# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:02:41 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-pyrrolo[2,3-b]pyridine-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]c4ncccc34
#
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
 7CS  7CS  '(3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-pyrrolo[2,3-b]pyridine-3-carboxylate'  ligand  40  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7CS
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
 7CS  C12   C  CR5   0  -0.240  -1.5682  -0.0918  -0.3594
 7CS  O4    O  O     0  -0.466  -0.5864  -2.1991   0.0087
 7CS  C9    C  C     0   0.543  -0.4640  -1.0363  -0.3111
 7CS  C11   C  CR15  0   0.028  -1.5066   1.2346  -0.7203
 7CS  O3    O  O2    0  -0.477   0.6863  -0.4746  -0.6615
 7CS  C7    C  CH2   0  -0.463   2.4596   1.1624   1.1740
 7CS  C6    C  CH2   0  -0.470   2.7648   1.6689  -0.2509
 7CS  N1    N  NT    0  -0.401   4.3553  -0.0143   0.3204
 7CS  C5    C  CH1   0  -0.128   3.6768   0.5677  -0.8375
 7CS  C4    C  CH2   0  -0.429   2.9069  -0.5565  -1.5285
 7CS  C1    C  CH1   0  -0.128   3.2437  -0.1680   1.2594
 7CS  C2    C  CH2   0  -0.444   2.4247  -1.3776   0.8142
 7CS  C3    C  CH1   0  -0.003   1.8999  -1.2530  -0.6163
 7CS  C13   C  CR16  0  -0.086  -5.6125  -0.0068   0.3623
 7CS  N14   N  N     0  -0.420  -4.9295   1.0533  -0.0458
 7CS  C15   C  CR56  0   0.472  -3.6384   0.8470  -0.2291
 7CS  C16   C  CR56  0   0.039  -2.9385  -0.3625  -0.0375
 7CS  C17   C  CR16  0  -0.243  -3.6851  -1.4566   0.3937
 7CS  C18   C  CR16  0  -0.335  -5.0411  -1.2623   0.5927
 7CS  N10   N  NR15  0  -0.657  -2.7352   1.7887  -0.6428
 7CS  H81   H  HCH3  0   0.200   5.1166   1.8437   1.1087
 7CS  H82   H  HCH3  0   0.232   5.8514   0.3610   1.7241
 7CS  H83   H  HCH3  0   0.232   6.2132   0.9068   0.0902
 7CS  H11   H  HCR5  0   0.308  -0.6583   1.8226  -1.0311
 7CS  H71   H  HCH2  0   0.237   2.8290   1.8655   1.9219
 7CS  H72   H  HCH2  0   0.236   1.3949   1.0327   1.3657
 7CS  H61   H  HCH2  0   0.245   1.8721   1.8386  -0.8510
 7CS  H62   H  HCH2  0   0.236   3.3009   2.6190  -0.2165
 7CS  H5    H  HCH1  0   0.237   4.4099   0.9730  -1.5389
 7CS  H41   H  HCH2  0   0.242   2.4019  -0.1944  -2.4272
 7CS  H42   H  HCH2  0   0.240   3.6293  -1.3062  -1.8597
 7CS  H1    H  HCH1  0   0.237   3.6261  -0.3574   2.2651
 7CS  H21   H  HCH2  0   0.239   3.0718  -2.2577   0.8535
 7CS  H22   H  HCH2  0   0.247   1.6069  -1.5656   1.5124
 7CS  H3    H  HCH1  0   0.254   1.6807  -2.2460  -1.0141
 7CS  H13   H  HCR6  0   0.261  -6.6753   0.1372   0.5191
 7CS  H17   H  HCR6  0   0.264  -3.2298  -2.4211   0.5694
 7CS  H18   H  HCR6  0   0.268  -5.6703  -2.0759   0.9265
 7CS  HN10  H  HNR5  0   0.422  -2.9546   2.7491  -0.8573
 7CS  C8    C  CH3   0  -0.528   5.4203   0.8240   0.8350

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
 7CS  C12  C16   aromatic  1.433  0.020  1.433
 7CS  C12  C11   aromatic  1.376  0.020  1.376
 7CS  C12  C9    single    1.454  0.020  1.454
 7CS  O4   C9    double    1.212  0.020  1.212
 7CS  C8   N1    single    1.450  0.020  1.450
 7CS  C8   H81   single    0.970  0.020  1.090
 7CS  C8   H82   single    0.970  0.020  1.090
 7CS  C8   H83   single    0.970  0.020  1.090
 7CS  C9   O3    single    1.327  0.020  1.327
 7CS  C11  N10   aromatic  1.350  0.020  1.350
 7CS  C11  H11   single    0.930  0.020  1.080
 7CS  O3   C3    single    1.443  0.020  1.443
 7CS  C7   C6    single    1.543  0.020  1.543
 7CS  C7   C1    single    1.547  0.020  1.547
 7CS  C7   H71   single    0.970  0.020  1.090
 7CS  C7   H72   single    0.970  0.020  1.090
 7CS  C6   C5    single    1.546  0.020  1.546
 7CS  C6   H61   single    0.970  0.020  1.090
 7CS  C6   H62   single    0.970  0.020  1.090
 7CS  N1   C5    single    1.463  0.020  1.463
 7CS  N1   C1    single    1.463  0.020  1.463
 7CS  C5   C4    single    1.528  0.020  1.528
 7CS  C5   H5    single    0.970  0.020  1.090
 7CS  C4   C3    single    1.527  0.020  1.527
 7CS  C4   H41   single    0.970  0.020  1.090
 7CS  C4   H42   single    0.970  0.020  1.090
 7CS  C1   C2    single    1.527  0.020  1.527
 7CS  C1   H1    single    0.970  0.020  1.090
 7CS  C2   C3    single    1.529  0.020  1.529
 7CS  C2   H21   single    0.970  0.020  1.090
 7CS  C2   H22   single    0.970  0.020  1.090
 7CS  C3   H3    single    0.970  0.020  1.090
 7CS  C13  N14   aromatic  1.325  0.020  1.325
 7CS  C13  C18   aromatic  1.398  0.020  1.398
 7CS  C13  H13   single    0.930  0.020  1.080
 7CS  N14  C15   aromatic  1.320  0.020  1.320
 7CS  C15  N10   aromatic  1.369  0.020  1.369
 7CS  C15  C16   aromatic  1.410  0.020  1.410
 7CS  C16  C17   aromatic  1.393  0.020  1.393
 7CS  C17  C18   aromatic  1.384  0.020  1.384
 7CS  C17  H17   single    0.930  0.020  1.080
 7CS  C18  H18   single    0.930  0.020  1.080
 7CS  N10  HN10  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
 7CS  C16   C12  C11  106.49  3.000
 7CS  C11   C12  C9   126.94  3.000
 7CS  C16   C12  C9   126.58  3.000
 7CS  O3    C9   O4   124.28  3.000
 7CS  O3    C9   C12  111.99  3.000
 7CS  O4    C9   C12  123.73  3.000
 7CS  H11   C11  N10  120.59  3.000
 7CS  H11   C11  C12  129.55  3.000
 7CS  N10   C11  C12  109.87  3.000
 7CS  C3    O3   C9   119.51  3.000
 7CS  H72   C7   H71  106.67  3.000
 7CS  H72   C7   C1   112.54  3.000
 7CS  H71   C7   C1   110.18  3.000
 7CS  H72   C7   C6   113.26  3.000
 7CS  H71   C7   C6   110.77  3.000
 7CS  C1    C7   C6   103.48  3.000
 7CS  H62   C6   H61  106.53  3.000
 7CS  H62   C6   C5   110.02  3.000
 7CS  H61   C6   C5   112.68  3.000
 7CS  H62   C6   C7   110.73  3.000
 7CS  H61   C6   C7   113.45  3.000
 7CS  C5    C6   C7   103.49  3.000
 7CS  C1    N1   C5   101.38  3.000
 7CS  C1    N1   C8   113.02  3.000
 7CS  C5    N1   C8   113.06  3.000
 7CS  H5    C5   C4   108.71  3.000
 7CS  H5    C5   N1   110.15  3.000
 7CS  C4    C5   N1   107.40  3.000
 7CS  H5    C5   C6   112.04  3.000
 7CS  C4    C5   C6   113.49  3.000
 7CS  N1    C5   C6   104.88  3.000
 7CS  H42   C4   H41  106.48  3.000
 7CS  H42   C4   C3   107.71  3.000
 7CS  H41   C4   C3   109.74  3.000
 7CS  H42   C4   C5   107.99  3.000
 7CS  H41   C4   C5   111.17  3.000
 7CS  C3    C4   C5   113.44  3.000
 7CS  H1    C1   C2   108.59  3.000
 7CS  H1    C1   N1   110.06  3.000
 7CS  C2    C1   N1   107.67  3.000
 7CS  H1    C1   C7   112.17  3.000
 7CS  C2    C1   C7   113.16  3.000
 7CS  N1    C1   C7   105.03  3.000
 7CS  H22   C2   H21  106.37  3.000
 7CS  H22   C2   C3   110.82  3.000
 7CS  H21   C2   C3   107.60  3.000
 7CS  H22   C2   C1   110.59  3.000
 7CS  H21   C2   C1   108.05  3.000
 7CS  C3    C2   C1   113.10  3.000
 7CS  H3    C3   C2   109.61  3.000
 7CS  H3    C3   C4   109.24  3.000
 7CS  C2    C3   C4   111.71  3.000
 7CS  H3    C3   O3   108.08  3.000
 7CS  C2    C3   O3   111.23  3.000
 7CS  C4    C3   O3   106.86  3.000
 7CS  H13   C13  C18  119.74  3.000
 7CS  H13   C13  N14  116.33  3.000
 7CS  C18   C13  N14  123.93  3.000
 7CS  C15   N14  C13  114.94  3.000
 7CS  N10   C15  C16  107.67  3.000
 7CS  C16   C15  N14  126.90  3.000
 7CS  N10   C15  N14  125.43  3.000
 7CS  C17   C16  C15  116.71  3.000
 7CS  C17   C16  C12  136.91  3.000
 7CS  C15   C16  C12  106.38  3.000
 7CS  H17   C17  C18  120.96  3.000
 7CS  H17   C17  C16  121.70  3.000
 7CS  C18   C17  C16  117.34  3.000
 7CS  H18   C18  C17  120.58  3.000
 7CS  H18   C18  C13  119.25  3.000
 7CS  C17   C18  C13  120.17  3.000
 7CS  HN10  N10  C15  125.17  3.000
 7CS  HN10  N10  C11  125.23  3.000
 7CS  C15   N10  C11  109.60  3.000
 7CS  H83   C8   H82  107.54  3.000
 7CS  H83   C8   H81  107.49  3.000
 7CS  H82   C8   H81  107.46  3.000
 7CS  H83   C8   N1   109.60  3.000
 7CS  H82   C8   N1   109.52  3.000
 7CS  H81   C8   N1   114.97  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
 7CS  CONST_01  N14   C15  C16  C12  180.00   0.0  0
 7CS  CONST_02  N10   C15  C16  C12    0.00   0.0  0
 7CS  CONST_03  C18   C17  C16  C12  180.00   0.0  0
 7CS  CONST_04  C15   N10  C11  C12    0.00   0.0  0
 7CS  CONST_05  C15   C16  C12  C11    0.00   0.0  0
 7CS  CONST_06  C17   C16  C12  C11  180.00   0.0  0
 7CS  CONST_07  N14   C15  N10  C11  180.00   0.0  0
 7CS  CONST_08  C16   C15  N10  C11    0.00   0.0  0
 7CS  CONST_09  N10   C15  N14  C13  180.00   0.0  0
 7CS  CONST_10  C16   C15  N14  C13    0.00   0.0  0
 7CS  CONST_11  C16   C17  C18  C13    0.00   0.0  0
 7CS  CONST_12  C17   C18  C13  N14    0.00   0.0  0
 7CS  CONST_13  C17   C16  C15  N14    0.00   0.0  0
 7CS  CONST_14  C18   C13  N14  C15    0.00   0.0  0
 7CS  CONST_15  C18   C17  C16  C15    0.00   0.0  0
 7CS  CONST_16  N10   C11  C12  C16    0.00   0.0  0
 7CS  CONST_17  N10   C15  C16  C17  180.00   0.0  0
 7CS  CONST_18  C15   C16  C12  C9   180.00   0.0  0
 7CS  CONST_19  C17   C16  C12  C9     0.00   0.0  0
 7CS  CONST_20  N10   C11  C12  C9   180.00   0.0  0
 7CS  CONST_21  H17   C17  C16  C12    0.00   0.0  0
 7CS  CONST_22  HN10  N10  C11  C12  180.00   0.0  0
 7CS  CONST_23  H18   C18  C13  N14  180.00   0.0  0
 7CS  CONST_24  H13   C13  N14  C15  180.00   0.0  0
 7CS  CONST_25  H11   C11  N10  C15  180.00   0.0  0
 7CS  Var_01    C1    C7   C6   C5     0.67  30.0  3
 7CS  Var_02    C16   C12  C9   O4     0.56  30.0  2
 7CS  Var_03    H81   C8   N1   C5    56.07  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
 7CS  chir_01  C5  C6  N1  C4  negativ
 7CS  chir_02  C1  N1  C7  C2  negativ
 7CS  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
 7CS  plan-1  C12   0.020
 7CS  plan-1  C9    0.020
 7CS  plan-1  C11   0.020
 7CS  plan-1  C13   0.020
 7CS  plan-1  N14   0.020
 7CS  plan-1  C15   0.020
 7CS  plan-1  C16   0.020
 7CS  plan-1  C17   0.020
 7CS  plan-1  C18   0.020
 7CS  plan-1  N10   0.020
 7CS  plan-1  H11   0.020
 7CS  plan-1  H13   0.020
 7CS  plan-1  H17   0.020
 7CS  plan-1  H18   0.020
 7CS  plan-1  HN10  0.020
 7CS  plan-2  C12   0.020
 7CS  plan-2  O4    0.020
 7CS  plan-2  C9    0.020
 7CS  plan-2  O3    0.020

