# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:07:21 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-methoxy-4-(3-phenyl-2H-pyrazolo[3,4-b]pyridin-6-yl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)c2ccc3c([nH]nc3n2)c4ccccc4
#
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
 3T9  3T9  2-methoxy-4-(3-phenyl-2H-pyrazolo[3,4-b]pyridin-6-yl)phenol  ligand  39  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3T9
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
 3T9  N1    N  NR15  0  -0.483   2.6575   1.8497   0.4607
 3T9  C2    C  CR56  0  -0.183   1.7265  -0.0644   0.0712
 3T9  C3    C  CR56  0   0.351   0.7724   0.9592   0.3177
 3T9  C4    C  CR5   0   0.409   2.9643   0.5757   0.1749
 3T9  N5    N  N     0  -0.297   1.3644   2.1290   0.5531
 3T9  N6    N  N     0  -0.464  -0.5585   0.7738   0.3322
 3T9  C7    C  CR6   0   0.213  -0.9847  -0.4469   0.1110
 3T9  C8    C  CR16  0  -0.225   1.2499  -1.3661  -0.1628
 3T9  C9    C  CR6   0   0.064  -2.4460  -0.6615   0.1232
 3T9  C10   C  CR16  0  -0.422  -3.3033   0.4192  -0.1226
 3T9  C11   C  CR6   0   0.325  -4.6739   0.2521  -0.1079
 3T9  C12   C  CR6   0   0.280  -5.2263  -1.0120   0.1723
 3T9  C13   C  CR6   0   0.059   4.3312   0.0859   0.0522
 3T9  C14   C  CR16  0  -0.344  -0.1034  -1.5456  -0.1437
 3T9  C15   C  CR16  0  -0.337  -3.0019  -1.9056   0.3968
 3T9  C16   C  CR16  0  -0.329  -4.3800  -2.0765   0.4257
 3T9  O17   O  O2    0  -0.490  -5.5831   1.2204  -0.3470
 3T9  O18   O  OH1   0  -0.625  -6.5566  -1.2038   0.1979
 3T9  C19   C  CR16  0  -0.300   5.3618   0.6322   0.8202
 3T9  C20   C  CR16  0  -0.318   4.6262  -0.9480  -0.8383
 3T9  C21   C  CH3   0  -0.433  -5.1219   2.5122  -0.6906
 3T9  C22   C  CR16  0  -0.238   5.9216  -1.4283  -0.9522
 3T9  C23   C  CR16  0  -0.242   6.6573   0.1549   0.6967
 3T9  C24   C  CR16  0  -0.257   6.9416  -0.8785  -0.1866
 3T9  H8    H  HCR6  0   0.265   1.9143  -2.1984  -0.3551
 3T9  H10   H  HCR6  0   0.280  -2.8698   1.3880  -0.3321
 3T9  H14   H  HCR6  0   0.268  -0.5118  -2.5250  -0.3459
 3T9  H15   H  HCR6  0   0.254  -2.3746  -2.7585   0.6175
 3T9  H16   H  HCR6  0   0.269  -4.8034  -3.0470   0.6515
 3T9  HO18  H  HOH1  0   0.474  -7.0168  -0.3833  -0.0186
 3T9  H19   H  HCR6  0   0.261   5.1545   1.4192   1.5347
 3T9  H20   H  HCR6  0   0.259   3.8481  -1.3662  -1.4635
 3T9  H21   H  HCH3  0   0.232  -4.5236   2.4969  -1.6051
 3T9  H21A  H  HCH3  0   0.264  -6.0054   3.1224  -0.8579
 3T9  H21B  H  HCH3  0   0.232  -4.5292   2.9566   0.1127
 3T9  H22   H  HCR6  0   0.265   6.1339  -2.2297  -1.6476
 3T9  H23   H  HCR6  0   0.265   7.4438   0.5841   1.3032
 3T9  H24   H  HCR6  0   0.264   7.9523  -1.2543  -0.2762
 3T9  HN1   H  HNR5  0   0.433   3.3227   2.6003   0.5827

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
 3T9  N5   N1    aromatic  1.326  0.020  1.326
 3T9  N1   C4    aromatic  1.341  0.020  1.341
 3T9  C3   C2    aromatic  1.421  0.020  1.421
 3T9  C2   C4    aromatic  1.397  0.020  1.397
 3T9  C2   C8    aromatic  1.406  0.020  1.406
 3T9  N6   C3    aromatic  1.344  0.020  1.344
 3T9  N5   C3    aromatic  1.332  0.020  1.332
 3T9  C4   C13   single    1.457  0.020  1.457
 3T9  N6   C7    aromatic  1.312  0.020  1.312
 3T9  C9   C7    single    1.477  0.020  1.477
 3T9  C7   C14   aromatic  1.431  0.020  1.431
 3T9  C14  C8    aromatic  1.365  0.020  1.365
 3T9  C8   H8    single    0.930  0.020  1.080
 3T9  C10  C9    aromatic  1.401  0.020  1.401
 3T9  C9   C15   aromatic  1.390  0.020  1.390
 3T9  C11  C10   aromatic  1.381  0.020  1.381
 3T9  C10  H10   single    0.930  0.020  1.080
 3T9  O17  C11   single    1.350  0.020  1.350
 3T9  C11  C12   aromatic  1.408  0.020  1.408
 3T9  O18  C12   single    1.344  0.020  1.344
 3T9  C12  C16   aromatic  1.383  0.020  1.383
 3T9  C13  C19   aromatic  1.397  0.020  1.397
 3T9  C13  C20   aromatic  1.396  0.020  1.396
 3T9  C14  H14   single    0.930  0.020  1.080
 3T9  C16  C15   aromatic  1.389  0.020  1.389
 3T9  C15  H15   single    0.930  0.020  1.080
 3T9  C16  H16   single    0.930  0.020  1.080
 3T9  C21  O17   single    1.414  0.020  1.414
 3T9  O18  HO18  single    0.850  0.020  0.980
 3T9  C19  C23   aromatic  1.386  0.020  1.386
 3T9  C19  H19   single    0.930  0.020  1.080
 3T9  C20  C22   aromatic  1.386  0.020  1.386
 3T9  C20  H20   single    0.930  0.020  1.080
 3T9  C21  H21   single    0.970  0.020  1.090
 3T9  C21  H21A  single    0.970  0.020  1.090
 3T9  C21  H21B  single    0.970  0.020  1.090
 3T9  C22  C24   aromatic  1.389  0.020  1.389
 3T9  C22  H22   single    0.930  0.020  1.080
 3T9  C23  C24   aromatic  1.389  0.020  1.389
 3T9  C23  H23   single    0.930  0.020  1.080
 3T9  C24  H24   single    0.930  0.020  1.080
 3T9  N1   HN1   single    0.860  0.020  1.020

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
 3T9  HN1   N1   N5    118.49  3.000
 3T9  HN1   N1   C4    125.51  3.000
 3T9  N5    N1   C4    115.97  3.000
 3T9  C8    C2   C4    137.46  3.000
 3T9  C8    C2   C3    117.93  3.000
 3T9  C4    C2   C3    104.59  3.000
 3T9  N6    C3   N5    124.01  3.000
 3T9  N5    C3   C2    111.40  3.000
 3T9  N6    C3   C2    124.58  3.000
 3T9  C13   C4   C2    132.12  3.000
 3T9  C13   C4   N1    123.49  3.000
 3T9  C2    C4   N1    104.38  3.000
 3T9  C3    N5   N1    103.66  3.000
 3T9  C7    N6   C3    116.64  3.000
 3T9  C14   C7   C9    119.94  3.000
 3T9  C14   C7   N6    122.97  3.000
 3T9  C9    C7   N6    117.08  3.000
 3T9  H8    C8   C14   120.66  3.000
 3T9  H8    C8   C2    122.25  3.000
 3T9  C14   C8   C2    117.09  3.000
 3T9  C15   C9   C10   118.70  3.000
 3T9  C15   C9   C7    121.83  3.000
 3T9  C10   C9   C7    119.46  3.000
 3T9  H10   C10  C11   120.54  3.000
 3T9  H10   C10  C9    118.65  3.000
 3T9  C11   C10  C9    120.80  3.000
 3T9  O17   C11  C12   114.53  3.000
 3T9  C12   C11  C10   120.02  3.000
 3T9  O17   C11  C10   125.44  3.000
 3T9  O18   C12  C16   119.48  3.000
 3T9  C16   C12  C11   119.17  3.000
 3T9  O18   C12  C11   121.35  3.000
 3T9  C20   C13  C19   118.98  3.000
 3T9  C20   C13  C4    120.06  3.000
 3T9  C19   C13  C4    120.96  3.000
 3T9  H14   C14  C8    119.43  3.000
 3T9  H14   C14  C7    119.76  3.000
 3T9  C8    C14  C7    120.79  3.000
 3T9  H15   C15  C16   118.30  3.000
 3T9  H15   C15  C9    120.94  3.000
 3T9  C16   C15  C9    120.74  3.000
 3T9  H16   C16  C15   120.17  3.000
 3T9  H16   C16  C12   119.26  3.000
 3T9  C15   C16  C12   120.56  3.000
 3T9  C21   O17  C11   118.61  3.000
 3T9  HO18  O18  C12   110.26  3.000
 3T9  H19   C19  C23   119.20  3.000
 3T9  H19   C19  C13   120.39  3.000
 3T9  C23   C19  C13   120.39  3.000
 3T9  H20   C20  C22   119.37  3.000
 3T9  H20   C20  C13   120.18  3.000
 3T9  C22   C20  C13   120.43  3.000
 3T9  H21B  C21  H21A  109.02  3.000
 3T9  H21B  C21  H21   108.89  3.000
 3T9  H21A  C21  H21   108.91  3.000
 3T9  H21B  C21  O17   111.70  3.000
 3T9  H21A  C21  O17   106.57  3.000
 3T9  H21   C21  O17   111.65  3.000
 3T9  H22   C22  C24   120.22  3.000
 3T9  H22   C22  C20   119.52  3.000
 3T9  C24   C22  C20   120.26  3.000
 3T9  H23   C23  C24   120.19  3.000
 3T9  H23   C23  C19   119.53  3.000
 3T9  C24   C23  C19   120.28  3.000
 3T9  H24   C24  C23   120.15  3.000
 3T9  H24   C24  C22   120.19  3.000
 3T9  C23   C24  C22   119.65  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
 3T9  CONST_01  C2   C3   N5   N1     0.00   0.0  0
 3T9  CONST_02  N6   C3   N5   N1   180.00   0.0  0
 3T9  CONST_03  C3   C2   C4   N1     0.00   0.0  0
 3T9  CONST_04  C8   C2   C4   N1   180.00   0.0  0
 3T9  CONST_07  C7   N6   C3   C2     0.00   0.0  0
 3T9  CONST_08  N5   N1   C4   C2     0.00   0.0  0
 3T9  CONST_11  C7   C14  C8   C2     0.00   0.0  0
 3T9  CONST_12  C13  C4   C2   C3   180.00   0.0  0
 3T9  CONST_13  C14  C8   C2   C3     0.00   0.0  0
 3T9  CONST_14  C9   C7   N6   C3   180.00   0.0  0
 3T9  CONST_15  C14  C7   N6   C3     0.00   0.0  0
 3T9  CONST_16  C4   N1   N5   C3     0.00   0.0  0
 3T9  CONST_17  N6   C3   C2   C4   180.00   0.0  0
 3T9  CONST_18  N5   C3   C2   C4     0.00   0.0  0
 3T9  CONST_19  C14  C8   C2   C4   180.00   0.0  0
 3T9  CONST_20  C23  C19  C13  C4   180.00   0.0  0
 3T9  CONST_21  C22  C20  C13  C4   180.00   0.0  0
 3T9  CONST_22  C13  C4   N1   N5   180.00   0.0  0
 3T9  CONST_23  C8   C2   C3   N5   180.00   0.0  0
 3T9  CONST_24  C7   N6   C3   N5   180.00   0.0  0
 3T9  CONST_25  C8   C2   C3   N6     0.00   0.0  0
 3T9  CONST_28  C8   C14  C7   N6     0.00   0.0  0
 3T9  CONST_29  C11  C10  C9   C7   180.00   0.0  0
 3T9  CONST_30  C16  C15  C9   C7   180.00   0.0  0
 3T9  CONST_31  C13  C4   C2   C8     0.00   0.0  0
 3T9  CONST_32  C9   C7   C14  C8   180.00   0.0  0
 3T9  CONST_33  C12  C11  C10  C9     0.00   0.0  0
 3T9  CONST_34  C12  C16  C15  C9     0.00   0.0  0
 3T9  CONST_36  C16  C15  C9   C10    0.00   0.0  0
 3T9  CONST_37  C16  C12  C11  C10    0.00   0.0  0
 3T9  CONST_38  C15  C9   C10  C11    0.00   0.0  0
 3T9  CONST_39  C15  C16  C12  C11    0.00   0.0  0
 3T9  CONST_40  C24  C23  C19  C13    0.00   0.0  0
 3T9  CONST_41  C24  C22  C20  C13    0.00   0.0  0
 3T9  CONST_43  C22  C20  C13  C19    0.00   0.0  0
 3T9  CONST_44  C22  C24  C23  C19    0.00   0.0  0
 3T9  CONST_45  C23  C19  C13  C20    0.00   0.0  0
 3T9  CONST_46  C23  C24  C22  C20    0.00   0.0  0
 3T9  CONST_47  O17  C11  C10  C9   180.00   0.0  0
 3T9  CONST_48  O18  C12  C11  C10  180.00   0.0  0
 3T9  CONST_49  O18  C12  C16  C15  180.00   0.0  0
 3T9  CONST_50  O17  C11  C12  C16  180.00   0.0  0
 3T9  CONST_51  HN1  N1   C4   C2   180.00   0.0  0
 3T9  CONST_52  H14  C14  C8   C2   180.00   0.0  0
 3T9  CONST_53  H8   C8   C2   C3   180.00   0.0  0
 3T9  CONST_54  H19  C19  C13  C4     0.00   0.0  0
 3T9  CONST_55  H20  C20  C13  C4     0.00   0.0  0
 3T9  CONST_56  H10  C10  C9   C7     0.00   0.0  0
 3T9  CONST_57  H15  C15  C9   C7     0.00   0.0  0
 3T9  CONST_58  H16  C16  C15  C9   180.00   0.0  0
 3T9  CONST_59  H23  C23  C19  C13  180.00   0.0  0
 3T9  CONST_60  H22  C22  C20  C13  180.00   0.0  0
 3T9  CONST_61  H24  C24  C23  C19  180.00   0.0  0
 3T9  Var_01    H21  C21  O17  C11   60.05  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
 3T9  plan-1  C7   0.020
 3T9  plan-1  C9   0.020
 3T9  plan-1  C10  0.020
 3T9  plan-1  C11  0.020
 3T9  plan-1  C12  0.020
 3T9  plan-1  C15  0.020
 3T9  plan-1  C16  0.020
 3T9  plan-1  O17  0.020
 3T9  plan-1  O18  0.020
 3T9  plan-1  H10  0.020
 3T9  plan-1  H15  0.020
 3T9  plan-1  H16  0.020
 3T9  plan-2  C4   0.020
 3T9  plan-2  C13  0.020
 3T9  plan-2  C19  0.020
 3T9  plan-2  C20  0.020
 3T9  plan-2  C22  0.020
 3T9  plan-2  C23  0.020
 3T9  plan-2  C24  0.020
 3T9  plan-2  H19  0.020
 3T9  plan-2  H20  0.020
 3T9  plan-2  H22  0.020
 3T9  plan-2  H23  0.020
 3T9  plan-2  H24  0.020
 3T9  plan-3  N1   0.020
 3T9  plan-3  C2   0.020
 3T9  plan-3  C3   0.020
 3T9  plan-3  C4   0.020
 3T9  plan-3  N5   0.020
 3T9  plan-3  N6   0.020
 3T9  plan-3  C7   0.020
 3T9  plan-3  C8   0.020
 3T9  plan-3  C9   0.020
 3T9  plan-3  C13  0.020
 3T9  plan-3  C14  0.020
 3T9  plan-3  H8   0.020
 3T9  plan-3  H14  0.020
 3T9  plan-3  HN1  0.020

