# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:57:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-cyano-4-(piperidin-4-yloxy)-1H-indole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(OC2CCNCC2)c3c1[nH]cc3C#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
 IEO  IEO  3-cyano-4-(piperidin-4-yloxy)-1H-indole-7-carboxamide  ligand  37  21  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IEO
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
 IEO  N01   N  NH2   0  -0.827   4.2195   2.8742  -0.1155
 IEO  C01   C  C     0   0.527   3.9636   1.5601  -0.0648
 IEO  O01   O  O     0  -0.502   4.8689   0.7277  -0.0193
 IEO  C02   C  CR6   0  -0.092   2.5465   1.1258  -0.0656
 IEO  C03   C  CR16  0  -0.311   1.4526   1.9741  -0.1403
 IEO  C04   C  CR16  0  -0.394   0.1296   1.5239  -0.1460
 IEO  C05   C  CR6   0   0.328  -0.1562   0.1667  -0.0768
 IEO  O1    O  O2    0  -0.473  -1.3637  -0.3954  -0.0954
 IEO  C06   C  CH1   0   0.018  -2.5445   0.3940  -0.2529
 IEO  C07   C  CH2   0  -0.440  -3.6107  -0.5106  -0.8473
 IEO  C08   C  CH2   0  -0.304  -4.9219   0.2548  -0.9707
 IEO  N02   N  NH1   0  -0.595  -5.3269   0.7576   0.3293
 IEO  C09   C  CH2   0  -0.300  -4.3502   1.6817   0.8750
 IEO  C10   C  CH2   0  -0.464  -3.0171   0.9700   1.0741
 IEO  C11   C  CR56  0  -0.013   0.9227  -0.7238   0.0081
 IEO  C12   C  CR5   0  -0.078   1.0018  -2.1532   0.0903
 IEO  C13   C  CR15  0   0.019   2.3394  -2.4703   0.1368
 IEO  N03   N  NR15  0  -0.671   3.0613  -1.3344   0.0878
 IEO  C14   C  CR56  0   0.362   2.2394  -0.2455   0.0091
 IEO  C1    C  CSP   0  -0.031  -0.0565  -3.0821   0.1221
 IEO  N1    N  NS    0  -0.271  -0.9107  -3.8581   0.1503
 IEO  H011  H  HNH2  0   0.407   5.1757   3.1897  -0.1240
 IEO  H012  H  HNH2  0   0.416   3.5095   3.5826  -0.1556
 IEO  H03   H  HCR6  0   0.255   1.5894   3.0458  -0.1982
 IEO  H04   H  HCR6  0   0.284  -0.6564   2.2627  -0.2051
 IEO  H06   H  HCH1  0   0.230  -2.3464   1.2079  -0.9626
 IEO  H071  H  HCH2  0   0.244  -3.2970  -0.8680  -1.8304
 IEO  H072  H  HCH2  0   0.231  -3.7525  -1.3839  -0.2042
 IEO  H101  H  HCH2  0   0.234  -3.1433   0.1572   1.7951
 IEO  H102  H  HCH2  0   0.245  -2.2891   1.6688   1.4919
 IEO  H081  H  HCH2  0   0.194  -4.7935   1.0587  -1.7137
 IEO  H082  H  HCH2  0   0.241  -5.6976  -0.4097  -1.3546
 IEO  H02   H  HNH1  0   0.355  -6.2212   1.2231   0.2472
 IEO  H091  H  HCH2  0   0.195  -4.1926   2.5632   0.2313
 IEO  H092  H  HCH2  0   0.241  -4.7106   2.0549   1.8351
 IEO  H13   H  HCR5  0   0.314   2.8122  -3.4364   0.2022
 IEO  HA    H  HNR5  0   0.428   4.0678  -1.2705   0.0980

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
 IEO  N01  C01   single    1.340  0.020  1.340
 IEO  C01  O01   double    1.231  0.020  1.231
 IEO  C01  C02   single    1.482  0.020  1.482
 IEO  C02  C03   aromatic  1.386  0.020  1.386
 IEO  C02  C14   aromatic  1.407  0.020  1.407
 IEO  C03  C04   aromatic  1.397  0.020  1.397
 IEO  C04  C05   aromatic  1.389  0.020  1.389
 IEO  C05  O1    single    1.332  0.020  1.332
 IEO  C05  C11   aromatic  1.402  0.020  1.402
 IEO  O1   C06   single    1.429  0.020  1.429
 IEO  C06  C07   single    1.519  0.020  1.519
 IEO  C06  C10   single    1.522  0.020  1.522
 IEO  C07  C08   single    1.523  0.020  1.523
 IEO  C08  N02   single    1.451  0.020  1.451
 IEO  N02  C09   single    1.451  0.020  1.451
 IEO  C09  C10   single    1.524  0.020  1.524
 IEO  C11  C12   aromatic  1.434  0.020  1.434
 IEO  C11  C14   aromatic  1.401  0.020  1.401
 IEO  C12  C13   aromatic  1.376  0.020  1.376
 IEO  C12  C1    single    1.409  0.020  1.409
 IEO  C13  N03   aromatic  1.347  0.020  1.347
 IEO  N03  C14   aromatic  1.367  0.020  1.367
 IEO  C1   N1    triple    1.154  0.020  1.154
 IEO  N01  H011  single    0.860  0.020  1.020
 IEO  N01  H012  single    0.860  0.020  1.020
 IEO  C03  H03   single    0.930  0.020  1.080
 IEO  C04  H04   single    0.930  0.020  1.080
 IEO  C06  H06   single    0.970  0.020  1.090
 IEO  C07  H071  single    0.970  0.020  1.090
 IEO  C07  H072  single    0.970  0.020  1.090
 IEO  C10  H101  single    0.970  0.020  1.090
 IEO  C10  H102  single    0.970  0.020  1.090
 IEO  C08  H081  single    0.970  0.020  1.090
 IEO  C08  H082  single    0.970  0.020  1.090
 IEO  N02  H02   single    0.890  0.020  1.040
 IEO  C09  H091  single    0.970  0.020  1.090
 IEO  C09  H092  single    0.970  0.020  1.090
 IEO  C13  H13   single    0.930  0.020  1.080
 IEO  N03  HA    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
 IEO  H012  N01  H011  116.76  3.000
 IEO  H012  N01  C01   123.96  3.000
 IEO  H011  N01  C01   119.28  3.000
 IEO  C02   C01  O01   120.35  3.000
 IEO  C02   C01  N01   118.03  3.000
 IEO  O01   C01  N01   121.62  3.000
 IEO  C14   C02  C03   115.27  3.000
 IEO  C14   C02  C01   119.61  3.000
 IEO  C03   C02  C01   125.12  3.000
 IEO  H03   C03  C04   116.02  3.000
 IEO  H03   C03  C02   120.61  3.000
 IEO  C04   C03  C02   123.37  3.000
 IEO  H04   C04  C05   121.42  3.000
 IEO  H04   C04  C03   117.94  3.000
 IEO  C05   C04  C03   120.63  3.000
 IEO  C11   C05  O1    115.50  3.000
 IEO  C11   C05  C04   117.75  3.000
 IEO  O1    C05  C04   126.75  3.000
 IEO  C06   O1   C05   121.16  3.000
 IEO  H06   C06  C10   109.82  3.000
 IEO  H06   C06  C07   108.37  3.000
 IEO  C10   C06  C07   110.40  3.000
 IEO  H06   C06  O1    109.37  3.000
 IEO  C10   C06  O1    111.69  3.000
 IEO  C07   C06  O1    107.10  3.000
 IEO  H072  C07  H071  107.77  3.000
 IEO  H072  C07  C08   109.70  3.000
 IEO  H071  C07  C08   109.80  3.000
 IEO  H072  C07  C06   109.65  3.000
 IEO  H071  C07  C06   110.21  3.000
 IEO  C08   C07  C06   109.67  3.000
 IEO  H082  C08  H081  106.84  3.000
 IEO  H082  C08  N02   109.13  3.000
 IEO  H081  C08  N02   112.55  3.000
 IEO  H082  C08  C07   109.54  3.000
 IEO  H081  C08  C07   108.71  3.000
 IEO  N02   C08  C07   109.99  3.000
 IEO  H02   N02  C09   109.42  3.000
 IEO  H02   N02  C08   109.48  3.000
 IEO  C09   N02  C08   111.70  3.000
 IEO  H092  C09  H091  106.70  3.000
 IEO  H092  C09  C10   109.49  3.000
 IEO  H091  C09  C10   108.93  3.000
 IEO  H092  C09  N02   109.05  3.000
 IEO  H091  C09  N02   112.69  3.000
 IEO  C10   C09  N02   109.90  3.000
 IEO  H102  C10  H101  107.47  3.000
 IEO  H102  C10  C09   109.52  3.000
 IEO  H101  C10  C09   109.40  3.000
 IEO  H102  C10  C06   111.64  3.000
 IEO  H101  C10  C06   109.23  3.000
 IEO  C09   C10  C06   109.54  3.000
 IEO  C14   C11  C12   106.77  3.000
 IEO  C14   C11  C05   120.44  3.000
 IEO  C12   C11  C05   132.79  3.000
 IEO  C1    C12  C13   125.30  3.000
 IEO  C1    C12  C11   128.12  3.000
 IEO  C13   C12  C11   106.58  3.000
 IEO  H13   C13  N03   121.55  3.000
 IEO  H13   C13  C12   129.45  3.000
 IEO  N03   C13  C12   109.00  3.000
 IEO  HA    N03  C14   123.39  3.000
 IEO  HA    N03  C13   126.01  3.000
 IEO  C14   N03  C13   110.59  3.000
 IEO  N03   C14  C11   107.05  3.000
 IEO  N03   C14  C02   130.41  3.000
 IEO  C11   C14  C02   122.54  3.000
 IEO  N1    C1   C12   180.00  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
 IEO  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 IEO  CONST_02  C05   C11  C14  C02     0.00   0.0  0
 IEO  CONST_03  C12   C11  C14  C02   180.00   0.0  0
 IEO  CONST_04  C13   N03  C14  C02   180.00   0.0  0
 IEO  CONST_05  C11   C14  C02  C03     0.00   0.0  0
 IEO  CONST_06  N03   C14  C02  C03   180.00   0.0  0
 IEO  CONST_07  C11   C05  C04  C03     0.00   0.0  0
 IEO  CONST_08  C14   C02  C03  C04     0.00   0.0  0
 IEO  CONST_09  C12   C11  C05  C04   180.00   0.0  0
 IEO  CONST_10  C14   C11  C05  C04     0.00   0.0  0
 IEO  CONST_11  C13   C12  C11  C05   180.00   0.0  0
 IEO  CONST_12  N03   C14  C11  C05   180.00   0.0  0
 IEO  CONST_13  N03   C13  C12  C11     0.00   0.0  0
 IEO  CONST_14  C13   N03  C14  C11     0.00   0.0  0
 IEO  CONST_15  N03   C14  C11  C12     0.00   0.0  0
 IEO  CONST_16  C14   N03  C13  C12     0.00   0.0  0
 IEO  CONST_17  C14   C11  C12  C13     0.00   0.0  0
 IEO  CONST_18  C04   C03  C02  C01   180.00   0.0  0
 IEO  CONST_19  C11   C14  C02  C01   180.00   0.0  0
 IEO  CONST_20  N03   C14  C02  C01     0.00   0.0  0
 IEO  CONST_21  O1    C05  C04  C03   180.00   0.0  0
 IEO  CONST_22  C1    C12  C11  C05     0.00   0.0  0
 IEO  CONST_23  C12   C11  C05  O1      0.00   0.0  0
 IEO  CONST_24  C14   C11  C05  O1    180.00   0.0  0
 IEO  CONST_25  C1    C12  C13  N03   180.00   0.0  0
 IEO  CONST_26  C1    C12  C11  C14   180.00   0.0  0
 IEO  CONST_27  H04   C04  C03  C02   180.00   0.0  0
 IEO  CONST_28  HA    N03  C14  C02     0.00   0.0  0
 IEO  CONST_29  H03   C03  C04  C05   180.00   0.0  0
 IEO  CONST_30  H13   C13  C12  C11   180.00   0.0  0
 IEO  CONST_31  H011  N01  C01  C02   180.00   0.0  0
 IEO  CONST_32  H012  N01  C01  C02     0.00   0.0  0
 IEO  Var_01    N02   C08  C07  C06   -57.47  30.0  1
 IEO  Var_02    N02   C09  C10  C06    57.68  30.0  1
 IEO  Var_03    C09   N02  C08  C07    61.54  30.0  1
 IEO  Var_04    C10   C09  N02  C08   -61.66  30.0  1
 IEO  Var_05    C11   C05  O1   C06  -176.56  30.0  3
 IEO  Var_06    C03   C02  C01  N01     1.28  30.0  2

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
 IEO  chir_01  C06  O1  C07  C10  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
 IEO  plan-1  C01   0.020
 IEO  plan-1  C02   0.020
 IEO  plan-1  C03   0.020
 IEO  plan-1  C04   0.020
 IEO  plan-1  C05   0.020
 IEO  plan-1  O1    0.020
 IEO  plan-1  C11   0.020
 IEO  plan-1  C12   0.020
 IEO  plan-1  C13   0.020
 IEO  plan-1  N03   0.020
 IEO  plan-1  C14   0.020
 IEO  plan-1  C1    0.020
 IEO  plan-1  N1    0.020
 IEO  plan-1  H03   0.020
 IEO  plan-1  H04   0.020
 IEO  plan-1  H13   0.020
 IEO  plan-1  HA    0.020
 IEO  plan-2  N01   0.020
 IEO  plan-2  C01   0.020
 IEO  plan-2  O01   0.020
 IEO  plan-2  C02   0.020
 IEO  plan-2  H011  0.020
 IEO  plan-2  H012  0.020

