# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:36:36 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: 2-(hydroxymethyl)cyclopent-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=CCCC1=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
 3RN  3RN  2-(hydroxymethyl)cyclopent-2-en-1-one  ligand  16  8  .  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_3RN
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
 3RN  C1   C  CR5   0   0.346  -0.9096   0.6874  -0.0094
 3RN  O1   O  O     0  -0.418  -1.0332   1.8948  -0.0113
 3RN  C2   C  CR5   0  -0.044   0.3654  -0.0448   0.0087
 3RN  O2   O  OH1   0  -0.667   2.7155  -0.2746   0.0380
 3RN  C3   C  CR15  0  -0.246   0.1190  -1.3592   0.0191
 3RN  C4   C  CH2   0  -0.480  -1.3400  -1.6900   0.0142
 3RN  C5   C  CH2   0  -0.573  -2.0330  -0.3283  -0.0277
 3RN  C6   C  CH2   0  -0.181   1.6728   0.6650   0.0183
 3RN  HO2  H  HOH1  0   0.461   3.5491   0.2040   0.0369
 3RN  H3   H  HCR5  0   0.272   0.8746  -2.1327   0.0329
 3RN  H4   H  HCH2  0   0.264  -1.5939  -2.3206  -0.8407
 3RN  H5   H  HCH2  0   0.282  -2.7010  -0.1641   0.8196
 3RN  H6   H  HCH2  0   0.219   1.7256   1.3190  -0.8635
 3RN  H6A  H  HCH2  0   0.218   1.7048   1.3331   0.8902
 3RN  H7   H  HCH2  0   0.265  -1.6044  -2.2652   0.9048
 3RN  H8   H  HCH2  0   0.283  -2.6326  -0.1927  -0.9300

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
 3RN  C1  C5   single  1.515  0.020  1.515
 3RN  C1  O1   double  1.214  0.020  1.214
 3RN  C2  C1   single  1.470  0.020  1.470
 3RN  O2  C6   single  1.404  0.020  1.404
 3RN  O2  HO2  single  0.850  0.020  0.980
 3RN  C3  C2   double  1.337  0.020  1.337
 3RN  C3  C4   single  1.496  0.020  1.496
 3RN  C3  H3   single  0.930  0.020  1.080
 3RN  C4  C5   single  1.528  0.020  1.528
 3RN  C4  H4   single  0.970  0.020  1.090
 3RN  C5  H5   single  0.970  0.020  1.090
 3RN  C6  C2   single  1.488  0.020  1.488
 3RN  C6  H6   single  0.970  0.020  1.090
 3RN  C6  H6A  single  0.970  0.020  1.090
 3RN  C4  H7   single  0.970  0.020  1.090
 3RN  C5  H8   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
 3RN  C5   C1  C2  108.03  3.000
 3RN  C2   C1  O1  125.71  3.000
 3RN  C5   C1  O1  126.26  3.000
 3RN  C6   C2  C3  129.11  3.000
 3RN  C6   C2  C1  121.64  3.000
 3RN  C3   C2  C1  109.25  3.000
 3RN  HO2  O2  C6  108.11  3.000
 3RN  H3   C3  C4  121.55  3.000
 3RN  H3   C3  C2  125.05  3.000
 3RN  C4   C3  C2  113.39  3.000
 3RN  H7   C4  H4  106.12  3.000
 3RN  H7   C4  C5  112.44  3.000
 3RN  H4   C4  C5  112.80  3.000
 3RN  H7   C4  C3  110.47  3.000
 3RN  H4   C4  C3  110.91  3.000
 3RN  C5   C4  C3  104.20  3.000
 3RN  H8   C5  H5  106.67  3.000
 3RN  H8   C5  C4  112.47  3.000
 3RN  H5   C5  C4  112.97  3.000
 3RN  H8   C5  C1  109.52  3.000
 3RN  H5   C5  C1  110.11  3.000
 3RN  C4   C5  C1  105.12  3.000
 3RN  H6A  C6  H6  105.86  3.000
 3RN  H6A  C6  O2  111.98  3.000
 3RN  H6   C6  O2  111.96  3.000
 3RN  H6A  C6  C2  108.71  3.000
 3RN  H6   C6  C2  108.72  3.000
 3RN  O2   C6  C2  109.48  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
 3RN  Var_01  C3  C4  C5  C1   -1.35  30.0  1
 3RN  Var_02  C4  C5  C1  C2    1.30  30.0  1
 3RN  Var_03  C5  C4  C3  C2    1.01  30.0  1
 3RN  Var_04  C5  C1  C2  C3   -0.73  30.0  1
 3RN  Var_05  O2  C6  C2  C1  179.87  30.0  1

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
 3RN  plan-1  C1  0.020
 3RN  plan-1  O1  0.020
 3RN  plan-1  C2  0.020
 3RN  plan-1  C5  0.020

