# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:25:15 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: (2~{S})-~{N}-[(4-methoxyphenyl)methyl]oxolane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)[C@@H]2CCCO2)cc1
#
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
 T9B  T9B  "(2S)-N-(4-Methoxybenzyl)tetrahydrofuran-2-carboxamide"
  ligand  34  17  .  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_T9B
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
 T9B  C13  C  CH1   0  -0.064   0.3290   -5.1592  5.9169
 T9B  C15  C  CH2   0  -0.503  -1.7830   -6.1560  5.5577
 T9B  C01  C  CH3   0  -0.435  -0.8886  -13.6977  8.7214
 T9B  C03  C  CR6   0   0.370  -0.3470  -11.3911  8.6620
 T9B  C04  C  CR16  0  -0.326  -0.6871  -10.0849  9.0287
 T9B  C05  C  CR16  0  -0.277   0.1247   -9.0274  8.6702
 T9B  C06  C  CR6   0   0.103   1.2956   -9.2303  7.9363
 T9B  C07  C  CR16  0  -0.294   1.6191  -10.5285  7.5767
 T9B  C08  C  CR16  0  -0.369   0.8159  -11.6091  7.9313
 T9B  C09  C  CH2   0  -0.386   2.1741   -8.0697  7.5466
 T9B  C11  C  C     0   0.510   1.0025   -5.9711  7.0221
 T9B  C14  C  CH2   0  -0.497  -1.1528   -4.9396  6.2247
 T9B  C16  C  CH2   0  -0.158  -0.9241   -6.2995  4.3114
 T9B  N10  N  NH1   0  -0.610   1.5174   -7.1471  6.6477
 T9B  O12  O  O     0  -0.503   1.0484   -5.5259  8.1617
 T9B  O17  O  O2    0  -0.505   0.3718   -5.8104  4.6638
 T9B  H1   H  HCH1  0   0.272   0.8726   -4.2108  5.8480
 T9B  H2   H  HCH2  0   0.257  -2.8366   -6.0191  5.3180
 T9B  H3   H  HCH2  0   0.242  -1.6977   -7.0369  6.1988
 T9B  H4   H  HCH3  0   0.257  -1.6893  -14.3106  9.1281
 T9B  H5   H  HCH3  0   0.226  -0.8459  -13.8496  7.6394
 T9B  H6   H  HCH3  0   0.227   0.0592  -14.0228  9.1591
 T9B  H7   H  HCR6  0   0.258  -1.5897   -9.9112  9.6017
 T9B  H8   H  HCR6  0   0.250  -0.1545   -8.0255  8.9745
 T9B  H9   H  HCR6  0   0.253   2.5198  -10.7174  7.0041
 T9B  H10  H  HCR6  0   0.275   1.1151  -12.6029  7.6270
 T9B  H11  H  HCH2  0   0.267   3.0802   -8.4379  7.0626
 T9B  H12  H  HCH2  0   0.260   2.4892   -7.5140  8.4295
 T9B  H13  H  HCH2  0   0.252  -1.4969   -4.0192  5.7492
 T9B  H14  H  HCH2  0   0.260  -1.3583   -4.8618  7.2904
 T9B  H15  H  HCH2  0   0.217  -1.3247   -5.6999  3.4878
 T9B  H16  H  HCH2  0   0.231  -0.8360   -7.3316  3.9670
 T9B  H17  H  HNH1  0   0.404   1.4141   -7.4185  5.6826
 T9B  O02  O  O2    0  -0.467  -1.1950  -12.3602  9.0565

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
 T9B  C16  O17  single    1.429  0.020  1.429
 T9B  C16  C15  single    1.520  0.020  1.520
 T9B  O17  C13  single    1.413  0.020  1.413
 T9B  C15  C14  single    1.524  0.020  1.524
 T9B  C13  C14  single    1.529  0.020  1.529
 T9B  C13  C11  single    1.528  0.020  1.528
 T9B  N10  C11  single    1.337  0.020  1.337
 T9B  N10  C09  single    1.446  0.020  1.446
 T9B  C11  O12  double    1.224  0.020  1.224
 T9B  C09  C06  single    1.507  0.020  1.507
 T9B  C07  C06  aromatic  1.385  0.020  1.385
 T9B  C07  C08  aromatic  1.392  0.020  1.392
 T9B  C06  C05  aromatic  1.397  0.020  1.397
 T9B  C08  C03  aromatic  1.391  0.020  1.391
 T9B  C05  C04  aromatic  1.381  0.020  1.381
 T9B  C03  C04  aromatic  1.399  0.020  1.399
 T9B  C03  O02  single    1.347  0.020  1.347
 T9B  O02  C01  single    1.413  0.020  1.413
 T9B  C13  H1   single    0.970  0.020  1.090
 T9B  C15  H2   single    0.970  0.020  1.090
 T9B  C15  H3   single    0.970  0.020  1.090
 T9B  C01  H4   single    0.970  0.020  1.090
 T9B  C01  H5   single    0.970  0.020  1.090
 T9B  C01  H6   single    0.970  0.020  1.090
 T9B  C04  H7   single    0.930  0.020  1.080
 T9B  C05  H8   single    0.930  0.020  1.080
 T9B  C07  H9   single    0.930  0.020  1.080
 T9B  C08  H10  single    0.930  0.020  1.080
 T9B  C09  H11  single    0.970  0.020  1.090
 T9B  C09  H12  single    0.970  0.020  1.090
 T9B  C14  H13  single    0.970  0.020  1.090
 T9B  C14  H14  single    0.970  0.020  1.090
 T9B  C16  H15  single    0.970  0.020  1.090
 T9B  C16  H16  single    0.970  0.020  1.090
 T9B  N10  H17  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
 T9B  H1   C13  O17  109.17  3.000
 T9B  H1   C13  C14  111.66  3.000
 T9B  O17  C13  C14  105.91  3.000
 T9B  H1   C13  C11  106.67  3.000
 T9B  C14  C13  C11  110.97  3.000
 T9B  O17  C13  C11  112.54  3.000
 T9B  H3   C15  H2   107.82  3.000
 T9B  H3   C15  C16  111.14  3.000
 T9B  H2   C15  C16  112.20  3.000
 T9B  H3   C15  C14  110.76  3.000
 T9B  H2   C15  C14  113.33  3.000
 T9B  C16  C15  C14  101.56  3.000
 T9B  H6   C01  H5   108.73  3.000
 T9B  H6   C01  H4   108.72  3.000
 T9B  H5   C01  H4   108.70  3.000
 T9B  H6   C01  O02  112.00  3.000
 T9B  H5   C01  O02  112.01  3.000
 T9B  H4   C01  O02  106.57  3.000
 T9B  O02  C03  C08  124.58  3.000
 T9B  O02  C03  C04  116.24  3.000
 T9B  C08  C03  C04  119.18  3.000
 T9B  H7   C04  C05  120.30  3.000
 T9B  H7   C04  C03  119.41  3.000
 T9B  C05  C04  C03  120.28  3.000
 T9B  H8   C05  C06  119.86  3.000
 T9B  H8   C05  C04  118.93  3.000
 T9B  C06  C05  C04  121.21  3.000
 T9B  C09  C06  C07  121.23  3.000
 T9B  C07  C06  C05  117.92  3.000
 T9B  C09  C06  C05  120.85  3.000
 T9B  H9   C07  C08  118.60  3.000
 T9B  H9   C07  C06  119.64  3.000
 T9B  C08  C07  C06  121.77  3.000
 T9B  H10  C08  C07  118.81  3.000
 T9B  H10  C08  C03  121.55  3.000
 T9B  C07  C08  C03  119.64  3.000
 T9B  H12  C09  H11  106.94  3.000
 T9B  H12  C09  N10  108.03  3.000
 T9B  H11  C09  N10  108.47  3.000
 T9B  H12  C09  C06  110.59  3.000
 T9B  H11  C09  C06  109.81  3.000
 T9B  N10  C09  C06  112.80  3.000
 T9B  O12  C11  N10  124.47  3.000
 T9B  O12  C11  C13  119.78  3.000
 T9B  N10  C11  C13  115.76  3.000
 T9B  H14  C14  H13  107.87  3.000
 T9B  H14  C14  C15  114.05  3.000
 T9B  H13  C14  C15  110.61  3.000
 T9B  H14  C14  C13  112.98  3.000
 T9B  H13  C14  C13  109.81  3.000
 T9B  C15  C14  C13  101.42  3.000
 T9B  H16  C16  H15  108.06  3.000
 T9B  H16  C16  O17  109.16  3.000
 T9B  H15  C16  O17  109.26  3.000
 T9B  H16  C16  C15  113.17  3.000
 T9B  H15  C16  C15  110.99  3.000
 T9B  O17  C16  C15  106.13  3.000
 T9B  H17  N10  C11  117.74  3.000
 T9B  H17  N10  C09  118.04  3.000
 T9B  C11  N10  C09  124.19  3.000
 T9B  C16  O17  C13  110.42  3.000
 T9B  C03  O02  C01  118.38  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
 T9B  CONST_01  C06  C07  C08  C03     0.00   0.0  0
 T9B  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 T9B  CONST_03  C07  C06  C05  C04     0.00   0.0  0
 T9B  CONST_04  C07  C08  C03  C04     0.00   0.0  0
 T9B  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 T9B  CONST_06  C08  C03  C04  C05     0.00   0.0  0
 T9B  CONST_07  C09  C06  C05  C04   180.00   0.0  0
 T9B  CONST_08  O02  C03  C04  C05   180.00   0.0  0
 T9B  CONST_09  O02  C03  C08  C07   180.00   0.0  0
 T9B  CONST_10  C09  C06  C07  C08   180.00   0.0  0
 T9B  CONST_11  H9   C07  C08  C03   180.00   0.0  0
 T9B  CONST_12  H8   C05  C04  C03   180.00   0.0  0
 T9B  CONST_13  H10  C08  C03  C04   180.00   0.0  0
 T9B  CONST_14  H9   C07  C06  C05   180.00   0.0  0
 T9B  CONST_15  H10  C08  C07  C06   180.00   0.0  0
 T9B  CONST_16  H7   C04  C05  C06   180.00   0.0  0
 T9B  CONST_17  H8   C05  C06  C07   180.00   0.0  0
 T9B  CONST_18  H7   C04  C03  C08   180.00   0.0  0
 T9B  CONST_19  C09  N10  C11  C13   180.00   0.0  0
 T9B  CONST_20  H17  N10  C11  C13     0.00   0.0  0
 T9B  CONST_21  O12  C11  N10  C09     0.00   0.0  0
 T9B  CONST_22  H17  N10  C11  O12   180.00   0.0  0
 T9B  Var_01    C15  C16  O17  C13   -10.71  30.0  1
 T9B  Var_02    C16  C15  C14  C13   -37.13  30.0  1
 T9B  Var_03    O17  C16  C15  C14    30.39  30.0  1
 T9B  Var_04    H15  C16  O17  C13   109.04  30.0  1
 T9B  Var_05    H16  C16  O17  C13  -132.99  30.0  1
 T9B  Var_06    H2   C15  C14  C13  -157.68  30.0  1
 T9B  Var_07    H3   C15  C14  C13    80.99  30.0  1
 T9B  Var_08    H15  C16  C15  C14   -88.22  30.0  1
 T9B  Var_09    H16  C16  C15  C14   150.08  30.0  1
 T9B  Var_10    H13  C14  C15  C16    79.32  30.0  1
 T9B  Var_11    H14  C14  C15  C16  -158.89  30.0  1
 T9B  Var_12    H2   C15  C16  O17   151.73  30.0  1
 T9B  Var_13    H3   C15  C16  O17   -87.45  30.0  1
 T9B  Var_14    C08  C03  O02  C01     0.57  30.0  2
 T9B  Var_15    C04  C03  O02  C01  -179.41  30.0  2
 T9B  Var_16    N10  C09  C06  C05   -64.11  30.0  3
 T9B  Var_17    N10  C09  C06  C07   115.69  30.0  3
 T9B  Var_18    H11  C09  C06  C05   174.78  30.0  3
 T9B  Var_19    H12  C09  C06  C05    56.99  30.0  3
 T9B  Var_20    H11  C09  C06  C07    -5.42  30.0  3
 T9B  Var_21    H12  C09  C06  C07  -123.21  30.0  3
 T9B  Var_22    C11  N10  C09  C06   102.32  30.0  2
 T9B  Var_23    H4   C01  O02  C03  -179.99  30.0  3
 T9B  Var_24    H5   C01  O02  C03   -61.23  30.0  3
 T9B  Var_25    H6   C01  O02  C03    61.23  30.0  3
 T9B  Var_26    H17  N10  C09  C06   -75.66  30.0  2
 T9B  Var_27    H11  C09  N10  C11  -135.81  30.0  3
 T9B  Var_28    H12  C09  N10  C11   -20.23  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
 T9B  chir_01  C13  O17  C14  C11  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
 T9B  plan-1  C03  0.020
 T9B  plan-1  C04  0.020
 T9B  plan-1  C05  0.020
 T9B  plan-1  C06  0.020
 T9B  plan-1  C07  0.020
 T9B  plan-1  C08  0.020
 T9B  plan-1  C09  0.020
 T9B  plan-1  H7   0.020
 T9B  plan-1  H8   0.020
 T9B  plan-1  H9   0.020
 T9B  plan-1  H10  0.020
 T9B  plan-1  O02  0.020
 T9B  plan-2  C13  0.020
 T9B  plan-2  C09  0.020
 T9B  plan-2  C11  0.020
 T9B  plan-2  N10  0.020
 T9B  plan-2  O12  0.020
 T9B  plan-2  H17  0.020

