# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:25:04 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-(4-{[3-(1-methyl-1H-pyrazol-4-yl)-1H-indol-5-yl]oxy}phenyl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2c[nH]c3ccc(Oc4ccc(NC(=O)CN)cc4)cc23
#
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
 87T  87T  N-(4-{[3-(1-methyl-1H-pyrazol-4-yl)-1H-indol-5-yl]oxy}phenyl)glycinamide  ligand  46  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_87T
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
 87T  C     C  CH3   0  -0.522   6.4967  -3.7712  -1.0087
 87T  N     N  NR5   0  -0.319   5.4314  -2.8585  -0.6716
 87T  O     O  O2    0  -0.557  -0.3397   1.5581  -1.6750
 87T  C1    C  CR15  0  -0.031   5.5515  -1.6091  -0.1908
 87T  N1    N  N     0  -0.181   4.1646  -3.2337  -0.7944
 87T  O1    O  O     0  -0.350  -5.2351  -1.1004   1.8900
 87T  C2    C  CR5   0  -0.212   4.2732  -1.1279   0.0200
 87T  N2    N  NR15  0  -0.531   3.8994   2.0762   1.7243
 87T  C3    C  CR15  0  -0.092   3.4509  -2.2016  -0.3820
 87T  N3    N  NH1   0  -0.613  -5.3531  -0.3921  -0.2704
 87T  C4    C  CR5   0  -0.048   3.8819   0.1683   0.5474
 87T  N4    N  NH2   0  -0.749  -7.8455  -1.9052   1.9314
 87T  C5    C  CR15  0  -0.115   4.5633   0.9134   1.4754
 87T  C6    C  CR56  0   0.343   2.7630   2.1193   0.9720
 87T  C7    C  CR56  0  -0.106   2.7153   0.9315   0.2096
 87T  C8    C  CR16  0  -0.362   1.6518   0.7338  -0.6793
 87T  C9    C  CR6   0   0.246   0.6853   1.7105  -0.7674
 87T  C10   C  CR16  0  -0.307   0.7327   2.8806   0.0060
 87T  C11   C  CR16  0  -0.246   1.7767   3.0989   0.8813
 87T  C12   C  CR6   0   0.352  -1.5362   1.0708  -1.2425
 87T  C13   C  CR16  0  -0.334  -1.7747   0.6105   0.0438
 87T  C14   C  CR16  0  -0.241  -3.0261   0.1184   0.3993
 87T  C15   C  CR6   0   0.236  -4.0610   0.0779  -0.5318
 87T  C16   C  CR16  0  -0.311  -3.8059   0.5430  -1.8250
 87T  C17   C  CR16  0  -0.289  -2.5653   1.0348  -2.1787
 87T  C18   C  C     0   0.489  -5.8653  -0.9345   0.8629
 87T  C19   C  CH2   0  -0.394  -7.3353  -1.3000   0.7251
 87T  H     H  HCH3  0   0.242   6.5455  -4.5896  -0.2919
 87T  HA    H  HCH3  0   0.257   6.3385  -4.1777  -2.0049
 87T  HB    H  HCH3  0   0.277   7.4402  -3.2333  -0.9932
 87T  H1    H  HCR5  0   0.283   6.5145  -1.1478  -0.0396
 87T  HN2   H  HNR5  0   0.397   4.2018   2.7839   2.3726
 87T  H3    H  HCR5  0   0.270   2.3724  -2.2575  -0.3714
 87T  HN3   H  HNH1  0   0.298  -5.9919  -0.3155  -1.0480
 87T  HN4   H  HNH2  0   0.323  -7.9042  -1.2153   2.6686
 87T  HN4A  H  HNH2  0   0.358  -8.7926  -2.2166   1.7632
 87T  H5    H  HCR5  0   0.316   5.4851   0.6868   1.9878
 87T  H8    H  HCR6  0   0.256   1.5891  -0.1529  -1.2979
 87T  H10   H  HCR6  0   0.253  -0.0515   3.6196  -0.0976
 87T  H11   H  HCR6  0   0.247   1.8249   4.0054   1.4708
 87T  H13   H  HCR6  0   0.242  -0.9953   0.6227   0.7936
 87T  H14   H  HCR6  0   0.264  -3.1741  -0.2285   1.4085
 87T  H16   H  HCR6  0   0.231  -4.5926   0.5230  -2.5700
 87T  H17   H  HCR6  0   0.271  -2.3934   1.3902  -3.1869
 87T  H19   H  HCH2  0   0.243  -7.4309  -2.0152  -0.0971
 87T  H19A  H  HCH2  0   0.218  -7.8718  -0.3973   0.3974

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
 87T  C    N     single    1.443  0.020  1.443
 87T  N    C1    aromatic  1.344  0.020  1.344
 87T  N    N1    aromatic  1.327  0.020  1.327
 87T  O    C9    single    1.378  0.020  1.378
 87T  O    C12   single    1.362  0.020  1.362
 87T  C1   C2    aromatic  1.382  0.020  1.382
 87T  N1   C3    aromatic  1.321  0.020  1.321
 87T  O1   C18   double    1.216  0.020  1.216
 87T  C2   C3    aromatic  1.411  0.020  1.411
 87T  C2   C4    single    1.453  0.020  1.453
 87T  N2   C5    aromatic  1.362  0.020  1.362
 87T  N2   C6    aromatic  1.364  0.020  1.364
 87T  N3   C15   single    1.400  0.020  1.400
 87T  N3   C18   single    1.357  0.020  1.357
 87T  C4   C5    aromatic  1.371  0.020  1.371
 87T  C4   C7    aromatic  1.434  0.020  1.434
 87T  N4   C19   single    1.443  0.020  1.443
 87T  C6   C7    aromatic  1.412  0.020  1.412
 87T  C6   C11   aromatic  1.393  0.020  1.393
 87T  C7   C8    aromatic  1.400  0.020  1.400
 87T  C8   C9    aromatic  1.377  0.020  1.377
 87T  C9   C10   aromatic  1.403  0.020  1.403
 87T  C10  C11   aromatic  1.380  0.020  1.380
 87T  C12  C13   aromatic  1.387  0.020  1.387
 87T  C12  C17   aromatic  1.392  0.020  1.392
 87T  C13  C14   aromatic  1.391  0.020  1.391
 87T  C14  C15   aromatic  1.393  0.020  1.393
 87T  C15  C16   aromatic  1.398  0.020  1.398
 87T  C16  C17   aromatic  1.381  0.020  1.381
 87T  C18  C19   single    1.521  0.020  1.521
 87T  C    H     single    0.970  0.020  1.090
 87T  C    HA    single    0.970  0.020  1.090
 87T  C    HB    single    0.970  0.020  1.090
 87T  C1   H1    single    0.930  0.020  1.080
 87T  N2   HN2   single    0.860  0.020  1.020
 87T  C3   H3    single    0.930  0.020  1.080
 87T  N3   HN3   single    0.860  0.020  1.020
 87T  N4   HN4   single    0.890  0.020  1.040
 87T  N4   HN4A  single    0.890  0.020  1.040
 87T  C5   H5    single    0.930  0.020  1.080
 87T  C8   H8    single    0.930  0.020  1.080
 87T  C10  H10   single    0.930  0.020  1.080
 87T  C11  H11   single    0.930  0.020  1.080
 87T  C13  H13   single    0.930  0.020  1.080
 87T  C14  H14   single    0.930  0.020  1.080
 87T  C16  H16   single    0.930  0.020  1.080
 87T  C17  H17   single    0.930  0.020  1.080
 87T  C19  H19   single    0.970  0.020  1.090
 87T  C19  H19A  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
 87T  HB    C    HA   108.94  3.000
 87T  HB    C    H    108.90  3.000
 87T  HA    C    H    109.19  3.000
 87T  HB    C    N    108.95  3.000
 87T  HA    C    N    110.06  3.000
 87T  H     C    N    110.77  3.000
 87T  N1    N    C1   112.41  3.000
 87T  N1    N    C    120.30  3.000
 87T  C1    N    C    127.27  3.000
 87T  C12   O    C9   118.94  3.000
 87T  H1    C1   C2   130.97  3.000
 87T  H1    C1   N    121.84  3.000
 87T  C2    C1   N    107.19  3.000
 87T  C3    N1   N    105.43  3.000
 87T  C4    C2   C3   128.70  3.000
 87T  C4    C2   C1   127.96  3.000
 87T  C3    C2   C1   103.34  3.000
 87T  HN2   N2   C6   125.71  3.000
 87T  HN2   N2   C5   124.87  3.000
 87T  C6    N2   C5   109.41  3.000
 87T  H3    C3   C2   128.22  3.000
 87T  H3    C3   N1   120.14  3.000
 87T  C2    C3   N1   111.63  3.000
 87T  HN3   N3   C18  115.78  3.000
 87T  HN3   N3   C15  114.52  3.000
 87T  C18   N3   C15  129.70  3.000
 87T  C7    C4   C5   105.93  3.000
 87T  C7    C4   C2   127.46  3.000
 87T  C5    C4   C2   126.61  3.000
 87T  HN4A  N4   HN4  106.08  3.000
 87T  HN4A  N4   C19  108.75  3.000
 87T  HN4   N4   C19  110.11  3.000
 87T  H5    C5   C4   129.19  3.000
 87T  H5    C5   N2   120.60  3.000
 87T  C4    C5   N2   110.20  3.000
 87T  C11   C6   C7   122.16  3.000
 87T  C11   C6   N2   130.41  3.000
 87T  C7    C6   N2   107.42  3.000
 87T  C8    C7   C6   119.16  3.000
 87T  C8    C7   C4   133.80  3.000
 87T  C6    C7   C4   107.03  3.000
 87T  H8    C8   C9   120.24  3.000
 87T  H8    C8   C7   121.48  3.000
 87T  C9    C8   C7   118.27  3.000
 87T  C10   C9   C8   122.17  3.000
 87T  C10   C9   O    118.72  3.000
 87T  C8    C9   O    119.07  3.000
 87T  H10   C10  C11  120.06  3.000
 87T  H10   C10  C9   119.47  3.000
 87T  C11   C10  C9   120.47  3.000
 87T  H11   C11  C10  120.78  3.000
 87T  H11   C11  C6   121.46  3.000
 87T  C10   C11  C6   117.76  3.000
 87T  C17   C12  C13  119.22  3.000
 87T  C17   C12  O    116.43  3.000
 87T  C13   C12  O    124.34  3.000
 87T  H13   C13  C14  118.36  3.000
 87T  H13   C13  C12  121.02  3.000
 87T  C14   C13  C12  120.61  3.000
 87T  H14   C14  C15  120.98  3.000
 87T  H14   C14  C13  118.49  3.000
 87T  C15   C14  C13  120.53  3.000
 87T  C16   C15  C14  118.25  3.000
 87T  C16   C15  N3   116.93  3.000
 87T  C14   C15  N3   124.82  3.000
 87T  H16   C16  C17  118.87  3.000
 87T  H16   C16  C15  119.83  3.000
 87T  C17   C16  C15  121.30  3.000
 87T  H17   C17  C16  119.88  3.000
 87T  H17   C17  C12  120.03  3.000
 87T  C16   C17  C12  120.09  3.000
 87T  C19   C18  N3   112.66  3.000
 87T  C19   C18  O1   122.99  3.000
 87T  N3    C18  O1   124.35  3.000
 87T  H19A  C19  H19  105.67  3.000
 87T  H19A  C19  C18  107.53  3.000
 87T  H19   C19  C18  108.04  3.000
 87T  H19A  C19  N4   114.88  3.000
 87T  H19   C19  N4   108.86  3.000
 87T  C18   C19  N4   111.51  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
 87T  CONST_01  C3   C2   C1   N      0.00   0.0  0
 87T  CONST_02  C4   C2   C1   N    180.00   0.0  0
 87T  CONST_03  C2   C3   N1   N      0.00   0.0  0
 87T  CONST_04  C3   N1   N    C1     0.00   0.0  0
 87T  CONST_05  N1   C3   C2   C1     0.00   0.0  0
 87T  CONST_08  C2   C1   N    N1     0.00   0.0  0
 87T  CONST_09  C4   C2   C3   N1   180.00   0.0  0
 87T  CONST_10  N2   C5   C4   C2   180.00   0.0  0
 87T  CONST_11  C6   C7   C4   C2   180.00   0.0  0
 87T  CONST_12  C8   C7   C4   C2     0.00   0.0  0
 87T  CONST_13  C7   C4   C5   N2     0.00   0.0  0
 87T  CONST_14  C4   C7   C6   N2     0.00   0.0  0
 87T  CONST_15  C8   C7   C6   N2   180.00   0.0  0
 87T  CONST_16  C10  C11  C6   N2   180.00   0.0  0
 87T  CONST_19  C6   N2   C5   C4     0.00   0.0  0
 87T  CONST_20  C11  C6   C7   C4   180.00   0.0  0
 87T  CONST_21  C9   C8   C7   C4   180.00   0.0  0
 87T  CONST_22  C7   C6   N2   C5     0.00   0.0  0
 87T  CONST_23  C11  C6   N2   C5   180.00   0.0  0
 87T  CONST_24  C6   C7   C4   C5     0.00   0.0  0
 87T  CONST_25  C8   C7   C4   C5   180.00   0.0  0
 87T  CONST_26  C9   C8   C7   C6     0.00   0.0  0
 87T  CONST_27  C9   C10  C11  C6     0.00   0.0  0
 87T  CONST_28  C10  C11  C6   C7     0.00   0.0  0
 87T  CONST_29  C10  C9   C8   C7     0.00   0.0  0
 87T  CONST_30  C11  C6   C7   C8     0.00   0.0  0
 87T  CONST_31  C11  C10  C9   C8     0.00   0.0  0
 87T  CONST_32  C15  C14  C13  C12    0.00   0.0  0
 87T  CONST_33  C15  C16  C17  C12    0.00   0.0  0
 87T  CONST_34  C16  C17  C12  C13    0.00   0.0  0
 87T  CONST_35  C16  C15  C14  C13    0.00   0.0  0
 87T  CONST_36  C17  C12  C13  C14    0.00   0.0  0
 87T  CONST_37  C17  C16  C15  C14    0.00   0.0  0
 87T  CONST_38  C2   C1   N    C    180.00   0.0  0
 87T  CONST_39  C3   N1   N    C    180.00   0.0  0
 87T  CONST_40  C7   C8   C9   O    180.00   0.0  0
 87T  CONST_41  C11  C10  C9   O    180.00   0.0  0
 87T  CONST_42  C14  C13  C12  O    180.00   0.0  0
 87T  CONST_43  C16  C17  C12  O    180.00   0.0  0
 87T  CONST_44  C13  C14  C15  N3   180.00   0.0  0
 87T  CONST_45  C17  C16  C15  N3   180.00   0.0  0
 87T  CONST_46  H3   C3   N1   N    180.00   0.0  0
 87T  CONST_47  H1   C1   N    N1   180.00   0.0  0
 87T  CONST_48  H5   C5   C4   C2     0.00   0.0  0
 87T  CONST_49  H11  C11  C6   N2     0.00   0.0  0
 87T  CONST_50  HN2  N2   C5   C4   180.00   0.0  0
 87T  CONST_51  H8   C8   C7   C4     0.00   0.0  0
 87T  CONST_52  H10  C10  C11  C6   180.00   0.0  0
 87T  CONST_53  H14  C14  C13  C12  180.00   0.0  0
 87T  CONST_54  H16  C16  C17  C12  180.00   0.0  0
 87T  CONST_55  H17  C17  C12  C13  180.00   0.0  0
 87T  CONST_56  H13  C13  C14  C15  180.00   0.0  0
 87T  CONST_57  C18  N3   C15  C14    0.00   0.0  0
 87T  CONST_58  C18  N3   C15  C16  180.00   0.0  0
 87T  CONST_59  HN3  N3   C15  C14  180.00   0.0  0
 87T  CONST_60  C15  N3   C18  O1     0.00   0.0  0
 87T  CONST_61  C19  C18  N3   C15  180.00   0.0  0
 87T  Var_01    C13  C12  O    C9    -5.33  30.0  2
 87T  Var_02    H    C    N    C1   109.17  30.0  2
 87T  Var_03    N4   C19  C18  O1    -2.36  30.0  3
 87T  Var_04    HN4  N4   C19  C18   69.92  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
 87T  plan-1  C    0.020
 87T  plan-1  N    0.020
 87T  plan-1  C1   0.020
 87T  plan-1  N1   0.020
 87T  plan-1  C2   0.020
 87T  plan-1  C3   0.020
 87T  plan-1  C4   0.020
 87T  plan-1  H1   0.020
 87T  plan-1  H3   0.020
 87T  plan-2  O    0.020
 87T  plan-2  N3   0.020
 87T  plan-2  C12  0.020
 87T  plan-2  C13  0.020
 87T  plan-2  C14  0.020
 87T  plan-2  C15  0.020
 87T  plan-2  C16  0.020
 87T  plan-2  C17  0.020
 87T  plan-2  H13  0.020
 87T  plan-2  H14  0.020
 87T  plan-2  H16  0.020
 87T  plan-2  H17  0.020
 87T  plan-3  O    0.020
 87T  plan-3  C2   0.020
 87T  plan-3  N2   0.020
 87T  plan-3  C4   0.020
 87T  plan-3  C5   0.020
 87T  plan-3  C6   0.020
 87T  plan-3  C7   0.020
 87T  plan-3  C8   0.020
 87T  plan-3  C9   0.020
 87T  plan-3  C10  0.020
 87T  plan-3  C11  0.020
 87T  plan-3  HN2  0.020
 87T  plan-3  H5   0.020
 87T  plan-3  H8   0.020
 87T  plan-3  H10  0.020
 87T  plan-3  H11  0.020
 87T  plan-4  O1   0.020
 87T  plan-4  N3   0.020
 87T  plan-4  C15  0.020
 87T  plan-4  C18  0.020
 87T  plan-4  C19  0.020
 87T  plan-4  HN3  0.020

