.69  3.000
 039  C2    N3   C4    112.54  3.000
 039  H2    C2   N1    115.72  3.000
 039  H2    C2   N3    116.67  3.000
 039  N1    C2   N3    127.61  3.000
 039  C2    N1   C6    119.03  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
 039  CONST_01  CAJ   CAR  CAQ  CAP     0.00   0.0  0
 039  CONST_02  CAJ   CAI  CAH  CAP     0.00   0.0  0
 039  CONST_05  CAI   CAH  CAP  CAQ     0.00   0.0  0
 039  CONST_06  NAG   CAH  CAP  CAQ   180.00   0.0  0
 039  CONST_07  CAI   CAJ  CAR  CAQ     0.00   0.0  0
 039  CONST_08  CAH   CAP  CAQ  CAR     0.00   0.0  0
 039  CONST_09  CAH   CAI  CAJ  CAR     0.00   0.0  0
 039  CONST_10  NAG   CAH  CAI  CAJ   180.00   0.0  0
 039  CONST_13  CAE   CAF  NAG  CAH   180.00   0.0  0
 039  CONST_14  NAN   CAO  NAG  CAH   180.00   0.0  0
 039  CONST_15  CAD   CAE  CAF  NAG   180.00   0.0  0
 039  CONST_16  CAM   CAE  CAF  NAG     0.00   0.0  0
 039  CONST_17  CAM   NAN  CAO  NAG     0.00   0.0  0
 039  CONST_18  NAN   CAO  NAG  CAF     0.00   0.0  0
 039  CONST_19  CAC   CAD  CAE  CAF   180.00   0.0  0
 039  CONST_20  CAL   CAM  CAE  CAF   180.00   0.0  0
 039  CONST_21  NAN   CAM  CAE  CAF     0.00   0.0  0
 039  CONST_22  CAO   NAG  CAF  CAE     0.00   0.0  0
 039  CONST_23  CAK   CAC  CAD  CAE     0.00   0.0  0
 039  CONST_24  CAK   CAL  CAM  CAE     0.00   0.0  0
 039  CONST_25  CAO   NAN  CAM  CAE     0.00   0.0  0
 039  CONST_26  CAL   CAM  CAE  CAD     0.00   0.0  0
 039  CONST_27  NAN   CAM  CAE  CAD   180.00   0.0  0
 039  CONST_28  CAL   CAK  CAC  CAD     0.00   0.0  0
 039  CONST_29  CAM   CAE  CAD  CAC     0.00   0.0  0
 039  CONST_30  CAM   CAL  CAK  CAC     0.00   0.0  0
 039  CONST_31  NAN   CAM  CAL  CAK   180.00   0.0  0
 039  CONST_32  CAO   NAN  CAM  CAL   180.00   0.0  0
 039  CONST_33  C8    N7   C5   C6    180.00   0.0  0
 039  CONST_34  N9    C4   C5   C6    180.00   0.0  0
 039  CONST_35  N3    C4   C5   C6      0.00   0.0  0
 039  CONST_36  N3    C2   N1   C6      0.00   0.0  0
 039  CONST_37  C2    N1   C6   C5      0.00   0.0  0
 039  CONST_38  N9    C8   N7   C5      0.00   0.0  0
 039  CONST_39  C8    N9   C4   C5      0.00   0.0  0
 039  CONST_40  C2    N3   C4   C5      0.00   0.0  0
 039  CONST_41  N1    C6   C5   N7    180.00   0.0  0
 039  CONST_42  N9    C4   C5   N7      0.00   0.0  0
 039  CONST_43  N3    C4   C5   N7    180.00   0.0  0
 039  CONST_44  C4    N9   C8   N7      0.00   0.0  0
 039  CONST_45  C4    C5   N7   C8      0.00   0.0  0
 039  CONST_46  N3    C4   N9   C8    180.00   0.0  0
 039  CONST_47  C2    N3   C4   N9    180.00   0.0  0
 039  CONST_48  N1    C6   C5   C4      0.00   0.0  0
 039  CONST_49  N1    C2   N3   C4      0.00   0.0  0
 039  CONST_50  CAR   CAQ  CAP  OAT   180.00   0.0  0
 039  CONST_51  CAI   CAH  CAP  OAT   180.00   0.0  0
 039  CONST_52  NAG   CAH  CAP  OAT     0.00   0.0  0
 039  CONST_53  OAB   CAF  NAG  CAH     0.00   0.0  0
 039  CONST_54  CAS   CAO  NAG  CAH     0.00   0.0  0
 039  CONST_55  CAS   CAO  NAG  CAF   180.00   0.0  0
 039  CONST_56  CL    CAD  CAE  CAF     0.00   0.0  0
 039  CONST_57  CAO   NAG  CAF  OAB   180.00   0.0  0
 039  CONST_58  CAD   CAE  CAF  OAB     0.00   0.0  0
 039  CONST_59  CAM   CAE  CAF  OAB   180.00   0.0  0
 039  CONST_60  CAM   CAE  CAD  CL    180.00   0.0  0
 039  CONST_61  CAK   CAC  CAD  CL    180.00   0.0  0
 039  CONST_62  CAS   CAO  NAN  CAM   180.00   0.0  0
 039  CONST_63  N7    C5   C6   S6      0.00   0.0  0
 039  CONST_64  C4    C5   C6   S6    180.00   0.0  0
 039  CONST_65  C2    N1   C6   S6    180.00   0.0  0
 039  CONST_66  HAR   CAR  CAQ  CAP   180.00   0.0  0
 039  CONST_67  HAI   CAI  CAH  CAP   180.00   0.0  0
 039  CONST_68  HAJ   CAJ  CAR  CAQ   180.00   0.0  0
 039  CONST_69  HAI   CAI  CAJ  CAR   180.00   0.0  0
 039  CONST_70  HAQ   CAQ  CAR  CAJ   180.00   0.0  0
 039  CONST_71  HAR   CAR  CAJ  CAI   180.00   0.0  0
 039  CONST_72  HAQ   CAQ  CAP  CAH   180.00   0.0  0
 039  CONST_73  HAJ   CAJ  CAI  CAH   180.00   0.0  0
 039  CONST_74  HAI   CAI  CAH  NAG     0.00   0.0  0
 039  CONST_75  HAC   CAC  CAD  CAE   180.00   0.0  0
 039  CONST_76  HAL   CAL  CAM  CAE   180.00   0.0  0
 039  CONST_77  HAK   CAK  CAC  CAD   180.00   0.0  0
 039  CONST_78  HAL   CAL  CAK  CAC   180.00   0.0  0
 039  CONST_79  HAC   CAC  CAK  CAL   180.00   0.0  0
 039  CONST_80  HAK   CAK  CAL  CAM   180.00   0.0  0
 039  CONST_81  HAL   CAL  CAM  NAN     0.00   0.0  0
 039  CONST_82  H2    C2   N1   C6    180.00   0.0  0
 039  CONST_83  H8    C8   N7   C5    180.00   0.0  0
 039  CONST_84  H9    N9   C4   C5    180.00   0.0  0
 039  CONST_85  H9    N9   C8   N7    180.00   0.0  0
 039  CONST_86  H8    C8   N9   C4    180.00   0.0  0
 039  CONST_87  H2    C2   N3   C4    180.00   0.0  0
 039  CONST_88  H9    N9   C4   N3      0.00   0.0  0
 039  Var_01    CAQ   CAP  OAT  CAU     1.12  30.0  2
 039  Var_02    CAH   CAP  OAT  CAU  -178.06  30.0  2
 039  Var_03    S6    CAS  CAO  NAG  -178.79  30.0  2
 039  Var_04    S6    CAS  CAO  NAN     1.19  30.0  2
 039  Var_05    C6    S6   CAS  CAO   178.60  30.0  3
 039  Var_06    C5    C6   S6   CAS   179.39  30.0  2
 039  Var_07    N1    C6   S6   CAS    -0.84  30.0  2
 039  Var_08    HAS1  CAS  CAO  NAG   -58.42  30.0  2
 039  Var_09    HAS2  CAS  CAO  NAG    60.64  30.0  2
 039  Var_10    HAS1  CAS  CAO  NAN   121.56  30.0  2
 039  Var_11    HAS2  CAS  CAO  NAN  -119.37  30.0  2
 039  Var_12    HAU1  CAU  OAT  CAP    60.05  30.0  3
 039  Var_13    HAU2  CAU  OAT  CAP   178.78  30.0  3
 039  Var_14    HAU3  CAU  OAT  CAP   -62.50  30.0  3
 039  Var_15    HAS1  CAS  S6   C6     57.51  30.0  1
 039  Var_16    HAS2  CAS  S6   C6    -59.89  30.0  1

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
 039  plan-1  OAT  0.020
 039  plan-1  CAP  0.020
 039  plan-1  CAQ  0.020
 039  plan-1  CAR  0.020
 039  plan-1  CAJ  0.020
 039  plan-1  CAI  0.020
 039  plan-1  CAH  0.020
 039  plan-1  NAG  0.020
 039  plan-1  HAQ  0.020
 039  plan-1  HAR  0.020
 039  plan-1  HAJ  0.020
 039  plan-1  HAI  0.020
 039  plan-2  S6   0.020
 039  plan-2  C6   0.020
 039  plan-2  C5   0.020
 039  plan-2  N7   0.020
 039  plan-2  C8   0.020
 039  plan-2  N9   0.020
 039  plan-2  C4   0.020
 039  plan-2  N3   0.020
 039  plan-2  C2   0.020
 039  plan-2  N1   0.020
 039  plan-2  H8   0.020
 039  plan-2  H9   0.020
 039  plan-2  H2   0.020
 039  plan-3  CAF  0.020
 039  plan-3  CAE  0.020
 039  plan-3  CAD  0.020
 039  plan-3  CL   0.020
 039  plan-3  CAC  0.020
 039  plan-3  CAK  0.020
 039  plan-3  CAL  0.020
 039  plan-3  CAM  0.020
 039  plan-3  NAN  0.020
 039  plan-3  HAC  0.020
 039  plan-3  HAK  0.020
 039  plan-3  HAL  0.020
 039  plan-4  NAG  0.020
 039  plan-4  CAF  0.020
 039  plan-4  OAB  0.020
 039  plan-4  CAE  0.020

