# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 15:58:23 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: methyl 2-(4-cyanophenoxy)ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)COc1ccc(cc1)C#N
#
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
 T9K  T9K  "methyl 2-(4-cyanophenoxy)ethanoate"  ligand  23  14  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T9K
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
 T9K  C10  C  CR6   0  -0.019   1.9350  -4.4966  5.4751
 T9K  C13  C  CSP   0   0.050   0.5224  -4.6058  5.6189
 T9K  C01  C  CH3   0  -0.415   7.4726  -1.6921  4.9365
 T9K  C03  C  C     0   0.546   8.2901  -3.8968  5.5483
 T9K  C05  C  CH2   0  -0.364   6.9080  -4.2777  6.0507
 T9K  C07  C  CR6   0   0.417   4.6899  -4.2784  5.2015
 T9K  C08  C  CR16  0  -0.332   3.8541  -4.0001  4.1162
 T9K  C09  C  CR16  0  -0.223   2.4882  -4.1082  4.2508
 T9K  C11  C  CR16  0  -0.223   2.7702  -4.7767  6.5533
 T9K  C12  C  CR16  0  -0.359   4.1440  -4.6711  6.4225
 T9K  N14  N  NS    0  -0.255  -0.6211  -4.6963  5.7346
 T9K  O02  O  O2    0  -0.421   8.4715  -2.7133  4.9855
 T9K  O04  O  O     0  -0.418   9.2285  -4.6384  5.6652
 T9K  O06  O  O2    0  -0.466   6.0060  -4.1465  4.9736
 T9K  H1   H  HCH3  0   0.264   8.0118  -0.7563  4.8180
 T9K  H2   H  HCH3  0   0.249   6.8098  -1.8325  4.0856
 T9K  H3   H  HCH3  0   0.243   6.8873  -1.6368  5.8537
 T9K  H4   H  HCH2  0   0.280   6.6291  -3.6331  6.8942
 T9K  H5   H  HCH2  0   0.291   6.9503  -5.3073  6.4133
 T9K  H6   H  HCR6  0   0.284   4.2868  -3.6957  3.1721
 T9K  H7   H  HCR6  0   0.283   1.8457  -3.8880  3.4090
 T9K  H8   H  HCR6  0   0.286   2.3491  -5.0821  7.5019
 T9K  H9   H  HCR6  0   0.301   4.7650  -4.9026  7.2769

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
 T9K  C08  C09  aromatic  1.377  0.020  1.377
 T9K  C08  C07  aromatic  1.398  0.020  1.398
 T9K  C09  C10  aromatic  1.398  0.020  1.398
 T9K  O06  C07  single    1.342  0.020  1.342
 T9K  O06  C05  single    1.411  0.020  1.411
 T9K  C07  C12  aromatic  1.394  0.020  1.394
 T9K  O02  C01  single    1.429  0.020  1.429
 T9K  O02  C03  single    1.323  0.020  1.323
 T9K  C10  C13  single    1.424  0.020  1.424
 T9K  C10  C11  aromatic  1.392  0.020  1.392
 T9K  C05  C03  single    1.519  0.020  1.519
 T9K  C13  N14  triple    1.153  0.020  1.153
 T9K  C03  O04  double    1.202  0.020  1.202
 T9K  C12  C11  aromatic  1.384  0.020  1.384
 T9K  C01  H1   single    0.970  0.020  1.090
 T9K  C01  H2   single    0.970  0.020  1.090
 T9K  C01  H3   single    0.970  0.020  1.090
 T9K  C05  H4   single    0.970  0.020  1.090
 T9K  C05  H5   single    0.970  0.020  1.090
 T9K  C08  H6   single    0.930  0.020  1.080
 T9K  C09  H7   single    0.930  0.020  1.080
 T9K  C11  H8   single    0.930  0.020  1.080
 T9K  C12  H9   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
 T9K  C11  C10  C09  119.77  3.000
 T9K  C11  C10  C13  120.09  3.000
 T9K  C09  C10  C13  120.14  3.000
 T9K  N14  C13  C10  180.00  3.000
 T9K  H3   C01  H2   109.74  3.000
 T9K  H3   C01  H1   108.34  3.000
 T9K  H2   C01  H1   109.16  3.000
 T9K  H3   C01  O02  112.51  3.000
 T9K  H2   C01  O02  111.13  3.000
 T9K  H1   C01  O02  105.80  3.000
 T9K  O04  C03  O02  119.10  3.000
 T9K  O04  C03  C05  121.57  3.000
 T9K  O02  C03  C05  119.33  3.000
 T9K  H5   C05  H4   107.96  3.000
 T9K  H5   C05  O06  111.46  3.000
 T9K  H4   C05  O06  111.69  3.000
 T9K  H5   C05  C03  108.11  3.000
 T9K  H4   C05  C03  109.76  3.000
 T9K  O06  C05  C03  107.81  3.000
 T9K  O06  C07  C12  124.08  3.000
 T9K  C12  C07  C08  120.14  3.000
 T9K  O06  C07  C08  115.78  3.000
 T9K  H6   C08  C09  120.27  3.000
 T9K  H6   C08  C07  119.63  3.000
 T9K  C09  C08  C07  120.11  3.000
 T9K  H7   C09  C08  119.82  3.000
 T9K  H7   C09  C10  120.19  3.000
 T9K  C08  C09  C10  119.99  3.000
 T9K  H8   C11  C12  119.39  3.000
 T9K  H8   C11  C10  120.16  3.000
 T9K  C12  C11  C10  120.46  3.000
 T9K  H9   C12  C11  118.62  3.000
 T9K  H9   C12  C07  121.84  3.000
 T9K  C11  C12  C07  119.54  3.000
 T9K  C03  O02  C01  123.91  3.000
 T9K  C07  O06  C05  119.22  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
 T9K  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 T9K  CONST_02  C07  C12  C11  C10     0.00   0.0  0
 T9K  CONST_03  C11  C10  C09  C08     0.00   0.0  0
 T9K  CONST_04  C11  C12  C07  C08     0.00   0.0  0
 T9K  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 T9K  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 T9K  CONST_07  C08  C09  C10  C13   180.00   0.0  0
 T9K  CONST_08  C12  C11  C10  C13   180.00   0.0  0
 T9K  CONST_09  O06  C07  C08  C09   180.00   0.0  0
 T9K  CONST_10  O06  C07  C12  C11   180.00   0.0  0
 T9K  CONST_11  H6   C08  C09  C10   180.00   0.0  0
 T9K  CONST_12  H9   C12  C11  C10   180.00   0.0  0
 T9K  CONST_13  H7   C09  C08  C07   180.00   0.0  0
 T9K  CONST_14  H8   C11  C12  C07   180.00   0.0  0
 T9K  CONST_15  H9   C12  C07  C08   180.00   0.0  0
 T9K  CONST_16  H8   C11  C10  C09   180.00   0.0  0
 T9K  CONST_17  H7   C09  C10  C11   180.00   0.0  0
 T9K  CONST_18  H6   C08  C07  C12   180.00   0.0  0
 T9K  Var_01    C08  C07  O06  C05   173.68  30.0  2
 T9K  Var_02    C12  C07  O06  C05    -6.62  30.0  2
 T9K  Var_03    C07  O06  C05  C03  -172.39  30.0  1
 T9K  Var_04    H4   C05  O06  C07   -51.73  30.0  3
 T9K  Var_05    H5   C05  O06  C07    69.12  30.0  3
 T9K  Var_06    C05  C03  O02  C01     6.76  30.0  3
 T9K  Var_07    O04  C03  O02  C01  -172.28  30.0  3
 T9K  Var_08    O06  C05  C03  O02    55.51  30.0  2
 T9K  Var_09    O06  C05  C03  O04  -125.47  30.0  2
 T9K  Var_10    H1   C01  O02  C03   156.62  30.0  3
 T9K  Var_11    H2   C01  O02  C03   -85.01  30.0  3
 T9K  Var_12    H3   C01  O02  C03    38.50  30.0  3
 T9K  Var_13    H4   C05  C03  O02   -66.35  30.0  2
 T9K  Var_14    H5   C05  C03  O02   176.13  30.0  2
 T9K  Var_15    H4   C05  C03  O04   112.67  30.0  2
 T9K  Var_16    H5   C05  C03  O04    -4.86  30.0  2

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
 T9K  plan-1  C10  0.020
 T9K  plan-1  C13  0.020
 T9K  plan-1  C07  0.020
 T9K  plan-1  C08  0.020
 T9K  plan-1  C09  0.020
 T9K  plan-1  C11  0.020
 T9K  plan-1  C12  0.020
 T9K  plan-1  N14  0.020
 T9K  plan-1  O06  0.020
 T9K  plan-1  H6   0.020
 T9K  plan-1  H7   0.020
 T9K  plan-1  H8   0.020
 T9K  plan-1  H9   0.020
 T9K  plan-2  C03  0.020
 T9K  plan-2  C05  0.020
 T9K  plan-2  O02  0.020
 T9K  plan-2  O04  0.020

