# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 13:27:00 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-chloro-5-{[4-methyl-2-oxo-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1,2-dihydropyridin-3-yl]oxy}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(Oc2cc(Cl)cc(c2)C#N)C(=O)N(Cc3[nH]nc4ncccc34)C=C1
#
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
 M06  M06  3-chloro-5-{[4-methyl-2-oxo-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1,2-dihydropyridin-3-yl]oxy}benzonitrile  ligand  42  28  .  2022-07-23  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_M06
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
 M06  C     C   CR6   0   0.147   0.3908  -2.5346  -0.8496
 M06  N     N   NR6   0  -0.505  -1.2239  -0.8959   0.6985
 M06  O     O   O2    0  -0.485   1.6613  -0.6265  -1.4494
 M06  CL    CL  CL    0  -0.098   4.5205  -0.3485   2.7599
 M06  C1    C   CR16  0  -0.438  -0.7340  -3.0493  -0.1555
 M06  C2    C   CR16  0   0.062  -1.4980  -2.2207   0.5939
 M06  C3    C   CR6   0   0.557  -0.1700  -0.2963   0.0342
 M06  C4    C   CR6   0   0.072   0.6395  -1.1991  -0.7414
 M06  C5    C   CR6   0   0.411   2.7420  -0.1501  -0.7898
 M06  C6    C   CH3   0  -0.722   1.2645  -3.4351  -1.6634
 M06  C7    C   CR16  0  -0.323   3.6006   0.6583  -1.5232
 M06  C8    C   CR6   0   0.013   4.7466   1.1467  -0.9089
 M06  C9    C   CR16  0  -0.229   5.0534   0.8552   0.4188
 M06  C10   C   CR6   0  -0.020   4.1756   0.0459   1.1150
 M06  C11   C   CR16  0  -0.276   3.0263  -0.4668   0.5328
 M06  O12   O   O     0  -0.500   0.0397   0.9106   0.1253
 M06  C13   C   CR5   0   0.399  -3.0689   0.7159   0.6693
 M06  N14   N   NR15  0  -0.444  -2.7962   1.8676   0.0454
 M06  N15   N   N     0  -0.291  -3.7822   2.3831  -0.6689
 M06  C16   C   CR56  0   0.357  -4.7795   1.5143  -0.5060
 M06  C17   C   CR56  0  -0.166  -4.3909   0.4329   0.3322
 M06  N18   N   N     0  -0.420  -5.9988   1.6462  -1.0641
 M06  C19   C   CR16  0  -0.074  -6.8429   0.6891  -0.7836
 M06  C20   C   CR16  0  -0.344  -6.5643  -0.4339   0.0429
 M06  C21   C   CR16  0  -0.212  -5.3298  -0.5760   0.6136
 M06  C22   C   CH2   0  -0.465  -2.0895  -0.0324   1.5032
 M06  C23   C   CSP   0   0.066   5.6377   1.9739  -1.6593
 M06  N24   N   NS    0  -0.240   6.3569   2.6396  -2.2637
 M06  H1    H   HCR6  0   0.284  -0.9817  -4.0989  -0.2092
 M06  H2    H   HCR6  0   0.312  -2.3577  -2.5751   1.1440
 M06  H16   H   HCH3  0   0.267   2.2026  -3.6335  -1.1412
 M06  H26   H   HCH3  0   0.261   0.7781  -4.3919  -1.8398
 M06  H36   H   HCH3  0   0.263   1.5165  -2.9947  -2.6265
 M06  H7    H   HCR6  0   0.300   3.3777   0.8987  -2.5539
 M06  H9    H   HCR6  0   0.303   5.9468   1.2473   0.8828
 M06  H11   H   HCR6  0   0.312   2.3733  -1.1093   1.1087
 M06  HN14  H   HNR5  0   0.432  -1.8991   2.3345   0.0601
 M06  H19   H   HCR6  0   0.265  -7.8314   0.7711  -1.2235
 M06  H20   H   HCR6  0   0.273  -7.3438  -1.1639   0.2095
 M06  H21   H   HCR6  0   0.267  -5.0966  -1.4216   1.2483
 M06  H122  H   HCH2  0   0.307  -2.6218  -0.6638   2.2118
 M06  H222  H   HCH2  0   0.320  -1.4684   0.6439   2.0882

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
 M06  N15  N14   aromatic  1.322  0.020  1.322
 M06  N15  C16   aromatic  1.333  0.020  1.333
 M06  N14  C13   aromatic  1.338  0.020  1.338
 M06  C16  N18   aromatic  1.347  0.020  1.347
 M06  C16  C17   aromatic  1.422  0.020  1.422
 M06  C2   C1    double    1.353  0.020  1.353
 M06  C2   N     single    1.357  0.020  1.357
 M06  N18  C19   aromatic  1.307  0.020  1.307
 M06  C13  C22   single    1.488  0.020  1.488
 M06  C13  C17   aromatic  1.393  0.020  1.393
 M06  C1   C     single    1.418  0.020  1.418
 M06  C22  N     single    1.464  0.020  1.464
 M06  C17  C21   aromatic  1.407  0.020  1.407
 M06  N    C3    single    1.383  0.020  1.383
 M06  C19  C20   aromatic  1.422  0.020  1.422
 M06  C    C6    single    1.495  0.020  1.495
 M06  C    C4    double    1.363  0.020  1.363
 M06  C21  C20   aromatic  1.367  0.020  1.367
 M06  C3   C4    single    1.439  0.020  1.439
 M06  C3   O12   double    1.228  0.020  1.228
 M06  C4   O     single    1.369  0.020  1.369
 M06  O    C5    single    1.353  0.020  1.353
 M06  C5   C11   aromatic  1.389  0.020  1.389
 M06  C5   C7    aromatic  1.389  0.020  1.389
 M06  C11  C10   aromatic  1.387  0.020  1.387
 M06  C7   C8    aromatic  1.389  0.020  1.389
 M06  C10  CL    single    1.726  0.020  1.726
 M06  C10  C9    aromatic  1.382  0.020  1.382
 M06  C8   C9    aromatic  1.394  0.020  1.394
 M06  C8   C23   single    1.429  0.020  1.429
 M06  C23  N24   triple    1.151  0.020  1.151
 M06  C1   H1    single    0.930  0.020  1.080
 M06  C2   H2    single    0.930  0.020  1.080
 M06  C6   H16   single    0.970  0.020  1.090
 M06  C6   H26   single    0.970  0.020  1.090
 M06  C6   H36   single    0.970  0.020  1.090
 M06  C7   H7    single    0.930  0.020  1.080
 M06  C9   H9    single    0.930  0.020  1.080
 M06  C11  H11   single    0.930  0.020  1.080
 M06  N14  HN14  single    0.860  0.020  1.020
 M06  C19  H19   single    0.930  0.020  1.080
 M06  C20  H20   single    0.930  0.020  1.080
 M06  C21  H21   single    0.930  0.020  1.080
 M06  C22  H122  single    0.970  0.020  1.090
 M06  C22  H222  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
 M06  C6    C    C4    121.78  3.000
 M06  C4    C    C1    117.48  3.000
 M06  C6    C    C1    120.74  3.000
 M06  C22   N    C3    117.33  3.000
 M06  C3    N    C2    122.71  3.000
 M06  C22   N    C2    119.93  3.000
 M06  C5    O    C4    119.44  3.000
 M06  H1    C1   C2    119.55  3.000
 M06  H1    C1   C     120.68  3.000
 M06  C2    C1   C     119.76  3.000
 M06  H2    C2   C1    122.02  3.000
 M06  H2    C2   N     116.21  3.000
 M06  C1    C2   N     121.76  3.000
 M06  O12   C3   C4    124.07  3.000
 M06  O12   C3   N     121.37  3.000
 M06  C4    C3   N     114.56  3.000
 M06  C3    C4   O     115.86  3.000
 M06  O     C4   C     120.34  3.000
 M06  C3    C4   C     123.70  3.000
 M06  C11   C5   C7    120.59  3.000
 M06  C7    C5   O     116.19  3.000
 M06  C11   C5   O     123.19  3.000
 M06  H36   C6   H26   108.41  3.000
 M06  H36   C6   H16   107.33  3.000
 M06  H26   C6   H16   107.57  3.000
 M06  H36   C6   C     111.91  3.000
 M06  H26   C6   C     110.89  3.000
 M06  H16   C6   C     110.56  3.000
 M06  H7    C7   C8    120.89  3.000
 M06  H7    C7   C5    120.35  3.000
 M06  C8    C7   C5    118.77  3.000
 M06  C23   C8   C9    118.96  3.000
 M06  C23   C8   C7    119.07  3.000
 M06  C9    C8   C7    121.97  3.000
 M06  H9    C9   C10   121.43  3.000
 M06  H9    C9   C8    121.02  3.000
 M06  C10   C9   C8    117.56  3.000
 M06  C11   C10  C9    122.10  3.000
 M06  C9    C10  CL    119.13  3.000
 M06  C11   C10  CL    118.76  3.000
 M06  H11   C11  C10   119.75  3.000
 M06  H11   C11  C5    121.23  3.000
 M06  C10   C11  C5    119.01  3.000
 M06  C22   C13  C17   131.14  3.000
 M06  C17   C13  N14   104.80  3.000
 M06  C22   C13  N14   124.05  3.000
 M06  HN14  N14  N15   119.29  3.000
 M06  HN14  N14  C13   124.85  3.000
 M06  N15   N14  C13   115.82  3.000
 M06  C16   N15  N14   103.76  3.000
 M06  N18   C16  C17   124.45  3.000
 M06  C17   C16  N15   111.30  3.000
 M06  N18   C16  N15   124.25  3.000
 M06  C21   C17  C16   118.74  3.000
 M06  C21   C17  C13   136.94  3.000
 M06  C16   C17  C13   104.32  3.000
 M06  C19   N18  C16   115.09  3.000
 M06  H19   C19  C20   118.28  3.000
 M06  H19   C19  N18   116.50  3.000
 M06  C20   C19  N18   125.22  3.000
 M06  H20   C20  C21   121.11  3.000
 M06  H20   C20  C19   118.79  3.000
 M06  C21   C20  C19   120.10  3.000
 M06  H21   C21  C20   121.35  3.000
 M06  H21   C21  C17   122.26  3.000
 M06  C20   C21  C17   116.40  3.000
 M06  H222  C22  H122  106.84  3.000
 M06  H222  C22  C13   111.36  3.000
 M06  H122  C22  C13   109.56  3.000
 M06  H222  C22  N     108.94  3.000
 M06  H122  C22  N     107.75  3.000
 M06  C13   C22  N     112.19  3.000
 M06  N24   C23  C8    180.00  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
 M06  CONST_01  C9    C10  C11  C5      0.00   0.0  0
 M06  CONST_02  C9    C8   C7   C5      0.00   0.0  0
 M06  CONST_03  C10   C11  C5   C7      0.00   0.0  0
 M06  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 M06  CONST_05  C11   C5   C7   C8      0.00   0.0  0
 M06  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 M06  CONST_07  C16   N15  N14  C13     0.00   0.0  0
 M06  CONST_08  N15   C16  C17  C13     0.00   0.0  0
 M06  CONST_09  N18   C16  C17  C13   180.00   0.0  0
 M06  CONST_10  C20   C21  C17  C13   180.00   0.0  0
 M06  CONST_11  N18   C16  N15  N14   180.00   0.0  0
 M06  CONST_12  C17   C16  N15  N14     0.00   0.0  0
 M06  CONST_13  C16   C17  C13  N14     0.00   0.0  0
 M06  CONST_14  C21   C17  C13  N14   180.00   0.0  0
 M06  CONST_15  C17   C13  N14  N15     0.00   0.0  0
 M06  CONST_16  C19   N18  C16  N15   180.00   0.0  0
 M06  CONST_17  C21   C17  C16  N15   180.00   0.0  0
 M06  CONST_18  C20   C19  N18  C16     0.00   0.0  0
 M06  CONST_19  C20   C21  C17  C16     0.00   0.0  0
 M06  CONST_20  C19   N18  C16  C17     0.00   0.0  0
 M06  CONST_21  C19   C20  C21  C17     0.00   0.0  0
 M06  CONST_22  C21   C17  C16  N18     0.00   0.0  0
 M06  CONST_23  C21   C20  C19  N18     0.00   0.0  0
 M06  CONST_24  C4    C3   N    C2      0.00   0.0  0
 M06  CONST_25  C10   C11  C5   O     180.00   0.0  0
 M06  CONST_26  C8    C7   C5   O     180.00   0.0  0
 M06  CONST_27  C5    C11  C10  CL    180.00   0.0  0
 M06  CONST_28  C8    C9   C10  CL    180.00   0.0  0
 M06  CONST_29  C23   C8   C7   C5    180.00   0.0  0
 M06  CONST_30  C23   C8   C9   C10   180.00   0.0  0
 M06  CONST_31  C22   C13  N14  N15   180.00   0.0  0
 M06  CONST_32  C22   C13  C17  C16   180.00   0.0  0
 M06  CONST_33  C22   C13  C17  C21     0.00   0.0  0
 M06  CONST_34  O12   C3   N    C2    180.00   0.0  0
 M06  CONST_35  C22   N    C3   C4    180.00   0.0  0
 M06  CONST_36  H11   C11  C5   C7    180.00   0.0  0
 M06  CONST_37  H9    C9   C8   C7    180.00   0.0  0
 M06  CONST_38  H7    C7   C8   C9    180.00   0.0  0
 M06  CONST_39  H21   C21  C17  C13     0.00   0.0  0
 M06  CONST_40  HN14  N14  N15  C16   180.00   0.0  0
 M06  CONST_41  H19   C19  N18  C16   180.00   0.0  0
 M06  CONST_42  H20   C20  C21  C17   180.00   0.0  0
 M06  CONST_43  C22   N    C3   O12     0.00   0.0  0
 M06  Var_01    N14   C13  C22  N     -83.97  30.0  2
 M06  Var_02    C13   C22  N    C2    -99.06  30.0  3
 M06  Var_03    C11   C5   O    C4     14.97  30.0  2
 M06  Var_04    H16   C6   C    C1   -104.53  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
 M06  plan-1  C     0.020
 M06  plan-1  N     0.020
 M06  plan-1  O     0.020
 M06  plan-1  C1    0.020
 M06  plan-1  C2    0.020
 M06  plan-1  C3    0.020
 M06  plan-1  C4    0.020
 M06  plan-1  C6    0.020
 M06  plan-1  O12   0.020
 M06  plan-1  C22   0.020
 M06  plan-1  H1    0.020
 M06  plan-1  H2    0.020
 M06  plan-2  O     0.020
 M06  plan-2  CL    0.020
 M06  plan-2  C5    0.020
 M06  plan-2  C7    0.020
 M06  plan-2  C8    0.020
 M06  plan-2  C9    0.020
 M06  plan-2  C10   0.020
 M06  plan-2  C11   0.020
 M06  plan-2  C23   0.020
 M06  plan-2  N24   0.020
 M06  plan-2  H7    0.020
 M06  plan-2  H9    0.020
 M06  plan-2  H11   0.020
 M06  plan-3  C13   0.020
 M06  plan-3  N14   0.020
 M06  plan-3  N15   0.020
 M06  plan-3  C16   0.020
 M06  plan-3  C17   0.020
 M06  plan-3  N18   0.020
 M06  plan-3  C19   0.020
 M06  plan-3  C20   0.020
 M06  plan-3  C21   0.020
 M06  plan-3  C22   0.020
 M06  plan-3  HN14  0.020
 M06  plan-3  H19   0.020
 M06  plan-3  H20   0.020
 M06  plan-3  H21   0.020

