# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:29:26 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: ~{N}-[3-[2-(3,5-dimethoxyphenyl)ethyl]-1~{H}-pyrazol-5-yl]-2-(propanoylamino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccccc1C(=O)Nc2[nH]nc(CCc3cc(OC)cc(OC)c3)c2
#
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
 9CT  9CT  ~{N}-[3-[2-(3,5-dimethoxyphenyl)ethyl]-1~{H}-pyrazol-5-yl]-2-(propanoylamino)benzamide  ligand  57  31  .  2022-07-24  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_9CT
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
 9CT  C1   C  CH3   0  -0.659   6.2588   4.4671   2.2519
 9CT  C2   C  CH2   0  -0.591   5.4218   3.5575   1.3722
 9CT  C3   C  C     0   0.546   6.1343   2.2840   0.9701
 9CT  C11  C  CR16  0  -0.292   7.0823  -0.0827  -0.6594
 9CT  C12  C  C     0   0.558   3.3055  -0.3363  -0.4907
 9CT  C15  C  CR5   0   0.643   1.1610  -1.3374   0.0613
 9CT  C18  C  CR5   0   0.280  -1.0081  -0.9917   0.2085
 9CT  C19  C  CH2   0  -0.497  -2.3717  -0.3790   0.1998
 9CT  C20  C  CH2   0  -0.514  -3.4749  -1.3573  -0.2126
 9CT  C21  C  CR6   0   0.161  -4.8256  -0.6968  -0.2133
 9CT  C22  C  CR16  0  -0.433  -5.2366   0.0419  -1.3166
 9CT  C23  C  CR6   0   0.431  -6.4720   0.6835  -1.3044
 9CT  C25  C  CH3   0  -0.439  -8.0419   2.0308  -2.4793
 9CT  C26  C  CR16  0  -0.547  -7.3078   0.5932  -0.1909
 9CT  C27  C  CR6   0   0.433  -6.8849  -0.1485   0.9113
 9CT  C29  C  CH3   0  -0.438  -8.8890   0.3209   2.1021
 9CT  C30  C  CR16  0  -0.440  -5.6487  -0.7909   0.9011
 9CT  O4   O  O     0  -0.462   7.2314   1.9747   1.3912
 9CT  N5   N  NH1   0  -0.762   5.4133   1.5203   0.0983
 9CT  C6   C  CR6   0   0.359   5.7535   0.2693  -0.4153
 9CT  C7   C  CR6   0  -0.126   4.7404  -0.6644  -0.7114
 9CT  C8   C  CR16  0  -0.298   5.0843  -1.8966  -1.2682
 9CT  C9   C  CR16  0  -0.254   6.4033  -2.2339  -1.5090
 9CT  C10  C  CR16  0  -0.246   7.3981  -1.3198  -1.1952
 9CT  O13  O  O     0  -0.467   2.8497   0.7865  -0.6476
 9CT  N14  N  NH1   0  -0.740   2.5327  -1.3821  -0.1034
 9CT  N16  N  NR15  0  -0.513   0.5024  -2.4416   0.4569
 9CT  N17  N  N     0  -0.306  -0.8158  -2.2505   0.5500
 9CT  O24  O  O2    0  -0.476  -6.7915   1.3755  -2.4153
 9CT  O28  O  O2    0  -0.475  -7.6201  -0.2969   2.0302
 9CT  C31  C  CR15  0  -0.529   0.2085  -0.3542  -0.1126
 9CT  H1   H  HCH3  0   0.230   6.5287   3.9838   3.1898
 9CT  H2   H  HCH3  0   0.230   7.1784   4.7721   1.7539
 9CT  H3   H  HCH3  0   0.237   5.6975   5.3688   2.4932
 9CT  H4   H  HCH2  0   0.274   4.4942   3.2818   1.8831
 9CT  H5   H  HCH2  0   0.270   5.1106   4.0815   0.4642
 9CT  H6   H  HCR6  0   0.279   7.8751   0.6177  -0.4519
 9CT  H7   H  HCH2  0   0.253  -2.6028   0.0238   1.1909
 9CT  H8   H  HCH2  0   0.250  -2.3680   0.4776  -0.4782
 9CT  H9   H  HCH2  0   0.245  -3.2513  -1.7511  -1.2068
 9CT  H10  H  HCH2  0   0.249  -3.4785  -2.2089   0.4697
 9CT  H11  H  HCR6  0   0.247  -4.6016   0.1193  -2.1916
 9CT  H12  H  HCH3  0   0.261  -8.0878   2.5123  -3.4530
 9CT  H13  H  HCH3  0   0.228  -8.8768   1.3304  -2.3946
 9CT  H14  H  HCH3  0   0.228  -8.1456   2.7958  -1.7054
 9CT  H15  H  HCR6  0   0.298  -8.2676   1.0890  -0.1838
 9CT  H16  H  HCH3  0   0.228  -8.8211   1.4087   2.0163
 9CT  H17  H  HCH3  0   0.228  -9.5702  -0.0516   1.3324
 9CT  H18  H  HCH3  0   0.260  -9.2978   0.0736   3.0786
 9CT  H19  H  HCR6  0   0.247  -5.3388  -1.3669   1.7653
 9CT  H20  H  HNH1  0   0.420   4.4754   1.8312  -0.1164
 9CT  H21  H  HCR6  0   0.273   4.3076  -2.5992  -1.5423
 9CT  H22  H  HCR6  0   0.266   6.6499  -3.1911  -1.9467
 9CT  H23  H  HCR6  0   0.269   8.4359  -1.5616  -1.3832
 9CT  H24  H  HNH1  0   0.431   2.9890  -2.2529   0.1253
 9CT  H25  H  HNR5  0   0.420   0.8923  -3.3491   0.6574
 9CT  H26  H  HCR5  0   0.269   0.3504   0.6645  -0.4228

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
 9CT  C1   C2   single    1.517  0.020  1.517
 9CT  C2   C3   single    1.514  0.020  1.514
 9CT  O4   C3   double    1.215  0.020  1.215
 9CT  C3   N5   single    1.365  0.020  1.365
 9CT  N5   C6   single    1.394  0.020  1.394
 9CT  C11  C6   aromatic  1.396  0.020  1.396
 9CT  C11  C10  aromatic  1.385  0.020  1.385
 9CT  C6   C7   aromatic  1.409  0.020  1.409
 9CT  C10  C9   aromatic  1.387  0.020  1.387
 9CT  C29  O28  single    1.413  0.020  1.413
 9CT  O13  C12  double    1.222  0.020  1.222
 9CT  C7   C12  single    1.488  0.020  1.488
 9CT  C7   C8   aromatic  1.395  0.020  1.395
 9CT  O28  C27  single    1.347  0.020  1.347
 9CT  C12  N14  single    1.357  0.020  1.357
 9CT  C9   C8   aromatic  1.383  0.020  1.383
 9CT  C30  C27  aromatic  1.393  0.020  1.393
 9CT  C30  C21  aromatic  1.389  0.020  1.389
 9CT  C27  C26  aromatic  1.394  0.020  1.394
 9CT  C20  C21  single    1.503  0.020  1.503
 9CT  C20  C19  single    1.531  0.020  1.531
 9CT  C21  C22  aromatic  1.390  0.020  1.390
 9CT  N14  C15  single    1.382  0.020  1.382
 9CT  C31  C15  aromatic  1.380  0.020  1.380
 9CT  C31  C18  aromatic  1.410  0.020  1.410
 9CT  C26  C23  aromatic  1.395  0.020  1.395
 9CT  C15  N16  aromatic  1.345  0.020  1.345
 9CT  C22  C23  aromatic  1.392  0.020  1.392
 9CT  C18  C19  single    1.495  0.020  1.495
 9CT  C18  N17  aromatic  1.318  0.020  1.318
 9CT  C23  O24  single    1.347  0.020  1.347
 9CT  N16  N17  aromatic  1.335  0.020  1.335
 9CT  C25  O24  single    1.413  0.020  1.413
 9CT  C1   H1   single    0.970  0.020  1.090
 9CT  C1   H2   single    0.970  0.020  1.090
 9CT  C1   H3   single    0.970  0.020  1.090
 9CT  C2   H4   single    0.970  0.020  1.090
 9CT  C2   H5   single    0.970  0.020  1.090
 9CT  C11  H6   single    0.930  0.020  1.080
 9CT  C19  H7   single    0.970  0.020  1.090
 9CT  C19  H8   single    0.970  0.020  1.090
 9CT  C20  H9   single    0.970  0.020  1.090
 9CT  C20  H10  single    0.970  0.020  1.090
 9CT  C22  H11  single    0.930  0.020  1.080
 9CT  C25  H12  single    0.970  0.020  1.090
 9CT  C25  H13  single    0.970  0.020  1.090
 9CT  C25  H14  single    0.970  0.020  1.090
 9CT  C26  H15  single    0.930  0.020  1.080
 9CT  C29  H16  single    0.970  0.020  1.090
 9CT  C29  H17  single    0.970  0.020  1.090
 9CT  C29  H18  single    0.970  0.020  1.090
 9CT  C30  H19  single    0.930  0.020  1.080
 9CT  N5   H20  single    0.860  0.020  1.020
 9CT  C8   H21  single    0.930  0.020  1.080
 9CT  C9   H22  single    0.930  0.020  1.080
 9CT  C10  H23  single    0.930  0.020  1.080
 9CT  N14  H24  single    0.860  0.020  1.020
 9CT  N16  H25  single    0.860  0.020  1.020
 9CT  C31  H26  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
 9CT  H3   C1   H2   107.73  3.000
 9CT  H3   C1   H1   107.72  3.000
 9CT  H2   C1   H1   107.99  3.000
 9CT  H3   C1   C2   109.90  3.000
 9CT  H2   C1   C2   111.63  3.000
 9CT  H1   C1   C2   111.71  3.000
 9CT  H5   C2   H4   105.50  3.000
 9CT  H5   C2   C3   108.45  3.000
 9CT  H4   C2   C3   108.12  3.000
 9CT  H5   C2   C1   110.56  3.000
 9CT  H4   C2   C1   110.37  3.000
 9CT  C3   C2   C1   113.50  3.000
 9CT  N5   C3   O4   123.76  3.000
 9CT  N5   C3   C2   113.07  3.000
 9CT  O4   C3   C2   123.17  3.000
 9CT  H6   C11  C10  119.16  3.000
 9CT  H6   C11  C6   120.16  3.000
 9CT  C10  C11  C6   120.66  3.000
 9CT  N14  C12  O13  122.18  3.000
 9CT  N14  C12  C7   114.93  3.000
 9CT  O13  C12  C7   122.90  3.000
 9CT  C31  C15  N16  106.50  3.000
 9CT  N16  C15  N14  119.63  3.000
 9CT  C31  C15  N14  133.87  3.000
 9CT  C31  C18  N17  111.39  3.000
 9CT  N17  C18  C19  121.72  3.000
 9CT  C31  C18  C19  126.88  3.000
 9CT  H8   C19  H7   105.91  3.000
 9CT  H8   C19  C20  109.65  3.000
 9CT  H7   C19  C20  109.08  3.000
 9CT  H8   C19  C18  108.78  3.000
 9CT  H7   C19  C18  109.77  3.000
 9CT  C20  C19  C18  113.39  3.000
 9CT  H10  C20  H9   106.76  3.000
 9CT  H10  C20  C21  109.89  3.000
 9CT  H9   C20  C21  109.99  3.000
 9CT  H10  C20  C19  109.43  3.000
 9CT  H9   C20  C19  109.14  3.000
 9CT  C21  C20  C19  111.51  3.000
 9CT  C30  C21  C22  119.85  3.000
 9CT  C22  C21  C20  119.97  3.000
 9CT  C30  C21  C20  120.16  3.000
 9CT  H11  C22  C23  119.60  3.000
 9CT  H11  C22  C21  120.37  3.000
 9CT  C23  C22  C21  120.03  3.000
 9CT  O24  C23  C26  123.32  3.000
 9CT  O24  C23  C22  116.11  3.000
 9CT  C26  C23  C22  120.58  3.000
 9CT  H14  C25  H13  108.73  3.000
 9CT  H14  C25  H12  108.67  3.000
 9CT  H13  C25  H12  108.72  3.000
 9CT  H14  C25  O24  112.11  3.000
 9CT  H13  C25  O24  112.04  3.000
 9CT  H12  C25  O24  106.46  3.000
 9CT  H15  C26  C27  120.56  3.000
 9CT  H15  C26  C23  120.51  3.000
 9CT  C27  C26  C23  118.93  3.000
 9CT  O28  C27  C30  116.08  3.000
 9CT  C30  C27  C26  120.57  3.000
 9CT  O28  C27  C26  123.35  3.000
 9CT  H18  C29  H17  108.70  3.000
 9CT  H18  C29  H16  108.67  3.000
 9CT  H17  C29  H16  108.82  3.000
 9CT  H18  C29  O28  106.49  3.000
 9CT  H17  C29  O28  112.01  3.000
 9CT  H16  C29  O28  112.04  3.000
 9CT  H19  C30  C27  119.53  3.000
 9CT  H19  C30  C21  120.43  3.000
 9CT  C27  C30  C21  120.04  3.000
 9CT  H20  N5   C6   115.08  3.000
 9CT  H20  N5   C3   116.96  3.000
 9CT  C6   N5   C3   127.48  3.000
 9CT  C7   C6   N5   119.76  3.000
 9CT  C7   C6   C11  118.71  3.000
 9CT  N5   C6   C11  121.52  3.000
 9CT  C8   C7   C6   119.46  3.000
 9CT  C8   C7   C12  119.44  3.000
 9CT  C6   C7   C12  121.05  3.000
 9CT  H21  C8   C9   118.82  3.000
 9CT  H21  C8   C7   119.82  3.000
 9CT  C9   C8   C7   121.34  3.000
 9CT  H22  C9   C10  120.77  3.000
 9CT  H22  C9   C8   120.28  3.000
 9CT  C10  C9   C8   118.95  3.000
 9CT  H23  C10  C9   120.09  3.000
 9CT  H23  C10  C11  119.05  3.000
 9CT  C9   C10  C11  120.85  3.000
 9CT  H24  N14  C15  116.71  3.000
 9CT  H24  N14  C12  118.18  3.000
 9CT  C15  N14  C12  125.05  3.000
 9CT  H25  N16  N17  119.80  3.000
 9CT  H25  N16  C15  127.46  3.000
 9CT  N17  N16  C15  112.73  3.000
 9CT  N16  N17  C18  105.22  3.000
 9CT  C25  O24  C23  119.04  3.000
 9CT  C29  O28  C27  118.96  3.000
 9CT  H26  C31  C18  127.46  3.000
 9CT  H26  C31  C15  128.38  3.000
 9CT  C18  C31  C15  104.16  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
 9CT  CONST_01  C8   C7   C6   C11     0.00   0.0  0
 9CT  CONST_02  C8   C9   C10  C11     0.00   0.0  0
 9CT  CONST_03  N17  C18  C31  C15     0.00   0.0  0
 9CT  CONST_04  C18  N17  N16  C15     0.00   0.0  0
 9CT  CONST_05  N16  C15  C31  C18     0.00   0.0  0
 9CT  CONST_06  C26  C27  C30  C21     0.00   0.0  0
 9CT  CONST_07  C26  C23  C22  C21     0.00   0.0  0
 9CT  CONST_08  C27  C30  C21  C22     0.00   0.0  0
 9CT  CONST_09  C27  C26  C23  C22     0.00   0.0  0
 9CT  CONST_10  C30  C27  C26  C23     0.00   0.0  0
 9CT  CONST_11  C30  C21  C22  C23     0.00   0.0  0
 9CT  CONST_12  C9   C10  C11  C6      0.00   0.0  0
 9CT  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 9CT  CONST_14  C10  C11  C6   C7      0.00   0.0  0
 9CT  CONST_15  C10  C9   C8   C7      0.00   0.0  0
 9CT  CONST_16  C31  C18  N17  N16     0.00   0.0  0
 9CT  CONST_17  C31  C15  N16  N17     0.00   0.0  0
 9CT  CONST_18  C12  C7   C6   C11   180.00   0.0  0
 9CT  CONST_19  C9   C8   C7   C12   180.00   0.0  0
 9CT  CONST_20  C19  C18  C31  C15   180.00   0.0  0
 9CT  CONST_21  N14  C15  C31  C18   180.00   0.0  0
 9CT  CONST_22  N16  N17  C18  C19   180.00   0.0  0
 9CT  CONST_23  C27  C30  C21  C20   180.00   0.0  0
 9CT  CONST_24  C23  C22  C21  C20   180.00   0.0  0
 9CT  CONST_25  O28  C27  C30  C21   180.00   0.0  0
 9CT  CONST_26  O24  C23  C22  C21   180.00   0.0  0
 9CT  CONST_27  O28  C27  C26  C23   180.00   0.0  0
 9CT  CONST_28  O24  C23  C26  C27   180.00   0.0  0
 9CT  CONST_29  C10  C11  C6   N5    180.00   0.0  0
 9CT  CONST_30  C8   C7   C6   N5    180.00   0.0  0
 9CT  CONST_31  N17  N16  C15  N14   180.00   0.0  0
 9CT  CONST_32  H22  C9   C10  C11   180.00   0.0  0
 9CT  CONST_33  H25  N16  N17  C18   180.00   0.0  0
 9CT  CONST_34  H19  C30  C21  C22   180.00   0.0  0
 9CT  CONST_35  H15  C26  C23  C22   180.00   0.0  0
 9CT  CONST_36  H11  C22  C23  C26   180.00   0.0  0
 9CT  CONST_37  H23  C10  C11  C6    180.00   0.0  0
 9CT  CONST_38  H21  C8   C7   C6    180.00   0.0  0
 9CT  CONST_39  H6   C11  C6   C7    180.00   0.0  0
 9CT  CONST_40  H26  C31  C15  N16   180.00   0.0  0
 9CT  CONST_41  C7   C12  N14  C15   180.00   0.0  0
 9CT  CONST_45  C31  C15  N14  C12     0.00   0.0  0
 9CT  CONST_46  N16  C15  N14  C12   180.00   0.0  0
 9CT  CONST_48  H24  N14  C15  N16     0.00   0.0  0
 9CT  CONST_49  C6   N5   C3   C2    180.00   0.0  0
 9CT  CONST_50  O13  C12  N14  C15     0.00   0.0  0
 9CT  CONST_51  C6   N5   C3   O4      0.00   0.0  0
 9CT  Var_01    C21  C20  C19  C18  -179.73  30.0  1
 9CT  Var_02    C30  C21  C20  C19   -94.99  30.0  2
 9CT  Var_03    C31  C18  C19  C20   146.29  30.0  1
 9CT  Var_04    C26  C23  O24  C25    -1.05  30.0  2
 9CT  Var_05    C30  C27  O28  C29  -179.53  30.0  2
 9CT  Var_06    H12  C25  O24  C23  -179.63  30.0  3
 9CT  Var_07    H16  C29  O28  C27   -61.23  30.0  3
 9CT  Var_08    O4   C3   C2   C1      5.14  30.0  3
 9CT  Var_09    H1   C1   C2   C3    -61.33  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
 9CT  plan-1  C15  0.020
 9CT  plan-1  C18  0.020
 9CT  plan-1  C19  0.020
 9CT  plan-1  N14  0.020
 9CT  plan-1  N16  0.020
 9CT  plan-1  N17  0.020
 9CT  plan-1  C31  0.020
 9CT  plan-1  H25  0.020
 9CT  plan-1  H26  0.020
 9CT  plan-2  C11  0.020
 9CT  plan-2  C12  0.020
 9CT  plan-2  C15  0.020
 9CT  plan-2  N5   0.020
 9CT  plan-2  C6   0.020
 9CT  plan-2  C7   0.020
 9CT  plan-2  C8   0.020
 9CT  plan-2  C9   0.020
 9CT  plan-2  C10  0.020
 9CT  plan-2  O13  0.020
 9CT  plan-2  N14  0.020
 9CT  plan-2  H6   0.020
 9CT  plan-2  H21  0.020
 9CT  plan-2  H22  0.020
 9CT  plan-2  H23  0.020
 9CT  plan-2  H24  0.020
 9CT  plan-3  C20  0.020
 9CT  plan-3  C21  0.020
 9CT  plan-3  C22  0.020
 9CT  plan-3  C23  0.020
 9CT  plan-3  C26  0.020
 9CT  plan-3  C27  0.020
 9CT  plan-3  C30  0.020
 9CT  plan-3  O24  0.020
 9CT  plan-3  O28  0.020
 9CT  plan-3  H11  0.020
 9CT  plan-3  H15  0.020
 9CT  plan-3  H19  0.020
 9CT  plan-4  C2   0.020
 9CT  plan-4  C3   0.020
 9CT  plan-4  O4   0.020
 9CT  plan-4  N5   0.020
 9CT  plan-4  C6   0.020
 9CT  plan-4  H20  0.020

