# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:22:06 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1Cc2cc(F)cc(C(N)=O)c2O1
#
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
 2UR  2UR  (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide  ligand  24  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2UR
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
 2UR  O    O  O     0  -0.475   0.2734  -2.7170   1.3598
 2UR  C8   C  C     0   0.490   0.9073  -2.1269   0.4979
 2UR  N    N  NH2   0  -0.804   1.8131  -2.7280  -0.2898
 2UR  C7   C  CR6   0  -0.152   0.7345  -0.6630   0.2683
 2UR  C6   C  CR16  0  -0.451   1.8191   0.1535  -0.0765
 2UR  C5   C  CR6   0   0.527   1.6395   1.5076  -0.2486
 2UR  F    F  F     0  -0.321   2.7037   2.2667  -0.5687
 2UR  C4   C  CR16  0  -0.470   0.4050   2.1228  -0.0966
 2UR  C9   C  CR56  0   0.418  -0.5009  -0.0478   0.4314
 2UR  C3   C  CR56  0  -0.012  -0.6632   1.3218   0.2426
 2UR  C2   C  CH2   0  -0.506  -2.0972   1.6570   0.5094
 2UR  O1   O  O     0  -0.478  -1.6487  -0.6690   0.7461
 2UR  C1   C  CR15  0  -0.004  -2.7424   0.2600   0.5318
 2UR  C    C  CH3   0  -0.675  -3.4436  -0.0887  -0.7639
 2UR  H1   H  HNH2  0   0.406   1.9871  -3.7150  -0.1891
 2UR  H2   H  HNH2  0   0.413   2.2189  -2.2700  -1.0873
 2UR  H3   H  HCR6  0   0.285   2.8109  -0.2662  -0.1896
 2UR  H4   H  HCR6  0   0.283   0.2950   3.1908  -0.2362
 2UR  H5   H  HCH2  0   0.279  -2.2034   2.1712   1.4676
 2UR  H6   H  HCH2  0   0.273  -2.5399   2.2973  -0.2546
 2UR  H7   H  HCR5  0   0.256  -3.4237   0.1396   1.3742
 2UR  H8   H  HCH3  0   0.232  -2.7737   0.0169  -1.6197
 2UR  H9   H  HCH3  0   0.245  -3.8249  -1.1097  -0.7469
 2UR  H10  H  HCH3  0   0.240  -4.2889   0.5829  -0.9151

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
 2UR  O   C8   double    1.222  0.020  1.222
 2UR  F   C5   single    1.346  0.020  1.346
 2UR  C6  C5   aromatic  1.377  0.020  1.377
 2UR  C6  C7   aromatic  1.401  0.020  1.401
 2UR  C5  C4   aromatic  1.388  0.020  1.388
 2UR  C8  C7   single    1.492  0.020  1.492
 2UR  C8  N    single    1.342  0.020  1.342
 2UR  C7  C9   aromatic  1.390  0.020  1.390
 2UR  C4  C3   aromatic  1.378  0.020  1.378
 2UR  C9  C3   aromatic  1.392  0.020  1.392
 2UR  C9  O1   single    1.343  0.020  1.343
 2UR  C3  C2   single    1.497  0.020  1.497
 2UR  O1  C1   single    1.451  0.020  1.451
 2UR  C2  C1   single    1.539  0.020  1.539
 2UR  C1  C    single    1.514  0.020  1.514
 2UR  N   H1   single    0.860  0.020  1.020
 2UR  N   H2   single    0.860  0.020  1.020
 2UR  C6  H3   single    0.930  0.020  1.080
 2UR  C4  H4   single    0.930  0.020  1.080
 2UR  C2  H5   single    0.970  0.020  1.090
 2UR  C2  H6   single    0.970  0.020  1.090
 2UR  C1  H7   single    0.970  0.020  1.090
 2UR  C   H8   single    0.970  0.020  1.090
 2UR  C   H9   single    0.970  0.020  1.090
 2UR  C   H10  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
 2UR  C7   C8  N   115.30  3.000
 2UR  N    C8  O   123.21  3.000
 2UR  C7   C8  O   121.49  3.000
 2UR  H2   N   H1  117.13  3.000
 2UR  H2   N   C8  122.27  3.000
 2UR  H1   N   C8  119.78  3.000
 2UR  C9   C7  C6  117.33  3.000
 2UR  C9   C7  C8  121.29  3.000
 2UR  C6   C7  C8  121.34  3.000
 2UR  H3   C6  C5  119.18  3.000
 2UR  H3   C6  C7  120.60  3.000
 2UR  C5   C6  C7  120.21  3.000
 2UR  C4   C5  F   118.65  3.000
 2UR  C4   C5  C6  122.57  3.000
 2UR  F    C5  C6  118.77  3.000
 2UR  H4   C4  C3  121.78  3.000
 2UR  H4   C4  C5  120.90  3.000
 2UR  C3   C4  C5  117.32  3.000
 2UR  O1   C9  C3  112.79  3.000
 2UR  O1   C9  C7  125.64  3.000
 2UR  C3   C9  C7  121.56  3.000
 2UR  C2   C3  C9  107.93  3.000
 2UR  C2   C3  C4  131.04  3.000
 2UR  C9   C3  C4  121.00  3.000
 2UR  H6   C2  H5  107.38  3.000
 2UR  H6   C2  C1  111.90  3.000
 2UR  H5   C2  C1  111.94  3.000
 2UR  H6   C2  C3  113.29  3.000
 2UR  H5   C2  C3  110.78  3.000
 2UR  C1   C2  C3  101.59  3.000
 2UR  C1   O1  C9  108.27  3.000
 2UR  H7   C1  C   110.27  3.000
 2UR  H7   C1  O1  106.63  3.000
 2UR  C    C1  O1  109.15  3.000
 2UR  H7   C1  C2  111.94  3.000
 2UR  C    C1  C2  113.00  3.000
 2UR  O1   C1  C2  105.51  3.000
 2UR  H10  C   H9  107.93  3.000
 2UR  H10  C   H8  107.90  3.000
 2UR  H9   C   H8  108.51  3.000
 2UR  H10  C   C1  109.63  3.000
 2UR  H9   C   C1  111.37  3.000
 2UR  H8   C   C1  111.37  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
 2UR  CONST_01  C4  C5  C6  C7    0.00   0.0  0
 2UR  CONST_02  C4  C3  C9  C7    0.00   0.0  0
 2UR  CONST_03  C3  C4  C5  C6    0.00   0.0  0
 2UR  CONST_04  C3  C9  C7  C6    0.00   0.0  0
 2UR  CONST_05  C9  C7  C6  C5    0.00   0.0  0
 2UR  CONST_06  C9  C3  C4  C5    0.00   0.0  0
 2UR  CONST_07  C5  C6  C7  C8  180.00   0.0  0
 2UR  CONST_08  C3  C9  C7  C8  180.00   0.0  0
 2UR  CONST_09  O1  C9  C7  C8    0.00   0.0  0
 2UR  CONST_10  F   C5  C6  C7  180.00   0.0  0
 2UR  CONST_11  C3  C4  C5  F   180.00   0.0  0
 2UR  CONST_12  H4  C4  C5  C6  180.00   0.0  0
 2UR  CONST_13  H3  C6  C5  C4  180.00   0.0  0
 2UR  CONST_14  H1  N   C8  C7  180.00   0.0  0
 2UR  CONST_15  H2  N   C8  C7    0.00   0.0  0
 2UR  Var_01    C1  C2  C3  C4  168.72  30.0  1
 2UR  Var_02    C6  C7  C8  O   143.47  30.0  2

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
 2UR  chir_01  C1  O1  C2  C  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
 2UR  plan-1  O   0.020
 2UR  plan-1  C8  0.020
 2UR  plan-1  N   0.020
 2UR  plan-1  C7  0.020
 2UR  plan-1  H1  0.020
 2UR  plan-1  H2  0.020
 2UR  plan-2  C8  0.020
 2UR  plan-2  C7  0.020
 2UR  plan-2  C6  0.020
 2UR  plan-2  C5  0.020
 2UR  plan-2  F   0.020
 2UR  plan-2  C4  0.020
 2UR  plan-2  C9  0.020
 2UR  plan-2  C3  0.020
 2UR  plan-2  C2  0.020
 2UR  plan-2  O1  0.020
 2UR  plan-2  H3  0.020
 2UR  plan-2  H4  0.020

