# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:10:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-ethyl-7-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-5-(trifluoromethyl)-1H-pyrrolo[3,2-b]pyridine-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1[nH]c2c(c1)nc(c(C#N)c2N3CC[C@](C)(O)C3)C(F)(F)F
#
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
 A3J  A3J  2-ethyl-7-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-5-(trifluoromethyl)-1H-pyrrolo[3,2-b]pyridine-6-carbonitrile  ligand  41  24  .  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_A3J
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
 A3J  N3   N  NS    0  -0.254  -1.7407   3.0725   0.2593
 A3J  C4   C  CR15  0  -0.406  -0.2956  -3.4132   0.0601
 A3J  N2   N  N     0  -0.457  -1.9894  -1.6299   0.3740
 A3J  C7   C  CR6   0   0.548   0.2877   0.1595   0.2955
 A3J  C6   C  CR56  0   0.249   0.4002  -1.2428   0.1665
 A3J  C9   C  CR6   0  -0.109  -2.1209  -0.3428   0.4805
 A3J  C13  C  CH2   0  -0.463   2.8366   2.6612   0.9911
 A3J  C8   C  CR6   0  -0.097  -1.0609   0.5983   0.4237
 A3J  C16  C  CH3   0  -0.639   4.9701   1.6830  -0.0293
 A3J  C1   C  CH3   0  -0.631   2.9044  -4.3591  -1.4627
 A3J  C3   C  CR5   0   0.387   1.0694  -3.3753  -0.0414
 A3J  C5   C  CR56  0   0.130  -0.7340  -2.0749   0.1998
 A3J  N1   N  NR15  0  -0.729   1.4785  -2.0766   0.0190
 A3J  C10  C  CT    0   1.069  -3.5430   0.1413   0.6638
 A3J  F1   F  F     0  -0.290  -4.3888  -0.8662   0.8317
 A3J  F2   F  F     0  -0.313  -3.6559   0.9414   1.7311
 A3J  F3   F  F     0  -0.319  -3.9622   0.8406  -0.4004
 A3J  C11  C  CSP   0  -0.002  -1.4121   1.9706   0.3597
 A3J  N4   N  NT    0  -0.534   1.3463   0.9914   0.2952
 A3J  C12  C  CH2   0  -0.273   1.3558   2.3553   0.8357
 A3J  C14  C  CT    0   0.152   3.4727   1.8879  -0.1640
 A3J  C15  C  CH2   0  -0.268   2.6881   0.5843  -0.0960
 A3J  O1   O  OH1   0  -0.638   3.1364   2.4732  -1.4066
 A3J  H7   H  HCR5  0   0.241  -0.9158  -4.2941   0.0388
 A3J  H10  H  HCH2  0   0.254   3.0399   3.7323   0.9561
 A3J  H11  H  HCH2  0   0.237   3.2126   2.2875   1.9455
 A3J  H15  H  HCH3  0   0.239   5.3557   1.0509  -0.8296
 A3J  H14  H  HCH3  0   0.225   5.5004   2.6360  -0.0744
 A3J  H16  H  HCH3  0   0.218   5.2261   1.2195   0.9229
 A3J  H2   H  HCH3  0   0.233   2.2844  -4.3203  -2.3572
 A3J  H4   H  HCH3  0   0.206   3.5266  -3.4640  -1.4485
 A3J  H3   H  HCH3  0   0.240   3.5728  -5.2139  -1.5514
 A3J  H5   H  HCH2  0   0.250   1.4992  -5.4232  -0.2193
 A3J  H6   H  HCH2  0   0.244   2.7009  -4.5255   0.6771
 A3J  H1   H  HNR5  0   0.398   2.4446  -1.8086   0.0577
 A3J  H8   H  HCH2  0   0.255   0.8207   2.3961   1.7846
 A3J  H9   H  HCH2  0   0.256   0.8947   3.0633   0.1490
 A3J  H12  H  HCH2  0   0.222   3.1507  -0.0568   0.6629
 A3J  H13  H  HCH2  0   0.266   2.6921   0.0684  -1.0582
 A3J  H17  H  HOH1  0   0.425   3.5729   3.3273  -1.4693
 A3J  C2   C  CH2   0  -0.523   2.0510  -4.4833  -0.2023

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
 A3J  O1   C14  single    1.414  0.020  1.414
 A3J  C16  C14  single    1.517  0.020  1.517
 A3J  C14  C15  single    1.523  0.020  1.523
 A3J  C14  C13  single    1.529  0.020  1.529
 A3J  C15  N4   single    1.456  0.020  1.456
 A3J  C13  C12  single    1.520  0.020  1.520
 A3J  N3   C11  triple    1.154  0.020  1.154
 A3J  N4   C12  single    1.467  0.020  1.467
 A3J  N4   C7   single    1.346  0.020  1.346
 A3J  C11  C8   single    1.418  0.020  1.418
 A3J  F3   C10  single    1.341  0.020  1.341
 A3J  C7   C8   aromatic  1.424  0.020  1.424
 A3J  C7   C6   aromatic  1.413  0.020  1.413
 A3J  C8   C9   aromatic  1.419  0.020  1.419
 A3J  C6   N1   aromatic  1.371  0.020  1.371
 A3J  C6   C5   aromatic  1.407  0.020  1.407
 A3J  C10  C9   single    1.513  0.020  1.513
 A3J  C10  F1   single    1.326  0.020  1.326
 A3J  C10  F2   single    1.339  0.020  1.339
 A3J  C9   N2   aromatic  1.298  0.020  1.298
 A3J  N1   C3   aromatic  1.363  0.020  1.363
 A3J  C5   N2   aromatic  1.343  0.020  1.343
 A3J  C5   C4   aromatic  1.415  0.020  1.415
 A3J  C3   C4   aromatic  1.369  0.020  1.369
 A3J  C3   C2   single    1.489  0.020  1.489
 A3J  C1   C2   single    1.527  0.020  1.527
 A3J  C4   H7   single    0.930  0.020  1.080
 A3J  C13  H10  single    0.970  0.020  1.090
 A3J  C13  H11  single    0.970  0.020  1.090
 A3J  C16  H15  single    0.970  0.020  1.090
 A3J  C16  H14  single    0.970  0.020  1.090
 A3J  C16  H16  single    0.970  0.020  1.090
 A3J  C1   H2   single    0.970  0.020  1.090
 A3J  C1   H4   single    0.970  0.020  1.090
 A3J  C1   H3   single    0.970  0.020  1.090
 A3J  C2   H5   single    0.970  0.020  1.090
 A3J  C2   H6   single    0.970  0.020  1.090
 A3J  N1   H1   single    0.860  0.020  1.020
 A3J  C12  H8   single    0.970  0.020  1.090
 A3J  C12  H9   single    0.970  0.020  1.090
 A3J  C15  H12  single    0.970  0.020  1.090
 A3J  C15  H13  single    0.970  0.020  1.090
 A3J  O1   H17  single    0.850  0.020  0.980

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
 A3J  H7   C4   C5   126.63  3.000
 A3J  H7   C4   C3   126.51  3.000
 A3J  C5   C4   C3   106.86  3.000
 A3J  C5   N2   C9   115.71  3.000
 A3J  N4   C7   C8   123.66  3.000
 A3J  C8   C7   C6   112.92  3.000
 A3J  N4   C7   C6   123.42  3.000
 A3J  N1   C6   C5   106.07  3.000
 A3J  C5   C6   C7   121.37  3.000
 A3J  N1   C6   C7   132.54  3.000
 A3J  C10  C9   C8   119.66  3.000
 A3J  C10  C9   N2   114.98  3.000
 A3J  C8   C9   N2   125.36  3.000
 A3J  H11  C13  H10  107.45  3.000
 A3J  H11  C13  C14  110.13  3.000
 A3J  H10  C13  C14  113.27  3.000
 A3J  H11  C13  C12  110.86  3.000
 A3J  H10  C13  C12  112.08  3.000
 A3J  C14  C13  C12  103.08  3.000
 A3J  C11  C8   C9   117.31  3.000
 A3J  C9   C8   C7   120.46  3.000
 A3J  C11  C8   C7   121.91  3.000
 A3J  H16  C16  H14  107.06  3.000
 A3J  H16  C16  H15  108.16  3.000
 A3J  H14  C16  H15  107.69  3.000
 A3J  H16  C16  C14  111.53  3.000
 A3J  H14  C16  C14  110.97  3.000
 A3J  H15  C16  C14  111.24  3.000
 A3J  H3   C1   H4   107.18  3.000
 A3J  H3   C1   H2   108.09  3.000
 A3J  H4   C1   H2   107.85  3.000
 A3J  H3   C1   C2   110.27  3.000
 A3J  H4   C1   C2   112.02  3.000
 A3J  H2   C1   C2   111.26  3.000
 A3J  N1   C3   C2   121.06  3.000
 A3J  C2   C3   C4   130.14  3.000
 A3J  N1   C3   C4   108.80  3.000
 A3J  C6   C5   N2   124.09  3.000
 A3J  N2   C5   C4   128.00  3.000
 A3J  C6   C5   C4   107.89  3.000
 A3J  H1   N1   C3   123.04  3.000
 A3J  H1   N1   C6   126.21  3.000
 A3J  C3   N1   C6   110.38  3.000
 A3J  F3   C10  F2   107.14  3.000
 A3J  F2   C10  F1   107.42  3.000
 A3J  F3   C10  F1   107.29  3.000
 A3J  F2   C10  C9   111.53  3.000
 A3J  F1   C10  C9   111.82  3.000
 A3J  F3   C10  C9   111.38  3.000
 A3J  C8   C11  N3   180.00  3.000
 A3J  C15  N4   C12  110.67  3.000
 A3J  C12  N4   C7   125.41  3.000
 A3J  C15  N4   C7   123.51  3.000
 A3J  H9   C12  H8   108.47  3.000
 A3J  H9   C12  N4   111.68  3.000
 A3J  H8   C12  N4   110.63  3.000
 A3J  H9   C12  C13  110.26  3.000
 A3J  H8   C12  C13  112.44  3.000
 A3J  N4   C12  C13  103.36  3.000
 A3J  O1   C14  C15  105.72  3.000
 A3J  C15  C14  C16  112.88  3.000
 A3J  O1   C14  C16  111.63  3.000
 A3J  C15  C14  C13  100.66  3.000
 A3J  C16  C14  C13  114.33  3.000
 A3J  O1   C14  C13  110.83  3.000
 A3J  H13  C15  H12  109.41  3.000
 A3J  H13  C15  C14  111.30  3.000
 A3J  H12  C15  C14  108.31  3.000
 A3J  H13  C15  N4   111.86  3.000
 A3J  H12  C15  N4   111.50  3.000
 A3J  C14  C15  N4   104.33  3.000
 A3J  H17  O1   C14  108.48  3.000
 A3J  H6   C2   H5   106.26  3.000
 A3J  H6   C2   C3   109.47  3.000
 A3J  H5   C2   C3   108.04  3.000
 A3J  H6   C2   C1   109.54  3.000
 A3J  H5   C2   C1   109.88  3.000
 A3J  C3   C2   C1   113.39  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
 A3J  CONST_01  C7   C6   C5   C4    180.00   0.0  0
 A3J  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 A3J  CONST_03  C9   N2   C5   C4    180.00   0.0  0
 A3J  CONST_04  C6   N1   C3   C4      0.00   0.0  0
 A3J  CONST_05  C7   C8   C9   N2      0.00   0.0  0
 A3J  CONST_06  C7   C6   C5   N2      0.00   0.0  0
 A3J  CONST_07  N1   C6   C5   N2    180.00   0.0  0
 A3J  CONST_08  C3   C4   C5   N2    180.00   0.0  0
 A3J  CONST_09  C3   N1   C6   C7    180.00   0.0  0
 A3J  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 A3J  CONST_11  C9   N2   C5   C6      0.00   0.0  0
 A3J  CONST_12  C3   C4   C5   C6      0.00   0.0  0
 A3J  CONST_13  N1   C6   C7   C8    180.00   0.0  0
 A3J  CONST_14  C5   C6   C7   C8      0.00   0.0  0
 A3J  CONST_15  C5   N2   C9   C8      0.00   0.0  0
 A3J  CONST_16  C5   C6   N1   C3      0.00   0.0  0
 A3J  CONST_17  N1   C3   C4   C5      0.00   0.0  0
 A3J  CONST_18  N4   C7   C8   C9    180.00   0.0  0
 A3J  CONST_19  N4   C7   C6   C5    180.00   0.0  0
 A3J  CONST_20  N4   C7   C6   N1      0.00   0.0  0
 A3J  CONST_21  C11  C8   C9   N2    180.00   0.0  0
 A3J  CONST_22  C10  C9   C8   C7    180.00   0.0  0
 A3J  CONST_23  C11  C8   C7   C6    180.00   0.0  0
 A3J  CONST_24  C2   C3   N1   C6    180.00   0.0  0
 A3J  CONST_25  C5   C4   C3   C2    180.00   0.0  0
 A3J  CONST_26  C10  C9   N2   C5    180.00   0.0  0
 A3J  CONST_27  N4   C7   C8   C11     0.00   0.0  0
 A3J  CONST_28  H1   N1   C3   C4    180.00   0.0  0
 A3J  CONST_29  H7   C4   C5   N2      0.00   0.0  0
 A3J  Var_01    C14  C15  N4   C7    170.72  30.0  1
 A3J  Var_02    C13  C12  N4   C7    162.53  30.0  1
 A3J  Var_03    C15  N4   C7   C6     12.50  30.0  2
 A3J  Var_04    C14  C13  C12  N4     32.61  30.0  1
 A3J  Var_05    C1   C2   C3   C4    121.30  30.0  2
 A3J  Var_06    F3   C10  C9   N2   -112.99  30.0  3
 A3J  Var_07    H2   C1   C2   C3    -57.71  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
 A3J  chir_01  C14  C16  C15  C13  negativ

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
 A3J  plan-1  N3   0.020
 A3J  plan-1  C4   0.020
 A3J  plan-1  N2   0.020
 A3J  plan-1  C7   0.020
 A3J  plan-1  C6   0.020
 A3J  plan-1  C9   0.020
 A3J  plan-1  C8   0.020
 A3J  plan-1  C3   0.020
 A3J  plan-1  C5   0.020
 A3J  plan-1  N1   0.020
 A3J  plan-1  C10  0.020
 A3J  plan-1  C11  0.020
 A3J  plan-1  N4   0.020
 A3J  plan-1  H7   0.020
 A3J  plan-1  H1   0.020
 A3J  plan-1  C2   0.020

