# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:25:46 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1nccc1c2c[nH]c3ncc(cc23)c4ccc(N)c(c4)C(=O)N(C)C
#
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
 SX7  SX7  2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide  ligand  50  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SX7
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
 SX7  O1    O  O     0  -0.490   5.7348  -1.0320   1.0830
 SX7  C7    C  CR15  0   0.021  -3.9420   2.1913   0.5366
 SX7  C6    C  CR5   0  -0.071  -3.4712   0.9072   0.5219
 SX7  C1    C  CH3   0  -0.631  -5.3722  -0.7174  -2.3114
 SX7  N1    N  NR5   0  -0.332  -5.3080  -0.7298   0.1510
 SX7  C5    C  CR5   0   0.378  -4.1875  -0.3278   0.7987
 SX7  C4    C  CR15  0  -0.534  -3.8930  -1.3231   1.7082
 SX7  C3    C  CR15  0  -0.064  -4.9003  -2.2796   1.5209
 SX7  C19   C  C     0   0.534   5.0971  -0.3149   0.3181
 SX7  N6    N  NT    0  -0.434   5.5330   0.9026  -0.0553
 SX7  C21   C  CH3   0  -0.500   6.7354   1.4291   0.5593
 SX7  C20   C  CH3   0  -0.510   5.0656   1.6299  -1.2181
 SX7  C17   C  CR6   0  -0.102   3.7653  -0.7626  -0.1915
 SX7  C16   C  CR6   0   0.323   3.5968  -2.0682  -0.6943
 SX7  N5    N  NH2   0  -0.837   4.6449  -2.9249  -0.8474
 SX7  C15   C  CR16  0  -0.290   2.3079  -2.4401  -1.1072
 SX7  C14   C  CR16  0  -0.308   1.2364  -1.5829  -0.9837
 SX7  C18   C  CR16  0  -0.321   2.6666   0.0744  -0.0578
 SX7  C13   C  CR6   0   0.060   1.3819  -0.3021  -0.4412
 SX7  C10   C  CR6   0  -0.011   0.2265   0.5970  -0.2672
 SX7  C9    C  CR16  0  -0.159   0.3715   1.9909  -0.4104
 SX7  N4    N  N     0  -0.426  -0.5976   2.8790  -0.2516
 SX7  C11   C  CR16  0  -0.326  -1.0378   0.1039   0.0492
 SX7  C12   C  CR56  0   0.045  -2.0801   1.0048   0.2043
 SX7  C8    C  CR56  0   0.484  -1.7832   2.3753   0.0415
 SX7  N3    N  NR15  0  -0.671  -2.9369   3.0674   0.2450
 SX7  N2    N  N     0  -0.238  -5.7413  -1.9111   0.5758
 SX7  H7    H  HCR5  0   0.283  -4.9304   2.5567   0.7609
 SX7  H1    H  HCH3  0   0.231  -5.8747  -0.2652  -3.1654
 SX7  H1A   H  HCH3  0   0.221  -4.3049  -0.5179  -2.4060
 SX7  H1B   H  HCH3  0   0.238  -5.5270  -1.7943  -2.3559
 SX7  H4    H  HCR5  0   0.238  -3.0875  -1.3326   2.4227
 SX7  H3    H  HCR5  0   0.236  -5.0442  -3.2112   2.0458
 SX7  H2    H  HCH2  0   0.237  -5.7717   0.9345  -0.9899
 SX7  H2A   H  HCH2  0   0.257  -6.9965  -0.3237  -0.9413
 SX7  H21   H  HCH3  0   0.236   7.6375   1.0553   0.0705
 SX7  H21A  H  HCH3  0   0.236   6.7261   2.5138   0.4739
 SX7  H21B  H  HCH3  0   0.249   6.7791   1.1727   1.6136
 SX7  H20   H  HCH3  0   0.227   4.5673   2.5602  -0.9381
 SX7  H20A  H  HCH3  0   0.253   5.9174   1.8889  -1.8485
 SX7  H20B  H  HCH3  0   0.256   4.3894   1.0327  -1.8204
 SX7  HN5   H  HNH2  0   0.387   5.4354  -2.7938  -0.2388
 SX7  HN5A  H  HNH2  0   0.363   4.4240  -3.8923  -1.0046
 SX7  H15   H  HCR6  0   0.235   2.1492  -3.4277  -1.5230
 SX7  H14   H  HCR6  0   0.232   0.2646  -1.9202  -1.3235
 SX7  H18   H  HCR6  0   0.237   2.8240   1.0492   0.3899
 SX7  H9    H  HCR6  0   0.233   1.3434   2.3968  -0.6756
 SX7  H11   H  HCR6  0   0.244  -1.2061  -0.9571   0.1940
 SX7  HN3   H  HNR5  0   0.381  -3.0457   4.0650   0.2022
 SX7  C2    C  CH2   0  -0.299  -5.9258  -0.1422  -1.0202

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
 SX7  O1   C19   double    1.227  0.020  1.227
 SX7  C7   C6    aromatic  1.368  0.020  1.368
 SX7  C7   N3    aromatic  1.365  0.020  1.365
 SX7  C6   C5    single    1.454  0.020  1.454
 SX7  C6   C12   aromatic  1.430  0.020  1.430
 SX7  C1   C2    single    1.518  0.020  1.518
 SX7  N1   C5    aromatic  1.355  0.020  1.355
 SX7  N1   C2    single    1.449  0.020  1.449
 SX7  N1   N2    aromatic  1.328  0.020  1.328
 SX7  C5   C4    aromatic  1.380  0.020  1.380
 SX7  C4   C3    aromatic  1.402  0.020  1.402
 SX7  C3   N2    aromatic  1.318  0.020  1.318
 SX7  C19  N6    single    1.346  0.020  1.346
 SX7  C19  C17   single    1.495  0.020  1.495
 SX7  N6   C21   single    1.449  0.020  1.449
 SX7  N6   C20   single    1.449  0.020  1.449
 SX7  C17  C16   aromatic  1.409  0.020  1.409
 SX7  C17  C18   aromatic  1.388  0.020  1.388
 SX7  C16  N5    single    1.362  0.020  1.362
 SX7  C16  C15   aromatic  1.404  0.020  1.404
 SX7  C15  C14   aromatic  1.378  0.020  1.378
 SX7  C14  C13   aromatic  1.398  0.020  1.398
 SX7  C18  C13   aromatic  1.393  0.020  1.393
 SX7  C13  C10   single    1.474  0.020  1.474
 SX7  C10  C9    aromatic  1.409  0.020  1.409
 SX7  C10  C11   aromatic  1.393  0.020  1.393
 SX7  C9   N4    aromatic  1.324  0.020  1.324
 SX7  N4   C8    aromatic  1.321  0.020  1.321
 SX7  C11  C12   aromatic  1.386  0.020  1.386
 SX7  C12  C8    aromatic  1.412  0.020  1.412
 SX7  C8   N3    aromatic  1.361  0.020  1.361
 SX7  C7   H7    single    0.930  0.020  1.080
 SX7  C1   H1    single    0.970  0.020  1.090
 SX7  C1   H1A   single    0.970  0.020  1.090
 SX7  C1   H1B   single    0.970  0.020  1.090
 SX7  C4   H4    single    0.930  0.020  1.080
 SX7  C3   H3    single    0.930  0.020  1.080
 SX7  C2   H2    single    0.970  0.020  1.090
 SX7  C2   H2A   single    0.970  0.020  1.090
 SX7  C21  H21   single    0.970  0.020  1.090
 SX7  C21  H21A  single    0.970  0.020  1.090
 SX7  C21  H21B  single    0.970  0.020  1.090
 SX7  C20  H20   single    0.970  0.020  1.090
 SX7  C20  H20A  single    0.970  0.020  1.090
 SX7  C20  H20B  single    0.970  0.020  1.090
 SX7  N5   HN5   single    0.890  0.020  1.040
 SX7  N5   HN5A  single    0.890  0.020  1.040
 SX7  C15  H15   single    0.930  0.020  1.080
 SX7  C14  H14   single    0.930  0.020  1.080
 SX7  C18  H18   single    0.930  0.020  1.080
 SX7  C9   H9    single    0.930  0.020  1.080
 SX7  C11  H11   single    0.930  0.020  1.080
 SX7  N3   HN3   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
 SX7  H7    C7   N3    120.15  3.000
 SX7  H7    C7   C6    129.53  3.000
 SX7  N3    C7   C6    110.30  3.000
 SX7  C12   C6   C5    125.40  3.000
 SX7  C12   C6   C7    105.85  3.000
 SX7  C5    C6   C7    128.73  3.000
 SX7  H1B   C1   H1A   108.46  3.000
 SX7  H1B   C1   H1    108.24  3.000
 SX7  H1A   C1   H1    107.93  3.000
 SX7  H1B   C1   C2    110.95  3.000
 SX7  H1A   C1   C2    111.20  3.000
 SX7  H1    C1   C2    109.96  3.000
 SX7  N2    N1   C2    118.70  3.000
 SX7  N2    N1   C5    112.38  3.000
 SX7  C2    N1   C5    128.22  3.000
 SX7  C4    C5   N1    106.11  3.000
 SX7  C4    C5   C6    129.26  3.000
 SX7  N1    C5   C6    124.62  3.000
 SX7  H4    C4   C3    128.34  3.000
 SX7  H4    C4   C5    127.10  3.000
 SX7  C3    C4   C5    104.52  3.000
 SX7  H3    C3   N2    120.36  3.000
 SX7  H3    C3   C4    128.32  3.000
 SX7  N2    C3   C4    111.32  3.000
 SX7  C17   C19  N6    117.71  3.000
 SX7  C17   C19  O1    120.03  3.000
 SX7  N6    C19  O1    122.22  3.000
 SX7  C20   N6   C21   115.19  3.000
 SX7  C20   N6   C19   124.90  3.000
 SX7  C21   N6   C19   118.66  3.000
 SX7  H21B  C21  H21A  108.17  3.000
 SX7  H21B  C21  H21   108.69  3.000
 SX7  H21A  C21  H21   108.26  3.000
 SX7  H21B  C21  N6    111.06  3.000
 SX7  H21A  C21  N6    108.77  3.000
 SX7  H21   C21  N6    111.79  3.000
 SX7  H20B  C20  H20A  107.25  3.000
 SX7  H20B  C20  H20   109.09  3.000
 SX7  H20A  C20  H20   107.59  3.000
 SX7  H20B  C20  N6    111.73  3.000
 SX7  H20A  C20  N6    109.33  3.000
 SX7  H20   C20  N6    111.66  3.000
 SX7  C18   C17  C16   119.91  3.000
 SX7  C18   C17  C19   119.47  3.000
 SX7  C16   C17  C19   120.38  3.000
 SX7  C15   C16  N5    120.45  3.000
 SX7  C15   C16  C17   117.40  3.000
 SX7  N5    C16  C17   122.06  3.000
 SX7  HN5A  N5   HN5   113.13  3.000
 SX7  HN5A  N5   C16   117.00  3.000
 SX7  HN5   N5   C16   117.04  3.000
 SX7  H15   C15  C14   119.19  3.000
 SX7  H15   C15  C16   119.28  3.000
 SX7  C14   C15  C16   121.53  3.000
 SX7  H14   C14  C13   120.01  3.000
 SX7  H14   C14  C15   118.41  3.000
 SX7  C13   C14  C15   121.58  3.000
 SX7  H18   C18  C13   119.39  3.000
 SX7  H18   C18  C17   117.85  3.000
 SX7  C13   C18  C17   122.74  3.000
 SX7  C10   C13  C18   121.71  3.000
 SX7  C10   C13  C14   121.51  3.000
 SX7  C18   C13  C14   116.77  3.000
 SX7  C11   C10  C9    117.81  3.000
 SX7  C11   C10  C13   121.47  3.000
 SX7  C9    C10  C13   120.71  3.000
 SX7  H9    C9   N4    115.69  3.000
 SX7  H9    C9   C10   119.12  3.000
 SX7  N4    C9   C10   125.18  3.000
 SX7  C8    N4   C9    115.32  3.000
 SX7  H11   C11  C12   120.29  3.000
 SX7  H11   C11  C10   121.17  3.000
 SX7  C12   C11  C10   118.53  3.000
 SX7  C8    C12  C11   117.38  3.000
 SX7  C8    C12  C6    107.24  3.000
 SX7  C11   C12  C6    135.38  3.000
 SX7  N3    C8   C12   107.36  3.000
 SX7  N3    C8   N4    126.88  3.000
 SX7  C12   C8   N4    125.76  3.000
 SX7  HN3   N3   C8    126.21  3.000
 SX7  HN3   N3   C7    124.53  3.000
 SX7  C8    N3   C7    109.25  3.000
 SX7  C3    N2   N1    105.66  3.000
 SX7  H2A   C2   H2    107.59  3.000
 SX7  H2A   C2   N1    107.05  3.000
 SX7  H2    C2   N1    108.57  3.000
 SX7  H2A   C2   C1    110.92  3.000
 SX7  H2    C2   C1    110.31  3.000
 SX7  N1    C2   C1    112.24  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
 SX7  CONST_03  C11   C12  C6   C7   180.00   0.0  0
 SX7  CONST_04  C8    C12  C6   C7     0.00   0.0  0
 SX7  CONST_05  N4    C8   N3   C7   180.00   0.0  0
 SX7  CONST_06  C12   C8   N3   C7     0.00   0.0  0
 SX7  CONST_07  C8    N3   C7   C6     0.00   0.0  0
 SX7  CONST_08  N2    N1   C5   C6   180.00   0.0  0
 SX7  CONST_09  C3    C4   C5   C6   180.00   0.0  0
 SX7  CONST_10  C10   C11  C12  C6   180.00   0.0  0
 SX7  CONST_11  N4    C8   C12  C6   180.00   0.0  0
 SX7  CONST_12  N3    C8   C12  C6     0.00   0.0  0
 SX7  CONST_14  C3    C4   C5   N1     0.00   0.0  0
 SX7  CONST_15  C4    C3   N2   N1     0.00   0.0  0
 SX7  CONST_16  N3    C7   C6   C5   180.00   0.0  0
 SX7  CONST_17  C11   C12  C6   C5     0.00   0.0  0
 SX7  CONST_18  C8    C12  C6   C5   180.00   0.0  0
 SX7  CONST_19  C3    N2   N1   C5     0.00   0.0  0
 SX7  CONST_20  N2    C3   C4   C5     0.00   0.0  0
 SX7  CONST_22  N2    N1   C5   C4     0.00   0.0  0
 SX7  CONST_23  C14   C15  C16  C17    0.00   0.0  0
 SX7  CONST_24  C14   C13  C18  C17    0.00   0.0  0
 SX7  CONST_25  C10   C13  C18  C17  180.00   0.0  0
 SX7  CONST_26  C13   C18  C17  C16    0.00   0.0  0
 SX7  CONST_27  C13   C14  C15  C16    0.00   0.0  0
 SX7  CONST_28  C18   C17  C16  C15    0.00   0.0  0
 SX7  CONST_29  C18   C13  C14  C15    0.00   0.0  0
 SX7  CONST_30  C10   C13  C14  C15  180.00   0.0  0
 SX7  CONST_35  N4    C9   C10  C13  180.00   0.0  0
 SX7  CONST_36  C12   C11  C10  C13  180.00   0.0  0
 SX7  CONST_37  C8    N4   C9   C10    0.00   0.0  0
 SX7  CONST_38  C8    C12  C11  C10    0.00   0.0  0
 SX7  CONST_39  C12   C11  C10  C9     0.00   0.0  0
 SX7  CONST_40  C12   C8   N4   C9     0.00   0.0  0
 SX7  CONST_41  N3    C8   N4   C9   180.00   0.0  0
 SX7  CONST_42  C11   C10  C9   N4     0.00   0.0  0
 SX7  CONST_43  C11   C12  C8   N4     0.00   0.0  0
 SX7  CONST_44  N3    C8   C12  C11  180.00   0.0  0
 SX7  CONST_45  N3    C7   C6   C12    0.00   0.0  0
 SX7  CONST_46  C2    N1   C5   C6     0.00   0.0  0
 SX7  CONST_47  C2    N1   C5   C4   180.00   0.0  0
 SX7  CONST_48  C2    N1   N2   C3   180.00   0.0  0
 SX7  CONST_49  C15   C16  C17  C19  180.00   0.0  0
 SX7  CONST_50  C13   C18  C17  C19  180.00   0.0  0
 SX7  CONST_51  C18   C17  C16  N5   180.00   0.0  0
 SX7  CONST_52  C14   C15  C16  N5   180.00   0.0  0
 SX7  CONST_53  HN3   N3   C7   C6   180.00   0.0  0
 SX7  CONST_54  H4    C4   C5   C6     0.00   0.0  0
 SX7  CONST_55  H11   C11  C12  C6     0.00   0.0  0
 SX7  CONST_56  H3    C3   N2   N1   180.00   0.0  0
 SX7  CONST_57  H7    C7   C6   C5     0.00   0.0  0
 SX7  CONST_58  H15   C15  C16  C17  180.00   0.0  0
 SX7  CONST_59  H18   C18  C17  C16  180.00   0.0  0
 SX7  CONST_60  H14   C14  C15  C16  180.00   0.0  0
 SX7  CONST_61  H9    C9   C10  C13    0.00   0.0  0
 SX7  CONST_63  HN5A  N5   C16  C17  180.00   0.0  0
 SX7  CONST_64  C17   C19  N6   C21  180.00   0.0  0
 SX7  CONST_66  C21   N6   C19  O1     0.00   0.0  0
 SX7  Var_01    C16   C17  C19  O1   -46.93  30.0  2
 SX7  Var_02    C5    N1   C2   C1    88.68  30.0  1
 SX7  Var_03    H1    C1   C2   N1   178.90  30.0  3
 SX7  Var_04    H21   C21  N6   C19   83.24  30.0  3
 SX7  Var_05    H20   C20  N6   C19  116.54  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
 SX7  plan-1  C6    0.020
 SX7  plan-1  N1    0.020
 SX7  plan-1  C5    0.020
 SX7  plan-1  C4    0.020
 SX7  plan-1  C3    0.020
 SX7  plan-1  N2    0.020
 SX7  plan-1  H4    0.020
 SX7  plan-1  H3    0.020
 SX7  plan-1  C2    0.020
 SX7  plan-2  C19   0.020
 SX7  plan-2  C17   0.020
 SX7  plan-2  C16   0.020
 SX7  plan-2  N5    0.020
 SX7  plan-2  C15   0.020
 SX7  plan-2  C14   0.020
 SX7  plan-2  C18   0.020
 SX7  plan-2  C13   0.020
 SX7  plan-2  C10   0.020
 SX7  plan-2  H15   0.020
 SX7  plan-2  H14   0.020
 SX7  plan-2  H18   0.020
 SX7  plan-3  C7    0.020
 SX7  plan-3  C6    0.020
 SX7  plan-3  C5    0.020
 SX7  plan-3  C13   0.020
 SX7  plan-3  C10   0.020
 SX7  plan-3  C9    0.020
 SX7  plan-3  N4    0.020
 SX7  plan-3  C11   0.020
 SX7  plan-3  C12   0.020
 SX7  plan-3  C8    0.020
 SX7  plan-3  N3    0.020
 SX7  plan-3  H7    0.020
 SX7  plan-3  H9    0.020
 SX7  plan-3  H11   0.020
 SX7  plan-3  HN3   0.020
 SX7  plan-4  O1    0.020
 SX7  plan-4  C19   0.020
 SX7  plan-4  N6    0.020
 SX7  plan-4  C21   0.020
 SX7  plan-4  C20   0.020
 SX7  plan-4  C17   0.020
 SX7  plan-5  C16   0.020
 SX7  plan-5  N5    0.020
 SX7  plan-5  HN5   0.020
 SX7  plan-5  HN5A  0.020

