# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:35:30 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-azanyl-3-[1-[[(3~{S})-1-methylpiperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@@H](C1)Cn2ccc3ccc(cc23)c4n[nH]c(N)c4C#N
#
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
 JE8  JE8  5-azanyl-3-[1-[[(3~{S})-1-methylpiperidin-3-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  47  25  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JE8
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
 JE8  C10  C  CR56  0   0.399   0.5246  -1.6123  -0.1980
 JE8  C13  C  CR5   0   0.320  -2.6069   0.4067  -0.1258
 JE8  C15  C  CSP   0  -0.038  -4.8725  -0.7898  -0.1880
 JE8  C17  C  CR5   0   0.618  -4.4484   1.6409  -0.4623
 JE8  C21  C  CR16  0  -0.337  -2.0077  -1.8022   0.8708
 JE8  C22  C  CR16  0  -0.328  -1.1151  -2.8253   1.1086
 JE8  C24  C  CR15  0  -0.425   1.3263  -3.5846   0.6187
 JE8  C01  C  CH3   0  -0.520   2.7554   2.6193   2.1420
 JE8  N02  N  NT    0  -0.409   3.5415   1.8326   1.2195
 JE8  C03  C  CH2   0  -0.251   2.6933   0.9683   0.4223
 JE8  C04  C  CH2   0  -0.277   4.3796   2.6799   0.3903
 JE8  C05  C  CH2   0  -0.441   5.2629   1.8497  -0.5261
 JE8  C06  C  CH2   0  -0.431   4.4196   0.9118  -1.3779
 JE8  C07  C  CH1   0  -0.259   3.5101   0.0638  -0.4939
 JE8  C08  C  CH2   0  -0.315   2.6181  -0.8225  -1.3600
 JE8  N09  N  NR5   0  -0.529   1.8228  -1.7678  -0.6046
 JE8  C11  C  CR16  0  -0.352  -0.3742  -0.5800  -0.4429
 JE8  C12  C  CR6   0   0.045  -1.6492  -0.6789   0.0968
 JE8  C14  C  CR5   0  -0.286  -4.0285   0.3274  -0.2244
 JE8  N16  N  NS    0  -0.267  -5.5894  -1.6970  -0.1661
 JE8  N18  N  NH2   0  -0.841  -5.6908   2.1534  -0.5845
 JE8  N19  N  NR15  0  -0.490  -3.3273   2.3672  -0.4920
 JE8  N20  N  N     0  -0.298  -2.2086   1.6431  -0.2875
 JE8  C23  C  CR56  0   0.046   0.1748  -2.7450   0.5741
 JE8  C25  C  CR15  0  -0.022   2.2952  -2.9496  -0.1028
 JE8  H1   H  HCR6  0   0.247  -2.9933  -1.8566   1.3138
 JE8  H2   H  HCR6  0   0.250  -1.4100  -3.6750   1.7115
 JE8  H3   H  HCR5  0   0.249   1.4231  -4.5365   1.1157
 JE8  H4   H  HCH3  0   0.232   2.1691   1.9655   2.7893
 JE8  H5   H  HCH3  0   0.232   3.4094   3.2198   2.7761
 JE8  H6   H  HCH3  0   0.190   2.0555   3.3050   1.6376
 JE8  H8   H  HCH2  0   0.239   2.0846   0.3684   1.1037
 JE8  H9   H  HCH2  0   0.177   1.9866   1.5555  -0.1973
 JE8  H10  H  HCH2  0   0.182   3.7700   3.3715  -0.2209
 JE8  H11  H  HCH2  0   0.233   4.9969   3.3017   1.0435
 JE8  H12  H  HCH2  0   0.234   5.8553   2.5135  -1.1589
 JE8  H13  H  HCH2  0   0.218   5.9670   1.2694   0.0776
 JE8  H14  H  HCH2  0   0.214   3.8037   1.5010  -2.0684
 JE8  H15  H  HCH2  0   0.238   5.0563   0.2703  -1.9924
 JE8  H16  H  HCH1  0   0.234   4.1376  -0.5845   0.1301
 JE8  H17  H  HCH2  0   0.259   1.9458  -0.2100  -1.9640
 JE8  H18  H  HCH2  0   0.272   3.2367  -1.3876  -2.0601
 JE8  H19  H  HCR6  0   0.257  -0.1017   0.2806  -1.0401
 JE8  H20  H  HNH2  0   0.409  -5.7865   3.0334  -1.0662
 JE8  H21  H  HNH2  0   0.407  -6.4270   1.5017  -0.8028
 JE8  H22  H  HNR5  0   0.429  -3.2560   3.3647  -0.6194
 JE8  H23  H  HCR5  0   0.285   3.3086  -3.2579  -0.3100

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
 JE8  N18  C17  single    1.350  0.020  1.350
 JE8  C17  N19  aromatic  1.336  0.020  1.336
 JE8  C17  C14  aromatic  1.399  0.020  1.399
 JE8  N19  N20  aromatic  1.348  0.020  1.348
 JE8  N16  C15  triple    1.156  0.020  1.156
 JE8  C15  C14  single    1.401  0.020  1.401
 JE8  C14  C13  aromatic  1.427  0.020  1.427
 JE8  N20  C13  aromatic  1.309  0.020  1.309
 JE8  C13  C12  single    1.465  0.020  1.465
 JE8  C12  C21  aromatic  1.410  0.020  1.410
 JE8  C12  C11  aromatic  1.388  0.020  1.388
 JE8  C21  C22  aromatic  1.378  0.020  1.378
 JE8  C11  C10  aromatic  1.390  0.020  1.390
 JE8  C22  C23  aromatic  1.399  0.020  1.399
 JE8  C10  C23  aromatic  1.415  0.020  1.415
 JE8  C10  N09  aromatic  1.369  0.020  1.369
 JE8  C23  C24  aromatic  1.426  0.020  1.426
 JE8  C08  N09  single    1.448  0.020  1.448
 JE8  C08  C07  single    1.527  0.020  1.527
 JE8  N09  C25  aromatic  1.368  0.020  1.368
 JE8  C24  C25  aromatic  1.365  0.020  1.365
 JE8  C06  C07  single    1.526  0.020  1.526
 JE8  C06  C05  single    1.522  0.020  1.522
 JE8  C07  C03  single    1.525  0.020  1.525
 JE8  C05  C04  single    1.520  0.020  1.520
 JE8  C03  N02  single    1.450  0.020  1.450
 JE8  C04  N02  single    1.452  0.020  1.452
 JE8  N02  C01  single    1.445  0.020  1.445
 JE8  C21  H1   single    0.930  0.020  1.080
 JE8  C22  H2   single    0.930  0.020  1.080
 JE8  C24  H3   single    0.930  0.020  1.080
 JE8  C01  H4   single    0.970  0.020  1.090
 JE8  C01  H5   single    0.970  0.020  1.090
 JE8  C01  H6   single    0.970  0.020  1.090
 JE8  C03  H8   single    0.970  0.020  1.090
 JE8  C03  H9   single    0.970  0.020  1.090
 JE8  C04  H10  single    0.970  0.020  1.090
 JE8  C04  H11  single    0.970  0.020  1.090
 JE8  C05  H12  single    0.970  0.020  1.090
 JE8  C05  H13  single    0.970  0.020  1.090
 JE8  C06  H14  single    0.970  0.020  1.090
 JE8  C06  H15  single    0.970  0.020  1.090
 JE8  C07  H16  single    0.970  0.020  1.090
 JE8  C08  H17  single    0.970  0.020  1.090
 JE8  C08  H18  single    0.970  0.020  1.090
 JE8  C11  H19  single    0.930  0.020  1.080
 JE8  N18  H20  single    0.890  0.020  1.040
 JE8  N18  H21  single    0.890  0.020  1.040
 JE8  N19  H22  single    0.860  0.020  1.020
 JE8  C25  H23  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
 JE8  C23  C10  C11  122.05  3.000
 JE8  C23  C10  N09  107.79  3.000
 JE8  C11  C10  N09  130.15  3.000
 JE8  N20  C13  C14  110.30  3.000
 JE8  N20  C13  C12  121.33  3.000
 JE8  C14  C13  C12  128.36  3.000
 JE8  N16  C15  C14  180.00  3.000
 JE8  N19  C17  N18  124.34  3.000
 JE8  N19  C17  C14  105.20  3.000
 JE8  N18  C17  C14  130.40  3.000
 JE8  H1   C21  C12  119.75  3.000
 JE8  H1   C21  C22  118.81  3.000
 JE8  C12  C21  C22  121.41  3.000
 JE8  H2   C22  C23  120.60  3.000
 JE8  H2   C22  C21  120.14  3.000
 JE8  C23  C22  C21  119.26  3.000
 JE8  H3   C24  C25  126.22  3.000
 JE8  H3   C24  C23  127.36  3.000
 JE8  C25  C24  C23  106.43  3.000
 JE8  H6   C01  H5   107.71  3.000
 JE8  H6   C01  H4   107.65  3.000
 JE8  H5   C01  H4   107.89  3.000
 JE8  H6   C01  N02  113.08  3.000
 JE8  H5   C01  N02  110.16  3.000
 JE8  H4   C01  N02  110.18  3.000
 JE8  C04  N02  C03  111.81  3.000
 JE8  C04  N02  C01  111.16  3.000
 JE8  C03  N02  C01  110.94  3.000
 JE8  H9   C03  H8   106.51  3.000
 JE8  H9   C03  C07  108.66  3.000
 JE8  H8   C03  C07  110.33  3.000
 JE8  H9   C03  N02  111.38  3.000
 JE8  H8   C03  N02  108.07  3.000
 JE8  C07  C03  N02  111.76  3.000
 JE8  H11  C04  H10  106.60  3.000
 JE8  H11  C04  C05  110.06  3.000
 JE8  H10  C04  C05  109.20  3.000
 JE8  H11  C04  N02  108.46  3.000
 JE8  H10  C04  N02  111.24  3.000
 JE8  C05  C04  N02  111.17  3.000
 JE8  H13  C05  H12  107.04  3.000
 JE8  H13  C05  C06  109.79  3.000
 JE8  H12  C05  C06  110.54  3.000
 JE8  H13  C05  C04  109.34  3.000
 JE8  H12  C05  C04  109.44  3.000
 JE8  C06  C05  C04  110.61  3.000
 JE8  H15  C06  H14  106.77  3.000
 JE8  H15  C06  C07  110.29  3.000
 JE8  H14  C06  C07  109.18  3.000
 JE8  H15  C06  C05  110.71  3.000
 JE8  H14  C06  C05  109.41  3.000
 JE8  C07  C06  C05  110.40  3.000
 JE8  H16  C07  C08  108.29  3.000
 JE8  H16  C07  C06  108.48  3.000
 JE8  C08  C07  C06  110.01  3.000
 JE8  H16  C07  C03  108.38  3.000
 JE8  C06  C07  C03  109.74  3.000
 JE8  C08  C07  C03  111.86  3.000
 JE8  H18  C08  H17  106.53  3.000
 JE8  H18  C08  N09  107.93  3.000
 JE8  H17  C08  N09  108.46  3.000
 JE8  H18  C08  C07  109.46  3.000
 JE8  H17  C08  C07  110.36  3.000
 JE8  N09  C08  C07  113.82  3.000
 JE8  C25  N09  C08  124.44  3.000
 JE8  C25  N09  C10  108.45  3.000
 JE8  C08  N09  C10  126.98  3.000
 JE8  H19  C11  C12  120.16  3.000
 JE8  H19  C11  C10  121.65  3.000
 JE8  C12  C11  C10  118.19  3.000
 JE8  C11  C12  C21  120.24  3.000
 JE8  C11  C12  C13  119.25  3.000
 JE8  C21  C12  C13  120.50  3.000
 JE8  C17  C14  C15  124.91  3.000
 JE8  C15  C14  C13  129.99  3.000
 JE8  C17  C14  C13  104.98  3.000
 JE8  H21  N18  H20  113.08  3.000
 JE8  H21  N18  C17  116.54  3.000
 JE8  H20  N18  C17  117.54  3.000
 JE8  H22  N19  N20  119.47  3.000
 JE8  H22  N19  C17  126.87  3.000
 JE8  N20  N19  C17  113.64  3.000
 JE8  N19  N20  C13  105.88  3.000
 JE8  C24  C23  C22  134.36  3.000
 JE8  C24  C23  C10  106.79  3.000
 JE8  C22  C23  C10  118.85  3.000
 JE8  H23  C25  N09  120.04  3.000
 JE8  H23  C25  C24  129.43  3.000
 JE8  N09  C25  C24  110.53  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
 JE8  CONST_01  C13  C12  C11  C10  180.00   0.0  0
 JE8  CONST_02  C21  C12  C11  C10    0.00   0.0  0
 JE8  CONST_03  C21  C22  C23  C10    0.00   0.0  0
 JE8  CONST_04  C25  C24  C23  C10    0.00   0.0  0
 JE8  CONST_05  C24  C25  N09  C10    0.00   0.0  0
 JE8  CONST_06  N19  C17  C14  C13    0.00   0.0  0
 JE8  CONST_07  C17  N19  N20  C13    0.00   0.0  0
 JE8  CONST_08  C22  C21  C12  C13  180.00   0.0  0
 JE8  CONST_09  N20  C13  C14  C17    0.00   0.0  0
 JE8  CONST_10  C12  C13  C14  C17  180.00   0.0  0
 JE8  CONST_13  C24  C23  C22  C21  180.00   0.0  0
 JE8  CONST_14  C11  C12  C21  C22    0.00   0.0  0
 JE8  CONST_15  C11  C10  C23  C22    0.00   0.0  0
 JE8  CONST_16  N09  C10  C23  C22  180.00   0.0  0
 JE8  CONST_17  C25  C24  C23  C22  180.00   0.0  0
 JE8  CONST_18  C11  C10  C23  C24  180.00   0.0  0
 JE8  CONST_19  N09  C10  C23  C24    0.00   0.0  0
 JE8  CONST_20  C12  C11  C10  N09  180.00   0.0  0
 JE8  CONST_21  C23  C24  C25  N09    0.00   0.0  0
 JE8  CONST_24  C25  N09  C10  C11  180.00   0.0  0
 JE8  CONST_25  N19  N20  C13  C12  180.00   0.0  0
 JE8  CONST_26  C23  C22  C21  C12    0.00   0.0  0
 JE8  CONST_27  C23  C10  C11  C12    0.00   0.0  0
 JE8  CONST_28  N20  N19  C17  C14    0.00   0.0  0
 JE8  CONST_29  N19  N20  C13  C14    0.00   0.0  0
 JE8  CONST_30  C25  N09  C10  C23    0.00   0.0  0
 JE8  CONST_31  N18  C17  C14  C13  180.00   0.0  0
 JE8  CONST_32  N19  C17  C14  C15  180.00   0.0  0
 JE8  CONST_33  N20  C13  C14  C15  180.00   0.0  0
 JE8  CONST_34  C12  C13  C14  C15    0.00   0.0  0
 JE8  CONST_35  C08  N09  C25  C24  180.00   0.0  0
 JE8  CONST_36  C11  C10  N09  C08    0.00   0.0  0
 JE8  CONST_37  C23  C10  N09  C08  180.00   0.0  0
 JE8  CONST_38  N20  N19  C17  N18  180.00   0.0  0
 JE8  CONST_39  H2   C22  C23  C10  180.00   0.0  0
 JE8  CONST_40  H3   C24  C23  C10  180.00   0.0  0
 JE8  CONST_41  H23  C25  N09  C10  180.00   0.0  0
 JE8  CONST_42  H22  N19  N20  C13  180.00   0.0  0
 JE8  CONST_43  H1   C21  C12  C13    0.00   0.0  0
 JE8  CONST_44  H19  C11  C12  C13    0.00   0.0  0
 JE8  Var_01    C06  C05  C04  N02   56.09  30.0  1
 JE8  Var_02    C05  C04  N02  C03  -58.57  30.0  1
 JE8  Var_03    C07  C06  C05  C04  -54.06  30.0  1
 JE8  Var_04    C07  C03  N02  C04   59.01  30.0  1
 JE8  Var_05    C07  C08  N09  C10   96.01  30.0  2
 JE8  Var_06    H4   C01  N02  C03   57.68  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
 JE8  chir_01  C07  C08  C06  C03  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
 JE8  plan-1  C13  0.020
 JE8  plan-1  C15  0.020
 JE8  plan-1  C17  0.020
 JE8  plan-1  C12  0.020
 JE8  plan-1  C14  0.020
 JE8  plan-1  N16  0.020
 JE8  plan-1  N18  0.020
 JE8  plan-1  N19  0.020
 JE8  plan-1  N20  0.020
 JE8  plan-1  H22  0.020
 JE8  plan-2  C10  0.020
 JE8  plan-2  C13  0.020
 JE8  plan-2  C21  0.020
 JE8  plan-2  C22  0.020
 JE8  plan-2  C24  0.020
 JE8  plan-2  C08  0.020
 JE8  plan-2  N09  0.020
 JE8  plan-2  C11  0.020
 JE8  plan-2  C12  0.020
 JE8  plan-2  C23  0.020
 JE8  plan-2  C25  0.020
 JE8  plan-2  H1   0.020
 JE8  plan-2  H2   0.020
 JE8  plan-2  H3   0.020
 JE8  plan-2  H19  0.020
 JE8  plan-2  H23  0.020
 JE8  plan-3  C17  0.020
 JE8  plan-3  N18  0.020
 JE8  plan-3  H20  0.020
 JE8  plan-3  H21  0.020

