# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:52:48 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2CC[C@@H]1CC(C2)OC(=O)c3c[nH]c4ccccc34
#
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
 TKT  TKT  '(3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate'  ligand  41  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TKT
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
 TKT  C12   C  CR5   0  -0.206   1.5866  -0.0491   0.3365
 TKT  O4    O  O     0  -0.470   0.5983  -2.1581  -0.0281
 TKT  C9    C  C     0   0.542   0.4829  -0.9923   0.2859
 TKT  C11   C  CR15  0   0.003   1.5156   1.2746   0.7087
 TKT  O3    O  O2    0  -0.478  -0.6698  -0.4276   0.6318
 TKT  C7    C  CH2   0  -0.462  -2.4859   1.1638  -1.2096
 TKT  C6    C  CH2   0  -0.469  -2.7754   1.6926   0.2105
 TKT  N1    N  NT    0  -0.401  -4.3584  -0.0141  -0.3077
 TKT  C5    C  CH1   0  -0.128  -3.6684   0.5939   0.8299
 TKT  C4    C  CH2   0  -0.428  -2.8776  -0.5097   1.5295
 TKT  C1    C  CH1   0  -0.128  -3.2592  -0.1745  -1.2599
 TKT  C2    C  CH2   0  -0.443  -2.4217  -1.3678  -0.8060
 TKT  C3    C  CH1   0  -0.001  -1.8778  -1.2140   0.6147
 TKT  C13   C  CR16  0  -0.282   5.7068  -0.0964  -0.4177
 TKT  C15   C  CR56  0   0.350   3.6554   0.8965   0.2221
 TKT  C16   C  CR56  0   0.085   2.9628  -0.3136   0.0170
 TKT  C17   C  CR16  0  -0.370   3.6786  -1.4334  -0.4210
 TKT  C18   C  CR16  0  -0.259   5.0387  -1.3116  -0.6328
 TKT  N10   N  NR15  0  -0.675   2.7409   1.8300   0.6402
 TKT  C21   C  CR16  0  -0.296   5.0252   1.0255   0.0122
 TKT  H11   H  HCR5  0   0.300   0.6646   1.8578   1.0208
 TKT  H81C  H  HCH3  0   0.200  -5.1488   1.8253  -1.1113
 TKT  H82C  H  HCH3  0   0.232  -5.8750   0.3265  -1.6979
 TKT  H83C  H  HCH3  0   0.232  -6.2228   0.8908  -0.0672
 TKT  H10   H  HNR5  0   0.421   2.9481   2.7900   0.8649
 TKT  H3    H  HCH1  0   0.252  -1.6472  -2.1992   1.0256
 TKT  H71C  H  HCH2  0   0.236  -2.8724   1.8504  -1.9641
 TKT  H72C  H  HCH2  0   0.237  -1.4229   1.0390  -1.4134
 TKT  H61C  H  HCH2  0   0.244  -1.8749   1.8811   0.7933
 TKT  H62C  H  HCH2  0   0.236  -3.3202   2.6374   0.1676
 TKT  H1    H  HCH1  0   0.236  -3.6544  -0.3855  -2.2564
 TKT  H5    H  HCH1  0   0.236  -4.3950   1.0053   1.5347
 TKT  H41C  H  HCH2  0   0.241  -2.3607  -0.1247   2.4117
 TKT  H42C  H  HCH2  0   0.239  -3.5872  -1.2594   1.8876
 TKT  H21C  H  HCH2  0   0.238  -3.0599  -2.2553  -0.8218
 TKT  H22C  H  HCH2  0   0.247  -1.6114  -1.5579  -1.5121
 TKT  H13   H  HCR6  0   0.255   6.7732  -0.0368  -0.5913
 TKT  H18   H  HCR6  0   0.251   5.6026  -2.1714  -0.9709
 TKT  H21   H  HCR6  0   0.266   5.5346   1.9657   0.1802
 TKT  H17   H  HCR6  0   0.247   3.1803  -2.3769  -0.5934
 TKT  C8    C  CH3   0  -0.528  -5.4381   0.8060  -0.8205

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
 TKT  C12  C9    single    1.453  0.020  1.453
 TKT  C12  C11   aromatic  1.377  0.020  1.377
 TKT  C12  C16   aromatic  1.437  0.020  1.437
 TKT  O4   C9    double    1.213  0.020  1.213
 TKT  C8   N1    single    1.450  0.020  1.450
 TKT  C9   O3    single    1.329  0.020  1.329
 TKT  C11  N10   aromatic  1.347  0.020  1.347
 TKT  O3   C3    single    1.441  0.020  1.441
 TKT  C7   C6    single    1.543  0.020  1.543
 TKT  C7   C1    single    1.546  0.020  1.546
 TKT  C6   C5    single    1.545  0.020  1.545
 TKT  N1   C5    single    1.463  0.020  1.463
 TKT  N1   C1    single    1.463  0.020  1.463
 TKT  C5   C4    single    1.527  0.020  1.527
 TKT  C4   C3    single    1.527  0.020  1.527
 TKT  C1   C2    single    1.527  0.020  1.527
 TKT  C2   C3    single    1.529  0.020  1.529
 TKT  C13  C18   aromatic  1.403  0.020  1.403
 TKT  C13  C21   aromatic  1.381  0.020  1.381
 TKT  C15  C16   aromatic  1.409  0.020  1.409
 TKT  C15  N10   aromatic  1.372  0.020  1.372
 TKT  C15  C21   aromatic  1.392  0.020  1.392
 TKT  C16  C17   aromatic  1.399  0.020  1.399
 TKT  C17  C18   aromatic  1.382  0.020  1.382
 TKT  C11  H11   single    0.930  0.020  1.080
 TKT  C8   H81C  single    0.970  0.020  1.090
 TKT  C8   H82C  single    0.970  0.020  1.090
 TKT  C8   H83C  single    0.970  0.020  1.090
 TKT  N10  H10   single    0.860  0.020  1.020
 TKT  C3   H3    single    0.970  0.020  1.090
 TKT  C7   H71C  single    0.970  0.020  1.090
 TKT  C7   H72C  single    0.970  0.020  1.090
 TKT  C6   H61C  single    0.970  0.020  1.090
 TKT  C6   H62C  single    0.970  0.020  1.090
 TKT  C1   H1    single    0.970  0.020  1.090
 TKT  C5   H5    single    0.970  0.020  1.090
 TKT  C4   H41C  single    0.970  0.020  1.090
 TKT  C4   H42C  single    0.970  0.020  1.090
 TKT  C2   H21C  single    0.970  0.020  1.090
 TKT  C2   H22C  single    0.970  0.020  1.090
 TKT  C13  H13   single    0.930  0.020  1.080
 TKT  C18  H18   single    0.930  0.020  1.080
 TKT  C21  H21   single    0.930  0.020  1.080
 TKT  C17  H17   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
 TKT  C16   C12  C11   106.64  3.000
 TKT  C16   C12  C9    126.89  3.000
 TKT  C11   C12  C9    126.47  3.000
 TKT  O3    C9   O4    123.93  3.000
 TKT  O3    C9   C12   111.96  3.000
 TKT  O4    C9   C12   124.11  3.000
 TKT  H11   C11  N10   120.65  3.000
 TKT  H11   C11  C12   129.73  3.000
 TKT  N10   C11  C12   109.62  3.000
 TKT  C3    O3   C9    119.46  3.000
 TKT  H72C  C7   H71C  106.76  3.000
 TKT  H72C  C7   C1    112.50  3.000
 TKT  H71C  C7   C1    110.18  3.000
 TKT  H72C  C7   C6    113.24  3.000
 TKT  H71C  C7   C6    110.76  3.000
 TKT  C1    C7   C6    103.46  3.000
 TKT  H62C  C6   H61C  106.49  3.000
 TKT  H62C  C6   C5    110.04  3.000
 TKT  H61C  C6   C5    112.73  3.000
 TKT  H62C  C6   C7    110.74  3.000
 TKT  H61C  C6   C7    113.38  3.000
 TKT  C5    C6   C7    103.51  3.000
 TKT  C1    N1   C5    101.38  3.000
 TKT  C1    N1   C8    113.04  3.000
 TKT  C5    N1   C8    113.03  3.000
 TKT  H5    C5   C4    108.71  3.000
 TKT  H5    C5   N1    110.15  3.000
 TKT  C4    C5   N1    107.46  3.000
 TKT  H5    C5   C6    112.03  3.000
 TKT  C4    C5   C6    113.46  3.000
 TKT  N1    C5   C6    104.86  3.000
 TKT  H42C  C4   H41C  106.53  3.000
 TKT  H42C  C4   C3    107.76  3.000
 TKT  H41C  C4   C3    109.66  3.000
 TKT  H42C  C4   C5    108.04  3.000
 TKT  H41C  C4   C5    111.11  3.000
 TKT  C3    C4   C5    113.44  3.000
 TKT  H1    C1   C2    108.58  3.000
 TKT  H1    C1   N1    110.06  3.000
 TKT  C2    C1   N1    107.71  3.000
 TKT  H1    C1   C7    112.19  3.000
 TKT  C2    C1   C7    113.10  3.000
 TKT  N1    C1   C7    105.05  3.000
 TKT  H22C  C2   H21C  106.42  3.000
 TKT  H22C  C2   C3    110.77  3.000
 TKT  H21C  C2   C3    107.62  3.000
 TKT  H22C  C2   C1    110.55  3.000
 TKT  H21C  C2   C1    108.06  3.000
 TKT  C3    C2   C1    113.12  3.000
 TKT  H3    C3   C2    109.51  3.000
 TKT  H3    C3   C4    109.20  3.000
 TKT  C2    C3   C4    111.72  3.000
 TKT  H3    C3   O3    108.11  3.000
 TKT  C2    C3   O3    111.34  3.000
 TKT  C4    C3   O3    106.86  3.000
 TKT  H13   C13  C21   119.44  3.000
 TKT  H13   C13  C18   119.49  3.000
 TKT  C21   C13  C18   121.07  3.000
 TKT  C21   C15  N10   129.71  3.000
 TKT  C21   C15  C16   122.78  3.000
 TKT  N10   C15  C16   107.51  3.000
 TKT  C17   C16  C15   118.77  3.000
 TKT  C17   C16  C12   134.96  3.000
 TKT  C15   C16  C12   106.27  3.000
 TKT  H17   C17  C18   120.41  3.000
 TKT  H17   C17  C16   120.84  3.000
 TKT  C18   C17  C16   118.75  3.000
 TKT  H18   C18  C17   119.39  3.000
 TKT  H18   C18  C13   119.19  3.000
 TKT  C17   C18  C13   121.42  3.000
 TKT  H10   N10  C15   125.39  3.000
 TKT  H10   N10  C11   124.66  3.000
 TKT  C15   N10  C11   109.95  3.000
 TKT  H21   C21  C15   121.35  3.000
 TKT  H21   C21  C13   121.43  3.000
 TKT  C15   C21  C13   117.21  3.000
 TKT  H83C  C8   H82C  107.54  3.000
 TKT  H83C  C8   H81C  107.46  3.000
 TKT  H82C  C8   H81C  107.48  3.000
 TKT  H83C  C8   N1    109.59  3.000
 TKT  H82C  C8   N1    109.52  3.000
 TKT  H81C  C8   N1    114.98  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
 TKT  CONST_01  C15   N10  C11  C12     0.00   0.0  0
 TKT  CONST_02  N10   C15  C16  C12     0.00   0.0  0
 TKT  CONST_03  C21   C15  C16  C12   180.00   0.0  0
 TKT  CONST_04  C18   C17  C16  C12   180.00   0.0  0
 TKT  CONST_05  C15   C16  C12  C11     0.00   0.0  0
 TKT  CONST_06  C17   C16  C12  C11   180.00   0.0  0
 TKT  CONST_07  C16   C15  N10  C11     0.00   0.0  0
 TKT  CONST_08  C21   C15  N10  C11   180.00   0.0  0
 TKT  CONST_09  C16   C17  C18  C13     0.00   0.0  0
 TKT  CONST_10  C16   C15  C21  C13     0.00   0.0  0
 TKT  CONST_11  N10   C15  C21  C13   180.00   0.0  0
 TKT  CONST_12  C18   C17  C16  C15     0.00   0.0  0
 TKT  CONST_13  C18   C13  C21  C15     0.00   0.0  0
 TKT  CONST_14  N10   C11  C12  C16     0.00   0.0  0
 TKT  CONST_15  N10   C15  C16  C17   180.00   0.0  0
 TKT  CONST_16  C21   C15  C16  C17     0.00   0.0  0
 TKT  CONST_17  C21   C13  C18  C17     0.00   0.0  0
 TKT  CONST_18  N10   C11  C12  C9    180.00   0.0  0
 TKT  CONST_19  C15   C16  C12  C9    180.00   0.0  0
 TKT  CONST_20  C17   C16  C12  C9      0.00   0.0  0
 TKT  CONST_21  H10   N10  C11  C12   180.00   0.0  0
 TKT  CONST_22  H17   C17  C16  C12     0.00   0.0  0
 TKT  CONST_23  H11   C11  N10  C15   180.00   0.0  0
 TKT  CONST_24  H13   C13  C21  C15   180.00   0.0  0
 TKT  CONST_25  H21   C21  C15  C16   180.00   0.0  0
 TKT  CONST_26  H18   C18  C17  C16   180.00   0.0  0
 TKT  Var_01    C1    C7   C6   C5      0.70  30.0  3
 TKT  Var_02    C11   C12  C9   O4   -178.72  30.0  1
 TKT  Var_03    H81C  C8   N1   C5     55.76  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
 TKT  chir_01  C5  C6  N1  C4  negativ
 TKT  chir_02  C1  N1  C7  C2  negativ
 TKT  chir_03  C3  O3  C4  C2  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
 TKT  plan-1  C12  0.020
 TKT  plan-1  C9   0.020
 TKT  plan-1  C11  0.020
 TKT  plan-1  C13  0.020
 TKT  plan-1  C15  0.020
 TKT  plan-1  C16  0.020
 TKT  plan-1  C17  0.020
 TKT  plan-1  C18  0.020
 TKT  plan-1  N10  0.020
 TKT  plan-1  C21  0.020
 TKT  plan-1  H11  0.020
 TKT  plan-1  H10  0.020
 TKT  plan-1  H13  0.020
 TKT  plan-1  H18  0.020
 TKT  plan-1  H21  0.020
 TKT  plan-1  H17  0.020
 TKT  plan-2  C12  0.020
 TKT  plan-2  O4   0.020
 TKT  plan-2  C9   0.020
 TKT  plan-2  O3   0.020

