# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 06:42:56 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2S)-pentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](O)CO
#
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
 1SP  1SP  '(2S)-pentane-1,2-diol    '  ligand  19  7  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1SP
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
 1SP  C3    C  CH2   0  -0.452  -0.7979   0.4617   0.2178
 1SP  O2    O  OH1   0  -0.665   0.6715  -1.4832   0.0908
 1SP  C4    C  CH2   0  -0.417  -2.0121  -0.2386  -0.3792
 1SP  C1    C  CH2   0  -0.153   1.6922   0.7128   0.2879
 1SP  O1    O  OH1   0  -0.671   2.9027   0.2182  -0.2348
 1SP  C5    C  CH3   0  -0.662  -3.3240   0.3769   0.0866
 1SP  C2    C  CH1   0   0.001   0.5354  -0.1166  -0.2442
 1SP  HA    H  HCH1  0   0.218   0.5672  -0.0826  -1.3393
 1SP  H31C  H  HCH2  0   0.221  -0.8302   1.5237  -0.0465
 1SP  H32C  H  HCH2  0   0.216  -0.8517   0.4238   1.3133
 1SP  H11C  H  HCH2  0   0.186   1.6809   0.6797   1.3881
 1SP  H12C  H  HCH2  0   0.196   1.5266   1.7601   0.0040
 1SP  H41C  H  HCH2  0   0.213  -1.9531  -0.1917  -1.4710
 1SP  H42C  H  HCH2  0   0.217  -1.9921  -1.2990  -0.1184
 1SP  H51C  H  HCH3  0   0.216  -3.4234   0.3198   1.1723
 1SP  H52C  H  HCH3  0   0.216  -3.3900   1.4300  -0.1930
 1SP  H53C  H  HCH3  0   0.227  -4.1822  -0.1351  -0.3501
 1SP  H1    H  HOH1  0   0.453   3.6142   0.7830   0.0783
 1SP  H2    H  HOH1  0   0.439   0.5886  -1.5676   1.0472

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
 1SP  O2  C2    single  1.414  0.020  1.414
 1SP  C2  C3    single  1.525  0.020  1.525
 1SP  C2  C1    single  1.520  0.020  1.520
 1SP  C3  C4    single  1.523  0.020  1.523
 1SP  C4  C5    single  1.522  0.020  1.522
 1SP  C1  O1    single  1.408  0.020  1.408
 1SP  O2  H2    single  0.850  0.020  0.980
 1SP  C2  HA    single  0.970  0.020  1.090
 1SP  C3  H31C  single  0.970  0.020  1.090
 1SP  C3  H32C  single  0.970  0.020  1.090
 1SP  C1  H11C  single  0.970  0.020  1.090
 1SP  C1  H12C  single  0.970  0.020  1.090
 1SP  C4  H41C  single  0.970  0.020  1.090
 1SP  C4  H42C  single  0.970  0.020  1.090
 1SP  C5  H51C  single  0.970  0.020  1.090
 1SP  C5  H52C  single  0.970  0.020  1.090
 1SP  C5  H53C  single  0.970  0.020  1.090
 1SP  O1  H1    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
 1SP  H32C  C3  H31C  105.84  3.000
 1SP  H32C  C3  C2    109.40  3.000
 1SP  H31C  C3  C2    108.69  3.000
 1SP  H32C  C3  C4    109.65  3.000
 1SP  H31C  C3  C4    109.13  3.000
 1SP  C2    C3  C4    113.82  3.000
 1SP  H2    O2  C2    108.16  3.000
 1SP  H42C  C4  H41C  106.18  3.000
 1SP  H42C  C4  C5    109.59  3.000
 1SP  H41C  C4  C5    109.53  3.000
 1SP  H42C  C4  C3    109.76  3.000
 1SP  H41C  C4  C3    109.17  3.000
 1SP  C5    C4  C3    112.41  3.000
 1SP  H12C  C1  H11C  106.59  3.000
 1SP  H12C  C1  C2    108.38  3.000
 1SP  H11C  C1  C2    109.01  3.000
 1SP  H12C  C1  O1    111.64  3.000
 1SP  H11C  C1  O1    111.67  3.000
 1SP  C2    C1  O1    109.43  3.000
 1SP  H1    O1  C1    108.00  3.000
 1SP  H53C  C5  H52C  107.63  3.000
 1SP  H53C  C5  H51C  107.58  3.000
 1SP  H52C  C5  H51C  107.44  3.000
 1SP  H53C  C5  C4    111.47  3.000
 1SP  H52C  C5  C4    111.33  3.000
 1SP  H51C  C5  C4    111.20  3.000
 1SP  HA    C2  C1    108.11  3.000
 1SP  HA    C2  O2    105.30  3.000
 1SP  C1    C2  O2    111.80  3.000
 1SP  HA    C2  C3    108.44  3.000
 1SP  C1    C2  C3    110.64  3.000
 1SP  O2    C2  C3    112.27  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
 1SP  Var_01  C2    C3  C4  C5  -179.14  30.0  1
 1SP  Var_02  H51C  C5  C4  C3   -60.00  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
 1SP  chir_01  C2  O2  C3  C1  negativ

