# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:45:53 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2,2-bis(hydroxymethyl)propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(CO)(CO)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
 3SY  3SY  2,2-bis(hydroxymethyl)propane-1,3-diol  ligand  21  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3SY
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
 3SY  O7   O  OH1   0  -0.675  -2.3837   0.0058   0.1593
 3SY  C3   C  CH2   0  -0.124  -1.2068   0.0106   0.9351
 3SY  C1   C  CT    0  -0.248   0.0221   0.0133   0.0207
 3SY  C2   C  CH2   0  -0.124   1.2469   0.0097   0.9406
 3SY  O6   O  OH1   0  -0.674   2.4274   0.0184   0.1706
 3SY  C4   C  CH2   0  -0.124   0.0237  -1.2109  -0.8999
 3SY  O8   O  OH1   0  -0.673   0.0202  -2.3912  -0.1300
 3SY  C5   C  CH2   0  -0.124   0.0242   1.2438  -0.8917
 3SY  O9   O  OH1   0  -0.674   0.0291   2.4189  -0.1136
 3SY  H1   H  HOH1  0   0.454  -3.1345   0.0044   0.7589
 3SY  H2   H  HCH2  0   0.203  -1.1670   0.8916   1.5870
 3SY  H3   H  HCH2  0   0.203  -1.1615  -0.8684   1.5894
 3SY  H4   H  HCH2  0   0.203   1.1990   0.8842   1.6006
 3SY  H5   H  HCH2  0   0.204   1.2034  -0.8751   1.5872
 3SY  H6   H  HOH1  0   0.454   3.1752   0.0098   0.7738
 3SY  H7   H  HCH2  0   0.203  -0.8539  -1.1642  -1.5560
 3SY  H8   H  HCH2  0   0.203   0.9051  -1.1659  -1.5512
 3SY  H9   H  HOH1  0   0.454   0.0033  -3.1389  -0.7333
 3SY  H10  H  HCH2  0   0.204   0.9028   1.1997  -1.5469
 3SY  H11  H  HCH2  0   0.203  -0.8568   1.2047  -1.5439
 3SY  H12  H  HOH1  0   0.454   0.0298   3.1710  -0.7115

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
 3SY  O6  C2   single  1.409  0.020  1.409
 3SY  C5  O9   single  1.409  0.020  1.409
 3SY  C5  C1   single  1.532  0.020  1.532
 3SY  C2  C1   single  1.532  0.020  1.532
 3SY  C1  C3   single  1.532  0.020  1.532
 3SY  C1  C4   single  1.532  0.020  1.532
 3SY  C3  O7   single  1.410  0.020  1.410
 3SY  C4  O8   single  1.409  0.020  1.409
 3SY  O7  H1   single  0.850  0.020  0.980
 3SY  C3  H2   single  0.970  0.020  1.090
 3SY  C3  H3   single  0.970  0.020  1.090
 3SY  C2  H4   single  0.970  0.020  1.090
 3SY  C2  H5   single  0.970  0.020  1.090
 3SY  O6  H6   single  0.850  0.020  0.980
 3SY  C4  H7   single  0.970  0.020  1.090
 3SY  C4  H8   single  0.970  0.020  1.090
 3SY  O8  H9   single  0.850  0.020  0.980
 3SY  C5  H10  single  0.970  0.020  1.090
 3SY  C5  H11  single  0.970  0.020  1.090
 3SY  O9  H12  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
 3SY  H1   O7  C3   108.00  3.000
 3SY  H3   C3  H2   106.72  3.000
 3SY  H3   C3  C1   108.93  3.000
 3SY  H2   C3  C1   108.92  3.000
 3SY  H3   C3  O7   111.11  3.000
 3SY  H2   C3  O7   111.11  3.000
 3SY  C1   C3  O7   109.96  3.000
 3SY  C5   C1  C4   106.50  3.000
 3SY  C4   C1  C2   110.99  3.000
 3SY  C5   C1  C2   111.01  3.000
 3SY  C4   C1  C3   110.99  3.000
 3SY  C2   C1  C3   106.44  3.000
 3SY  C5   C1  C3   110.98  3.000
 3SY  H5   C2  H4   106.66  3.000
 3SY  H5   C2  O6   111.12  3.000
 3SY  H4   C2  O6   111.13  3.000
 3SY  H5   C2  C1   108.92  3.000
 3SY  H4   C2  C1   108.94  3.000
 3SY  O6   C2  C1   109.97  3.000
 3SY  H6   O6  C2   107.99  3.000
 3SY  H8   C4  H7   106.63  3.000
 3SY  H8   C4  O8   111.15  3.000
 3SY  H7   C4  O8   111.13  3.000
 3SY  H8   C4  C1   108.96  3.000
 3SY  H7   C4  C1   108.95  3.000
 3SY  O8   C4  C1   109.94  3.000
 3SY  H9   O8  C4   107.98  3.000
 3SY  H11  C5  H10  106.67  3.000
 3SY  H11  C5  O9   111.14  3.000
 3SY  H10  C5  O9   111.13  3.000
 3SY  H11  C5  C1   108.93  3.000
 3SY  H10  C5  C1   108.94  3.000
 3SY  O9   C5  C1   109.93  3.000
 3SY  H12  O9  C5   108.01  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
 3SY  Var_01  C5  C1  C3  O7    59.44  30.0  3
 3SY  Var_02  O9  C5  C1  C3    59.36  30.0  3
 3SY  Var_03  O6  C2  C1  C3  -179.72  30.0  3
 3SY  Var_04  O8  C4  C1  C3   -59.02  30.0  3

