# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 01:33:39 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)\C=C\[C@H]1C=CC(=O)[C@@H]1CCCCCCC(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
 RPG  RPG  '7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]heptanoic acid'  ligand  55  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RPG
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
 RPG  O9   O  O      0  -0.416  -1.6570   4.0011  -0.2375
 RPG  C9   C  C      0   0.386  -0.5900   3.5183   0.0779
 RPG  C10  C  C1     0  -0.339   0.5670   4.2560   0.6010
 RPG  C11  C  C1     0  -0.138   1.5335   3.3992   0.9341
 RPG  C12  C  CH1    0  -0.383   1.1707   1.9632   0.6838
 RPG  C13  C  C1     0  -0.181   2.2003   1.2547  -0.1428
 RPG  C14  C  C1     0  -0.260   2.8607   0.1709   0.2490
 RPG  C15  C  CH1    0   0.006   3.9099  -0.5488  -0.5516
 RPG  C16  C  CH2    0  -0.463   5.1875  -0.7124   0.2749
 RPG  C17  C  CH2    0  -0.413   6.2752  -1.5164  -0.4258
 RPG  C18  C  CH2    0  -0.408   7.5107  -1.7116   0.4438
 RPG  C19  C  CH2    0  -0.419   8.6114  -2.5064  -0.2481
 RPG  C20  C  CH3    0  -0.663   9.8408  -2.6980   0.6291
 RPG  O15  O  OH1    0  -0.661   4.1539   0.0485  -1.8032
 RPG  C8   C  CH1    0  -0.361  -0.2110   2.0450   0.0022
 RPG  C7   C  CH2    0  -0.421  -1.2426   1.0895   0.6019
 RPG  C6   C  CH2    0  -0.418  -2.4867   0.8646  -0.2494
 RPG  C5   C  CH2    0  -0.413  -3.4826  -0.0756   0.4186
 RPG  C4   C  CH2    0  -0.410  -4.7215  -0.3359  -0.4289
 RPG  C3   C  CH2    0  -0.402  -5.7521  -1.2214   0.2623
 RPG  C2   C  CH2    0  -0.582  -6.9770  -1.4748  -0.6010
 RPG  C1   C  C      0   0.410  -8.0805  -2.3496   0.0187
 RPG  O1   O  OC    -1  -0.636  -9.0765  -2.5660  -0.7051
 RPG  O2   O  O      0  -0.610  -7.9090  -2.7739   1.1783
 RPG  H1   H  H      0   0.271   0.5917   5.3314   0.7124
 RPG  H3   H  H      0   0.281   2.4918   3.6739   1.3567
 RPG  H5   H  HCH1   0   0.282   1.0847   1.4567   1.6530
 RPG  H6   H  H      0   0.245   2.3852   1.6805  -1.1257
 RPG  H7   H  H      0   0.245   2.6576  -0.2515   1.2304
 RPG  H8   H  HCH1   0   0.236   3.5299  -1.5534  -0.7775
 RPG  H9   H  HCH2   0   0.225   5.5711   0.2786   0.5465
 RPG  H10  H  HCH2   0   0.227   4.9253  -1.2013   1.2185
 RPG  H11  H  HCH2   0   0.211   5.8751  -2.4954  -0.7134
 RPG  H12  H  HCH2   0   0.214   6.5635  -1.0185  -1.3558
 RPG  H13  H  HCH2   0   0.208   7.9042  -0.7333   0.7425
 RPG  H14  H  HCH2   0   0.207   7.2279  -2.2190   1.3729
 RPG  H15  H  HCH2   0   0.211   8.2177  -3.4829  -0.5472
 RPG  H16  H  HCH2   0   0.210   8.8945  -1.9980  -1.1750
 RPG  H17  H  HCH3   0   0.216   9.5879  -3.2306   1.5481
 RPG  H18  H  HCH3   0   0.226  10.6152  -3.2712   0.1183
 RPG  H19  H  HCH3   0   0.216  10.2742  -1.7377   0.9154
 RPG  H20  H  HOH1   0   0.444   4.5746   0.9025  -1.6518
 RPG  H21  H  HCH1   0   0.284  -0.0906   1.8108  -1.0638
 RPG  H22  H  HCH2   0   0.231  -0.7512   0.1240   0.7608
 RPG  H23  H  HCH2   0   0.226  -1.5288   1.4469   1.5969
 RPG  H24  H  HCH2   0   0.224  -2.9778   1.8165  -0.4613
 RPG  H25  H  HCH2   0   0.209  -2.1887   0.4505  -1.2189
 RPG  H26  H  HCH2   0   0.205  -2.9918  -1.0280   0.6492
 RPG  H27  H  HCH2   0   0.206  -3.7847   0.3491   1.3827
 RPG  H28  H  HCH2   0   0.202  -5.1850   0.6216  -0.6943
 RPG  H29  H  HCH2   0   0.203  -4.4229  -0.7963  -1.3776
 RPG  H30  H  HCH2   0   0.200  -5.2855  -2.1729   0.5353
 RPG  H31  H  HCH2   0   0.200  -6.0503  -0.7528   1.2047
 RPG  H32  H  HCH2   0   0.216  -7.4245  -0.5163  -0.8908
 RPG  H33  H  HCH2   0   0.215  -6.6705  -1.9362  -1.5474

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
 RPG  C20  C19  single  1.522  0.020  1.522
 RPG  C19  C18  single  1.524  0.020  1.524
 RPG  C18  C17  single  1.523  0.020  1.523
 RPG  C17  C16  single  1.523  0.020  1.523
 RPG  C16  C15  single  1.530  0.020  1.530
 RPG  C15  O15  single  1.408  0.020  1.408
 RPG  C15  C14  single  1.503  0.020  1.503
 RPG  C14  C13  double  1.328  0.020  1.328
 RPG  C13  C12  single  1.498  0.020  1.498
 RPG  C6   C5   single  1.524  0.020  1.524
 RPG  C6   C7   single  1.524  0.020  1.524
 RPG  C4   C5   single  1.523  0.020  1.523
 RPG  C4   C3   single  1.524  0.020  1.524
 RPG  C8   C12  single  1.543  0.020  1.543
 RPG  C8   C7   single  1.529  0.020  1.529
 RPG  C8   C9   single  1.523  0.020  1.523
 RPG  C12  C11  single  1.502  0.020  1.502
 RPG  C3   C2   single  1.520  0.020  1.520
 RPG  C9   O9   double  1.213  0.020  1.213
 RPG  C9   C10  single  1.469  0.020  1.469
 RPG  C11  C10  double  1.334  0.020  1.334
 RPG  C2   C1   single  1.538  0.020  1.538
 RPG  O2   C1   deloc   1.247  0.020  1.247
 RPG  C1   O1   deloc   1.250  0.020  1.250
 RPG  C10  H1   single  0.930  0.020  1.080
 RPG  C11  H3   single  0.930  0.020  1.080
 RPG  C12  H5   single  0.970  0.020  1.090
 RPG  C13  H6   single  0.930  0.020  1.080
 RPG  C14  H7   single  0.930  0.020  1.080
 RPG  C15  H8   single  0.970  0.020  1.090
 RPG  C16  H9   single  0.970  0.020  1.090
 RPG  C16  H10  single  0.970  0.020  1.090
 RPG  C17  H11  single  0.970  0.020  1.090
 RPG  C17  H12  single  0.970  0.020  1.090
 RPG  C18  H13  single  0.970  0.020  1.090
 RPG  C18  H14  single  0.970  0.020  1.090
 RPG  C19  H15  single  0.970  0.020  1.090
 RPG  C19  H16  single  0.970  0.020  1.090
 RPG  C20  H17  single  0.970  0.020  1.090
 RPG  C20  H18  single  0.970  0.020  1.090
 RPG  C20  H19  single  0.970  0.020  1.090
 RPG  O15  H20  single  0.850  0.020  0.980
 RPG  C8   H21  single  0.970  0.020  1.090
 RPG  C7   H22  single  0.970  0.020  1.090
 RPG  C7   H23  single  0.970  0.020  1.090
 RPG  C6   H24  single  0.970  0.020  1.090
 RPG  C6   H25  single  0.970  0.020  1.090
 RPG  C5   H26  single  0.970  0.020  1.090
 RPG  C5   H27  single  0.970  0.020  1.090
 RPG  C4   H28  single  0.970  0.020  1.090
 RPG  C4   H29  single  0.970  0.020  1.090
 RPG  C3   H30  single  0.970  0.020  1.090
 RPG  C3   H31  single  0.970  0.020  1.090
 RPG  C2   H32  single  0.970  0.020  1.090
 RPG  C2   H33  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
 RPG  C8   C9   C10  107.91  3.000
 RPG  C10  C9   O9   125.86  3.000
 RPG  C8   C9   O9   126.22  3.000
 RPG  H1   C10  C11  126.62  3.000
 RPG  H1   C10  C9   123.66  3.000
 RPG  C11  C10  C9   109.70  3.000
 RPG  H3   C11  C12  121.42  3.000
 RPG  H3   C11  C10  125.16  3.000
 RPG  C12  C11  C10  113.42  3.000
 RPG  H5   C12  C8   110.16  3.000
 RPG  H5   C12  C13  108.84  3.000
 RPG  C8   C12  C13  113.37  3.000
 RPG  H5   C12  C11  108.24  3.000
 RPG  C8   C12  C11  103.84  3.000
 RPG  C13  C12  C11  112.21  3.000
 RPG  H6   C13  C14  120.12  3.000
 RPG  H6   C13  C12  115.49  3.000
 RPG  C14  C13  C12  124.38  3.000
 RPG  H7   C14  C15  115.14  3.000
 RPG  H7   C14  C13  119.36  3.000
 RPG  C15  C14  C13  125.49  3.000
 RPG  H8   C15  O15  105.38  3.000
 RPG  H8   C15  C16  107.60  3.000
 RPG  O15  C15  C16  112.38  3.000
 RPG  H8   C15  C14  107.83  3.000
 RPG  O15  C15  C14  113.03  3.000
 RPG  C16  C15  C14  110.26  3.000
 RPG  H10  C16  H9   105.89  3.000
 RPG  H10  C16  C17  109.39  3.000
 RPG  H9   C16  C17  109.94  3.000
 RPG  H10  C16  C15  108.26  3.000
 RPG  H9   C16  C15  109.21  3.000
 RPG  C17  C16  C15  113.83  3.000
 RPG  H12  C17  H11  106.25  3.000
 RPG  H12  C17  C18  109.26  3.000
 RPG  H11  C17  C18  109.35  3.000
 RPG  H12  C17  C16  109.83  3.000
 RPG  H11  C17  C16  109.36  3.000
 RPG  C18  C17  C16  112.59  3.000
 RPG  H14  C18  H13  105.96  3.000
 RPG  H14  C18  C19  109.26  3.000
 RPG  H13  C18  C19  109.27  3.000
 RPG  H14  C18  C17  109.51  3.000
 RPG  H13  C18  C17  109.41  3.000
 RPG  C19  C18  C17  113.17  3.000
 RPG  H16  C19  H15  106.02  3.000
 RPG  H16  C19  C20  109.73  3.000
 RPG  H15  C19  C20  109.62  3.000
 RPG  H16  C19  C18  109.21  3.000
 RPG  H15  C19  C18  109.25  3.000
 RPG  C20  C19  C18  112.79  3.000
 RPG  H19  C20  H18  107.65  3.000
 RPG  H19  C20  H17  107.48  3.000
 RPG  H18  C20  H17  107.60  3.000
 RPG  H19  C20  C19  111.16  3.000
 RPG  H18  C20  C19  111.69  3.000
 RPG  H17  C20  C19  111.06  3.000
 RPG  H20  O15  C15  108.17  3.000
 RPG  H21  C8   C7   108.76  3.000
 RPG  H21  C8   C12  108.62  3.000
 RPG  C7   C8   C12  113.44  3.000
 RPG  H21  C8   C9   106.37  3.000
 RPG  C7   C8   C9   114.66  3.000
 RPG  C12  C8   C9   104.61  3.000
 RPG  H23  C7   H22  105.85  3.000
 RPG  H23  C7   C6   110.01  3.000
 RPG  H22  C7   C6   108.50  3.000
 RPG  H23  C7   C8   109.19  3.000
 RPG  H22  C7   C8   107.78  3.000
 RPG  C6   C7   C8   115.08  3.000
 RPG  H25  C6   H24  106.27  3.000
 RPG  H25  C6   C5   109.42  3.000
 RPG  H24  C6   C5   109.21  3.000
 RPG  H25  C6   C7   109.15  3.000
 RPG  H24  C6   C7   110.30  3.000
 RPG  C5   C6   C7   112.31  3.000
 RPG  H27  C5   H26  105.97  3.000
 RPG  H27  C5   C4   109.35  3.000
 RPG  H26  C5   C4   109.43  3.000
 RPG  H27  C5   C6   109.07  3.000
 RPG  H26  C5   C6   109.62  3.000
 RPG  C4   C5   C6   113.14  3.000
 RPG  H29  C4   H28  105.81  3.000
 RPG  H29  C4   C3   109.43  3.000
 RPG  H28  C4   C3   109.34  3.000
 RPG  H29  C4   C5   109.37  3.000
 RPG  H28  C4   C5   109.22  3.000
 RPG  C3   C4   C5   113.38  3.000
 RPG  H31  C3   H30  105.89  3.000
 RPG  H31  C3   C2   109.94  3.000
 RPG  H30  C3   C2   109.89  3.000
 RPG  H31  C3   C4   109.03  3.000
 RPG  H30  C3   C4   109.27  3.000
 RPG  C2   C3   C4   112.59  3.000
 RPG  H33  C2   H32  104.70  3.000
 RPG  H33  C2   C1   107.99  3.000
 RPG  H32  C2   C1   108.10  3.000
 RPG  H33  C2   C3   109.58  3.000
 RPG  H32  C2   C3   109.46  3.000
 RPG  C1   C2   C3   116.36  3.000
 RPG  O2   C1   O1   126.10  3.000
 RPG  O1   C1   C2   115.89  3.000
 RPG  O2   C1   C2   118.01  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
 RPG  Var_01  C12  C11  C10  C9      0.06  30.0  1
 RPG  Var_02  C8   C9   C10  C11    -4.62  30.0  1
 RPG  Var_03  C15  C14  C13  C12  -179.17   0.0  2
 RPG  Var_04  C5   C6   C7   C8   -178.91  30.0  1
 RPG  Var_05  C18  C17  C16  C15  -177.59  30.0  1
 RPG  Var_06  C19  C18  C17  C16  -179.61  30.0  1
 RPG  Var_07  C20  C19  C18  C17  -179.92  30.0  1
 RPG  Var_08  C4   C5   C6   C7   -178.84  30.0  3
 RPG  Var_09  C3   C4   C5   C6   -177.20  30.0  1
 RPG  Var_10  C2   C3   C4   C5   -179.73  30.0  3
 RPG  Var_11  C1   C2   C3   C4   -179.45  30.0  3
 RPG  Var_12  O2   C1   C2   C3      0.88  30.0  3
 RPG  Var_13  H17  C20  C19  C18    59.70  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
 RPG  chir_01  C12  C13  C8   C11  positiv
 RPG  chir_02  C15  O15  C16  C14  negativ
 RPG  chir_03  C8   C12  C7   C9   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
 RPG  plan-1  O9   0.020
 RPG  plan-1  C9   0.020
 RPG  plan-1  C10  0.020
 RPG  plan-1  C8   0.020
 RPG  plan-2  C2   0.020
 RPG  plan-2  C1   0.020
 RPG  plan-2  O1   0.020
 RPG  plan-2  O2   0.020
 RPG  plan-3  C12  0.020
 RPG  plan-3  C13  0.020
 RPG  plan-3  C14  0.020
 RPG  plan-3  C15  0.020
 RPG  plan-3  H6   0.020
 RPG  plan-3  H7   0.020

