# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 03:22:22 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-2-(1H-pyrazol-4-yl)-1H-pyrrolo[3,2-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1CCN(CC1)c2nccc(Nc3cc4[nH]c(cc4cn3)c5c[nH]nc5)n2
#
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
 3QY  3QY  N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-2-(1H-pyrazol-4-yl)-1H-pyrrolo[3,2-c]pyridin-6-amine  ligand  51  29  .  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_3QY
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
 3QY  C4   C  CH2   0  -0.463   5.5444   0.9545   0.4498
 3QY  C5   C  CH2   0  -0.331   5.4464  -0.0363  -0.7076
 3QY  C11  C  CR16  0  -0.021   3.8657  -3.6436   0.3934
 3QY  C7   C  CH2   0  -0.332   3.2124   0.7169  -1.2462
 3QY  C8   C  CH2   0  -0.470   3.2310   1.7372  -0.1111
 3QY  C9   C  CR6   0   0.625   3.5532  -1.5714  -0.4441
 3QY  C12  C  CR16  0  -0.468   2.5136  -3.8840   0.4241
 3QY  C13  C  CR6   0   0.531   1.7017  -2.8217  -0.0151
 3QY  C3   C  CH1   0   0.083   4.6644   2.1697   0.1921
 3QY  O2   O  O2    0  -0.494   4.7585   3.0183   1.3152
 3QY  N6   N  NT    0  -0.481   4.0668  -0.4144  -0.9413
 3QY  N10  N  N     0  -0.501   4.4129  -2.5087  -0.0327
 3QY  N14  N  N     0  -0.496   2.2234  -1.6819  -0.4303
 3QY  N15  N  NH1   0  -0.752   0.3476  -2.9557   0.0077
 3QY  C16  C  CR6   0   0.451  -0.5853  -1.9722  -0.3556
 3QY  C17  C  CR16  0  -0.448  -1.6112  -1.6753   0.5283
 3QY  C18  C  CR56  0   0.446  -2.5410  -0.7418   0.0894
 3QY  C19  C  CR56  0  -0.007  -2.4097  -0.1213  -1.1704
 3QY  C20  C  CR15  0  -0.477  -3.5013   0.7862  -1.3049
 3QY  C21  C  CR5   0   0.389  -4.2396   0.6923  -0.1547
 3QY  N22  N  NR15  0  -0.763  -3.6503  -0.2331   0.6804
 3QY  C24  C  CR5   0  -0.161  -5.4467   1.3854   0.2331
 3QY  C25  C  CR15  0  -0.012  -6.1585   2.3095  -0.5097
 3QY  N26  N  NR15  0  -0.422  -7.1980   2.6797   0.2460
 3QY  N28  N  N     0  -0.256  -7.2337   2.0759   1.4271
 3QY  C29  C  CR15  0  -0.103  -6.1781   1.2870   1.4372
 3QY  C30  C  CR16  0  -0.148  -1.3242  -0.5063  -1.9556
 3QY  N31  N  N     0  -0.419  -0.4521  -1.4160  -1.5634
 3QY  H1   H  HCH2  0   0.228   5.2326   0.4622   1.3766
 3QY  H2   H  HCH2  0   0.242   6.5844   1.2655   0.5764
 3QY  H3   H  HCH2  0   0.237   5.8322   0.4259  -1.6215
 3QY  H4   H  HCH2  0   0.270   6.0433  -0.9219  -0.5135
 3QY  H5   H  HCR6  0   0.259   4.5574  -4.4100   0.7286
 3QY  H6   H  HCH2  0   0.281   2.2017   0.3687  -1.4378
 3QY  H7   H  HCH2  0   0.237   3.5817   1.1799  -2.1673
 3QY  H8   H  HCH2  0   0.241   2.6131   2.5924  -0.3967
 3QY  H9   H  HCH2  0   0.227   2.7844   1.2935   0.7847
 3QY  H10  H  HCR6  0   0.268   2.1051  -4.8213   0.7734
 3QY  H11  H  HCH1  0   0.190   5.0564   2.6938  -0.6964
 3QY  H12  H  HCH3  0   0.234   4.5188   4.9145   1.9832
 3QY  H13  H  HCH3  0   0.202   4.8058   4.7960   0.2382
 3QY  H14  H  HCH3  0   0.206   3.2211   4.3785   0.9083
 3QY  H15  H  HNH1  0   0.409  -0.0097  -3.7333   0.5400
 3QY  H16  H  HCR6  0   0.277  -1.6720  -2.1429   1.5024
 3QY  H17  H  HCR5  0   0.251  -3.7147   1.4281  -2.1450
 3QY  H18  H  HNR5  0   0.414  -3.9870  -0.4960   1.5922
 3QY  H19  H  HCR5  0   0.293  -5.9958   2.7131  -1.4956
 3QY  H20  H  HNR5  0   0.428  -7.9207   3.3364  -0.0036
 3QY  H21  H  HCR5  0   0.259  -5.9709   0.6746   2.3022
 3QY  H22  H  HCR6  0   0.254  -1.1687  -0.0745  -2.9391
 3QY  C1   C  CH3   0  -0.406   4.2997   4.3277   1.0913

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
 3QY  N26  N28  aromatic  1.327  0.020  1.327
 3QY  N26  C25  aromatic  1.337  0.020  1.337
 3QY  N28  C29  aromatic  1.318  0.020  1.318
 3QY  C25  C24  aromatic  1.383  0.020  1.383
 3QY  C29  C24  aromatic  1.412  0.020  1.412
 3QY  C24  C21  single    1.445  0.020  1.445
 3QY  C21  C20  aromatic  1.370  0.020  1.370
 3QY  C21  N22  aromatic  1.379  0.020  1.379
 3QY  C20  C19  aromatic  1.426  0.020  1.426
 3QY  N22  C18  aromatic  1.356  0.020  1.356
 3QY  C19  C18  aromatic  1.411  0.020  1.411
 3QY  C19  C30  aromatic  1.394  0.020  1.394
 3QY  C18  C17  aromatic  1.389  0.020  1.389
 3QY  C30  N31  aromatic  1.320  0.020  1.320
 3QY  C17  C16  aromatic  1.386  0.020  1.386
 3QY  N31  C16  aromatic  1.336  0.020  1.336
 3QY  C1   O2   single    1.405  0.020  1.405
 3QY  C16  N15  single    1.403  0.020  1.403
 3QY  C4   C5   single    1.527  0.020  1.527
 3QY  C4   C3   single    1.522  0.020  1.522
 3QY  O2   C3   single    1.411  0.020  1.411
 3QY  C5   N6   single    1.449  0.020  1.449
 3QY  C3   C8   single    1.528  0.020  1.528
 3QY  N15  C13  single    1.361  0.020  1.361
 3QY  N14  C13  aromatic  1.320  0.020  1.320
 3QY  N14  C9   aromatic  1.334  0.020  1.334
 3QY  N6   C9   single    1.360  0.020  1.360
 3QY  N6   C7   single    1.450  0.020  1.450
 3QY  C8   C7   single    1.526  0.020  1.526
 3QY  C13  C12  aromatic  1.407  0.020  1.407
 3QY  C9   N10  aromatic  1.337  0.020  1.337
 3QY  C12  C11  aromatic  1.374  0.020  1.374
 3QY  N10  C11  aromatic  1.330  0.020  1.330
 3QY  C4   H1   single    0.970  0.020  1.090
 3QY  C4   H2   single    0.970  0.020  1.090
 3QY  C5   H3   single    0.970  0.020  1.090
 3QY  C5   H4   single    0.970  0.020  1.090
 3QY  C11  H5   single    0.930  0.020  1.080
 3QY  C7   H6   single    0.970  0.020  1.090
 3QY  C7   H7   single    0.970  0.020  1.090
 3QY  C8   H8   single    0.970  0.020  1.090
 3QY  C8   H9   single    0.970  0.020  1.090
 3QY  C12  H10  single    0.930  0.020  1.080
 3QY  C3   H11  single    0.970  0.020  1.090
 3QY  C1   H12  single    0.970  0.020  1.090
 3QY  C1   H13  single    0.970  0.020  1.090
 3QY  C1   H14  single    0.970  0.020  1.090
 3QY  N15  H15  single    0.860  0.020  1.020
 3QY  C17  H16  single    0.930  0.020  1.080
 3QY  C20  H17  single    0.930  0.020  1.080
 3QY  N22  H18  single    0.860  0.020  1.020
 3QY  C25  H19  single    0.930  0.020  1.080
 3QY  N26  H20  single    0.860  0.020  1.020
 3QY  C29  H21  single    0.930  0.020  1.080
 3QY  C30  H22  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
 3QY  H2   C4   H1   107.51  3.000
 3QY  H2   C4   C3   110.03  3.000
 3QY  H1   C4   C3   109.74  3.000
 3QY  H2   C4   C5   109.48  3.000
 3QY  H1   C4   C5   109.37  3.000
 3QY  C3   C4   C5   110.65  3.000
 3QY  H4   C5   H3   107.46  3.000
 3QY  H4   C5   N6   109.84  3.000
 3QY  H3   C5   N6   108.13  3.000
 3QY  H4   C5   C4   111.02  3.000
 3QY  H3   C5   C4   109.65  3.000
 3QY  N6   C5   C4   110.65  3.000
 3QY  H5   C11  N10  116.06  3.000
 3QY  H5   C11  C12  119.79  3.000
 3QY  N10  C11  C12  124.16  3.000
 3QY  H7   C7   H6   107.52  3.000
 3QY  H7   C7   N6   107.94  3.000
 3QY  H6   C7   N6   109.59  3.000
 3QY  H7   C7   C8   109.80  3.000
 3QY  H6   C7   C8   110.91  3.000
 3QY  N6   C7   C8   110.97  3.000
 3QY  H9   C8   H8   107.47  3.000
 3QY  H9   C8   C3   109.57  3.000
 3QY  H8   C8   C3   111.15  3.000
 3QY  H9   C8   C7   109.43  3.000
 3QY  H8   C8   C7   108.77  3.000
 3QY  C3   C8   C7   110.38  3.000
 3QY  N14  C9   N10  125.42  3.000
 3QY  N10  C9   N6   117.79  3.000
 3QY  N14  C9   N6   116.78  3.000
 3QY  H10  C12  C13  122.52  3.000
 3QY  H10  C12  C11  122.09  3.000
 3QY  C13  C12  C11  115.39  3.000
 3QY  N15  C13  N14  118.91  3.000
 3QY  N14  C13  C12  121.45  3.000
 3QY  N15  C13  C12  119.64  3.000
 3QY  H11  C3   O2   109.36  3.000
 3QY  H11  C3   C8   107.94  3.000
 3QY  O2   C3   C8   113.01  3.000
 3QY  H11  C3   C4   108.06  3.000
 3QY  C8   C3   C4   110.49  3.000
 3QY  O2   C3   C4   107.87  3.000
 3QY  C1   O2   C3   114.32  3.000
 3QY  C9   N6   C7   121.20  3.000
 3QY  C7   N6   C5   113.03  3.000
 3QY  C9   N6   C5   121.49  3.000
 3QY  C9   N10  C11  115.61  3.000
 3QY  C13  N14  C9   117.94  3.000
 3QY  H15  N15  C16  116.22  3.000
 3QY  H15  N15  C13  115.95  3.000
 3QY  C16  N15  C13  126.02  3.000
 3QY  N31  C16  C17  124.12  3.000
 3QY  N31  C16  N15  117.35  3.000
 3QY  C17  C16  N15  118.48  3.000
 3QY  H16  C17  C18  122.50  3.000
 3QY  H16  C17  C16  121.53  3.000
 3QY  C18  C17  C16  115.97  3.000
 3QY  N22  C18  C19  107.48  3.000
 3QY  C19  C18  C17  121.04  3.000
 3QY  N22  C18  C17  131.47  3.000
 3QY  C30  C19  C20  135.96  3.000
 3QY  C30  C19  C18  117.01  3.000
 3QY  C20  C19  C18  107.04  3.000
 3QY  H17  C20  C21  126.02  3.000
 3QY  H17  C20  C19  127.13  3.000
 3QY  C21  C20  C19  106.84  3.000
 3QY  C24  C21  N22  121.09  3.000
 3QY  N22  C21  C20  108.92  3.000
 3QY  C24  C21  C20  129.99  3.000
 3QY  H18  N22  C21  125.51  3.000
 3QY  H18  N22  C18  124.77  3.000
 3QY  C21  N22  C18  109.72  3.000
 3QY  C29  C24  C25  103.77  3.000
 3QY  C29  C24  C21  128.91  3.000
 3QY  C25  C24  C21  127.33  3.000
 3QY  H19  C25  N26  122.05  3.000
 3QY  H19  C25  C24  131.60  3.000
 3QY  N26  C25  C24  106.35  3.000
 3QY  H20  N26  N28  119.84  3.000
 3QY  H20  N26  C25  126.70  3.000
 3QY  N28  N26  C25  113.45  3.000
 3QY  C29  N28  N26  104.93  3.000
 3QY  H21  C29  N28  119.96  3.000
 3QY  H21  C29  C24  128.54  3.000
 3QY  N28  C29  C24  111.51  3.000
 3QY  H22  C30  N31  116.67  3.000
 3QY  H22  C30  C19  120.81  3.000
 3QY  N31  C30  C19  122.52  3.000
 3QY  C30  N31  C16  119.31  3.000
 3QY  H14  C1   H13  107.74  3.000
 3QY  H14  C1   H12  108.05  3.000
 3QY  H13  C1   H12  108.29  3.000
 3QY  H14  C1   O2   113.04  3.000
 3QY  H13  C1   O2   111.78  3.000
 3QY  H12  C1   O2   107.80  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
 3QY  CONST_01  N14  C13  C12  C11     0.00   0.0  0
 3QY  CONST_02  N14  C9   N10  C11     0.00   0.0  0
 3QY  CONST_03  C12  C13  N14  C9      0.00   0.0  0
 3QY  CONST_04  C12  C11  N10  C9      0.00   0.0  0
 3QY  CONST_05  N10  C9   N14  C13     0.00   0.0  0
 3QY  CONST_06  N10  C11  C12  C13     0.00   0.0  0
 3QY  CONST_07  N22  C18  C17  C16   180.00   0.0  0
 3QY  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 3QY  CONST_09  C19  C30  N31  C16     0.00   0.0  0
 3QY  CONST_10  C21  N22  C18  C17   180.00   0.0  0
 3QY  CONST_11  C20  C19  C18  C17   180.00   0.0  0
 3QY  CONST_12  C30  C19  C18  C17     0.00   0.0  0
 3QY  CONST_13  C30  N31  C16  C17     0.00   0.0  0
 3QY  CONST_14  C24  C21  N22  C18   180.00   0.0  0
 3QY  CONST_15  C20  C21  N22  C18     0.00   0.0  0
 3QY  CONST_16  C21  C20  C19  C18     0.00   0.0  0
 3QY  CONST_17  N31  C30  C19  C18     0.00   0.0  0
 3QY  CONST_18  N31  C16  C17  C18     0.00   0.0  0
 3QY  CONST_19  C24  C21  C20  C19   180.00   0.0  0
 3QY  CONST_20  N22  C21  C20  C19     0.00   0.0  0
 3QY  CONST_21  C21  N22  C18  C19     0.00   0.0  0
 3QY  CONST_22  C25  C24  C21  C20     0.00   0.0  0
 3QY  CONST_23  C29  C24  C21  C20   180.00   0.0  0
 3QY  CONST_24  N22  C18  C19  C20     0.00   0.0  0
 3QY  CONST_25  N31  C30  C19  C20   180.00   0.0  0
 3QY  CONST_26  N26  C25  C24  C21   180.00   0.0  0
 3QY  CONST_27  N28  C29  C24  C21   180.00   0.0  0
 3QY  CONST_28  C30  C19  C20  C21   180.00   0.0  0
 3QY  CONST_29  C25  C24  C21  N22   180.00   0.0  0
 3QY  CONST_30  C29  C24  C21  N22     0.00   0.0  0
 3QY  CONST_31  C30  C19  C18  N22   180.00   0.0  0
 3QY  CONST_32  N28  N26  C25  C24     0.00   0.0  0
 3QY  CONST_33  N26  N28  C29  C24     0.00   0.0  0
 3QY  CONST_34  C29  N28  N26  C25     0.00   0.0  0
 3QY  CONST_35  N28  C29  C24  C25     0.00   0.0  0
 3QY  CONST_36  C29  C24  C25  N26     0.00   0.0  0
 3QY  CONST_37  N6   C9   N10  C11   180.00   0.0  0
 3QY  CONST_38  N6   C9   N14  C13   180.00   0.0  0
 3QY  CONST_39  N15  C13  C12  C11   180.00   0.0  0
 3QY  CONST_40  N15  C13  N14  C9    180.00   0.0  0
 3QY  CONST_41  C18  C17  C16  N15   180.00   0.0  0
 3QY  CONST_42  C30  N31  C16  N15   180.00   0.0  0
 3QY  CONST_43  H5   C11  N10  C9    180.00   0.0  0
 3QY  CONST_44  H10  C12  C11  N10   180.00   0.0  0
 3QY  CONST_45  H22  C30  N31  C16   180.00   0.0  0
 3QY  CONST_46  H18  N22  C18  C17     0.00   0.0  0
 3QY  CONST_47  H17  C20  C19  C18   180.00   0.0  0
 3QY  CONST_48  H16  C17  C18  C19   180.00   0.0  0
 3QY  CONST_49  H19  C25  C24  C21     0.00   0.0  0
 3QY  CONST_50  H21  C29  C24  C21     0.00   0.0  0
 3QY  CONST_51  H20  N26  C25  C24   180.00   0.0  0
 3QY  Var_01    C9   N6   C5   C4    -98.29  30.0  1
 3QY  Var_02    N14  C9   N6   C5    164.36  30.0  2
 3QY  Var_03    C8   C7   N6   C5    -58.74  30.0  1
 3QY  Var_04    N6   C5   C4   C3    -55.69  30.0  1
 3QY  Var_05    N6   C7   C8   C3     55.29  30.0  1
 3QY  Var_06    C16  N15  C13  C12   177.78  30.0  2
 3QY  Var_07    C17  C16  N15  C13  -128.81  30.0  2
 3QY  Var_08    H12  C1   O2   C3   -173.98  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
 3QY  chir_01  C3  C4  O2  C8  positiv

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
 3QY  plan-1  C21  0.020
 3QY  plan-1  C24  0.020
 3QY  plan-1  C25  0.020
 3QY  plan-1  N26  0.020
 3QY  plan-1  N28  0.020
 3QY  plan-1  C29  0.020
 3QY  plan-1  H19  0.020
 3QY  plan-1  H20  0.020
 3QY  plan-1  H21  0.020
 3QY  plan-2  C11  0.020
 3QY  plan-2  C9   0.020
 3QY  plan-2  C12  0.020
 3QY  plan-2  C13  0.020
 3QY  plan-2  N6   0.020
 3QY  plan-2  N10  0.020
 3QY  plan-2  N14  0.020
 3QY  plan-2  N15  0.020
 3QY  plan-2  H5   0.020
 3QY  plan-2  H10  0.020
 3QY  plan-3  N15  0.020
 3QY  plan-3  C16  0.020
 3QY  plan-3  C17  0.020
 3QY  plan-3  C18  0.020
 3QY  plan-3  C19  0.020
 3QY  plan-3  C20  0.020
 3QY  plan-3  C21  0.020
 3QY  plan-3  N22  0.020
 3QY  plan-3  C24  0.020
 3QY  plan-3  C30  0.020
 3QY  plan-3  N31  0.020
 3QY  plan-3  H16  0.020
 3QY  plan-3  H17  0.020
 3QY  plan-3  H18  0.020
 3QY  plan-3  H22  0.020

