# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:08:18 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: ethyl 1,3-dihydro-2H-pyrrolo[3,4-c]pyridine-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1Cc2ccncc2C1
#
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
 T9S  T9S  'ethyl 1,3-dihydro-2H-pyrrolo[3,4-c]pyridine-2-carboxylate'  ligand  26  14  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_T9S
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
 T9S  C4   C  CR56  0   0.151  45.8658  27.2293  28.6481
 T9S  C5   C  CR16  0  -0.387  45.2745  26.1542  28.0111
 T9S  C6   C  CR16  0  -0.063  45.9495  25.6161  26.9232
 T9S  N1   N  N     0  -0.411  47.1136  26.0735  26.4716
 T9S  C7   C  CR16  0  -0.097  47.6702  27.1081  27.0929
 T9S  C8   C  CR56  0  -0.059  47.0766  27.7145  28.1853
 T9S  C9   C  CH2   0  -0.278  47.5397  28.8742  29.0071
 T9S  O1   O  O     0  -0.528  47.3891  30.7763  31.0243
 T9S  O    O  O2    0  -0.482  45.4228  29.9095  31.7091
 T9S  C1   C  CH2   0  -0.169  45.3192  30.8930  32.7457
 T9S  C    C  CH3   0  -0.690  44.0308  30.6382  33.4899
 T9S  N    N  NR5   0  -0.546  46.4632  28.9959  29.9821
 T9S  C3   C  CH2   0  -0.270  45.3956  28.0142  29.8293
 T9S  H1   H  HCR6  0   0.272  44.3282  25.7398  28.3326
 T9S  H2   H  HCR6  0   0.267  45.5255  24.7722  26.3907
 T9S  H3   H  HCR6  0   0.266  48.6197  27.4610  26.7041
 T9S  H4   H  HCH2  0   0.265  48.5018  28.6798  29.4888
 T9S  H5   H  HCH2  0   0.265  47.6484  29.7844  28.4109
 T9S  H6   H  HCH2  0   0.231  46.1762  30.8162  33.4176
 T9S  H7   H  HCH2  0   0.231  45.3227  31.8943  32.3103
 T9S  H8   H  HCH3  0   0.239  43.9260  31.3740  34.2867
 T9S  H9   H  HCH3  0   0.235  43.1641  30.7282  32.8349
 T9S  H10  H  HCH3  0   0.235  44.0204  29.6484  33.9467
 T9S  H11  H  HCH2  0   0.271  44.4275  28.4849  29.6386
 T9S  H12  H  HCH2  0   0.271  45.2880  27.3810  30.7142
 T9S  C2   C  C     0   0.781  46.4936  29.9603  30.9173

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
 T9S  N1  C6   aromatic  1.330  0.020  1.330
 T9S  N1  C7   aromatic  1.329  0.020  1.329
 T9S  C6  C5   aromatic  1.389  0.020  1.389
 T9S  C7  C8   aromatic  1.383  0.020  1.383
 T9S  C5  C4   aromatic  1.383  0.020  1.383
 T9S  C8  C4   aromatic  1.384  0.020  1.384
 T9S  C8  C9   single    1.495  0.020  1.495
 T9S  C4  C3   single    1.494  0.020  1.494
 T9S  C9  N    single    1.457  0.020  1.457
 T9S  C3  N    single    1.458  0.020  1.458
 T9S  N   C2   single    1.344  0.020  1.344
 T9S  C2  O1   double    1.216  0.020  1.216
 T9S  C2  O    single    1.333  0.020  1.333
 T9S  O   C1   single    1.433  0.020  1.433
 T9S  C1  C    single    1.510  0.020  1.510
 T9S  C5  H1   single    0.930  0.020  1.080
 T9S  C6  H2   single    0.930  0.020  1.080
 T9S  C7  H3   single    0.930  0.020  1.080
 T9S  C9  H4   single    0.970  0.020  1.090
 T9S  C9  H5   single    0.970  0.020  1.090
 T9S  C1  H6   single    0.970  0.020  1.090
 T9S  C1  H7   single    0.970  0.020  1.090
 T9S  C   H8   single    0.970  0.020  1.090
 T9S  C   H9   single    0.970  0.020  1.090
 T9S  C   H10  single    0.970  0.020  1.090
 T9S  C3  H11  single    0.970  0.020  1.090
 T9S  C3  H12  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
 T9S  C3   C4  C8   110.82  3.000
 T9S  C3   C4  C5   129.66  3.000
 T9S  C8   C4  C5   119.52  3.000
 T9S  H1   C5  C6   120.63  3.000
 T9S  H1   C5  C4   122.35  3.000
 T9S  C6   C5  C4   117.02  3.000
 T9S  H2   C6  N1   116.31  3.000
 T9S  H2   C6  C5   119.75  3.000
 T9S  N1   C6  C5   123.94  3.000
 T9S  C7   N1  C6   118.40  3.000
 T9S  H3   C7  C8   121.06  3.000
 T9S  H3   C7  N1   116.88  3.000
 T9S  C8   C7  N1   122.06  3.000
 T9S  C9   C8  C7   129.89  3.000
 T9S  C9   C8  C4   111.05  3.000
 T9S  C7   C8  C4   119.07  3.000
 T9S  H5   C9  H4   107.50  3.000
 T9S  H5   C9  N    111.64  3.000
 T9S  H4   C9  N    111.71  3.000
 T9S  H5   C9  C8   112.14  3.000
 T9S  H4   C9  C8   112.14  3.000
 T9S  N    C9  C8   101.75  3.000
 T9S  C1   O   C2   117.50  3.000
 T9S  H7   C1  H6   107.91  3.000
 T9S  H7   C1  C    110.74  3.000
 T9S  H6   C1  C    110.78  3.000
 T9S  H7   C1  O    109.92  3.000
 T9S  H6   C1  O    109.89  3.000
 T9S  C    C1  O    107.61  3.000
 T9S  H10  C   H9   108.61  3.000
 T9S  H10  C   H8   107.81  3.000
 T9S  H9   C   H8   107.89  3.000
 T9S  H10  C   C1   111.59  3.000
 T9S  H9   C   C1   111.62  3.000
 T9S  H8   C   C1   109.19  3.000
 T9S  C3   N   C2   124.93  3.000
 T9S  C2   N   C9   120.58  3.000
 T9S  C3   N   C9   114.48  3.000
 T9S  H12  C3  H11  107.66  3.000
 T9S  H12  C3  N    112.15  3.000
 T9S  H11  C3  N    112.13  3.000
 T9S  H12  C3  C4   111.50  3.000
 T9S  H11  C3  C4   111.53  3.000
 T9S  N    C3  C4   101.89  3.000
 T9S  N    C2  O    111.59  3.000
 T9S  O    C2  O1   124.40  3.000
 T9S  N    C2  O1   124.01  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
 T9S  CONST_01  N1  C6  C5  C4     0.00   0.0  0
 T9S  CONST_02  N1  C7  C8  C4     0.00   0.0  0
 T9S  CONST_03  C7  N1  C6  C5     0.00   0.0  0
 T9S  CONST_04  C7  C8  C4  C5     0.00   0.0  0
 T9S  CONST_05  C8  C7  N1  C6     0.00   0.0  0
 T9S  CONST_06  C8  C4  C5  C6     0.00   0.0  0
 T9S  CONST_07  H2  C6  C5  C4   180.00   0.0  0
 T9S  CONST_08  H3  C7  C8  C4   180.00   0.0  0
 T9S  CONST_09  H1  C5  C6  N1   180.00   0.0  0
 T9S  Var_01    N   C9  C8  C4    -0.08  30.0  1
 T9S  Var_02    C9  N   C3  C4    -0.28  30.0  1
 T9S  Var_03    N   C3  C4  C5  -179.76  30.0  1
 T9S  Var_04    C3  N   C9  C8     0.24  30.0  1
 T9S  Var_05    O1  C2  N   C9    -0.21  30.0  2
 T9S  Var_06    N   C2  O   C1  -179.36  30.0  2
 T9S  Var_07    C   C1  O   C2   179.49  30.0  3
 T9S  Var_08    H8  C   C1  O    179.99  30.0  3

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
 T9S  plan-1  O1  0.020
 T9S  plan-1  O   0.020
 T9S  plan-1  N   0.020
 T9S  plan-1  C2  0.020
 T9S  plan-2  C4  0.020
 T9S  plan-2  C5  0.020
 T9S  plan-2  C6  0.020
 T9S  plan-2  N1  0.020
 T9S  plan-2  C7  0.020
 T9S  plan-2  C8  0.020
 T9S  plan-2  C9  0.020
 T9S  plan-2  C3  0.020
 T9S  plan-2  H1  0.020
 T9S  plan-2  H2  0.020
 T9S  plan-2  H3  0.020

