# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 19:37:39 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (2R,4S)-2,4,7-trihydroxyheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC[C@H](O)C[C@@H](O)C(O)=O
#
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
 1N5  1N5  '(2R,4S)-2,4,7-trihydroxyheptanoic acid'  ligand  25  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1N5
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
 1N5  C1   C  C      0   0.392   3.2634   0.2493  -0.3826
 1N5  C2   C  CH1    0  -0.075   1.9959  -0.2892   0.3159
 1N5  C3   C  CH2    0  -0.474   0.7389   0.2963  -0.3206
 1N5  O4   O  OH1    0  -0.671  -0.6144   0.0704   1.6930
 1N5  C4   C  CH1    0   0.047  -0.5629  -0.1971   0.3027
 1N5  C5   C  CH2    0  -0.451  -1.7717   0.3779  -0.4303
 1N5  C6   C  CH2    0  -0.452  -3.1074  -0.1406   0.0857
 1N5  O2   O  OH1    0  -0.703   1.9918  -1.6958   0.2553
 1N5  O7   O  OH1    0  -0.676  -5.4787  -0.0922  -0.1872
 1N5  O1A  O  OC    -1  -0.597   3.4498   1.4758  -0.3804
 1N5  O1B  O  O      0  -0.611   3.9940  -0.6301  -0.8962
 1N5  H2   H  HCH1   0   0.196   2.0337   0.0336   1.3658
 1N5  H3   H  HCH2   0   0.219   0.7825   1.3882  -0.2511
 1N5  H3A  H  HCH2   0   0.219   0.7255   0.0573  -1.3898
 1N5  H7   H  HCH2   0   0.186  -4.2463   1.5158  -0.6632
 1N5  H7A  H  HCH2   0   0.187  -4.1476   0.1487  -1.7681
 1N5  H4   H  HCH1   0   0.215  -0.6017  -1.2882   0.2198
 1N5  H5   H  HCH2   0   0.215  -1.7451   1.4729  -0.3667
 1N5  H5A  H  HCH2   0   0.221  -1.6721   0.1371  -1.4937
 1N5  H6   H  HCH2   0   0.222  -3.2282   0.1231   1.1395
 1N5  H6A  H  HCH2   0   0.217  -3.1220  -1.2341   0.0266
 1N5  HO2  H  HOH1   0   0.425   2.7901  -1.8773  -0.2756
 1N5  HO7  H  HOH1   0   0.451  -6.2014   0.2393  -0.7271
 1N5  C7   C  CH2    0  -0.138  -4.2699   0.4182  -0.7103
 1N5  HO4  H  HOH1   0   0.437  -0.5498   1.0241   1.8145

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
 1N5  O1B  C1   deloc   1.253  0.020  1.253
 1N5  C1   C2   single  1.544  0.020  1.544
 1N5  C1   O1A  deloc   1.241  0.020  1.241
 1N5  C3   C2   single  1.526  0.020  1.526
 1N5  C2   O2   single  1.408  0.020  1.408
 1N5  C2   H2   single  0.970  0.020  1.090
 1N5  C3   C4   single  1.525  0.020  1.525
 1N5  C3   H3   single  0.970  0.020  1.090
 1N5  C3   H3A  single  0.970  0.020  1.090
 1N5  C4   O4   single  1.417  0.020  1.417
 1N5  O4   HO4  single  0.850  0.020  0.980
 1N5  C7   O7   single  1.413  0.020  1.413
 1N5  C7   C6   single  1.516  0.020  1.516
 1N5  C7   H7   single  0.970  0.020  1.090
 1N5  C7   H7A  single  0.970  0.020  1.090
 1N5  C5   C4   single  1.526  0.020  1.526
 1N5  C4   H4   single  0.970  0.020  1.090
 1N5  C5   C6   single  1.523  0.020  1.523
 1N5  C5   H5   single  0.970  0.020  1.090
 1N5  C5   H5A  single  0.970  0.020  1.090
 1N5  C6   H6   single  0.970  0.020  1.090
 1N5  C6   H6A  single  0.970  0.020  1.090
 1N5  O2   HO2  single  0.850  0.020  0.980
 1N5  O7   HO7  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
 1N5  O1B  C1  O1A  127.36  3.000
 1N5  O1A  C1  C2   117.86  3.000
 1N5  O1B  C1  C2   114.78  3.000
 1N5  H2   C2  O2   109.55  3.000
 1N5  H2   C2  C3   108.31  3.000
 1N5  O2   C2  C3   111.29  3.000
 1N5  H2   C2  C1   107.54  3.000
 1N5  O2   C2  C1   109.35  3.000
 1N5  C3   C2  C1   110.72  3.000
 1N5  H3A  C3  H3   106.25  3.000
 1N5  H3A  C3  C4   108.53  3.000
 1N5  H3   C3  C4   109.31  3.000
 1N5  H3A  C3  C2   109.48  3.000
 1N5  H3   C3  C2   108.87  3.000
 1N5  C4   C3  C2   114.11  3.000
 1N5  HO4  O4  C4   107.95  3.000
 1N5  H4   C4  C5   108.12  3.000
 1N5  H4   C4  O4   105.14  3.000
 1N5  C5   C4  O4   111.80  3.000
 1N5  H4   C4  C3   108.76  3.000
 1N5  C5   C4  C3   110.97  3.000
 1N5  O4   C4  C3   111.77  3.000
 1N5  H5A  C5  H5   105.88  3.000
 1N5  H5A  C5  C6   109.52  3.000
 1N5  H5   C5  C6   109.96  3.000
 1N5  H5A  C5  C4   108.16  3.000
 1N5  H5   C5  C4   109.20  3.000
 1N5  C6   C5  C4   113.81  3.000
 1N5  H6A  C6  H6   106.95  3.000
 1N5  H6A  C6  C5   109.47  3.000
 1N5  H6   C6  C5   109.97  3.000
 1N5  H6A  C6  C7   109.24  3.000
 1N5  H6   C6  C7   109.43  3.000
 1N5  C5   C6  C7   111.66  3.000
 1N5  HO2  O2  C2   101.94  3.000
 1N5  HO7  O7  C7   108.11  3.000
 1N5  H7A  C7  H7   106.50  3.000
 1N5  H7A  C7  O7   111.30  3.000
 1N5  H7   C7  O7   111.31  3.000
 1N5  H7A  C7  C6   109.26  3.000
 1N5  H7   C7  C6   109.23  3.000
 1N5  O7   C7  C6   109.18  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
 1N5  Var_01  C4  C5  C6  C7  -177.75  30.0  1
 1N5  Var_02  O7  C7  C6  C5  -179.86  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
 1N5  chir_01  C2  C1  C3  O2  negativ
 1N5  chir_02  C4  O4  C3  C5  positiv

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
 1N5  plan-1  C1   0.020
 1N5  plan-1  C2   0.020
 1N5  plan-1  O1A  0.020
 1N5  plan-1  O1B  0.020

