# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:23:19 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (1R,5S)-5-hydroxy-3-(hydroxymethyl)-1-(3-methylbut-2-en-1-yl)cyclopent-2-ene-1-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CC[C@@]1(C=O)C=C(CO)C[C@@H]1O
#
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
 1Y9  1Y9  (1R,5S)-5-hydroxy-3-(hydroxymethyl)-1-(3-methylbut-2-en-1-yl)cyclopent-2-ene-1-carbaldehyde  ligand  33  15  .  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_1Y9
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
 1Y9  O1   O  OH1   0  -0.669   1.6418   2.3891   0.2352
 1Y9  C2   C  CR15  0   0.075   1.1665   1.4687  -0.7226
 1Y9  C3   C  CR5   0  -0.277   0.1145   0.5677  -0.0221
 1Y9  C4   C  C1    0   0.217  -0.4890   1.3146   1.1500
 1Y9  O5   O  O     0  -0.371  -1.5145   1.9444   1.1030
 1Y9  C6   C  CH2   0  -0.472  -0.9726   0.1388  -1.0263
 1Y9  C7   C  C1    0  -0.258  -1.8920  -0.9059  -0.4770
 1Y9  C8   C  C     0   0.089  -3.2050  -0.8144  -0.2509
 1Y9  C9   C  CH3   0  -0.706  -3.9600  -1.9737   0.3333
 1Y9  C10  C  CH3   0  -0.714  -4.0476   0.3943  -0.5269
 1Y9  C11  C  CR15  0  -0.240   0.9550  -0.5992   0.4383
 1Y9  C12  C  CR5   0   0.054   2.1226  -0.6491  -0.1969
 1Y9  C13  C  CH2   0  -0.199   3.1926  -1.6729  -0.0734
 1Y9  O14  O  OH1   0  -0.665   2.8097  -2.6786   0.8277
 1Y9  C15  C  CH2   0  -0.512   2.2621   0.4911  -1.1650
 1Y9  H1   H  HOH1  0   0.457   2.2370   3.0053  -0.2030
 1Y9  H2   H  HCR5  0   0.231   0.7187   1.9943  -1.5738
 1Y9  H3   H  H     0   0.195   0.0819   1.2412   2.0937
 1Y9  H6   H  HCH2  0   0.248  -1.5160   1.0216  -1.3641
 1Y9  H7   H  HCH2  0   0.246  -0.4628  -0.2645  -1.9084
 1Y9  H8   H  H     0   0.224  -1.4131  -1.8503  -0.2287
 1Y9  H9   H  HCH3  0   0.235  -3.3161  -2.8347   0.5122
 1Y9  H10  H  HCH3  0   0.231  -4.4261  -1.6963   1.2826
 1Y9  H11  H  HCH3  0   0.230  -4.7724  -2.2891  -0.3267
 1Y9  H12  H  HCH3  0   0.229  -4.9129   0.1214  -1.1358
 1Y9  H13  H  HCH3  0   0.234  -4.4418   0.8050   0.4059
 1Y9  H14  H  HCH3  0   0.239  -3.5157   1.1915  -1.0391
 1Y9  H15  H  HCR5  0   0.254   0.5963  -1.3235   1.1580
 1Y9  H18  H  HCH2  0   0.211   3.4023  -2.0762  -1.0756
 1Y9  H19  H  HCH2  0   0.215   4.1181  -1.1690   0.2420
 1Y9  H20  H  HOH1  0   0.460   3.5429  -3.2935   0.9185
 1Y9  H21  H  HCH2  0   0.254   2.1027   0.1461  -2.1918
 1Y9  H22  H  HCH2  0   0.254   3.2515   0.9584  -1.1494

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
 1Y9  O5   C4   double  1.204  0.020  1.204
 1Y9  C4   C3   single  1.515  0.020  1.515
 1Y9  O1   C2   single  1.411  0.020  1.411
 1Y9  C6   C3   single  1.541  0.020  1.541
 1Y9  C6   C7   single  1.496  0.020  1.496
 1Y9  C9   C8   single  1.502  0.020  1.502
 1Y9  C3   C2   single  1.552  0.020  1.552
 1Y9  C3   C11  single  1.510  0.020  1.510
 1Y9  C2   C15  single  1.534  0.020  1.534
 1Y9  C7   C8   double  1.335  0.020  1.335
 1Y9  C8   C10  single  1.499  0.020  1.499
 1Y9  C11  C12  double  1.330  0.020  1.330
 1Y9  C15  C12  single  1.502  0.020  1.502
 1Y9  C12  C13  single  1.486  0.020  1.486
 1Y9  C13  O14  single  1.404  0.020  1.404
 1Y9  O1   H1   single  0.850  0.020  0.980
 1Y9  C2   H2   single  0.970  0.020  1.090
 1Y9  C4   H3   single  0.930  0.020  1.080
 1Y9  C6   H6   single  0.970  0.020  1.090
 1Y9  C6   H7   single  0.970  0.020  1.090
 1Y9  C7   H8   single  0.930  0.020  1.080
 1Y9  C9   H9   single  0.970  0.020  1.090
 1Y9  C9   H10  single  0.970  0.020  1.090
 1Y9  C9   H11  single  0.970  0.020  1.090
 1Y9  C10  H12  single  0.970  0.020  1.090
 1Y9  C10  H13  single  0.970  0.020  1.090
 1Y9  C10  H14  single  0.970  0.020  1.090
 1Y9  C11  H15  single  0.930  0.020  1.080
 1Y9  C13  H18  single  0.970  0.020  1.090
 1Y9  C13  H19  single  0.970  0.020  1.090
 1Y9  O14  H20  single  0.850  0.020  0.980
 1Y9  C15  H21  single  0.970  0.020  1.090
 1Y9  C15  H22  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
 1Y9  H1   O1   C2   108.48  3.000
 1Y9  H2   C2   C15  111.93  3.000
 1Y9  H2   C2   C3   110.60  3.000
 1Y9  C15  C2   C3   104.14  3.000
 1Y9  H2   C2   O1   110.61  3.000
 1Y9  C15  C2   O1   111.79  3.000
 1Y9  C3   C2   O1   107.49  3.000
 1Y9  C11  C3   C6   112.11  3.000
 1Y9  C11  C3   C4   111.52  3.000
 1Y9  C6   C3   C4   111.12  3.000
 1Y9  C11  C3   C2   102.06  3.000
 1Y9  C6   C3   C2   110.22  3.000
 1Y9  C4   C3   C2   109.45  3.000
 1Y9  H3   C4   O5   120.52  3.000
 1Y9  H3   C4   C3   114.96  3.000
 1Y9  O5   C4   C3   124.52  3.000
 1Y9  H7   C6   H6   106.29  3.000
 1Y9  H7   C6   C7   108.93  3.000
 1Y9  H6   C6   C7   111.89  3.000
 1Y9  H7   C6   C3   107.39  3.000
 1Y9  H6   C6   C3   109.16  3.000
 1Y9  C7   C6   C3   112.87  3.000
 1Y9  H8   C7   C8   116.98  3.000
 1Y9  H8   C7   C6   114.81  3.000
 1Y9  C8   C7   C6   128.21  3.000
 1Y9  C10  C8   C9   114.29  3.000
 1Y9  C10  C8   C7   125.22  3.000
 1Y9  C9   C8   C7   120.48  3.000
 1Y9  H11  C9   H10  106.30  3.000
 1Y9  H11  C9   H9   108.07  3.000
 1Y9  H10  C9   H9   108.04  3.000
 1Y9  H11  C9   C8   111.19  3.000
 1Y9  H10  C9   C8   110.87  3.000
 1Y9  H9   C9   C8   112.13  3.000
 1Y9  H14  C10  H13  107.65  3.000
 1Y9  H14  C10  H12  107.95  3.000
 1Y9  H13  C10  H12  106.49  3.000
 1Y9  H14  C10  C8   113.77  3.000
 1Y9  H13  C10  C8   110.41  3.000
 1Y9  H12  C10  C8   110.27  3.000
 1Y9  H15  C11  C12  125.69  3.000
 1Y9  H15  C11  C3   122.38  3.000
 1Y9  C12  C11  C3   111.84  3.000
 1Y9  C15  C12  C13  120.64  3.000
 1Y9  C13  C12  C11  128.19  3.000
 1Y9  C15  C12  C11  111.15  3.000
 1Y9  H19  C13  H18  105.59  3.000
 1Y9  H19  C13  O14  111.94  3.000
 1Y9  H18  C13  O14  111.97  3.000
 1Y9  H19  C13  C12  108.30  3.000
 1Y9  H18  C13  C12  108.30  3.000
 1Y9  O14  C13  C12  110.52  3.000
 1Y9  H20  O14  C13  108.12  3.000
 1Y9  H22  C15  H21  106.23  3.000
 1Y9  H22  C15  C12  113.51  3.000
 1Y9  H21  C15  C12  110.59  3.000
 1Y9  H22  C15  C2   111.69  3.000
 1Y9  H21  C15  C2   111.56  3.000
 1Y9  C12  C15  C2   103.39  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
 1Y9  Var_01  C11  C12  C15  C2     15.96  30.0  1
 1Y9  Var_02  C15  C12  C11  C3      1.09  30.0  1
 1Y9  Var_03  O14  C13  C12  C11     1.42  30.0  3
 1Y9  Var_04  C8   C7   C6   C3    116.57  30.0  3
 1Y9  Var_05  C9   C8   C7   C6   -178.90   0.0  2
 1Y9  Var_06  H9   C9   C8   C7     -0.84  30.0  3
 1Y9  Var_07  H12  C10  C8   C7    127.58  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
 1Y9  chir_01  C2  O1  C3   C15  positiv
 1Y9  chir_02  C3  C2  C11  C4   negativ

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
 1Y9  plan-1  C3   0.020
 1Y9  plan-1  C4   0.020
 1Y9  plan-1  O5   0.020
 1Y9  plan-1  H3   0.020
 1Y9  plan-2  C6   0.020
 1Y9  plan-2  C7   0.020
 1Y9  plan-2  C8   0.020
 1Y9  plan-2  C9   0.020
 1Y9  plan-2  C10  0.020
 1Y9  plan-2  H8   0.020

