# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:40:30 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 5-methyl-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-3-pyridin-4-yl-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CN1C(=O)N(C)C(=O)c2c1nn(Cc3cccc4ccccc34)c2c5ccncc5
#
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
 003  003  5-methyl-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-3-pyridin-4-yl-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione  ligand  58  33  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_003
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
 003  C2    C  CR6   0   0.760   0.0602  -2.0820  -2.5713
 003  O11   O  OC    0  -0.483  -0.0441  -1.4260  -3.5879
 003  N3    N  NR6   0  -0.609  -0.2311  -1.5570  -1.3370
 003  C7    C  CH2   0  -0.300  -0.6389  -0.1638  -1.1879
 003  C8    C  CH1   0  -0.256   0.4825   0.7534  -0.7001
 003  C10   C  CH3   0  -0.656   1.6699   0.7702  -1.6557
 003  C9    C  CH3   0  -0.657  -0.0817   2.1569  -0.5063
 003  C4    C  CR56  0   0.609  -0.1161  -2.3484  -0.2293
 003  N16   N  N     0  -0.312  -0.3952  -1.9857   1.0002
 003  N15   N  NR5   0  -0.350  -0.1487  -3.0875   1.7356
 003  C23   C  CH2   0  -0.424  -0.2692  -3.0015   3.1883
 003  C24   C  CR6   0   0.081   0.9751  -3.4590   3.8998
 003  C29   C  CR66  0   0.104   2.2176  -2.7884   3.7122
 003  C30   C  CR16  0  -0.335   2.3571  -1.6261   2.9145
 003  C31   C  CR16  0  -0.250   3.5736  -1.0150   2.7658
 003  C32   C  CR16  0  -0.260   4.7198  -1.5322   3.4006
 003  C33   C  CR16  0  -0.309   4.6176  -2.6496   4.1824
 003  C28   C  CR66  0   0.111   3.3737  -3.2982   4.3626
 003  C27   C  CR16  0  -0.324   3.2631  -4.4389   5.1920
 003  C26   C  CR16  0  -0.238   2.0536  -5.0422   5.3843
 003  C25   C  CR16  0  -0.297   0.9100  -4.5465   4.7302
 003  C14   C  CR5   0   0.522   0.2740  -4.1261   1.0049
 003  C17   C  CR6   0   0.115   0.5877  -5.4400   1.5759
 003  C22   C  CR16  0  -0.317   1.8928  -5.9124   1.6014
 003  C21   C  CR16  0  -0.050   2.1384  -7.1346   2.2053
 003  N20   N  N     0  -0.401   1.1890  -7.8915   2.7438
 003  C19   C  CR16  0  -0.055  -0.0590  -7.4438   2.6940
 003  C18   C  CR16  0  -0.345  -0.4131  -6.2293   2.1266
 003  C5    C  CR56  0  -0.418   0.3129  -3.6744  -0.3054
 003  C6    C  CR6   0   0.512   0.6433  -4.2847  -1.5612
 003  O13   O  OC    0  -0.440   1.0197  -5.4304  -1.7046
 003  N1    N  NR6   0  -0.609   0.4855  -3.4102  -2.6370
 003  C12   C  CH3   0  -0.527   0.7859  -3.8942  -3.9805
 003  H7C1  H  HCH2  0   0.263  -1.4735  -0.1422  -0.4846
 003  H7C2  H  HCH2  0   0.267  -1.0165   0.1797  -2.1490
 003  H8    H  HCH1  0   0.236   0.8240   0.3902   0.2750
 003  H101  H  HCH3  0   0.220   1.3689   1.1000  -2.6520
 003  H102  H  HCH3  0   0.233   2.4384   1.4587  -1.3004
 003  H103  H  HCH3  0   0.228   2.1377  -0.2103  -1.7536
 003  H9C1  H  HCH3  0   0.220  -0.4557   2.5644  -1.4482
 003  H9C2  H  HCH3  0   0.234   0.6900   2.8335  -0.1374
 003  H9C3  H  HCH3  0   0.231  -0.9024   2.1695   0.2136
 003  H231  H  HCH2  0   0.302  -1.1286  -3.5887   3.5141
 003  H232  H  HCH2  0   0.304  -0.4973  -1.9567   3.4004
 003  H25   H  HCR6  0   0.257  -0.0352  -5.0550   4.8708
 003  H30   H  HCR6  0   0.257   1.4971  -1.1954   2.4202
 003  H31   H  HCR6  0   0.257   3.6544  -0.1230   2.1581
 003  H32   H  HCR6  0   0.259   5.6754  -1.0411   3.2718
 003  H33   H  HCR6  0   0.257   5.4910  -3.0517   4.6818
 003  H27   H  HCR6  0   0.257   4.1524  -4.8234   5.6767
 003  H26   H  HCR6  0   0.259   1.9686  -5.9087   6.0260
 003  H22   H  HCR6  0   0.271   2.7074  -5.3372   1.1840
 003  H18   H  HCR6  0   0.281  -1.4471  -5.9115   2.1244
 003  H21   H  HCR6  0   0.269   3.1508  -7.5187   2.2527
 003  H19   H  HCR6  0   0.270  -0.8223  -8.0769   3.1321
 003  H121  H  HCH3  0   0.255   1.5748  -3.2984  -4.4341
 003  H122  H  HCH3  0   0.255  -0.0989  -3.8528  -4.6115
 003  H123  H  HCH3  0   0.267   1.1208  -4.9219  -3.9138

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
 003  C2   O11   double    1.214  0.020  1.214
 003  C2   N3    aromatic  1.373  0.020  1.373
 003  C2   N1    aromatic  1.396  0.020  1.396
 003  N3   C7    single    1.459  0.020  1.459
 003  N3   C4    aromatic  1.366  0.020  1.366
 003  C7   C8    single    1.529  0.020  1.529
 003  C7   H7C1  single    0.970  0.020  1.090
 003  C7   H7C2  single    0.970  0.020  1.090
 003  C8   C10   single    1.524  0.020  1.524
 003  C8   C9    single    1.525  0.020  1.525
 003  C8   H8    single    0.970  0.020  1.090
 003  C10  H101  single    0.970  0.020  1.090
 003  C10  H102  single    0.970  0.020  1.090
 003  C10  H103  single    0.970  0.020  1.090
 003  C9   H9C1  single    0.970  0.020  1.090
 003  C9   H9C2  single    0.970  0.020  1.090
 003  C9   H9C3  single    0.970  0.020  1.090
 003  C4   N16   aromatic  1.312  0.020  1.312
 003  C4   C5    aromatic  1.396  0.020  1.396
 003  N16  N15   aromatic  1.347  0.020  1.347
 003  N15  C23   single    1.460  0.020  1.460
 003  N15  C14   aromatic  1.338  0.020  1.338
 003  C23  C24   single    1.505  0.020  1.505
 003  C23  H231  single    0.970  0.020  1.090
 003  C23  H232  single    0.970  0.020  1.090
 003  C24  C29   aromatic  1.424  0.020  1.424
 003  C24  C25   aromatic  1.370  0.020  1.370
 003  C29  C30   aromatic  1.417  0.020  1.417
 003  C29  C28   aromatic  1.421  0.020  1.421
 003  C30  C31   aromatic  1.369  0.020  1.369
 003  C30  H30   single    0.930  0.020  1.080
 003  C31  C32   aromatic  1.409  0.020  1.409
 003  C31  H31   single    0.930  0.020  1.080
 003  C32  C33   aromatic  1.368  0.020  1.368
 003  C32  H32   single    0.930  0.020  1.080
 003  C33  C28   aromatic  1.414  0.020  1.414
 003  C33  H33   single    0.930  0.020  1.080
 003  C28  C27   aromatic  1.415  0.020  1.415
 003  C27  C26   aromatic  1.365  0.020  1.365
 003  C27  H27   single    0.930  0.020  1.080
 003  C26  C25   aromatic  1.408  0.020  1.408
 003  C26  H26   single    0.930  0.020  1.080
 003  C25  H25   single    0.930  0.020  1.080
 003  C14  C17   single    1.467  0.020  1.467
 003  C14  C5    aromatic  1.386  0.020  1.386
 003  C17  C22   aromatic  1.388  0.020  1.388
 003  C17  C18   aromatic  1.389  0.020  1.389
 003  C22  C21   aromatic  1.385  0.020  1.385
 003  C22  H22   single    0.930  0.020  1.080
 003  C21  N20   aromatic  1.328  0.020  1.328
 003  C21  H21   single    0.930  0.020  1.080
 003  N20  C19   aromatic  1.327  0.020  1.327
 003  C19  C18   aromatic  1.387  0.020  1.387
 003  C19  H19   single    0.930  0.020  1.080
 003  C18  H18   single    0.930  0.020  1.080
 003  C5   C6    aromatic  1.435  0.020  1.435
 003  C6   O13   double    1.215  0.020  1.215
 003  C6   N1    aromatic  1.395  0.020  1.395
 003  N1   C12   single    1.459  0.020  1.459
 003  C12  H121  single    0.970  0.020  1.090
 003  C12  H122  single    0.970  0.020  1.090
 003  C12  H123  single    0.970  0.020  1.090

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
 003  N1    C2   N3    118.09  3.000
 003  N1    C2   O11   120.05  3.000
 003  N3    C2   O11   121.87  3.000
 003  C4    N3   C7    119.59  3.000
 003  C4    N3   C2    119.32  3.000
 003  C7    N3   C2    121.09  3.000
 003  H7C2  C7   H7C1  107.30  3.000
 003  H7C2  C7   C8    110.30  3.000
 003  H7C1  C7   C8    110.08  3.000
 003  H7C2  C7   N3    107.95  3.000
 003  H7C1  C7   N3    107.37  3.000
 003  C8    C7   N3    113.60  3.000
 003  H8    C8   C9    107.90  3.000
 003  H8    C8   C10   108.60  3.000
 003  C9    C8   C10   110.96  3.000
 003  H8    C8   C7    108.29  3.000
 003  C9    C8   C7    108.75  3.000
 003  C10   C8   C7    112.21  3.000
 003  H103  C10  H102  107.11  3.000
 003  H103  C10  H101  107.94  3.000
 003  H102  C10  H101  107.50  3.000
 003  H103  C10  C8    112.36  3.000
 003  H102  C10  C8    110.58  3.000
 003  H101  C10  C8    111.14  3.000
 003  H9C3  C9   H9C2  107.56  3.000
 003  H9C3  C9   H9C1  107.87  3.000
 003  H9C2  C9   H9C1  107.61  3.000
 003  H9C3  C9   C8    111.87  3.000
 003  H9C2  C9   C8    110.62  3.000
 003  H9C1  C9   C8    111.13  3.000
 003  C5    C4   N16   112.28  3.000
 003  C5    C4   N3    122.14  3.000
 003  N16   C4   N3    125.58  3.000
 003  N15   N16  C4    104.27  3.000
 003  C14   N15  C23   127.95  3.000
 003  C14   N15  N16   113.23  3.000
 003  C23   N15  N16   118.67  3.000
 003  H232  C23  H231  107.04  3.000
 003  H232  C23  C24   111.86  3.000
 003  H231  C23  C24   110.28  3.000
 003  H232  C23  N15   105.50  3.000
 003  H231  C23  N15   109.30  3.000
 003  C24   C23  N15   112.60  3.000
 003  C25   C24  C29   119.68  3.000
 003  C25   C24  C23   119.26  3.000
 003  C29   C24  C23   121.06  3.000
 003  C28   C29  C30   118.16  3.000
 003  C28   C29  C24   118.72  3.000
 003  C30   C29  C24   123.12  3.000
 003  H30   C30  C31   118.62  3.000
 003  H30   C30  C29   120.39  3.000
 003  C31   C30  C29   120.98  3.000
 003  H31   C31  C32   119.66  3.000
 003  H31   C31  C30   119.67  3.000
 003  C32   C31  C30   120.66  3.000
 003  H32   C32  C33   120.32  3.000
 003  H32   C32  C31   119.89  3.000
 003  C33   C32  C31   119.79  3.000
 003  H33   C33  C28   118.69  3.000
 003  H33   C33  C32   120.43  3.000
 003  C28   C33  C32   120.88  3.000
 003  C27   C28  C33   120.88  3.000
 003  C27   C28  C29   119.60  3.000
 003  C33   C28  C29   119.52  3.000
 003  H27   C27  C26   120.49  3.000
 003  H27   C27  C28   118.97  3.000
 003  C26   C27  C28   120.54  3.000
 003  H26   C26  C25   119.60  3.000
 003  H26   C26  C27   120.48  3.000
 003  C25   C26  C27   119.91  3.000
 003  H25   C25  C26   118.92  3.000
 003  H25   C25  C24   119.55  3.000
 003  C26   C25  C24   121.51  3.000
 003  C5    C14  C17   130.83  3.000
 003  C5    C14  N15   105.78  3.000
 003  C17   C14  N15   123.38  3.000
 003  C18   C17  C22   118.49  3.000
 003  C18   C17  C14   120.63  3.000
 003  C22   C17  C14   120.87  3.000
 003  H22   C22  C21   120.28  3.000
 003  H22   C22  C17   121.35  3.000
 003  C21   C22  C17   118.35  3.000
 003  H21   C21  N20   116.61  3.000
 003  H21   C21  C22   119.82  3.000
 003  N20   C21  C22   123.56  3.000
 003  C19   N20  C21   117.70  3.000
 003  H19   C19  C18   119.81  3.000
 003  H19   C19  N20   116.74  3.000
 003  C18   C19  N20   123.45  3.000
 003  H18   C18  C19   120.15  3.000
 003  H18   C18  C17   121.41  3.000
 003  C19   C18  C17   118.43  3.000
 003  C6    C5   C14   134.03  3.000
 003  C6    C5   C4    121.50  3.000
 003  C14   C5   C4    104.44  3.000
 003  N1    C6   O13   122.36  3.000
 003  N1    C6   C5    112.47  3.000
 003  O13   C6   C5    125.17  3.000
 003  C12   N1   C6    118.60  3.000
 003  C12   N1   C2    114.93  3.000
 003  C6    N1   C2    126.47  3.000
 003  H123  C12  H122  108.87  3.000
 003  H123  C12  H121  108.74  3.000
 003  H122  C12  H121  109.10  3.000
 003  H123  C12  N1    108.77  3.000
 003  H122  C12  N1    110.74  3.000
 003  H121  C12  N1    110.58  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
 003  CONST_01  N16   C4   N3   C2    180.00   0.0  0
 003  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 003  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 003  CONST_04  C6    N1   C2   N3      0.00   0.0  0
 003  CONST_05  N15   N16  C4   N3    180.00   0.0  0
 003  CONST_06  C14   C5   C4   N3    180.00   0.0  0
 003  CONST_07  C6    C5   C4   N3      0.00   0.0  0
 003  CONST_08  N1    C2   N3   C4      0.00   0.0  0
 003  CONST_09  C14   N15  N16  C4      0.00   0.0  0
 003  CONST_10  N15   C14  C5   C4      0.00   0.0  0
 003  CONST_11  C17   C14  C5   C4    180.00   0.0  0
 003  CONST_12  N1    C6   C5   C4      0.00   0.0  0
 003  CONST_13  C14   C5   C4   N16     0.00   0.0  0
 003  CONST_14  C6    C5   C4   N16   180.00   0.0  0
 003  CONST_15  C17   C14  N15  N16   180.00   0.0  0
 003  CONST_16  C5    C14  N15  N16     0.00   0.0  0
 003  CONST_17  C5    C4   N16  N15     0.00   0.0  0
 003  CONST_20  C6    C5   C14  N15   180.00   0.0  0
 003  CONST_21  C31   C30  C29  C24   180.00   0.0  0
 003  CONST_22  C33   C28  C29  C24   180.00   0.0  0
 003  CONST_23  C27   C28  C29  C24     0.00   0.0  0
 003  CONST_24  C27   C26  C25  C24     0.00   0.0  0
 003  CONST_25  C26   C25  C24  C29     0.00   0.0  0
 003  CONST_26  C32   C31  C30  C29     0.00   0.0  0
 003  CONST_27  C32   C33  C28  C29     0.00   0.0  0
 003  CONST_28  C26   C27  C28  C29     0.00   0.0  0
 003  CONST_29  C25   C24  C29  C30   180.00   0.0  0
 003  CONST_30  C33   C28  C29  C30     0.00   0.0  0
 003  CONST_31  C27   C28  C29  C30   180.00   0.0  0
 003  CONST_32  C33   C32  C31  C30     0.00   0.0  0
 003  CONST_33  C28   C29  C30  C31     0.00   0.0  0
 003  CONST_34  C28   C33  C32  C31     0.00   0.0  0
 003  CONST_35  C27   C28  C33  C32   180.00   0.0  0
 003  CONST_36  C26   C27  C28  C33   180.00   0.0  0
 003  CONST_37  C25   C24  C29  C28     0.00   0.0  0
 003  CONST_38  C25   C26  C27  C28     0.00   0.0  0
 003  CONST_39  C21   C22  C17  C14   180.00   0.0  0
 003  CONST_40  C19   C18  C17  C14   180.00   0.0  0
 003  CONST_41  N1    C6   C5   C14   180.00   0.0  0
 003  CONST_42  C6    C5   C14  C17     0.00   0.0  0
 003  CONST_43  N20   C21  C22  C17     0.00   0.0  0
 003  CONST_44  N20   C19  C18  C17     0.00   0.0  0
 003  CONST_46  C19   C18  C17  C22     0.00   0.0  0
 003  CONST_47  C19   N20  C21  C22     0.00   0.0  0
 003  CONST_48  C18   C17  C22  C21     0.00   0.0  0
 003  CONST_49  C18   C19  N20  C21     0.00   0.0  0
 003  CONST_51  O13   C6   N1   C2    180.00   0.0  0
 003  CONST_52  C4    N3   C2   O11   180.00   0.0  0
 003  CONST_53  C6    N1   C2   O11   180.00   0.0  0
 003  CONST_54  C12   N1   C2   N3    180.00   0.0  0
 003  CONST_55  N1    C2   N3   C7    180.00   0.0  0
 003  CONST_56  N16   C4   N3   C7      0.00   0.0  0
 003  CONST_57  C5    C4   N3   C7    180.00   0.0  0
 003  CONST_58  C23   N15  N16  C4    180.00   0.0  0
 003  CONST_59  O13   C6   C5   C4    180.00   0.0  0
 003  CONST_60  C17   C14  N15  C23     0.00   0.0  0
 003  CONST_61  C5    C14  N15  C23   180.00   0.0  0
 003  CONST_62  C30   C29  C24  C23     0.00   0.0  0
 003  CONST_63  C28   C29  C24  C23   180.00   0.0  0
 003  CONST_64  C26   C25  C24  C23   180.00   0.0  0
 003  CONST_65  O13   C6   C5   C14     0.00   0.0  0
 003  CONST_66  C12   N1   C6   C5    180.00   0.0  0
 003  CONST_67  H30   C30  C29  C24     0.00   0.0  0
 003  CONST_68  H26   C26  C25  C24   180.00   0.0  0
 003  CONST_69  H25   C25  C24  C29   180.00   0.0  0
 003  CONST_70  H31   C31  C30  C29   180.00   0.0  0
 003  CONST_71  H33   C33  C28  C29   180.00   0.0  0
 003  CONST_72  H27   C27  C28  C29   180.00   0.0  0
 003  CONST_73  H32   C32  C31  C30   180.00   0.0  0
 003  CONST_74  H22   C22  C17  C14     0.00   0.0  0
 003  CONST_75  H18   C18  C17  C14     0.00   0.0  0
 003  CONST_76  H21   C21  C22  C17   180.00   0.0  0
 003  CONST_77  H19   C19  C18  C17   180.00   0.0  0
 003  CONST_78  C7    N3   C2   O11     0.00   0.0  0
 003  CONST_79  C12   N1   C2   O11     0.00   0.0  0
 003  CONST_80  C12   N1   C6   O13     0.00   0.0  0
 003  Var_01    C24   C23  N15  N16  -125.78  30.0  2
 003  Var_02    C29   C24  C23  N15    61.80  30.0  2
 003  Var_03    C8    C7   N3   C2   -101.32  30.0  2
 003  Var_04    H121  C12  N1   C2     59.66  30.0  2
 003  Var_05    C10   C8   C7   N3     60.12  30.0  3
 003  Var_06    H101  C10  C8   C7     58.70  30.0  3
 003  Var_07    H9C1  C9   C8   C7    -61.73  30.0  3

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
 003  plan-1  C14  0.020
 003  plan-1  C17  0.020
 003  plan-1  C22  0.020
 003  plan-1  C21  0.020
 003  plan-1  N20  0.020
 003  plan-1  C19  0.020
 003  plan-1  C18  0.020
 003  plan-1  H22  0.020
 003  plan-1  H18  0.020
 003  plan-1  H21  0.020
 003  plan-1  H19  0.020
 003  plan-2  C2   0.020
 003  plan-2  O11  0.020
 003  plan-2  N3   0.020
 003  plan-2  C7   0.020
 003  plan-2  C4   0.020
 003  plan-2  N16  0.020
 003  plan-2  N15  0.020
 003  plan-2  C23  0.020
 003  plan-2  C14  0.020
 003  plan-2  C17  0.020
 003  plan-2  C5   0.020
 003  plan-2  C6   0.020
 003  plan-2  O13  0.020
 003  plan-2  N1   0.020
 003  plan-2  C12  0.020
 003  plan-3  C23  0.020
 003  plan-3  C24  0.020
 003  plan-3  C29  0.020
 003  plan-3  C30  0.020
 003  plan-3  C31  0.020
 003  plan-3  C32  0.020
 003  plan-3  C33  0.020
 003  plan-3  C28  0.020
 003  plan-3  C27  0.020
 003  plan-3  C26  0.020
 003  plan-3  C25  0.020
 003  plan-3  H25  0.020
 003  plan-3  H30  0.020
 003  plan-3  H31  0.020
 003  plan-3  H32  0.020
 003  plan-3  H33  0.020
 003  plan-3  H27  0.020
 003  plan-3  H26  0.020

