# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:49:05 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: 4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1coc2CCCCc12
#
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
 NXT  NXT  '4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid'  ligand  22  12  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NXT
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
 NXT  C7   C  CH2   0  -0.501  -47.4241  13.8623  28.6094
 NXT  C6   C  CH2   0  -0.455  -47.6179  13.6586  30.1142
 NXT  C5   C  CH2   0  -0.451  -47.4233  14.9509  30.9054
 NXT  C4   C  CH2   0  -0.523  -48.4729  16.0023  30.5315
 NXT  C8   C  CR5   0   0.024  -48.1325  15.1036  28.1704
 NXT  C3   C  CR5   0   0.325  -48.5908  16.0185  29.0539
 NXT  O2   O  O     0  -0.408  -49.2094  17.0393  28.4060
 NXT  C2   C  CR15  0   0.032  -49.1464  16.7856  27.0969
 NXT  C1   C  CR5   0  -0.178  -48.4934  15.6125  26.8739
 NXT  C    C  C     0   0.456  -48.2562  15.0731  25.5370
 NXT  O1   O  O     0  -0.449  -48.6552  15.5890  24.5179
 NXT  O    O  OH1   0  -0.594  -47.5481  13.9508  25.5581
 NXT  H1   H  HCH2  0   0.246  -47.7944  12.9912  28.0667
 NXT  H2   H  HCH2  0   0.239  -46.3587  13.9378  28.3713
 NXT  H3   H  HCH2  0   0.227  -48.6265  13.2761  30.2988
 NXT  H4   H  HCH2  0   0.240  -46.9247  12.8944  30.4701
 NXT  H5   H  HCH2  0   0.244  -47.4779  14.7491  31.9761
 NXT  H6   H  HCH2  0   0.229  -46.4244  15.3507  30.7088
 NXT  H7   H  HCH2  0   0.261  -48.1868  16.9852  30.9138
 NXT  H8   H  HCH2  0   0.252  -49.4353  15.7538  30.9917
 NXT  H9   H  HCR5  0   0.298  -49.5931  17.5073  26.4319
 NXT  H10  H  HOH1  0   0.486  -47.4220  13.6238  24.6548

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
 NXT  O1  C    double    1.210  0.020  1.210
 NXT  O   C    single    1.327  0.020  1.327
 NXT  C   C1   single    1.461  0.020  1.461
 NXT  C1  C2   aromatic  1.361  0.020  1.361
 NXT  C1  C8   aromatic  1.439  0.020  1.439
 NXT  C2  O2   aromatic  1.335  0.020  1.335
 NXT  C8  C7   single    1.495  0.020  1.495
 NXT  C8  C3   aromatic  1.352  0.020  1.352
 NXT  O2  C3   aromatic  1.358  0.020  1.358
 NXT  C7  C6   single    1.531  0.020  1.531
 NXT  C3  C4   single    1.482  0.020  1.482
 NXT  C6  C5   single    1.528  0.020  1.528
 NXT  C4  C5   single    1.532  0.020  1.532
 NXT  C7  H1   single    0.970  0.020  1.090
 NXT  C7  H2   single    0.970  0.020  1.090
 NXT  C6  H3   single    0.970  0.020  1.090
 NXT  C6  H4   single    0.970  0.020  1.090
 NXT  C5  H5   single    0.970  0.020  1.090
 NXT  C5  H6   single    0.970  0.020  1.090
 NXT  C4  H7   single    0.970  0.020  1.090
 NXT  C4  H8   single    0.970  0.020  1.090
 NXT  C2  H9   single    0.930  0.020  1.080
 NXT  O   H10  single    0.850  0.020  0.980

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
 NXT  H2   C7  H1  106.10  3.000
 NXT  H2   C7  C8  109.89  3.000
 NXT  H1   C7  C8  110.85  3.000
 NXT  H2   C7  C6  110.26  3.000
 NXT  H1   C7  C6  109.86  3.000
 NXT  C8   C7  C6  109.82  3.000
 NXT  H4   C6  H3  106.59  3.000
 NXT  H4   C6  C5  110.03  3.000
 NXT  H3   C6  C5  109.00  3.000
 NXT  H4   C6  C7  109.47  3.000
 NXT  H3   C6  C7  109.21  3.000
 NXT  C5   C6  C7  112.36  3.000
 NXT  H6   C5  H5  106.84  3.000
 NXT  H6   C5  C4  109.33  3.000
 NXT  H5   C5  C4  109.40  3.000
 NXT  H6   C5  C6  109.42  3.000
 NXT  H5   C5  C6  110.21  3.000
 NXT  C4   C5  C6  111.52  3.000
 NXT  H8   C4  H7  106.69  3.000
 NXT  H8   C4  C3  110.58  3.000
 NXT  H7   C4  C3  111.08  3.000
 NXT  H8   C4  C5  110.10  3.000
 NXT  H7   C4  C5  110.64  3.000
 NXT  C3   C4  C5  107.77  3.000
 NXT  C1   C8  C3  105.33  3.000
 NXT  C3   C8  C7  122.05  3.000
 NXT  C1   C8  C7  132.62  3.000
 NXT  O2   C3  C8  110.57  3.000
 NXT  O2   C3  C4  121.33  3.000
 NXT  C8   C3  C4  128.10  3.000
 NXT  C2   O2  C3  107.67  3.000
 NXT  H9   C2  C1  132.42  3.000
 NXT  H9   C2  O2  117.26  3.000
 NXT  C1   C2  O2  110.32  3.000
 NXT  C    C1  C2  123.10  3.000
 NXT  C2   C1  C8  106.11  3.000
 NXT  C    C1  C8  130.78  3.000
 NXT  O    C   O1  123.36  3.000
 NXT  O    C   C1  112.60  3.000
 NXT  O1   C   C1  124.04  3.000
 NXT  H10  O   C   109.88  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
 NXT  CONST_01  O2   C2  C1  C8     0.00   0.0  0
 NXT  CONST_02  C2   O2  C3  C8     0.00   0.0  0
 NXT  CONST_03  C2   C1  C8  C3     0.00   0.0  0
 NXT  CONST_04  C1   C2  O2  C3     0.00   0.0  0
 NXT  CONST_05  C1   C8  C3  O2     0.00   0.0  0
 NXT  CONST_06  C    C1  C8  C7     0.00   0.0  0
 NXT  CONST_07  C    C1  C8  C3   180.00   0.0  0
 NXT  CONST_08  C    C1  C2  O2   180.00   0.0  0
 NXT  CONST_09  H9   C2  C1  C8   180.00   0.0  0
 NXT  CONST_10  H10  O   C   C1   180.00   0.0  0
 NXT  Var_01    C4   C5  C6  C7    63.49  30.0  1
 NXT  Var_02    C1   C8  C7  C6  -165.91  30.0  1
 NXT  Var_03    C3   C4  C5  C6   -44.75  30.0  1
 NXT  Var_04    C8   C7  C6  C5   -44.65  30.0  1
 NXT  Var_05    C8   C3  C4  C5    14.47  30.0  1
 NXT  Var_06    O1   C   C1  C8   177.58  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
 NXT  plan-1  C1   0.020
 NXT  plan-1  C    0.020
 NXT  plan-1  O1   0.020
 NXT  plan-1  O    0.020
 NXT  plan-1  H10  0.020
 NXT  plan-2  C7   0.020
 NXT  plan-2  C4   0.020
 NXT  plan-2  C8   0.020
 NXT  plan-2  C3   0.020
 NXT  plan-2  O2   0.020
 NXT  plan-2  C2   0.020
 NXT  plan-2  C1   0.020
 NXT  plan-2  C    0.020
 NXT  plan-2  H9   0.020

