# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:09:48 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: retinoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(/C=C/C(C)=C/C=C/C(C)=C/C(O)=O)C(C)(C)CCC1
#
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
 3KV  3KV  'retinoic acid            '  ligand  49  22  .  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_3KV
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
 3KV  C4   C  CH2    0  -0.468   5.4733  -2.0103  -0.0134
 3KV  C5   C  C      0   0.007   4.1453  -1.4296  -0.4217
 3KV  C6   C  C      0   0.125   3.8146  -0.1458  -0.1896
 3KV  C7   C  C1     0  -0.314   2.5211   0.4299  -0.5825
 3KV  C8   C  C1     0  -0.255   1.3174  -0.0687  -0.2622
 3KV  C10  C  C1     0  -0.305  -1.0881  -0.0688  -0.1326
 3KV  C13  C  C      0   0.166  -4.9004   0.0708   0.0820
 3KV  C15  C  C      0   0.391  -7.3087  -0.5647   0.7927
 3KV  C20  C  CH3    0  -0.769  -5.2202   1.2974  -0.7199
 3KV  O1   O  OC    -1  -0.617  -7.8318  -1.1772   1.7491
 3KV  O2   O  O      0  -0.594  -7.9143   0.1095  -0.0657
 3KV  C14  C  C1     0  -0.477  -5.8082  -0.7019   0.7135
 3KV  C12  C  C1     0  -0.286  -3.4972  -0.2988   0.2139
 3KV  C11  C  C1     0  -0.255  -2.4499   0.3610  -0.3207
 3KV  C9   C  C      0   0.117   0.0348   0.5294  -0.5977
 3KV  C19  C  CH3    0  -0.762   0.0330   1.7775  -1.4271
 3KV  C18  C  CH3    0  -0.727   3.2430  -2.4227  -1.0984
 3KV  C3   C  CH2    0  -0.448   6.5152  -0.9718   0.3665
 3KV  C2   C  CH2    0  -0.412   5.8813   0.1086   1.2209
 3KV  C1   C  CT     0  -0.152   4.7600   0.8489   0.4862
 3KV  C16  C  CH3    0  -0.647   5.3551   1.7967  -0.5648
 3KV  H1   H  HCH2   0   0.231   5.3074  -2.7017   0.8229
 3KV  H2   H  HCH2   0   0.232   5.8502  -2.6363  -0.8279
 3KV  H5   H  H      0   0.246   2.5660   1.3765  -1.1158
 3KV  H6   H  H      0   0.235   1.2738  -0.9824   0.3242
 3KV  H7   H  H      0   0.236  -0.9613  -0.9705   0.4620
 3KV  H8   H  HCH3   0   0.225   3.4626   1.0417   2.2281
 3KV  H9   H  HCH3   0   0.224   4.6921   2.3011   2.0910
 3KV  H10  H  HCH3   0   0.226   3.2625   2.3489   1.0634
 3KV  H11  H  HCH3   0   0.233  -4.9119   1.1703  -1.7604
 3KV  H12  H  HCH3   0   0.268  -6.2812   1.5158  -0.7041
 3KV  H13  H  HCH3   0   0.230  -4.6737   2.1610  -0.3354
 3KV  H15  H  H      0   0.218  -5.4119  -1.5381   1.2854
 3KV  H16  H  H      0   0.235  -3.2928  -1.1904   0.8021
 3KV  H18  H  H      0   0.250  -2.6303   1.2528  -0.9097
 3KV  H20  H  HCH3   0   0.244   0.6031   2.5721  -0.9409
 3KV  H21  H  HCH3   0   0.246   0.5058   1.5998  -2.3954
 3KV  H22  H  HCH3   0   0.255  -0.9659   2.1627  -1.6144
 3KV  H23  H  HCH3   0   0.231   3.8174  -3.0575  -1.7769
 3KV  H24  H  HCH3   0   0.236   2.7767  -3.0931  -0.3707
 3KV  H25  H  HCH3   0   0.244   2.4414  -1.9566  -1.6671
 3KV  H26  H  HCH2   0   0.231   7.3422  -1.4475   0.8980
 3KV  H27  H  HCH2   0   0.220   6.9433  -0.5317  -0.5381
 3KV  H28  H  HCH2   0   0.219   5.4718  -0.3519   2.1277
 3KV  H29  H  HCH2   0   0.224   6.6295   0.8340   1.5539
 3KV  H30  H  HCH3   0   0.229   4.5792   2.3349  -1.1122
 3KV  H31  H  HCH3   0   0.224   5.9927   2.5442  -0.0859
 3KV  H32  H  HCH3   0   0.229   5.9616   1.2637  -1.2986
 3KV  C17  C  CH3    0  -0.639   3.9944   1.6825   1.5222

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
 3KV  C20  C13  single  1.500  0.020  1.500
 3KV  O2   C15  deloc   1.248  0.020  1.248
 3KV  C13  C12  single  1.457  0.020  1.457
 3KV  C13  C14  double  1.349  0.020  1.349
 3KV  C12  C11  double  1.348  0.020  1.348
 3KV  C15  C14  single  1.509  0.020  1.509
 3KV  C15  O1   deloc   1.250  0.020  1.250
 3KV  C11  C10  single  1.440  0.020  1.440
 3KV  C18  C5   single  1.503  0.020  1.503
 3KV  C10  C9   double  1.355  0.020  1.355
 3KV  C9   C8   single  1.454  0.020  1.454
 3KV  C9   C19  single  1.499  0.020  1.499
 3KV  C4   C5   single  1.506  0.020  1.506
 3KV  C4   C3   single  1.519  0.020  1.519
 3KV  C5   C6   double  1.346  0.020  1.346
 3KV  C8   C7   double  1.342  0.020  1.342
 3KV  C7   C6   single  1.469  0.020  1.469
 3KV  C6   C1   single  1.530  0.020  1.530
 3KV  C3   C2   single  1.516  0.020  1.516
 3KV  C16  C1   single  1.535  0.020  1.535
 3KV  C1   C2   single  1.531  0.020  1.531
 3KV  C1   C17  single  1.534  0.020  1.534
 3KV  C4   H1   single  0.970  0.020  1.090
 3KV  C4   H2   single  0.970  0.020  1.090
 3KV  C7   H5   single  0.930  0.020  1.080
 3KV  C8   H6   single  0.930  0.020  1.080
 3KV  C10  H7   single  0.930  0.020  1.080
 3KV  C17  H8   single  0.970  0.020  1.090
 3KV  C17  H9   single  0.970  0.020  1.090
 3KV  C17  H10  single  0.970  0.020  1.090
 3KV  C20  H11  single  0.970  0.020  1.090
 3KV  C20  H12  single  0.970  0.020  1.090
 3KV  C20  H13  single  0.970  0.020  1.090
 3KV  C14  H15  single  0.930  0.020  1.080
 3KV  C12  H16  single  0.930  0.020  1.080
 3KV  C11  H18  single  0.930  0.020  1.080
 3KV  C19  H20  single  0.970  0.020  1.090
 3KV  C19  H21  single  0.970  0.020  1.090
 3KV  C19  H22  single  0.970  0.020  1.090
 3KV  C18  H23  single  0.970  0.020  1.090
 3KV  C18  H24  single  0.970  0.020  1.090
 3KV  C18  H25  single  0.970  0.020  1.090
 3KV  C3   H26  single  0.970  0.020  1.090
 3KV  C3   H27  single  0.970  0.020  1.090
 3KV  C2   H28  single  0.970  0.020  1.090
 3KV  C2   H29  single  0.970  0.020  1.090
 3KV  C16  H30  single  0.970  0.020  1.090
 3KV  C16  H31  single  0.970  0.020  1.090
 3KV  C16  H32  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
 3KV  H2   C4   H1   105.00  3.000
 3KV  H2   C4   C3   109.93  3.000
 3KV  H1   C4   C3   110.10  3.000
 3KV  H2   C4   C5   108.82  3.000
 3KV  H1   C4   C5   108.44  3.000
 3KV  C3   C4   C5   114.14  3.000
 3KV  C18  C5   C6   124.09  3.000
 3KV  C6   C5   C4   122.54  3.000
 3KV  C18  C5   C4   113.38  3.000
 3KV  C1   C6   C7   114.04  3.000
 3KV  C1   C6   C5   123.00  3.000
 3KV  C7   C6   C5   122.95  3.000
 3KV  H5   C7   C8   118.53  3.000
 3KV  H5   C7   C6   115.84  3.000
 3KV  C8   C7   C6   125.47  3.000
 3KV  H6   C8   C9   115.78  3.000
 3KV  H6   C8   C7   118.51  3.000
 3KV  C9   C8   C7   125.68  3.000
 3KV  H7   C10  C9   117.21  3.000
 3KV  H7   C10  C11  115.40  3.000
 3KV  C9   C10  C11  127.38  3.000
 3KV  C12  C13  C14  117.41  3.000
 3KV  C14  C13  C20  125.11  3.000
 3KV  C12  C13  C20  117.46  3.000
 3KV  C14  C15  O2   119.70  3.000
 3KV  C14  C15  O1   114.31  3.000
 3KV  O2   C15  O1   125.99  3.000
 3KV  H13  C20  H12  109.00  3.000
 3KV  H13  C20  H11  106.62  3.000
 3KV  H12  C20  H11  108.29  3.000
 3KV  H13  C20  C13  110.60  3.000
 3KV  H12  C20  C13  111.46  3.000
 3KV  H11  C20  C13  110.72  3.000
 3KV  H15  C14  C15  113.86  3.000
 3KV  H15  C14  C13  116.18  3.000
 3KV  C15  C14  C13  129.92  3.000
 3KV  H16  C12  C11  118.01  3.000
 3KV  H16  C12  C13  115.97  3.000
 3KV  C11  C12  C13  126.02  3.000
 3KV  H18  C11  C12  119.26  3.000
 3KV  H18  C11  C10  118.28  3.000
 3KV  C12  C11  C10  122.45  3.000
 3KV  C19  C9   C10  123.83  3.000
 3KV  C19  C9   C8   118.11  3.000
 3KV  C10  C9   C8   118.05  3.000
 3KV  H22  C19  H21  107.62  3.000
 3KV  H22  C19  H20  107.37  3.000
 3KV  H21  C19  H20  106.69  3.000
 3KV  H22  C19  C9   113.06  3.000
 3KV  H21  C19  C9   110.78  3.000
 3KV  H20  C19  C9   111.04  3.000
 3KV  H25  C18  H24  107.23  3.000
 3KV  H25  C18  H23  108.16  3.000
 3KV  H24  C18  H23  106.33  3.000
 3KV  H25  C18  C5   113.25  3.000
 3KV  H24  C18  C5   111.19  3.000
 3KV  H23  C18  C5   110.37  3.000
 3KV  H27  C3   H26  106.35  3.000
 3KV  H27  C3   C2   110.07  3.000
 3KV  H26  C3   C2   110.66  3.000
 3KV  H27  C3   C4   109.68  3.000
 3KV  H26  C3   C4   110.07  3.000
 3KV  C2   C3   C4   109.95  3.000
 3KV  H29  C2   H28  106.39  3.000
 3KV  H29  C2   C1   109.04  3.000
 3KV  H28  C2   C1   109.05  3.000
 3KV  H29  C2   C3   110.98  3.000
 3KV  H28  C2   C3   108.84  3.000
 3KV  C1   C2   C3   112.35  3.000
 3KV  C16  C1   C2   110.06  3.000
 3KV  C2   C1   C17  107.70  3.000
 3KV  C16  C1   C17  108.67  3.000
 3KV  C17  C1   C6   110.07  3.000
 3KV  C2   C1   C6   110.50  3.000
 3KV  C16  C1   C6   109.79  3.000
 3KV  H32  C16  H31  107.73  3.000
 3KV  H32  C16  H30  107.38  3.000
 3KV  H31  C16  H30  107.29  3.000
 3KV  H32  C16  C1   111.98  3.000
 3KV  H31  C16  C1   110.39  3.000
 3KV  H30  C16  C1   111.85  3.000
 3KV  H10  C17  H9   107.55  3.000
 3KV  H10  C17  H8   107.68  3.000
 3KV  H9   C17  H8   107.88  3.000
 3KV  H10  C17  C1   112.49  3.000
 3KV  H9   C17  C1   109.91  3.000
 3KV  H8   C17  C1   111.14  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
 3KV  Var_01  C1   C6   C5   C4      1.09  30.0  1
 3KV  Var_02  C1   C2   C3   C4    -61.01  30.0  1
 3KV  Var_03  C2   C3   C4   C5     42.72  30.0  1
 3KV  Var_04  C2   C1   C6   C5    -17.56  30.0  1
 3KV  Var_05  C3   C4   C5   C6    -13.99  30.0  1
 3KV  Var_06  C3   C2   C1   C6     47.35  30.0  1
 3KV  Var_07  C8   C7   C6   C5     53.29  30.0  2
 3KV  Var_08  H23  C18  C5   C4    -40.18  30.0  3
 3KV  Var_09  H30  C16  C1   C6     57.73  30.0  3
 3KV  Var_10  H8   C17  C1   C6     53.51  30.0  3
 3KV  Var_11  C9   C8   C7   C6    177.08   0.0  2
 3KV  Var_12  C11  C10  C9   C8    178.79   0.0  2
 3KV  Var_13  C13  C12  C11  C10   179.54   0.0  2
 3KV  Var_14  C20  C13  C14  C15    -0.08   0.0  2
 3KV  Var_15  C10  C9   C8   C7   -176.44  30.0  2
 3KV  Var_16  O2   C15  C14  C13    20.81  30.0  2
 3KV  Var_17  C11  C12  C13  C20    -0.04  30.0  2
 3KV  Var_18  C9   C10  C11  C12  -178.54  30.0  2
 3KV  Var_19  H20  C19  C9   C8    -58.27  30.0  3
 3KV  Var_20  H11  C20  C13  C14  -118.54  30.0  3

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
 3KV  plan-1  C15  0.020
 3KV  plan-1  O1   0.020
 3KV  plan-1  O2   0.020
 3KV  plan-1  C14  0.020
 3KV  plan-2  C13  0.020
 3KV  plan-2  C15  0.020
 3KV  plan-2  C20  0.020
 3KV  plan-2  C14  0.020
 3KV  plan-2  C12  0.020
 3KV  plan-2  H15  0.020
 3KV  plan-3  C10  0.020
 3KV  plan-3  C13  0.020
 3KV  plan-3  C12  0.020
 3KV  plan-3  C11  0.020
 3KV  plan-3  H16  0.020
 3KV  plan-3  H18  0.020
 3KV  plan-4  C8   0.020
 3KV  plan-4  C10  0.020
 3KV  plan-4  C11  0.020
 3KV  plan-4  C9   0.020
 3KV  plan-4  C19  0.020
 3KV  plan-4  H7   0.020
 3KV  plan-5  C6   0.020
 3KV  plan-5  C7   0.020
 3KV  plan-5  C8   0.020
 3KV  plan-5  C9   0.020
 3KV  plan-5  H5   0.020
 3KV  plan-5  H6   0.020

