# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:33:21 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: 1-(3-methoxybenzyl)-N-[1-(1-methylethyl)piperidin-4-yl]-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cn2c(cc3ccccc23)C(=O)NC4CCN(CC4)C(C)C)c1
#
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
 IID  IID  1-(3-methoxybenzyl)-N-[1-(1-methylethyl)piperidin-4-yl]-1H-indole-2-carboxamide  ligand  61  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IID
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
 IID  C1    C  CR16  0  -0.276   4.3602  -3.2904  -0.5021
 IID  C2    C  CR16  0  -0.304   3.7497  -2.1782   0.0411
 IID  C3    C  CR56  0   0.369   2.4174  -1.9447  -0.3059
 IID  C4    C  CR56  0   0.072   1.7076  -2.8089  -1.1652
 IID  C5    C  CR16  0  -0.345   2.3544  -3.9286  -1.7044
 IID  C6    C  CR16  0  -0.271   3.6720  -4.1579  -1.3694
 IID  N7    N  NR5   0  -0.580   1.5799  -0.9351   0.0786
 IID  C8    C  CR5   0   0.242   0.3540  -1.1403  -0.5133
 IID  C9    C  CR15  0  -0.435   0.3939  -2.2757  -1.2786
 IID  C11   C  C     0   0.509  -0.7711  -0.1830  -0.3950
 IID  N12   N  NH1   0  -0.647  -1.9839  -0.7510  -0.4630
 IID  C13   C  CH1   0  -0.070  -3.2250  -0.0031  -0.4490
 IID  C14   C  CH2   0  -0.446  -4.2922  -0.7361  -1.2456
 IID  C17   C  CH2   0  -0.381   1.9724   0.0938   1.0170
 IID  C18   C  CR6   0   0.110   2.9265   1.1010   0.4230
 IID  C21   C  CR16  0  -0.299   2.7846   1.5488  -0.8896
 IID  C22   C  CR16  0  -0.228   3.6695   2.4894  -1.3861
 IID  C23   C  CR16  0  -0.395   4.6952   3.0068  -0.6014
 IID  C24   C  CR6   0   0.398   4.8329   2.5634   0.7105
 IID  C25   C  CR16  0  -0.406   3.9471   1.6061   1.2112
 IID  C26   C  CH2   0  -0.290  -5.6150   0.0100  -1.1755
 IID  O1    O  O2    0  -0.473   5.7857   2.9890   1.5621
 IID  O45   O  O     0  -0.485  -0.5895   1.0241  -0.2866
 IID  C7    C  CH3   0  -0.436   6.7183   3.9472   1.1033
 IID  C10   C  CH2   0  -0.425  -3.7381   0.2457   0.9641
 IID  C12   C  CH2   0  -0.290  -5.0851   0.9540   0.9386
 IID  N1    N  NT    0  -0.422  -6.0727   0.1895   0.1937
 IID  C16   C  CH1   0  -0.046  -7.4269   0.7557   0.2251
 IID  C19   C  CH3   0  -0.665  -8.4521  -0.2874  -0.2176
 IID  C20   C  CH3   0  -0.698  -7.8280   1.2586   1.6083
 IID  H1    H  HCR6  0   0.255   5.3939  -3.4974  -0.2575
 IID  H2    H  HCR6  0   0.265   4.2943  -1.5151   0.7005
 IID  H5    H  HCR6  0   0.251   1.8268  -4.6015  -2.3687
 IID  H6    H  HCR6  0   0.251   4.1890  -5.0170  -1.7766
 IID  H9    H  HCR5  0   0.264  -0.4105  -2.6603  -1.8860
 IID  H12   H  HNH1  0   0.404  -2.0480  -1.7565  -0.4158
 IID  H13   H  HCH1  0   0.241  -3.0350   0.9622  -0.9266
 IID  H141  H  HCH2  0   0.245  -3.9879  -0.8364  -2.2897
 IID  H142  H  HCH2  0   0.225  -4.4268  -1.7464  -0.8451
 IID  H171  H  HCH2  0   0.274   2.4312  -0.3875   1.8836
 IID  H172  H  HCH2  0   0.296   1.0803   0.5961   1.3826
 IID  H21   H  HCR6  0   0.246   1.9964   1.1624  -1.5212
 IID  H22   H  HCR6  0   0.258   3.5664   2.8356  -2.4065
 IID  H23   H  HCR6  0   0.278   5.3677   3.7392  -1.0271
 IID  H25   H  HCR6  0   0.258   4.0747   1.2570   2.2301
 IID  H261  H  HCH2  0   0.190  -5.5092   0.9838  -1.6876
 IID  H262  H  HCH2  0   0.243  -6.3540  -0.5550  -1.7422
 IID  H7C1  H  HCH3  0   0.228   6.2324   4.8803   0.8061
 IID  H7C2  H  HCH3  0   0.259   7.3880   4.1507   1.9353
 IID  H7C3  H  HCH3  0   0.228   7.3065   3.5734   0.2611
 IID  H101  H  HCH2  0   0.219  -3.8387  -0.7103   1.4867
 IID  H102  H  HCH2  0   0.240  -3.0242   0.8519   1.5260
 IID  H121  H  HCH2  0   0.186  -4.9503   1.9683   0.5199
 IID  H122  H  HCH2  0   0.249  -5.4167   1.0832   1.9675
 IID  H16   H  HCH1  0   0.188  -7.4857   1.6138  -0.4683
 IID  H191  H  HCH3  0   0.217  -8.4691  -1.1235   0.4844
 IID  H192  H  HCH3  0   0.225  -9.4486   0.1551  -0.2380
 IID  H193  H  HCH3  0   0.232  -8.2634  -0.6890  -1.2122
 IID  H201  H  HCH3  0   0.223  -7.7025   0.4779   2.3618
 IID  H202  H  HCH3  0   0.238  -7.2663   2.1358   1.9258
 IID  H203  H  HCH3  0   0.238  -8.8808   1.5415   1.5961

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
 IID  C1   C2    aromatic  1.380  0.020  1.380
 IID  C1   C6    aromatic  1.407  0.020  1.407
 IID  C1   H1    single    0.930  0.020  1.080
 IID  C2   C3    aromatic  1.396  0.020  1.396
 IID  C2   H2    single    0.930  0.020  1.080
 IID  C3   C4    aromatic  1.410  0.020  1.410
 IID  C3   N7    aromatic  1.367  0.020  1.367
 IID  C4   C5    aromatic  1.401  0.020  1.401
 IID  C4   C9    aromatic  1.422  0.020  1.422
 IID  C5   C6    aromatic  1.379  0.020  1.379
 IID  C5   H5    single    0.930  0.020  1.080
 IID  C6   H6    single    0.930  0.020  1.080
 IID  N7   C8    aromatic  1.377  0.020  1.377
 IID  N7   C17   single    1.447  0.020  1.447
 IID  C8   C9    aromatic  1.370  0.020  1.370
 IID  C8   C11   single    1.482  0.020  1.482
 IID  C9   H9    single    0.930  0.020  1.080
 IID  C11  N12   single    1.341  0.020  1.341
 IID  C11  O45   double    1.225  0.020  1.225
 IID  N12  C13   single    1.449  0.020  1.449
 IID  N12  H12   single    0.860  0.020  1.020
 IID  C13  C14   single    1.520  0.020  1.520
 IID  C13  C10   single    1.524  0.020  1.524
 IID  C13  H13   single    0.970  0.020  1.090
 IID  C14  C26   single    1.520  0.020  1.520
 IID  C14  H141  single    0.970  0.020  1.090
 IID  C14  H142  single    0.970  0.020  1.090
 IID  C17  C18   single    1.509  0.020  1.509
 IID  C17  H171  single    0.970  0.020  1.090
 IID  C17  H172  single    0.970  0.020  1.090
 IID  C18  C21   aromatic  1.394  0.020  1.394
 IID  C18  C25   aromatic  1.385  0.020  1.385
 IID  C21  C22   aromatic  1.384  0.020  1.384
 IID  C21  H21   single    0.930  0.020  1.080
 IID  C22  C23   aromatic  1.391  0.020  1.391
 IID  C22  H22   single    0.930  0.020  1.080
 IID  C23  C24   aromatic  1.392  0.020  1.392
 IID  C23  H23   single    0.930  0.020  1.080
 IID  C24  C25   aromatic  1.397  0.020  1.397
 IID  C24  O1    single    1.347  0.020  1.347
 IID  C25  H25   single    0.930  0.020  1.080
 IID  C26  N1    single    1.455  0.020  1.455
 IID  C26  H261  single    0.970  0.020  1.090
 IID  C26  H262  single    0.970  0.020  1.090
 IID  O1   C7    single    1.414  0.020  1.414
 IID  C7   H7C1  single    0.970  0.020  1.090
 IID  C7   H7C2  single    0.970  0.020  1.090
 IID  C7   H7C3  single    0.970  0.020  1.090
 IID  C10  C12   single    1.522  0.020  1.522
 IID  C10  H101  single    0.970  0.020  1.090
 IID  C10  H102  single    0.970  0.020  1.090
 IID  C12  N1    single    1.454  0.020  1.454
 IID  C12  H121  single    0.970  0.020  1.090
 IID  C12  H122  single    0.970  0.020  1.090
 IID  N1   C16   single    1.468  0.020  1.468
 IID  C16  C19   single    1.528  0.020  1.528
 IID  C16  C20   single    1.525  0.020  1.525
 IID  C16  H16   single    0.970  0.020  1.090
 IID  C19  H191  single    0.970  0.020  1.090
 IID  C19  H192  single    0.970  0.020  1.090
 IID  C19  H193  single    0.970  0.020  1.090
 IID  C20  H201  single    0.970  0.020  1.090
 IID  C20  H202  single    0.970  0.020  1.090
 IID  C20  H203  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
 IID  H1    C1   C6    119.26  3.000
 IID  H1    C1   C2    119.19  3.000
 IID  C6    C1   C2    121.55  3.000
 IID  H2    C2   C3    121.94  3.000
 IID  H2    C2   C1    120.73  3.000
 IID  C3    C2   C1    117.32  3.000
 IID  N7    C3   C4    108.40  3.000
 IID  N7    C3   C2    129.66  3.000
 IID  C4    C3   C2    121.95  3.000
 IID  C9    C4   C5    134.06  3.000
 IID  C9    C4   C3    106.48  3.000
 IID  C5    C4   C3    119.46  3.000
 IID  H5    C5   C6    120.76  3.000
 IID  H5    C5   C4    120.52  3.000
 IID  C6    C5   C4    118.73  3.000
 IID  H6    C6   C5    119.81  3.000
 IID  H6    C6   C1    119.20  3.000
 IID  C5    C6   C1    120.99  3.000
 IID  C17   N7   C8    128.79  3.000
 IID  C17   N7   C3    122.78  3.000
 IID  C8    N7   C3    108.33  3.000
 IID  C11   C8   C9    127.02  3.000
 IID  C11   C8   N7    123.06  3.000
 IID  C9    C8   N7    109.75  3.000
 IID  H9    C9   C8    126.04  3.000
 IID  H9    C9   C4    126.86  3.000
 IID  C8    C9   C4    107.04  3.000
 IID  O45   C11  N12   123.76  3.000
 IID  O45   C11  C8    122.06  3.000
 IID  N12   C11  C8    114.14  3.000
 IID  H12   N12  C13   117.37  3.000
 IID  H12   N12  C11   118.51  3.000
 IID  C13   N12  C11   123.74  3.000
 IID  H13   C13  C10   108.63  3.000
 IID  H13   C13  C14   108.59  3.000
 IID  C10   C13  C14   109.17  3.000
 IID  H13   C13  N12   107.61  3.000
 IID  C10   C13  N12   112.43  3.000
 IID  C14   C13  N12   110.32  3.000
 IID  H142  C14  H141  107.40  3.000
 IID  H142  C14  C26   109.20  3.000
 IID  H141  C14  C26   109.36  3.000
 IID  H142  C14  C13   109.85  3.000
 IID  H141  C14  C13   110.47  3.000
 IID  C26   C14  C13   110.49  3.000
 IID  H172  C17  H171  106.35  3.000
 IID  H172  C17  C18   110.05  3.000
 IID  H171  C17  C18   109.92  3.000
 IID  H172  C17  N7    108.91  3.000
 IID  H171  C17  N7    108.37  3.000
 IID  C18   C17  N7    113.01  3.000
 IID  C25   C18  C21   119.59  3.000
 IID  C25   C18  C17   119.03  3.000
 IID  C21   C18  C17   121.37  3.000
 IID  H21   C21  C22   119.96  3.000
 IID  H21   C21  C18   120.62  3.000
 IID  C22   C21  C18   119.41  3.000
 IID  H22   C22  C23   118.88  3.000
 IID  H22   C22  C21   119.65  3.000
 IID  C23   C22  C21   121.46  3.000
 IID  H23   C23  C24   121.68  3.000
 IID  H23   C23  C22   119.22  3.000
 IID  C24   C23  C22   119.09  3.000
 IID  O1    C24  C25   116.01  3.000
 IID  O1    C24  C23   124.43  3.000
 IID  C25   C24  C23   119.56  3.000
 IID  H25   C25  C24   118.86  3.000
 IID  H25   C25  C18   120.27  3.000
 IID  C24   C25  C18   120.88  3.000
 IID  H262  C26  H261  106.31  3.000
 IID  H262  C26  N1    109.89  3.000
 IID  H261  C26  N1    110.95  3.000
 IID  H262  C26  C14   108.16  3.000
 IID  H261  C26  C14   109.13  3.000
 IID  N1    C26  C14   112.19  3.000
 IID  C7    O1   C24   118.40  3.000
 IID  H7C3  C7   H7C2  108.79  3.000
 IID  H7C3  C7   H7C1  108.75  3.000
 IID  H7C2  C7   H7C1  108.79  3.000
 IID  H7C3  C7   O1    111.92  3.000
 IID  H7C2  C7   O1    106.56  3.000
 IID  H7C1  C7   O1    111.94  3.000
 IID  H102  C10  H101  107.41  3.000
 IID  H102  C10  C12   109.20  3.000
 IID  H101  C10  C12   109.46  3.000
 IID  H102  C10  C13   110.35  3.000
 IID  H101  C10  C13   109.34  3.000
 IID  C12   C10  C13   111.01  3.000
 IID  H122  C12  H121  106.62  3.000
 IID  H122  C12  N1    109.86  3.000
 IID  H121  C12  N1    111.79  3.000
 IID  H122  C12  C10   108.00  3.000
 IID  H121  C12  C10   108.98  3.000
 IID  N1    C12  C10   111.40  3.000
 IID  C16   N1   C12   114.37  3.000
 IID  C16   N1   C26   110.97  3.000
 IID  C12   N1   C26   109.47  3.000
 IID  H16   C16  C20   107.40  3.000
 IID  H16   C16  C19   108.22  3.000
 IID  C20   C16  C19   108.14  3.000
 IID  H16   C16  N1    109.58  3.000
 IID  C20   C16  N1    112.89  3.000
 IID  C19   C16  N1    110.45  3.000
 IID  H193  C19  H192  106.91  3.000
 IID  H193  C19  H191  107.91  3.000
 IID  H192  C19  H191  107.97  3.000
 IID  H193  C19  C16   113.58  3.000
 IID  H192  C19  C16   109.97  3.000
 IID  H191  C19  C16   110.30  3.000
 IID  H203  C20  H202  107.00  3.000
 IID  H203  C20  H201  107.71  3.000
 IID  H202  C20  H201  108.39  3.000
 IID  H203  C20  C16   109.22  3.000
 IID  H202  C20  C16   113.22  3.000
 IID  H201  C20  C16   111.08  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
 IID  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 IID  CONST_02  N7    C3   C2   C1    180.00   0.0  0
 IID  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 IID  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 IID  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 IID  CONST_06  C9    C4   C3   C2    180.00   0.0  0
 IID  CONST_07  C8    N7   C3   C2    180.00   0.0  0
 IID  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 IID  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 IID  CONST_10  C8    C9   C4   C3      0.00   0.0  0
 IID  CONST_11  C9    C8   N7   C3      0.00   0.0  0
 IID  CONST_12  C8    N7   C3   C4      0.00   0.0  0
 IID  CONST_13  N7    C8   C9   C4      0.00   0.0  0
 IID  CONST_14  N7    C3   C4   C5    180.00   0.0  0
 IID  CONST_15  C8    C9   C4   C5    180.00   0.0  0
 IID  CONST_16  C9    C4   C5   C6    180.00   0.0  0
 IID  CONST_17  C9    C4   C3   N7      0.00   0.0  0
 IID  CONST_18  C23   C22  C21  C18     0.00   0.0  0
 IID  CONST_19  C23   C24  C25  C18     0.00   0.0  0
 IID  CONST_20  C24   C25  C18  C21     0.00   0.0  0
 IID  CONST_21  C24   C23  C22  C21     0.00   0.0  0
 IID  CONST_22  C25   C18  C21  C22     0.00   0.0  0
 IID  CONST_23  C25   C24  C23  C22     0.00   0.0  0
 IID  CONST_24  C17   N7   C3   C2      0.00   0.0  0
 IID  CONST_25  C11   C8   N7   C3    180.00   0.0  0
 IID  CONST_26  C17   N7   C3   C4    180.00   0.0  0
 IID  CONST_27  C11   C8   C9   C4    180.00   0.0  0
 IID  CONST_28  C17   N7   C8   C9    180.00   0.0  0
 IID  CONST_29  C22   C21  C18  C17   180.00   0.0  0
 IID  CONST_30  C24   C25  C18  C17   180.00   0.0  0
 IID  CONST_31  O1    C24  C25  C18   180.00   0.0  0
 IID  CONST_32  O1    C24  C23  C22   180.00   0.0  0
 IID  CONST_33  H5    C5   C6   C1    180.00   0.0  0
 IID  CONST_34  H6    C6   C1   C2    180.00   0.0  0
 IID  CONST_35  H1    C1   C2   C3    180.00   0.0  0
 IID  CONST_36  H9    C9   C4   C3    180.00   0.0  0
 IID  CONST_37  H2    C2   C3   C4    180.00   0.0  0
 IID  CONST_38  H22   C22  C21  C18   180.00   0.0  0
 IID  CONST_39  H25   C25  C18  C21   180.00   0.0  0
 IID  CONST_40  H23   C23  C22  C21   180.00   0.0  0
 IID  CONST_41  H21   C21  C22  C23   180.00   0.0  0
 IID  CONST_42  C13   N12  C11  C8    180.00   0.0  0
 IID  CONST_43  O45   C11  N12  C13     0.00   0.0  0
 IID  CONST_44  H12   N12  C11  C8      0.00   0.0  0
 IID  Var_01    N1    C26  C14  C13   -57.66  30.0  1
 IID  Var_02    N1    C12  C10  C13    57.81  30.0  1
 IID  Var_03    C12   N1   C26  C14    60.10  30.0  1
 IID  Var_04    C10   C12  N1   C26   -59.79  30.0  1
 IID  Var_05    C18   C17  N7   C3     73.73  30.0  2
 IID  Var_06    C21   C18  C17  N7     38.71  30.0  2
 IID  Var_07    N12   C11  C8   N7   -150.73  30.0  2
 IID  Var_08    C19   C16  N1   C26    71.97  30.0  3
 IID  Var_09    H7C1  C7   O1   C24    61.10  30.0  3
 IID  Var_10    H191  C19  C16  N1     63.77  30.0  3
 IID  Var_11    H201  C20  C16  N1    -53.87  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
 IID  chir_01  C13  N12  C14  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
 IID  plan-1  C17  0.020
 IID  plan-1  C18  0.020
 IID  plan-1  C21  0.020
 IID  plan-1  C22  0.020
 IID  plan-1  C23  0.020
 IID  plan-1  C24  0.020
 IID  plan-1  C25  0.020
 IID  plan-1  O1   0.020
 IID  plan-1  H21  0.020
 IID  plan-1  H22  0.020
 IID  plan-1  H23  0.020
 IID  plan-1  H25  0.020
 IID  plan-2  C1   0.020
 IID  plan-2  C2   0.020
 IID  plan-2  C3   0.020
 IID  plan-2  C4   0.020
 IID  plan-2  C5   0.020
 IID  plan-2  C6   0.020
 IID  plan-2  N7   0.020
 IID  plan-2  C8   0.020
 IID  plan-2  C9   0.020
 IID  plan-2  C11  0.020
 IID  plan-2  C17  0.020
 IID  plan-2  H1   0.020
 IID  plan-2  H2   0.020
 IID  plan-2  H5   0.020
 IID  plan-2  H6   0.020
 IID  plan-2  H9   0.020
 IID  plan-3  C8   0.020
 IID  plan-3  C11  0.020
 IID  plan-3  N12  0.020
 IID  plan-3  C13  0.020
 IID  plan-3  O45  0.020
 IID  plan-3  H12  0.020

