# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:52:54 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-[(5S,8R)-6,7,8,9-tetrahydro-5H-5,8-epiminocyclohepta[b]pyridin-10-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1[C@@H]2CC[C@H]1c3cccnc3C2
#
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
 W27  W27  1-[(5S,8R)-6,7,8,9-tetrahydro-5H-5,8-epiminocyclohepta[b]pyridin-10-yl]ethan-1-one  ligand  29  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W27
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
 W27  N1   N  N     0  -0.425  -0.9374  14.1334   2.0116
 W27  C4   C  CR6   0   0.084  -2.0999  14.2530  -0.0730
 W27  C5   C  CR16  0  -0.193  -0.8935  14.2202  -0.7546
 W27  C6   C  CR16  0  -0.323   0.2895  14.1419  -0.0369
 W27  C7   C  CR16  0  -0.088   0.2106  14.1018   1.3465
 W27  C8   C  CH1   0  -0.228  -3.4277  14.3728  -0.7816
 W27  O    O  O     0  -0.501  -4.5124  11.7941  -1.1678
 W27  C11  C  CH3   0  -0.797  -5.8377  11.8934   0.8222
 W27  N    N  NT    0  -0.420  -4.4369  13.7042   0.0175
 W27  C9   C  CH2   0  -0.418  -3.9245  15.8231  -0.7424
 W27  C1   C  CH1   0  -0.147  -4.5627  14.5129   1.2237
 W27  C3   C  CR6   0   0.197  -2.0726  14.2096   1.3242
 W27  C2   C  CH2   0  -0.483  -3.3565  14.2173   2.1154
 W27  H1   H  HCR6  0   0.266  -0.8791  14.2509  -1.8378
 W27  H2   H  HCR6  0   0.267   1.2493  14.1078  -0.5338
 W27  H3   H  HCR6  0   0.261   1.1133  14.0395   1.9445
 W27  H4   H  HCH1  0   0.278  -3.3750  13.9653  -1.7893
 W27  H5   H  HCH2  0   0.251  -3.9536  16.6074   1.3134
 W27  H6   H  HCH2  0   0.259  -5.5440  16.3614   0.6178
 W27  H7   H  HCH3  0   0.268  -6.2239  10.9395   0.4720
 W27  H8   H  HCH3  0   0.265  -5.3500  11.7280   1.7843
 W27  H9   H  HCH3  0   0.266  -6.6764  12.5679   0.9932
 W27  H10  H  HCH2  0   0.252  -3.1237  16.5382  -0.9276
 W27  H11  H  HCH2  0   0.254  -4.6839  15.9677  -1.5119
 W27  H12  H  HCH1  0   0.280  -5.4892  14.3009   1.7537
 W27  H13  H  HCH2  0   0.264  -3.2910  14.9521   2.9212
 W27  H14  H  HCH2  0   0.267  -3.4769  13.2424   2.5987
 W27  C10  C  CH2   0  -0.454  -4.5361  15.9508   0.6673
 W27  C    C  C     0   0.500  -4.8682  12.4457  -0.1942

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
 W27  O    C    double    1.224  0.020  1.224
 W27  C8   C9   single    1.534  0.020  1.534
 W27  C8   C4   single    1.510  0.020  1.510
 W27  C8   N    single    1.450  0.020  1.450
 W27  C9   C10  single    1.542  0.020  1.542
 W27  C5   C6   aromatic  1.386  0.020  1.386
 W27  C5   C4   aromatic  1.386  0.020  1.386
 W27  C    N    single    1.347  0.020  1.347
 W27  C    C11  single    1.509  0.020  1.509
 W27  C6   C7   aromatic  1.386  0.020  1.386
 W27  C4   C3   aromatic  1.398  0.020  1.398
 W27  N    C1   single    1.458  0.020  1.458
 W27  C10  C1   single    1.542  0.020  1.542
 W27  C1   C2   single    1.529  0.020  1.529
 W27  C7   N1   aromatic  1.327  0.020  1.327
 W27  C3   N1   aromatic  1.329  0.020  1.329
 W27  C3   C2   single    1.508  0.020  1.508
 W27  C5   H1   single    0.930  0.020  1.080
 W27  C6   H2   single    0.930  0.020  1.080
 W27  C7   H3   single    0.930  0.020  1.080
 W27  C8   H4   single    0.970  0.020  1.090
 W27  C10  H5   single    0.970  0.020  1.090
 W27  C10  H6   single    0.970  0.020  1.090
 W27  C11  H7   single    0.970  0.020  1.090
 W27  C11  H8   single    0.970  0.020  1.090
 W27  C11  H9   single    0.970  0.020  1.090
 W27  C9   H10  single    0.970  0.020  1.090
 W27  C9   H11  single    0.970  0.020  1.090
 W27  C1   H12  single    0.970  0.020  1.090
 W27  C2   H13  single    0.970  0.020  1.090
 W27  C2   H14  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
 W27  C3   N1   C7   118.74  3.000
 W27  C3   C4   C8   119.25  3.000
 W27  C3   C4   C5   118.28  3.000
 W27  C8   C4   C5   122.45  3.000
 W27  H1   C5   C6   120.52  3.000
 W27  H1   C5   C4   120.16  3.000
 W27  C6   C5   C4   119.32  3.000
 W27  H2   C6   C7   120.55  3.000
 W27  H2   C6   C5   121.42  3.000
 W27  C7   C6   C5   118.03  3.000
 W27  H3   C7   C6   120.30  3.000
 W27  H3   C7   N1   116.42  3.000
 W27  C6   C7   N1   123.28  3.000
 W27  H4   C8   C9   113.17  3.000
 W27  H4   C8   N    111.79  3.000
 W27  C9   C8   N    101.33  3.000
 W27  H4   C8   C4   111.24  3.000
 W27  N    C8   C4   108.47  3.000
 W27  C9   C8   C4   110.36  3.000
 W27  H9   C11  H8   107.43  3.000
 W27  H9   C11  H7   108.68  3.000
 W27  H8   C11  H7   108.05  3.000
 W27  H9   C11  C    111.94  3.000
 W27  H8   C11  C    111.23  3.000
 W27  H7   C11  C    109.41  3.000
 W27  C1   N    C    128.36  3.000
 W27  C1   N    C8   105.09  3.000
 W27  C    N    C8   124.53  3.000
 W27  H11  C9   H10  107.75  3.000
 W27  H11  C9   C10  110.97  3.000
 W27  H10  C9   C10  113.12  3.000
 W27  H11  C9   C8   109.44  3.000
 W27  H10  C9   C8   112.22  3.000
 W27  C10  C9   C8   103.31  3.000
 W27  H12  C1   C2   110.48  3.000
 W27  H12  C1   N    111.62  3.000
 W27  C2   C1   N    107.90  3.000
 W27  H12  C1   C10  111.84  3.000
 W27  C2   C1   C10  112.16  3.000
 W27  N    C1   C10  102.55  3.000
 W27  C2   C3   C4   120.50  3.000
 W27  C2   C3   N1   117.13  3.000
 W27  C4   C3   N1   122.36  3.000
 W27  H14  C2   H13  106.26  3.000
 W27  H14  C2   C3   108.71  3.000
 W27  H13  C2   C3   109.84  3.000
 W27  H14  C2   C1   110.05  3.000
 W27  H13  C2   C1   110.33  3.000
 W27  C3   C2   C1   111.51  3.000
 W27  H6   C10  H5   107.12  3.000
 W27  H6   C10  C1   110.60  3.000
 W27  H5   C10  C1   110.92  3.000
 W27  H6   C10  C9   110.90  3.000
 W27  H5   C10  C9   112.32  3.000
 W27  C1   C10  C9   105.04  3.000
 W27  N    C    C11  116.21  3.000
 W27  C11  C    O    121.83  3.000
 W27  N    C    O    121.94  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
 W27  CONST_01  C5   C6   C7  N1     0.00   0.0  0
 W27  CONST_02  C5   C4   C3  N1     0.00   0.0  0
 W27  CONST_03  C7   C6   C5  C4     0.00   0.0  0
 W27  CONST_04  C7   N1   C3  C4     0.00   0.0  0
 W27  CONST_05  C3   C4   C5  C6     0.00   0.0  0
 W27  CONST_06  C3   N1   C7  C6     0.00   0.0  0
 W27  CONST_07  H2   C6   C7  N1   180.00   0.0  0
 W27  CONST_08  H3   C7   C6  C5   180.00   0.0  0
 W27  CONST_09  H1   C5   C6  C7   180.00   0.0  0
 W27  CONST_10  O    C    N   C8     0.00   0.0  0
 W27  CONST_11  C11  C    N   C8   180.00   0.0  0
 W27  CONST_12  C1   N    C   O    180.00   0.0  0
 W27  CONST_13  C1   N    C   C11    0.00   0.0  0
 W27  Var_01    C1   C2   C3  N1   171.67  30.0  1
 W27  Var_02    C1   C10  C9  C8    -9.55  30.0  3
 W27  Var_03    H7   C11  C   N    171.73  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
 W27  chir_01  C8  C9  C4   N   negativ
 W27  chir_02  C1  N   C10  C2  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
 W27  plan-1  C8   0.020
 W27  plan-1  O    0.020
 W27  plan-1  C11  0.020
 W27  plan-1  N    0.020
 W27  plan-1  C1   0.020
 W27  plan-1  C    0.020
 W27  plan-2  N1   0.020
 W27  plan-2  C4   0.020
 W27  plan-2  C5   0.020
 W27  plan-2  C6   0.020
 W27  plan-2  C7   0.020
 W27  plan-2  C8   0.020
 W27  plan-2  C3   0.020
 W27  plan-2  C2   0.020
 W27  plan-2  H1   0.020
 W27  plan-2  H2   0.020
 W27  plan-2  H3   0.020

