# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:46:15 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 5-azanyl-3-[1-[[(2~{R})-1-methylpiperidin-2-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCC[C@@H]1Cn2ccc3ccc(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
 JD8  JD8  5-azanyl-3-[1-[[(2~{R})-1-methylpiperidin-2-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  47  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JD8
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
 JD8  C10  C  CR16  0  -0.331   1.0445   3.0044  -0.2582
 JD8  C13  C  CR15  0  -0.016  -2.4155   2.6293   0.7442
 JD8  C15  C  CH2   0  -0.341  -2.5830   0.2426   1.4922
 JD8  C17  C  CH2   0  -0.435  -3.4979  -2.0479   0.9191
 JD8  C20  C  CH2   0  -0.321  -3.9270  -1.0624  -1.7659
 JD8  C24  C  CSP   0  -0.037   4.2415   0.2113  -1.6199
 JD8  C02  C  CR5   0   0.623   4.5088  -1.6261   0.0288
 JD8  N03  N  NR15  0  -0.492   3.7809  -2.0124   1.0808
 JD8  N04  N  N     0  -0.301   2.7130  -1.2236   1.3176
 JD8  C05  C  CR5   0   0.322   2.7400  -0.2977   0.3930
 JD8  C06  C  CR6   0   0.042   1.7026   0.7333   0.3159
 JD8  C07  C  CR16  0  -0.352   0.4162   0.4358   0.7460
 JD8  C08  C  CR56  0   0.394  -0.5485   1.4340   0.6655
 JD8  C09  C  CR56  0   0.052  -0.2595   2.7235   0.1618
 JD8  C11  C  CR16  0  -0.335   2.0052   2.0183  -0.1794
 JD8  C12  C  CR15  0  -0.433  -1.4733   3.4694   0.2243
 JD8  N14  N  NR5   0  -0.518  -1.8694   1.4077   1.0214
 JD8  C16  C  CH1   0  -0.101  -2.9307  -0.7346   0.3728
 JD8  C18  C  CH2   0  -0.439  -3.6978  -3.0365  -0.2294
 JD8  C19  C  CH2   0  -0.446  -4.5136  -2.4150  -1.3610
 JD8  N21  N  NT    0  -0.394  -3.7773  -0.1344  -0.6520
 JD8  C23  C  CR5   0  -0.288   3.8617  -0.4888  -0.4678
 JD8  N25  N  NS    0  -0.268   4.5746   0.7717  -2.5751
 JD8  H1   H  HCR6  0   0.250   1.3048   3.9856  -0.6344
 JD8  H2   H  HCR5  0   0.285  -3.4565   2.8183   0.9540
 JD8  H3   H  HCH2  0   0.271  -1.9631  -0.2723   2.2287
 JD8  H4   H  HCH2  0   0.272  -3.4722   0.5771   2.0276
 JD8  H5   H  HCH2  0   0.233  -2.8166  -2.4681   1.6636
 JD8  H6   H  HCH2  0   0.222  -4.4483  -1.8664   1.4317
 JD8  H7   H  HCH2  0   0.225  -2.9376  -1.2195  -2.2101
 JD8  H8   H  HCH2  0   0.234  -4.5449  -0.5901  -2.5339
 JD8  H12  H  HNH2  0   0.409   6.0538  -2.9270   0.1843
 JD8  H13  H  HNH2  0   0.409   6.2113  -1.7795  -1.0379
 JD8  H14  H  HNR5  0   0.429   3.9630  -2.7972   1.6868
 JD8  H15  H  HCR6  0   0.258   0.1819  -0.5532   1.1187
 JD8  H16  H  HCR6  0   0.247   3.0171   2.2516  -0.4827
 JD8  H17  H  HCR5  0   0.249  -1.6298   4.4947  -0.0703
 JD8  H18  H  HCH1  0   0.237  -1.9867  -0.9850  -0.1305
 JD8  H19  H  HCH2  0   0.214  -2.7160  -3.3308  -0.6159
 JD8  H20  H  HCH2  0   0.232  -4.1759  -3.9504   0.1295
 JD8  H21  H  HCH2  0   0.220  -5.5542  -2.2940  -1.0448
 JD8  H22  H  HCH2  0   0.231  -4.5308  -3.0797  -2.2281
 JD8  C22  C  CH3   0  -0.547  -5.0603   0.3544  -0.1826
 JD8  N01  N  NH2   0  -0.843   5.5835  -2.2917  -0.4401
 JD8  H9   H  HCH3  0   0.234  -4.9355   1.1662   0.5327
 JD8  H10  H  HCH3  0   0.238  -5.6099   0.7655  -1.0297
 JD8  H11  H  HCH3  0   0.206  -5.7042  -0.3971   0.2923

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
 JD8  N01  C02  single    1.348  0.020  1.348
 JD8  C02  N03  aromatic  1.336  0.020  1.336
 JD8  C02  C23  aromatic  1.400  0.020  1.400
 JD8  N03  N04  aromatic  1.349  0.020  1.349
 JD8  N25  C24  triple    1.156  0.020  1.156
 JD8  C24  C23  single    1.401  0.020  1.401
 JD8  C23  C05  aromatic  1.427  0.020  1.427
 JD8  N04  C05  aromatic  1.309  0.020  1.309
 JD8  C05  C06  single    1.465  0.020  1.465
 JD8  C06  C11  aromatic  1.410  0.020  1.410
 JD8  C06  C07  aromatic  1.389  0.020  1.389
 JD8  C11  C10  aromatic  1.379  0.020  1.379
 JD8  C07  C08  aromatic  1.390  0.020  1.390
 JD8  C10  C09  aromatic  1.398  0.020  1.398
 JD8  C08  C09  aromatic  1.414  0.020  1.414
 JD8  C08  N14  aromatic  1.368  0.020  1.368
 JD8  C09  C12  aromatic  1.426  0.020  1.426
 JD8  C15  N14  single    1.445  0.020  1.445
 JD8  C15  C16  single    1.526  0.020  1.526
 JD8  N14  C13  aromatic  1.367  0.020  1.367
 JD8  C12  C13  aromatic  1.365  0.020  1.365
 JD8  C22  N21  single    1.451  0.020  1.451
 JD8  N21  C16  single    1.458  0.020  1.458
 JD8  N21  C20  single    1.457  0.020  1.457
 JD8  C16  C17  single    1.531  0.020  1.531
 JD8  C17  C18  single    1.528  0.020  1.528
 JD8  C20  C19  single    1.529  0.020  1.529
 JD8  C18  C19  single    1.527  0.020  1.527
 JD8  C10  H1   single    0.930  0.020  1.080
 JD8  C13  H2   single    0.930  0.020  1.080
 JD8  C15  H3   single    0.970  0.020  1.090
 JD8  C15  H4   single    0.970  0.020  1.090
 JD8  C17  H5   single    0.970  0.020  1.090
 JD8  C17  H6   single    0.970  0.020  1.090
 JD8  C20  H7   single    0.970  0.020  1.090
 JD8  C20  H8   single    0.970  0.020  1.090
 JD8  C22  H9   single    0.970  0.020  1.090
 JD8  C22  H10  single    0.970  0.020  1.090
 JD8  C22  H11  single    0.970  0.020  1.090
 JD8  N01  H12  single    0.890  0.020  1.040
 JD8  N01  H13  single    0.890  0.020  1.040
 JD8  N03  H14  single    0.860  0.020  1.020
 JD8  C07  H15  single    0.930  0.020  1.080
 JD8  C11  H16  single    0.930  0.020  1.080
 JD8  C12  H17  single    0.930  0.020  1.080
 JD8  C16  H18  single    0.970  0.020  1.090
 JD8  C18  H19  single    0.970  0.020  1.090
 JD8  C18  H20  single    0.970  0.020  1.090
 JD8  C19  H21  single    0.970  0.020  1.090
 JD8  C19  H22  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
 JD8  H1   C10  C11  120.03  3.000
 JD8  H1   C10  C09  120.70  3.000
 JD8  C11  C10  C09  119.27  3.000
 JD8  H2   C13  N14  120.19  3.000
 JD8  H2   C13  C12  129.22  3.000
 JD8  N14  C13  C12  110.58  3.000
 JD8  H4   C15  H3   106.05  3.000
 JD8  H4   C15  C16  111.77  3.000
 JD8  H3   C15  C16  108.80  3.000
 JD8  H4   C15  N14  108.38  3.000
 JD8  H3   C15  N14  108.64  3.000
 JD8  C16  C15  N14  112.94  3.000
 JD8  H6   C17  H5   106.61  3.000
 JD8  H6   C17  C18  110.21  3.000
 JD8  H5   C17  C18  110.15  3.000
 JD8  H6   C17  C16  110.27  3.000
 JD8  H5   C17  C16  109.99  3.000
 JD8  C18  C17  C16  109.58  3.000
 JD8  H8   C20  H7   106.71  3.000
 JD8  H8   C20  N21  108.66  3.000
 JD8  H7   C20  N21  107.96  3.000
 JD8  H8   C20  C19  110.58  3.000
 JD8  H7   C20  C19  109.08  3.000
 JD8  N21  C20  C19  113.60  3.000
 JD8  N25  C24  C23  180.00  3.000
 JD8  C23  C02  N03  105.21  3.000
 JD8  C23  C02  N01  130.26  3.000
 JD8  N03  C02  N01  124.42  3.000
 JD8  H14  N03  N04  119.52  3.000
 JD8  H14  N03  C02  126.86  3.000
 JD8  N04  N03  C02  113.61  3.000
 JD8  C05  N04  N03  105.87  3.000
 JD8  C23  C05  C06  128.27  3.000
 JD8  C06  C05  N04  121.37  3.000
 JD8  C23  C05  N04  110.34  3.000
 JD8  C11  C06  C07  120.18  3.000
 JD8  C07  C06  C05  119.28  3.000
 JD8  C11  C06  C05  120.53  3.000
 JD8  H15  C07  C08  121.70  3.000
 JD8  H15  C07  C06  120.19  3.000
 JD8  C08  C07  C06  118.10  3.000
 JD8  N14  C08  C09  107.90  3.000
 JD8  N14  C08  C07  129.86  3.000
 JD8  C09  C08  C07  122.24  3.000
 JD8  C12  C09  C08  106.70  3.000
 JD8  C12  C09  C10  134.58  3.000
 JD8  C08  C09  C10  118.72  3.000
 JD8  H16  C11  C06  119.72  3.000
 JD8  H16  C11  C10  118.78  3.000
 JD8  C06  C11  C10  121.49  3.000
 JD8  H17  C12  C09  127.51  3.000
 JD8  H17  C12  C13  126.09  3.000
 JD8  C09  C12  C13  106.40  3.000
 JD8  C08  N14  C15  125.24  3.000
 JD8  C15  N14  C13  126.12  3.000
 JD8  C08  N14  C13  108.41  3.000
 JD8  H18  C16  N21  105.70  3.000
 JD8  H18  C16  C17  106.63  3.000
 JD8  N21  C16  C17  112.86  3.000
 JD8  H18  C16  C15  106.63  3.000
 JD8  C17  C16  C15  111.83  3.000
 JD8  N21  C16  C15  112.59  3.000
 JD8  H20  C18  H19  106.46  3.000
 JD8  H20  C18  C19  110.50  3.000
 JD8  H19  C18  C19  109.07  3.000
 JD8  H20  C18  C17  110.59  3.000
 JD8  H19  C18  C17  108.77  3.000
 JD8  C19  C18  C17  111.31  3.000
 JD8  H22  C19  H21  106.35  3.000
 JD8  H22  C19  C18  110.42  3.000
 JD8  H21  C19  C18  109.81  3.000
 JD8  H22  C19  C20  109.51  3.000
 JD8  H21  C19  C20  110.09  3.000
 JD8  C18  C19  C20  110.57  3.000
 JD8  C16  N21  C22  115.12  3.000
 JD8  C16  N21  C20  109.55  3.000
 JD8  C22  N21  C20  111.77  3.000
 JD8  C05  C23  C02  104.97  3.000
 JD8  C05  C23  C24  129.98  3.000
 JD8  C02  C23  C24  124.93  3.000
 JD8  H11  C22  H10  107.37  3.000
 JD8  H11  C22  H9   107.06  3.000
 JD8  H10  C22  H9   106.68  3.000
 JD8  H11  C22  N21  115.34  3.000
 JD8  H10  C22  N21  108.75  3.000
 JD8  H9   C22  N21  111.24  3.000
 JD8  H13  N01  H12  113.44  3.000
 JD8  H13  N01  C02  116.89  3.000
 JD8  H12  N01  C02  117.90  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
 JD8  CONST_01  C05  C06  C11  C10   180.00   0.0  0
 JD8  CONST_02  C07  C06  C11  C10     0.00   0.0  0
 JD8  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 JD8  CONST_04  N14  C08  C09  C10   180.00   0.0  0
 JD8  CONST_05  C13  C12  C09  C10   180.00   0.0  0
 JD8  CONST_06  C07  C08  N14  C13   180.00   0.0  0
 JD8  CONST_07  C09  C08  N14  C13     0.00   0.0  0
 JD8  CONST_08  C08  C09  C12  C13     0.00   0.0  0
 JD8  CONST_09  C05  N04  N03  C02     0.00   0.0  0
 JD8  CONST_10  N04  C05  C23  C02     0.00   0.0  0
 JD8  CONST_11  C06  C05  C23  C02   180.00   0.0  0
 JD8  CONST_12  C05  C23  C02  N03     0.00   0.0  0
 JD8  CONST_13  C23  C05  N04  N03     0.00   0.0  0
 JD8  CONST_14  C06  C05  N04  N03   180.00   0.0  0
 JD8  CONST_15  C23  C02  N03  N04     0.00   0.0  0
 JD8  CONST_18  C08  C07  C06  C05   180.00   0.0  0
 JD8  CONST_19  C09  C10  C11  C06     0.00   0.0  0
 JD8  CONST_20  C09  C08  C07  C06     0.00   0.0  0
 JD8  CONST_21  N14  C08  C07  C06   180.00   0.0  0
 JD8  CONST_23  C12  C09  C08  C07   180.00   0.0  0
 JD8  CONST_24  C11  C06  C07  C08     0.00   0.0  0
 JD8  CONST_25  C11  C10  C09  C08     0.00   0.0  0
 JD8  CONST_26  C12  C13  N14  C08     0.00   0.0  0
 JD8  CONST_27  N14  C13  C12  C09     0.00   0.0  0
 JD8  CONST_29  C12  C09  C10  C11   180.00   0.0  0
 JD8  CONST_30  N14  C08  C09  C12     0.00   0.0  0
 JD8  CONST_31  C07  C08  N14  C15     0.00   0.0  0
 JD8  CONST_32  C09  C08  N14  C15   180.00   0.0  0
 JD8  CONST_33  C12  C13  N14  C15   180.00   0.0  0
 JD8  CONST_34  N03  C02  C23  C24   180.00   0.0  0
 JD8  CONST_35  N04  C05  C23  C24   180.00   0.0  0
 JD8  CONST_36  C06  C05  C23  C24     0.00   0.0  0
 JD8  CONST_37  N04  N03  C02  N01   180.00   0.0  0
 JD8  CONST_38  C05  C23  C02  N01   180.00   0.0  0
 JD8  CONST_39  H17  C12  C09  C10     0.00   0.0  0
 JD8  CONST_40  H14  N03  N04  C05   180.00   0.0  0
 JD8  CONST_41  H16  C11  C06  C05     0.00   0.0  0
 JD8  CONST_42  H15  C07  C06  C05     0.00   0.0  0
 JD8  CONST_43  H1   C10  C11  C06   180.00   0.0  0
 JD8  CONST_44  H2   C13  N14  C08   180.00   0.0  0
 JD8  Var_01    C20  C19  C18  C17    50.82  30.0  1
 JD8  Var_02    C19  C20  N21  C16    57.71  30.0  1
 JD8  Var_03    C19  C18  C17  C16   -52.26  30.0  1
 JD8  Var_04    N21  C20  C19  C18   -54.14  30.0  1
 JD8  Var_05    C16  C15  N14  C13    97.95  30.0  2
 JD8  Var_06    H9   C22  N21  C20  -170.57  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
 JD8  chir_01  C16  C15  N21  C17  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
 JD8  plan-1  C24  0.020
 JD8  plan-1  C02  0.020
 JD8  plan-1  N03  0.020
 JD8  plan-1  N04  0.020
 JD8  plan-1  C05  0.020
 JD8  plan-1  C06  0.020
 JD8  plan-1  C23  0.020
 JD8  plan-1  N25  0.020
 JD8  plan-1  H14  0.020
 JD8  plan-1  N01  0.020
 JD8  plan-2  C10  0.020
 JD8  plan-2  C13  0.020
 JD8  plan-2  C15  0.020
 JD8  plan-2  C05  0.020
 JD8  plan-2  C06  0.020
 JD8  plan-2  C07  0.020
 JD8  plan-2  C08  0.020
 JD8  plan-2  C09  0.020
 JD8  plan-2  C11  0.020
 JD8  plan-2  C12  0.020
 JD8  plan-2  N14  0.020
 JD8  plan-2  H1   0.020
 JD8  plan-2  H2   0.020
 JD8  plan-2  H15  0.020
 JD8  plan-2  H16  0.020
 JD8  plan-2  H17  0.020
 JD8  plan-3  C02  0.020
 JD8  plan-3  H12  0.020
 JD8  plan-3  H13  0.020
 JD8  plan-3  N01  0.020

