# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 21:11:09 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2E,4E,6Z,8E)-8-[3-cyclopropyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethylocta-2,4,6-trienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC1=C(CCC/C1=C\C(C)=C/C=C/C(C)=C/C(O)=O)C2CC2
#
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
 3SW  3SW  '(2E,4E,6Z,8E)-8-[3-cyclopropyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethylocta-2,4,6-trienoic acid'  ligand  60  26  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3SW
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
 3SW  C1   C  CH2   0  -0.532  -2.5659  -2.5253  -0.7449
 3SW  C10  C  C1    0  -0.230   1.9529  -1.3831   0.4658
 3SW  C11  C  C1    0  -0.286   3.2977  -1.2930   0.4453
 3SW  C9   C  C1    0  -0.288   1.2503  -2.5613   0.9056
 3SW  O2   O  OH1   0  -0.610   7.6478   0.3381   0.0203
 3SW  C14  C  C     0   0.520   6.4020   0.8032  -0.1132
 3SW  C20  C  CH3   0  -0.746   3.3832   1.0923  -0.4601
 3SW  C19  C  CH3   0  -0.725  -0.7101  -3.9209   1.5442
 3SW  C12  C  C     0   0.191   4.0794  -0.1360   0.0465
 3SW  C13  C  C1    0  -0.461   5.4233  -0.2410   0.1796
 3SW  C2   C  CH2   0  -0.443  -3.1576  -2.0435  -2.0583
 3SW  C4   C  C     0   0.013  -3.8742   0.0190  -0.8238
 3SW  C5   C  C     0   0.128  -2.8250  -0.1150   0.0159
 3SW  C6   C  C     0   0.136  -2.0590  -1.3727   0.0813
 3SW  C7   C  C1    0  -0.420  -0.9454  -1.4715   0.8330
 3SW  C8   C  C     0   0.091  -0.0916  -2.6528   1.0344
 3SW  C3   C  CH2   0  -0.498  -4.2762  -1.0542  -1.7963
 3SW  O1   O  O     0  -0.457   6.1744   1.9520  -0.4277
 3SW  C4'  C  CH3   0  -0.666   0.2882   2.1485   2.1618
 3SW  C3'  C  CH1   0  -0.232  -0.5641   2.8615   1.1157
 3SW  C5'  C  CH3   0  -0.655   0.2964   3.8108   0.2872
 3SW  C2'  C  CH2   0  -0.408  -1.2864   1.8716   0.1993
 3SW  C1'  C  CH2   0  -0.574  -2.3806   1.0393   0.8794
 3SW  C6'  C  CH1   0  -0.318  -4.6664   1.2847  -0.8738
 3SW  C7'  C  CH2   0  -0.470  -5.6905   1.6041   0.1798
 3SW  C8'  C  CH2   0  -0.495  -6.1250   1.2782  -1.2150
 3SW  H1   H  HCH2  0   0.242  -3.3350  -3.0671  -0.1812
 3SW  H2   H  HCH2  0   0.246  -1.7623  -3.2353  -0.9412
 3SW  H3   H  H     0   0.246   1.3499  -0.5417   0.1418
 3SW  H4   H  H     0   0.249   3.8685  -2.1552   0.7790
 3SW  H5   H  H     0   0.241   1.8567  -3.4286   1.1501
 3SW  H6   H  HOH1  0   0.477   8.2803   1.0471  -0.1657
 3SW  H7   H  HCH3  0   0.258   3.3092   1.8442   0.3274
 3SW  H8   H  HCH3  0   0.267   3.9220   1.5483  -1.2852
 3SW  H9   H  HCH3  0   0.239   2.3750   0.8764  -0.8040
 3SW  H10  H  HCH3  0   0.248  -1.1378  -3.7553   2.5361
 3SW  H11  H  HCH3  0   0.252  -1.5259  -4.2744   0.9149
 3SW  H12  H  HCH3  0   0.243   0.0261  -4.7202   1.6229
 3SW  H13  H  H     0   0.265   5.8302  -1.1763   0.5457
 3SW  H14  H  HCH2  0   0.226  -2.3767  -1.5634  -2.6552
 3SW  H15  H  HCH2  0   0.237  -3.5243  -2.8919  -2.6390
 3SW  H16  H  H     0   0.249  -0.5990  -0.5888   1.3574
 3SW  H17  H  HCH2  0   0.248  -4.5958  -0.5842  -2.7305
 3SW  H18  H  HCH2  0   0.240  -5.1617  -1.5811  -1.4196
 3SW  H19  H  HCH3  0   0.205   1.0353   1.5071   1.6844
 3SW  H20  H  HCH3  0   0.234   0.8266   2.8628   2.7867
 3SW  H21  H  HCH3  0   0.229  -0.3061   1.5222   2.8277
 3SW  H22  H  HCH1  0   0.214  -1.3210   3.4583   1.6398
 3SW  H23  H  HCH3  0   0.214   1.0341   3.2574  -0.3004
 3SW  H24  H  HCH3  0   0.226  -0.3092   4.3924  -0.4098
 3SW  H25  H  HCH3  0   0.225   0.8411   4.5128   0.9206
 3SW  H26  H  HCH2  0   0.229  -1.7399   2.4190  -0.6334
 3SW  H27  H  HCH2  0   0.215  -0.5401   1.2103  -0.2572
 3SW  H28  H  HCH2  0   0.265  -3.2272   1.6913   1.0989
 3SW  H29  H  HCH2  0   0.237  -2.0377   0.6726   1.8495
 3SW  H30  H  HCH1  0   0.272  -4.1148   2.1447  -1.2450
 3SW  H31  H  HCH2  0   0.246  -5.8599   0.8600   0.9486
 3SW  H32  H  HCH2  0   0.250  -5.7685   2.6277   0.5241
 3SW  H33  H  HCH2  0   0.250  -6.5038   2.0801  -1.8357
 3SW  H34  H  HCH2  0   0.248  -6.6111   0.3250  -1.3829

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
 3SW  C19  C8   single  1.500  0.020  1.500
 3SW  C9   C8   double  1.351  0.020  1.351
 3SW  C9   C10  single  1.441  0.020  1.441
 3SW  C11  C10  double  1.348  0.020  1.348
 3SW  C11  C12  single  1.452  0.020  1.452
 3SW  C8   C7   single  1.471  0.020  1.471
 3SW  C13  C12  double  1.354  0.020  1.354
 3SW  C13  C14  single  1.461  0.020  1.461
 3SW  C1   C2   single  1.519  0.020  1.519
 3SW  C1   C6   single  1.506  0.020  1.506
 3SW  C12  C20  single  1.500  0.020  1.500
 3SW  O1   C14  double  1.213  0.020  1.213
 3SW  C2   C3   single  1.516  0.020  1.516
 3SW  C14  O2   single  1.337  0.020  1.337
 3SW  C7   C6   double  1.347  0.020  1.347
 3SW  C6   C5   single  1.474  0.020  1.474
 3SW  C3   C4   single  1.503  0.020  1.503
 3SW  C5   C4   double  1.351  0.020  1.351
 3SW  C5   C1'  single  1.508  0.020  1.508
 3SW  C4   C6'  single  1.494  0.020  1.494
 3SW  C1'  C2'  single  1.534  0.020  1.534
 3SW  C2'  C3'  single  1.530  0.020  1.530
 3SW  C6'  C7'  single  1.504  0.020  1.504
 3SW  C6'  C8'  single  1.498  0.020  1.498
 3SW  C7'  C8'  single  1.497  0.020  1.497
 3SW  C3'  C5'  single  1.526  0.020  1.526
 3SW  C3'  C4'  single  1.526  0.020  1.526
 3SW  C1   H1   single  0.970  0.020  1.090
 3SW  C1   H2   single  0.970  0.020  1.090
 3SW  C10  H3   single  0.930  0.020  1.080
 3SW  C11  H4   single  0.930  0.020  1.080
 3SW  C9   H5   single  0.930  0.020  1.080
 3SW  O2   H6   single  0.850  0.020  0.980
 3SW  C20  H7   single  0.970  0.020  1.090
 3SW  C20  H8   single  0.970  0.020  1.090
 3SW  C20  H9   single  0.970  0.020  1.090
 3SW  C19  H10  single  0.970  0.020  1.090
 3SW  C19  H11  single  0.970  0.020  1.090
 3SW  C19  H12  single  0.970  0.020  1.090
 3SW  C13  H13  single  0.930  0.020  1.080
 3SW  C2   H14  single  0.970  0.020  1.090
 3SW  C2   H15  single  0.970  0.020  1.090
 3SW  C7   H16  single  0.930  0.020  1.080
 3SW  C3   H17  single  0.970  0.020  1.090
 3SW  C3   H18  single  0.970  0.020  1.090
 3SW  C4'  H19  single  0.970  0.020  1.090
 3SW  C4'  H20  single  0.970  0.020  1.090
 3SW  C4'  H21  single  0.970  0.020  1.090
 3SW  C3'  H22  single  0.970  0.020  1.090
 3SW  C5'  H23  single  0.970  0.020  1.090
 3SW  C5'  H24  single  0.970  0.020  1.090
 3SW  C5'  H25  single  0.970  0.020  1.090
 3SW  C2'  H26  single  0.970  0.020  1.090
 3SW  C2'  H27  single  0.970  0.020  1.090
 3SW  C1'  H28  single  0.970  0.020  1.090
 3SW  C1'  H29  single  0.970  0.020  1.090
 3SW  C6'  H30  single  0.970  0.020  1.090
 3SW  C7'  H31  single  0.970  0.020  1.090
 3SW  C7'  H32  single  0.970  0.020  1.090
 3SW  C8'  H33  single  0.970  0.020  1.090
 3SW  C8'  H34  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
 3SW  H2   C1   H1   106.73  3.000
 3SW  H2   C1   C6   110.43  3.000
 3SW  H1   C1   C6   109.40  3.000
 3SW  H2   C1   C2   109.76  3.000
 3SW  H1   C1   C2   109.14  3.000
 3SW  C6   C1   C2   111.26  3.000
 3SW  H3   C10  C9   117.04  3.000
 3SW  H3   C10  C11  119.88  3.000
 3SW  C9   C10  C11  123.08  3.000
 3SW  H4   C11  C12  115.71  3.000
 3SW  H4   C11  C10  117.80  3.000
 3SW  C12  C11  C10  126.47  3.000
 3SW  H5   C9   C8   118.61  3.000
 3SW  H5   C9   C10  116.72  3.000
 3SW  C8   C9   C10  124.67  3.000
 3SW  H6   O2   C14  109.57  3.000
 3SW  O1   C14  C13  127.12  3.000
 3SW  O1   C14  O2   122.04  3.000
 3SW  C13  C14  O2   110.84  3.000
 3SW  H9   C20  H8   107.65  3.000
 3SW  H9   C20  H7   107.60  3.000
 3SW  H8   C20  H7   107.02  3.000
 3SW  H9   C20  C12  112.01  3.000
 3SW  H8   C20  C12  111.73  3.000
 3SW  H7   C20  C12  110.60  3.000
 3SW  H12  C19  H11  108.04  3.000
 3SW  H12  C19  H10  108.07  3.000
 3SW  H11  C19  H10  106.29  3.000
 3SW  H12  C19  C8   111.47  3.000
 3SW  H11  C19  C8   112.75  3.000
 3SW  H10  C19  C8   109.98  3.000
 3SW  C13  C12  C20  123.86  3.000
 3SW  C20  C12  C11  119.69  3.000
 3SW  C13  C12  C11  116.44  3.000
 3SW  H13  C13  C12  118.21  3.000
 3SW  H13  C13  C14  115.66  3.000
 3SW  C12  C13  C14  126.13  3.000
 3SW  H15  C2   H14  106.89  3.000
 3SW  H15  C2   C3   110.56  3.000
 3SW  H14  C2   C3   109.55  3.000
 3SW  H15  C2   C1   110.14  3.000
 3SW  H14  C2   C1   109.45  3.000
 3SW  C3   C2   C1   110.18  3.000
 3SW  C6'  C4   C3   116.20  3.000
 3SW  C6'  C4   C5   121.12  3.000
 3SW  C3   C4   C5   122.63  3.000
 3SW  C1'  C5   C6   118.32  3.000
 3SW  C1'  C5   C4   120.58  3.000
 3SW  C6   C5   C4   121.06  3.000
 3SW  C7   C6   C5   121.12  3.000
 3SW  C5   C6   C1   116.99  3.000
 3SW  C7   C6   C1   121.88  3.000
 3SW  H16  C7   C8   113.72  3.000
 3SW  H16  C7   C6   118.33  3.000
 3SW  C8   C7   C6   127.94  3.000
 3SW  C7   C8   C19  119.07  3.000
 3SW  C7   C8   C9   120.59  3.000
 3SW  C19  C8   C9   119.94  3.000
 3SW  H18  C3   H17  105.30  3.000
 3SW  H18  C3   C4   109.67  3.000
 3SW  H17  C3   C4   108.91  3.000
 3SW  H18  C3   C2   109.96  3.000
 3SW  H17  C3   C2   110.40  3.000
 3SW  C4   C3   C2   112.36  3.000
 3SW  H21  C4'  H20  107.16  3.000
 3SW  H21  C4'  H19  107.57  3.000
 3SW  H20  C4'  H19  107.27  3.000
 3SW  H21  C4'  C3'  112.49  3.000
 3SW  H20  C4'  C3'  111.24  3.000
 3SW  H19  C4'  C3'  110.86  3.000
 3SW  H22  C3'  C2'  108.20  3.000
 3SW  H22  C3'  C5'  108.06  3.000
 3SW  C2'  C3'  C5'  110.10  3.000
 3SW  H22  C3'  C4'  108.18  3.000
 3SW  C5'  C3'  C4'  110.36  3.000
 3SW  C2'  C3'  C4'  111.83  3.000
 3SW  H25  C5'  H24  107.76  3.000
 3SW  H25  C5'  H23  107.50  3.000
 3SW  H24  C5'  H23  107.51  3.000
 3SW  H25  C5'  C3'  111.51  3.000
 3SW  H24  C5'  C3'  111.43  3.000
 3SW  H23  C5'  C3'  110.94  3.000
 3SW  H27  C2'  H26  105.47  3.000
 3SW  H27  C2'  C1'  110.05  3.000
 3SW  H26  C2'  C1'  108.25  3.000
 3SW  H27  C2'  C3'  108.55  3.000
 3SW  H26  C2'  C3'  109.12  3.000
 3SW  C1'  C2'  C3'  114.98  3.000
 3SW  H29  C1'  H28  105.40  3.000
 3SW  H29  C1'  C2'  110.61  3.000
 3SW  H28  C1'  C2'  108.57  3.000
 3SW  H29  C1'  C5   110.12  3.000
 3SW  H28  C1'  C5   110.12  3.000
 3SW  C2'  C1'  C5   111.81  3.000
 3SW  H30  C6'  C8'  114.82  3.000
 3SW  H30  C6'  C7'  114.64  3.000
 3SW  C8'  C6'  C7'   59.82  3.000
 3SW  H30  C6'  C4   114.37  3.000
 3SW  C8'  C6'  C4   121.35  3.000
 3SW  C7'  C6'  C4   121.17  3.000
 3SW  H32  C7'  H31  114.36  3.000
 3SW  H32  C7'  C8'  118.76  3.000
 3SW  H31  C7'  C8'  117.80  3.000
 3SW  H32  C7'  C6'  118.20  3.000
 3SW  H31  C7'  C6'  117.26  3.000
 3SW  C8'  C7'  C6'   59.90  3.000
 3SW  H34  C8'  H33  113.95  3.000
 3SW  H34  C8'  C7'  117.80  3.000
 3SW  H33  C8'  C7'  118.34  3.000
 3SW  H34  C8'  C6'  118.43  3.000
 3SW  H33  C8'  C6'  117.91  3.000
 3SW  C7'  C8'  C6'   60.28  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
 3SW  CONST_01  H6   O2   C14  C13   180.00   0.0  0
 3SW  Var_01    C4   C3   C2   C1     49.09  30.0  1
 3SW  Var_02    C4   C5   C6   C1     -4.70  30.0  1
 3SW  Var_03    C5   C6   C1   C2     35.51  30.0  1
 3SW  Var_04    C5   C4   C3   C2    -19.17  30.0  1
 3SW  Var_05    C8'  C7'  C6'  C4   -110.58  30.0  1
 3SW  Var_06    C7'  C6'  C4   C5    -77.95  30.0  3
 3SW  Var_07    C3   C2   C1   C6    -57.42  30.0  1
 3SW  Var_08    C3   C4   C5   C6     -3.88  30.0  1
 3SW  Var_09    C8   C7   C6   C1     -2.75  30.0  2
 3SW  Var_10    C2'  C1'  C5   C4    -92.56  30.0  3
 3SW  Var_11    C6   C7   C8   C9    131.50  30.0  2
 3SW  Var_12    C3'  C2'  C1'  C5   -167.00  30.0  3
 3SW  Var_13    C19  C8   C9   C10  -178.05   0.0  2
 3SW  Var_14    C14  C13  C12  C11  -177.81   0.0  2
 3SW  Var_15    C12  C11  C10  C9   -178.53   0.0  2
 3SW  Var_16    C13  C12  C11  C10   176.20  30.0  2
 3SW  Var_17    C8   C9   C10  C11   174.79  30.0  2
 3SW  Var_18    C12  C13  C14  O2   -174.90  30.0  3
 3SW  Var_19    C1'  C2'  C3'  C4'    67.94  30.0  1
 3SW  Var_20    H7   C20  C12  C11    99.91  30.0  3
 3SW  Var_21    H10  C19  C8   C9    111.20  30.0  3
 3SW  Var_22    H23  C5'  C3'  C4'    65.06  30.0  3
 3SW  Var_23    H19  C4'  C3'  C5'   -64.21  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
 3SW  chir_01  C6'  C4  C7'  C8'  both

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
 3SW  plan-1  O2   0.020
 3SW  plan-1  C14  0.020
 3SW  plan-1  C13  0.020
 3SW  plan-1  O1   0.020
 3SW  plan-1  H6   0.020
 3SW  plan-2  C10  0.020
 3SW  plan-2  C9   0.020
 3SW  plan-2  C19  0.020
 3SW  plan-2  C7   0.020
 3SW  plan-2  C8   0.020
 3SW  plan-2  H5   0.020
 3SW  plan-3  C10  0.020
 3SW  plan-3  C11  0.020
 3SW  plan-3  C9   0.020
 3SW  plan-3  C12  0.020
 3SW  plan-3  H3   0.020
 3SW  plan-3  H4   0.020
 3SW  plan-4  C11  0.020
 3SW  plan-4  C14  0.020
 3SW  plan-4  C20  0.020
 3SW  plan-4  C12  0.020
 3SW  plan-4  C13  0.020
 3SW  plan-4  H13  0.020

