# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 15:29:39 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-methoxy-~{N}-(phenylmethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC(=O)NCc1ccccc1
#
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
 T9Q  T9Q  "N-Benzyl-2-methoxyacetamide"
  ligand  26  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T9Q
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
 T9Q  C10  C  CR16  0  -0.238  -0.6547  -6.0850  6.5758
 T9Q  C13  C  CR16  0  -0.309  -0.1719  -4.7269  4.2105
 T9Q  C01  C  CH3   0  -0.411   4.4233  -6.8094  7.3108
 T9Q  C03  C  CH2   0  -0.283   5.3008  -4.7749  6.5396
 T9Q  C04  C  C     0   0.482   4.0904  -3.8769  6.3044
 T9Q  C07  C  CH2   0  -0.336   1.9310  -3.7038  5.1352
 T9Q  C08  C  CR6   0   0.093   0.7208  -4.5922  5.2678
 T9Q  C09  C  CR16  0  -0.289   0.4687  -5.2812  6.4526
 T9Q  C11  C  CR16  0  -0.266  -1.5435  -6.2120  5.5142
 T9Q  C12  C  CR16  0  -0.238  -1.3003  -5.5292  4.3317
 T9Q  N06  N  NH1   0  -0.615   3.1466  -4.3913  5.5037
 T9Q  O02  O  O2    0  -0.477   5.0890  -6.1299  6.2677
 T9Q  O05  O  O     0  -0.491   4.0481  -2.7588  6.7965
 T9Q  H1   H  HCR6  0   0.254  -0.8387  -6.6139  7.5022
 T9Q  H2   H  HCR6  0   0.251   0.0174  -4.2031  3.2808
 T9Q  H3   H  HCH3  0   0.240   4.3068  -7.8484  7.0069
 T9Q  H4   H  HCH3  0   0.218   5.0010  -6.7806  8.2409
 T9Q  H5   H  HCH3  0   0.215   3.4290  -6.3973  7.5137
 T9Q  H6   H  HCH2  0   0.238   5.6457  -4.6066  7.5671
 T9Q  H7   H  HCH2  0   0.273   6.0964  -4.4250  5.8747
 T9Q  H8   H  HCH2  0   0.259   2.0007  -3.3280  4.1107
 T9Q  H9   H  HCH2  0   0.265   1.8323  -2.8325  5.7831
 T9Q  H10  H  HCR6  0   0.253   1.1561  -5.1908  7.2858
 T9Q  H11  H  HCR6  0   0.254  -2.4186  -6.8417  5.6100
 T9Q  H12  H  HCR6  0   0.254  -1.9839  -5.6252  3.4978
 T9Q  H13  H  HNH1  0   0.403   3.3105  -5.3036  5.1052

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
 T9Q  C12  C13  aromatic  1.390  0.020  1.390
 T9Q  C12  C11  aromatic  1.387  0.020  1.387
 T9Q  C13  C08  aromatic  1.390  0.020  1.390
 T9Q  C11  C10  aromatic  1.390  0.020  1.390
 T9Q  C08  C07  single    1.507  0.020  1.507
 T9Q  C08  C09  aromatic  1.394  0.020  1.394
 T9Q  C07  N06  single    1.444  0.020  1.444
 T9Q  N06  C04  single    1.340  0.020  1.340
 T9Q  O02  C03  single    1.398  0.020  1.398
 T9Q  O02  C01  single    1.412  0.020  1.412
 T9Q  O05  C04  double    1.222  0.020  1.222
 T9Q  C04  C03  single    1.525  0.020  1.525
 T9Q  C10  C09  aromatic  1.387  0.020  1.387
 T9Q  C10  H1   single    0.930  0.020  1.080
 T9Q  C13  H2   single    0.930  0.020  1.080
 T9Q  C01  H3   single    0.970  0.020  1.090
 T9Q  C01  H4   single    0.970  0.020  1.090
 T9Q  C01  H5   single    0.970  0.020  1.090
 T9Q  C03  H6   single    0.970  0.020  1.090
 T9Q  C03  H7   single    0.970  0.020  1.090
 T9Q  C07  H8   single    0.970  0.020  1.090
 T9Q  C07  H9   single    0.970  0.020  1.090
 T9Q  C09  H10  single    0.930  0.020  1.080
 T9Q  C11  H11  single    0.930  0.020  1.080
 T9Q  C12  H12  single    0.930  0.020  1.080
 T9Q  N06  H13  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
 T9Q  H1   C10  C11  120.01  3.000
 T9Q  H1   C10  C09  119.79  3.000
 T9Q  C11  C10  C09  120.20  3.000
 T9Q  H2   C13  C12  119.71  3.000
 T9Q  H2   C13  C08  119.57  3.000
 T9Q  C12  C13  C08  120.73  3.000
 T9Q  H5   C01  H4   108.16  3.000
 T9Q  H5   C01  H3   108.27  3.000
 T9Q  H4   C01  H3   108.58  3.000
 T9Q  H5   C01  O02  112.57  3.000
 T9Q  H4   C01  O02  111.48  3.000
 T9Q  H3   C01  O02  107.67  3.000
 T9Q  H7   C03  H6   106.94  3.000
 T9Q  H7   C03  O02  107.57  3.000
 T9Q  H6   C03  O02  112.24  3.000
 T9Q  H7   C03  C04  107.16  3.000
 T9Q  H6   C03  C04  107.68  3.000
 T9Q  O02  C03  C04  114.86  3.000
 T9Q  O05  C04  N06  124.55  3.000
 T9Q  O05  C04  C03  120.26  3.000
 T9Q  N06  C04  C03  115.14  3.000
 T9Q  H9   C07  H8   106.73  3.000
 T9Q  H9   C07  N06  107.75  3.000
 T9Q  H8   C07  N06  110.42  3.000
 T9Q  H9   C07  C08  110.25  3.000
 T9Q  H8   C07  C08  109.65  3.000
 T9Q  N06  C07  C08  111.89  3.000
 T9Q  C09  C08  C07  120.76  3.000
 T9Q  C09  C08  C13  118.85  3.000
 T9Q  C07  C08  C13  120.38  3.000
 T9Q  H10  C09  C08  119.84  3.000
 T9Q  H10  C09  C10  119.59  3.000
 T9Q  C08  C09  C10  120.57  3.000
 T9Q  H11  C11  C12  120.24  3.000
 T9Q  H11  C11  C10  120.16  3.000
 T9Q  C12  C11  C10  119.60  3.000
 T9Q  H12  C12  C11  120.16  3.000
 T9Q  H12  C12  C13  119.78  3.000
 T9Q  C11  C12  C13  120.06  3.000
 T9Q  H13  N06  C07  117.80  3.000
 T9Q  H13  N06  C04  117.94  3.000
 T9Q  C07  N06  C04  124.22  3.000
 T9Q  C03  O02  C01  113.22  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
 T9Q  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 T9Q  CONST_02  C13  C08  C09  C10     0.00   0.0  0
 T9Q  CONST_03  C11  C12  C13  C08     0.00   0.0  0
 T9Q  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 T9Q  CONST_05  C12  C13  C08  C09     0.00   0.0  0
 T9Q  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 T9Q  CONST_07  C07  C08  C09  C10   180.00   0.0  0
 T9Q  CONST_08  C12  C13  C08  C07   180.00   0.0  0
 T9Q  CONST_09  H12  C12  C11  C10   180.00   0.0  0
 T9Q  CONST_10  H11  C11  C12  C13   180.00   0.0  0
 T9Q  CONST_11  H10  C09  C08  C13   180.00   0.0  0
 T9Q  CONST_12  H12  C12  C13  C08   180.00   0.0  0
 T9Q  CONST_13  H1   C10  C09  C08   180.00   0.0  0
 T9Q  CONST_14  H2   C13  C08  C09   180.00   0.0  0
 T9Q  CONST_15  H11  C11  C10  C09   180.00   0.0  0
 T9Q  CONST_16  H2   C13  C12  C11   180.00   0.0  0
 T9Q  CONST_17  H10  C09  C10  C11   180.00   0.0  0
 T9Q  CONST_18  H1   C10  C11  C12   180.00   0.0  0
 T9Q  CONST_19  C07  N06  C04  C03   180.00   0.0  0
 T9Q  CONST_20  O05  C04  N06  C07     0.00   0.0  0
 T9Q  CONST_21  H13  N06  C04  C03     0.00   0.0  0
 T9Q  CONST_22  H13  N06  C04  O05   180.00   0.0  0
 T9Q  Var_01    N06  C07  C08  C13  -128.63  30.0  2
 T9Q  Var_02    N06  C07  C08  C09    52.02  30.0  2
 T9Q  Var_03    H8   C07  C08  C13    -5.76  30.0  2
 T9Q  Var_04    H9   C07  C08  C13   111.47  30.0  2
 T9Q  Var_05    H8   C07  C08  C09   174.89  30.0  2
 T9Q  Var_06    H9   C07  C08  C09   -67.88  30.0  2
 T9Q  Var_07    C08  C07  N06  C04  -133.63  30.0  2
 T9Q  Var_08    H13  N06  C07  C08    48.71  30.0  3
 T9Q  Var_09    C04  C03  O02  C01   -80.16  30.0  3
 T9Q  Var_10    O02  C03  C04  N06   -19.67  30.0  3
 T9Q  Var_11    O05  C04  C03  O02   162.56  30.0  2
 T9Q  Var_12    H6   C03  O02  C01    43.28  30.0  3
 T9Q  Var_13    H7   C03  O02  C01   160.65  30.0  3
 T9Q  Var_14    H3   C01  O02  C03  -179.97  30.0  3
 T9Q  Var_15    H4   C01  O02  C03   -60.98  30.0  3
 T9Q  Var_16    H5   C01  O02  C03    60.77  30.0  3
 T9Q  Var_17    H8   C07  N06  C04   103.93  30.0  2
 T9Q  Var_18    H9   C07  N06  C04   -12.28  30.0  2
 T9Q  Var_19    H6   C03  C04  N06  -145.51  30.0  3
 T9Q  Var_20    H7   C03  C04  N06    99.75  30.0  3
 T9Q  Var_21    H6   C03  C04  O05    36.72  30.0  3
 T9Q  Var_22    H7   C03  C04  O05   -78.02  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
 T9Q  plan-1  C10  0.020
 T9Q  plan-1  C13  0.020
 T9Q  plan-1  C07  0.020
 T9Q  plan-1  C08  0.020
 T9Q  plan-1  C09  0.020
 T9Q  plan-1  C11  0.020
 T9Q  plan-1  C12  0.020
 T9Q  plan-1  H1   0.020
 T9Q  plan-1  H2   0.020
 T9Q  plan-1  H10  0.020
 T9Q  plan-1  H11  0.020
 T9Q  plan-1  H12  0.020
 T9Q  plan-2  C03  0.020
 T9Q  plan-2  C04  0.020
 T9Q  plan-2  C07  0.020
 T9Q  plan-2  N06  0.020
 T9Q  plan-2  O05  0.020
 T9Q  plan-2  H13  0.020

