# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:07:19 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 3-[[1-(cyclopropylmethyl)-5-ethanoyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]amino]-~{N}-propan-2-yl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)c1cccc(Nc2nn(CC3CC3)c4CCN(Cc24)C(C)=O)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
 6XG  6XG  3-[[1-(cyclopropylmethyl)-5-ethanoyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]amino]-~{N}-propan-2-yl-benzamide  ligand  58  29  .  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_6XG
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
 6XG  C7   C  CR6   0  -0.016  -3.2036  -1.1749   0.4321
 6XG  C9   C  CR16  0  -0.233  -2.7863  -3.5261   0.2725
 6XG  C2   C  CH1   0  -0.090  -6.2218   0.9915  -0.3284
 6XG  C10  C  CR16  0  -0.366  -1.4284  -3.2998   0.3879
 6XG  C1   C  CH3   0  -0.649  -5.8253   2.0172  -1.3853
 6XG  C3   C  CH3   0  -0.669  -7.5876   0.3872  -0.6172
 6XG  N4   N  NH1   0  -0.637  -5.2399  -0.0779  -0.2337
 6XG  C5   C  C     0   0.529  -4.1079   0.0187   0.4822
 6XG  O6   O  O     0  -0.488  -3.8168   1.0084   1.1419
 6XG  C8   C  CR16  0  -0.334  -3.6898  -2.4698   0.2867
 6XG  C11  C  CR6   0   0.384  -0.9296  -1.9964   0.5346
 6XG  C12  C  CR16  0  -0.382  -1.8403  -0.9374   0.5737
 6XG  N13  N  NH1   0  -0.799   0.4360  -1.8351   0.6309
 6XG  C14  C  CR5   0   0.503   1.1655  -0.6698   0.7235
 6XG  C15  C  CR5   0  -0.282   2.5631  -0.5696   0.5500
 6XG  C16  C  CR5   0   0.457   2.8305   0.7630   0.7466
 6XG  N17  N  NR5   0  -0.349   1.6629   1.3707   1.0125
 6XG  N18  N  N     0  -0.345   0.6362   0.5065   1.0007
 6XG  C19  C  CH2   0  -0.316   1.3940   2.7826   1.1613
 6XG  C20  C  CH1   0  -0.243   0.8380   3.4025  -0.0926
 6XG  C21  C  CH2   0  -0.495  -0.0677   4.5903   0.0244
 6XG  C22  C  CH2   0  -0.476  -0.6172   3.2664  -0.4127
 6XG  C23  C  CH2   0  -0.506   4.1900   1.3591   0.6798
 6XG  C24  C  CH2   0  -0.355   5.1885   0.2070   0.7996
 6XG  N25  N  NT    0  -0.455   4.8493  -0.8834  -0.0987
 6XG  C26  C  CH2   0  -0.357   3.6128  -1.5814   0.2240
 6XG  C27  C  C     0   0.514   5.5527  -1.2116  -1.2080
 6XG  O28  O  O     0  -0.512   5.2145  -2.1334  -1.9399
 6XG  C29  C  CH3   0  -0.845   6.7949  -0.4053  -1.5072
 6XG  H1   H  HCR6  0   0.259  -3.1459  -4.5420   0.1734
 6XG  H2   H  HCH1  0   0.243  -6.2543   1.4847   0.6447
 6XG  H3   H  HCR6  0   0.264  -0.7412  -4.1377   0.3673
 6XG  H4   H  HCH3  0   0.227  -6.5543   2.8276  -1.4253
 6XG  H5   H  HCH3  0   0.239  -4.8504   2.4523  -1.1668
 6XG  H6   H  HCH3  0   0.218  -5.7811   1.5565  -2.3742
 6XG  H7   H  HCH3  0   0.224  -7.5936  -0.1258  -1.5818
 6XG  H8   H  HCH3  0   0.240  -7.8770  -0.3290   0.1523
 6XG  H9   H  HCH3  0   0.239  -8.3459   1.1685  -0.6546
 6XG  H10  H  HNH1  0   0.395  -5.3383  -0.8473  -0.8779
 6XG  H11  H  HCR6  0   0.249  -4.7511  -2.6696   0.2169
 6XG  H12  H  HCR6  0   0.313  -1.4891   0.0735   0.7053
 6XG  H13  H  HNH1  0   0.407   0.9818  -2.6738   0.5210
 6XG  H14  H  HCH2  0   0.257   0.6978   2.9094   1.9929
 6XG  H15  H  HCH2  0   0.263   2.3283   3.2682   1.4453
 6XG  H16  H  HCH1  0   0.257   1.5221   3.4009  -0.9352
 6XG  H17  H  HCH2  0   0.244  -0.3161   4.9412   1.0191
 6XG  H18  H  HCH2  0   0.251   0.0296   5.3788  -0.7103
 6XG  H19  H  HCH2  0   0.246  -0.8968   3.1463  -1.4515
 6XG  H20  H  HCH2  0   0.256  -1.2429   2.7157   0.2788
 6XG  H21  H  HCH2  0   0.260   4.3380   1.8962  -0.2614
 6XG  H22  H  HCH2  0   0.272   4.3619   2.0751   1.4862
 6XG  H23  H  HCH2  0   0.308   6.1967   0.5601   0.6108
 6XG  H24  H  HCH2  0   0.277   5.1750  -0.1768   1.8231
 6XG  H25  H  HCH2  0   0.270   3.7835  -2.2647   1.0647
 6XG  H26  H  HCH2  0   0.284   3.3238  -2.1949  -0.6278
 6XG  H27  H  HCH3  0   0.294   7.5561  -0.5503  -0.7395
 6XG  H28  H  HCH3  0   0.276   7.2058  -0.7346  -2.4581
 6XG  H29  H  HCH3  0   0.281   6.5919   0.6638  -1.5719

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
 6XG  C9   C8   aromatic  1.390  0.020  1.390
 6XG  C9   C10  aromatic  1.381  0.020  1.381
 6XG  C8   C7   aromatic  1.391  0.020  1.391
 6XG  C1   C2   single    1.525  0.020  1.525
 6XG  C10  C11  aromatic  1.403  0.020  1.403
 6XG  N4   C2   single    1.455  0.020  1.455
 6XG  N4   C5   single    1.343  0.020  1.343
 6XG  C2   C3   single    1.521  0.020  1.521
 6XG  C7   C5   single    1.498  0.020  1.498
 6XG  C7   C12  aromatic  1.391  0.020  1.391
 6XG  C5   O6   double    1.225  0.020  1.225
 6XG  C11  C12  aromatic  1.397  0.020  1.397
 6XG  C11  N13  single    1.378  0.020  1.378
 6XG  N13  C14  single    1.378  0.020  1.378
 6XG  C14  N18  aromatic  1.319  0.020  1.319
 6XG  C14  C15  aromatic  1.412  0.020  1.412
 6XG  N18  N17  aromatic  1.342  0.020  1.342
 6XG  C15  C26  single    1.494  0.020  1.494
 6XG  C15  C16  aromatic  1.373  0.020  1.373
 6XG  C26  N25  single    1.456  0.020  1.456
 6XG  N17  C16  aromatic  1.343  0.020  1.343
 6XG  N17  C19  single    1.445  0.020  1.445
 6XG  C20  C19  single    1.505  0.020  1.505
 6XG  C20  C21  single    1.498  0.020  1.498
 6XG  C20  C22  single    1.496  0.020  1.496
 6XG  C16  C23  single    1.486  0.020  1.486
 6XG  C29  C27  single    1.511  0.020  1.511
 6XG  C21  C22  single    1.499  0.020  1.499
 6XG  N25  C27  single    1.354  0.020  1.354
 6XG  N25  C24  single    1.453  0.020  1.453
 6XG  C27  O28  double    1.225  0.020  1.225
 6XG  C23  C24  single    1.529  0.020  1.529
 6XG  C9   H1   single    0.930  0.020  1.080
 6XG  C2   H2   single    0.970  0.020  1.090
 6XG  C10  H3   single    0.930  0.020  1.080
 6XG  C1   H4   single    0.970  0.020  1.090
 6XG  C1   H5   single    0.970  0.020  1.090
 6XG  C1   H6   single    0.970  0.020  1.090
 6XG  C3   H7   single    0.970  0.020  1.090
 6XG  C3   H8   single    0.970  0.020  1.090
 6XG  C3   H9   single    0.970  0.020  1.090
 6XG  N4   H10  single    0.860  0.020  1.020
 6XG  C8   H11  single    0.930  0.020  1.080
 6XG  C12  H12  single    0.930  0.020  1.080
 6XG  N13  H13  single    0.860  0.020  1.020
 6XG  C19  H14  single    0.970  0.020  1.090
 6XG  C19  H15  single    0.970  0.020  1.090
 6XG  C20  H16  single    0.970  0.020  1.090
 6XG  C21  H17  single    0.970  0.020  1.090
 6XG  C21  H18  single    0.970  0.020  1.090
 6XG  C22  H19  single    0.970  0.020  1.090
 6XG  C22  H20  single    0.970  0.020  1.090
 6XG  C23  H21  single    0.970  0.020  1.090
 6XG  C23  H22  single    0.970  0.020  1.090
 6XG  C24  H23  single    0.970  0.020  1.090
 6XG  C24  H24  single    0.970  0.020  1.090
 6XG  C26  H25  single    0.970  0.020  1.090
 6XG  C26  H26  single    0.970  0.020  1.090
 6XG  C29  H27  single    0.970  0.020  1.090
 6XG  C29  H28  single    0.970  0.020  1.090
 6XG  C29  H29  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
 6XG  C12  C7   C8   120.82  3.000
 6XG  C12  C7   C5   116.87  3.000
 6XG  C8   C7   C5   122.29  3.000
 6XG  H1   C9   C8   119.89  3.000
 6XG  H1   C9   C10  119.21  3.000
 6XG  C8   C9   C10  120.90  3.000
 6XG  H2   C2   N4   107.11  3.000
 6XG  H2   C2   C3   108.79  3.000
 6XG  N4   C2   C3   109.04  3.000
 6XG  H2   C2   C1   108.77  3.000
 6XG  C3   C2   C1   111.66  3.000
 6XG  N4   C2   C1   111.34  3.000
 6XG  H3   C10  C11  119.65  3.000
 6XG  H3   C10  C9   119.67  3.000
 6XG  C11  C10  C9   120.68  3.000
 6XG  H6   C1   H5   108.30  3.000
 6XG  H6   C1   H4   107.90  3.000
 6XG  H5   C1   H4   107.97  3.000
 6XG  H6   C1   C2   110.76  3.000
 6XG  H5   C1   C2   111.23  3.000
 6XG  H4   C1   C2   110.56  3.000
 6XG  H9   C3   H8   108.09  3.000
 6XG  H9   C3   H7   107.62  3.000
 6XG  H8   C3   H7   108.26  3.000
 6XG  H9   C3   C2   110.27  3.000
 6XG  H8   C3   C2   111.43  3.000
 6XG  H7   C3   C2   111.04  3.000
 6XG  H10  N4   C5   118.54  3.000
 6XG  H10  N4   C2   116.97  3.000
 6XG  C5   N4   C2   123.42  3.000
 6XG  O6   C5   N4   123.08  3.000
 6XG  O6   C5   C7   121.23  3.000
 6XG  N4   C5   C7   115.70  3.000
 6XG  H11  C8   C9   119.76  3.000
 6XG  H11  C8   C7   121.43  3.000
 6XG  C9   C8   C7   118.77  3.000
 6XG  N13  C11  C12  123.71  3.000
 6XG  N13  C11  C10  117.91  3.000
 6XG  C12  C11  C10  118.37  3.000
 6XG  H12  C12  C11  120.11  3.000
 6XG  H12  C12  C7   119.46  3.000
 6XG  C11  C12  C7   120.43  3.000
 6XG  H13  N13  C14  115.14  3.000
 6XG  H13  N13  C11  115.60  3.000
 6XG  C14  N13  C11  128.92  3.000
 6XG  N18  C14  C15  111.08  3.000
 6XG  C15  C14  N13  125.16  3.000
 6XG  N18  C14  N13  123.76  3.000
 6XG  C26  C15  C16  123.47  3.000
 6XG  C16  C15  C14  104.13  3.000
 6XG  C26  C15  C14  132.40  3.000
 6XG  C23  C16  N17  128.53  3.000
 6XG  C23  C16  C15  124.13  3.000
 6XG  N17  C16  C15  107.34  3.000
 6XG  C19  N17  N18  119.19  3.000
 6XG  C19  N17  C16  128.64  3.000
 6XG  N18  N17  C16  111.84  3.000
 6XG  N17  N18  C14  105.61  3.000
 6XG  H15  C19  H14  107.23  3.000
 6XG  H15  C19  C20  110.48  3.000
 6XG  H14  C19  C20  110.55  3.000
 6XG  H15  C19  N17  107.61  3.000
 6XG  H14  C19  N17  108.09  3.000
 6XG  C20  C19  N17  112.66  3.000
 6XG  H16  C20  C22  116.54  3.000
 6XG  H16  C20  C21  116.28  3.000
 6XG  C22  C20  C21   60.06  3.000
 6XG  H16  C20  C19  114.41  3.000
 6XG  C22  C20  C19  120.00  3.000
 6XG  C21  C20  C19  118.99  3.000
 6XG  H18  C21  H17  114.07  3.000
 6XG  H18  C21  C22  118.60  3.000
 6XG  H17  C21  C22  118.02  3.000
 6XG  H18  C21  C20  118.05  3.000
 6XG  H17  C21  C20  117.84  3.000
 6XG  C22  C21  C20   59.90  3.000
 6XG  H20  C22  H19  114.03  3.000
 6XG  H20  C22  C21  118.35  3.000
 6XG  H19  C22  C21  118.21  3.000
 6XG  H20  C22  C20  118.13  3.000
 6XG  H19  C22  C20  117.81  3.000
 6XG  C21  C22  C20   60.04  3.000
 6XG  H22  C23  H21  106.99  3.000
 6XG  H22  C23  C24  109.47  3.000
 6XG  H21  C23  C24  110.43  3.000
 6XG  H22  C23  C16  111.95  3.000
 6XG  H21  C23  C16  111.07  3.000
 6XG  C24  C23  C16  106.95  3.000
 6XG  H24  C24  H23  106.78  3.000
 6XG  H24  C24  N25  108.21  3.000
 6XG  H23  C24  N25  110.71  3.000
 6XG  H24  C24  C23  109.26  3.000
 6XG  H23  C24  C23  110.36  3.000
 6XG  N25  C24  C23  111.38  3.000
 6XG  C27  N25  C26  120.44  3.000
 6XG  C27  N25  C24  124.56  3.000
 6XG  C26  N25  C24  114.89  3.000
 6XG  H26  C26  H25  106.85  3.000
 6XG  H26  C26  N25  108.79  3.000
 6XG  H25  C26  N25  109.66  3.000
 6XG  H26  C26  C15  111.46  3.000
 6XG  H25  C26  C15  111.35  3.000
 6XG  N25  C26  C15  108.69  3.000
 6XG  C29  C27  O28  120.69  3.000
 6XG  O28  C27  N25  121.92  3.000
 6XG  C29  C27  N25  117.39  3.000
 6XG  H29  C29  H28  108.40  3.000
 6XG  H29  C29  H27  107.58  3.000
 6XG  H28  C29  H27  108.16  3.000
 6XG  H29  C29  C27  112.46  3.000
 6XG  H28  C29  C27  108.81  3.000
 6XG  H27  C29  C27  111.31  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
 6XG  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 6XG  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 6XG  CONST_03  C12  C7   C8   C9      0.00   0.0  0
 6XG  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 6XG  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 6XG  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 6XG  CONST_07  C16  N17  N18  C14     0.00   0.0  0
 6XG  CONST_08  N17  C16  C15  C14     0.00   0.0  0
 6XG  CONST_09  N17  N18  C14  C15     0.00   0.0  0
 6XG  CONST_10  N18  N17  C16  C15     0.00   0.0  0
 6XG  CONST_11  N18  C14  C15  C16     0.00   0.0  0
 6XG  CONST_12  N13  C11  C12  C7    180.00   0.0  0
 6XG  CONST_13  C5   C7   C8   C9    180.00   0.0  0
 6XG  CONST_14  N13  C11  C10  C9    180.00   0.0  0
 6XG  CONST_15  C11  C12  C7   C5    180.00   0.0  0
 6XG  CONST_16  N17  N18  C14  N13   180.00   0.0  0
 6XG  CONST_17  C26  C15  C14  N13     0.00   0.0  0
 6XG  CONST_18  C16  C15  C14  N13   180.00   0.0  0
 6XG  CONST_19  C19  N17  N18  C14   180.00   0.0  0
 6XG  CONST_20  C19  N17  C16  C15   180.00   0.0  0
 6XG  CONST_21  C23  C16  N17  C19     0.00   0.0  0
 6XG  CONST_22  H1   C9   C8   C7    180.00   0.0  0
 6XG  CONST_23  H11  C8   C9   C10   180.00   0.0  0
 6XG  CONST_24  H12  C12  C11  C10   180.00   0.0  0
 6XG  CONST_25  H3   C10  C9   C8    180.00   0.0  0
 6XG  CONST_26  C29  C27  N25  C24     0.00   0.0  0
 6XG  CONST_27  O28  C27  N25  C24   180.00   0.0  0
 6XG  CONST_28  C29  C27  N25  C26   180.00   0.0  0
 6XG  CONST_29  O28  C27  N25  C26     0.00   0.0  0
 6XG  CONST_30  C2   N4   C5   C7    180.00   0.0  0
 6XG  CONST_31  H10  N4   C5   C7      0.00   0.0  0
 6XG  CONST_32  O6   C5   N4   C2      0.00   0.0  0
 6XG  Var_01    N25  C26  C15  C14   168.62  30.0  1
 6XG  Var_02    C24  N25  C26  C15    44.39  30.0  1
 6XG  Var_03    C24  C23  C16  C15   -17.24  30.0  1
 6XG  Var_04    N25  C24  C23  C16    48.25  30.0  1
 6XG  Var_05    C26  N25  C24  C23   -67.05  30.0  1
 6XG  Var_06    C14  N13  C11  C10   177.05  30.0  2
 6XG  Var_07    N18  C14  N13  C11    14.05  30.0  2
 6XG  Var_08    C20  C19  N17  C16    98.13  30.0  2
 6XG  Var_09    C21  C20  C19  N17   151.36  30.0  2
 6XG  Var_10    C22  C21  C20  C19  -109.91  30.0  1
 6XG  Var_11    H19  C22  C21  C20  -107.57  30.0  1
 6XG  Var_12    C8   C7   C5   N4    -31.56  30.0  1
 6XG  Var_13    H27  C29  C27  N25    65.04  30.0  3
 6XG  Var_14    C5   N4   C2   C1     82.72  30.0  2
 6XG  Var_15    H7   C3   C2   C1     60.50  30.0  3
 6XG  Var_16    H4   C1   C2   C3     59.52  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 6XG  chir_01  C20  C19  C21  C22  both

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
 6XG  plan-1  C7   0.020
 6XG  plan-1  C9   0.020
 6XG  plan-1  C10  0.020
 6XG  plan-1  C5   0.020
 6XG  plan-1  C8   0.020
 6XG  plan-1  C11  0.020
 6XG  plan-1  C12  0.020
 6XG  plan-1  N13  0.020
 6XG  plan-1  H1   0.020
 6XG  plan-1  H3   0.020
 6XG  plan-1  H11  0.020
 6XG  plan-1  H12  0.020
 6XG  plan-2  N13  0.020
 6XG  plan-2  C14  0.020
 6XG  plan-2  C15  0.020
 6XG  plan-2  C16  0.020
 6XG  plan-2  N17  0.020
 6XG  plan-2  N18  0.020
 6XG  plan-2  C19  0.020
 6XG  plan-2  C23  0.020
 6XG  plan-2  C26  0.020
 6XG  plan-3  C7   0.020
 6XG  plan-3  C2   0.020
 6XG  plan-3  N4   0.020
 6XG  plan-3  C5   0.020
 6XG  plan-3  O6   0.020
 6XG  plan-3  H10  0.020
 6XG  plan-4  C24  0.020
 6XG  plan-4  N25  0.020
 6XG  plan-4  C26  0.020
 6XG  plan-4  C27  0.020
 6XG  plan-4  O28  0.020
 6XG  plan-4  C29  0.020

