# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 20:20:54 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2~{Z},4~{E})-3-cyclopropyl-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]penta-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)CC(C)(C)[C@@]1(O)\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
 A4H  A4H  '(2~{Z},4~{E})-3-cyclopropyl-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]penta-2,4-dienoic acid'  ligand  42  21  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A4H
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
 A4H  C1   C  C      0   0.398  -3.4251  -1.8990   0.6271
 A4H  C2   C  C1     0  -0.485  -3.5985  -0.4060   0.6850
 A4H  C3   C  C      0   0.164  -2.7328   0.5281   0.2679
 A4H  C5   C  C1     0  -0.233  -0.2462   0.4318   0.1930
 A4H  C6   C  CH1    0  -0.335  -3.1173   1.9609   0.3820
 A4H  C24  C  CH2    0  -0.479  -2.1949   3.0339   0.8983
 A4H  O11  O  O      0  -0.584  -2.5561  -2.3668  -0.1365
 A4H  O12  O  OC    -1  -0.624  -4.1973  -2.5569   1.3590
 A4H  C23  C  CH2    0  -0.475  -2.5691   3.0135  -0.5441
 A4H  C4   C  C1     0  -0.277  -1.4316   0.2010  -0.3628
 A4H  C7   C  CT     0   0.157   1.0881   0.1207  -0.4444
 A4H  O7   O  OH1    0  -0.660   0.9654  -0.1604  -1.8233
 A4H  C12  C  CT     0  -0.110   1.7190  -1.1361   0.2223
 A4H  C14  C  CH3    0  -0.673   0.9649  -2.4012  -0.1829
 A4H  C8   C  C      0   0.185   2.0069   1.3429  -0.3248
 A4H  C9   C  C1     0  -0.420   3.3208   1.2340  -0.0891
 A4H  C10  C  C      0   0.400   4.0016  -0.0504   0.0720
 A4H  O10  O  O      0  -0.430   5.1810  -0.1096   0.3734
 A4H  C11  C  CH2    0  -0.551   3.1789  -1.2684  -0.2253
 A4H  H1   H  H      0   0.213  -4.5270  -0.0590   1.1330
 A4H  H2   H  H      0   0.260  -0.1917   0.8365   1.1984
 A4H  H3   H  HCH1   0   0.256  -4.1556   2.0990   0.6641
 A4H  H4   H  HCH3   0   0.260   0.6678   2.9351   0.2078
 A4H  H5   H  HCH3   0   0.263   2.1419   3.4680  -0.6072
 A4H  H6   H  HCH3   0   0.246   0.8371   2.6979  -1.5107
 A4H  H7   H  HCH3   0   0.242   0.6571  -1.1410   2.1281
 A4H  H8   H  HCH3   0   0.238   2.2736  -1.8236   2.1927
 A4H  H9   H  HCH3   0   0.232   2.0601  -0.0774   2.1309
 A4H  H10  H  HCH2   0   0.260  -2.6348   3.7876   1.5388
 A4H  H11  H  HCH2   0   0.245  -1.1844   2.7616   1.1677
 A4H  H13  H  HCH2   0   0.247  -1.8075   2.7154  -1.2545
 A4H  H14  H  HCH2   0   0.256  -3.2574   3.7624  -0.9143
 A4H  H15  H  H      0   0.247  -1.4811  -0.2381  -1.3533
 A4H  H16  H  HOH1   0   0.450   0.4595   0.5435  -2.2443
 A4H  H17  H  HCH3   0   0.223   1.0748  -2.6227  -1.2444
 A4H  H18  H  HCH3   0   0.219   1.3666  -3.2537   0.3694
 A4H  H19  H  HCH3   0   0.277  -0.0997  -2.3220   0.0380
 A4H  H20  H  H      0   0.256   3.9384   2.1246  -0.0324
 A4H  H21  H  HCH2   0   0.260   3.6387  -2.1455   0.2359
 A4H  H22  H  HCH2   0   0.277   3.2239  -1.4258  -1.3093
 A4H  C13  C  CH3    0  -0.729   1.3902   2.6823  -0.5685
 A4H  C15  C  CH3    0  -0.664   1.6739  -1.0253   1.7524

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
 A4H  O10  C10  double  1.219  0.020  1.219
 A4H  C14  C12  single  1.528  0.020  1.528
 A4H  C10  C9   single  1.463  0.020  1.463
 A4H  C10  C11  single  1.500  0.020  1.500
 A4H  C9   C8   double  1.339  0.020  1.339
 A4H  C11  C12  single  1.533  0.020  1.533
 A4H  C8   C13  single  1.495  0.020  1.495
 A4H  C8   C7   single  1.534  0.020  1.534
 A4H  C12  C7   single  1.556  0.020  1.556
 A4H  C12  C15  single  1.535  0.020  1.535
 A4H  C7   O7   single  1.413  0.020  1.413
 A4H  C7   C5   single  1.511  0.020  1.511
 A4H  C5   C4   double  1.329  0.020  1.329
 A4H  C4   C3   single  1.483  0.020  1.483
 A4H  C24  C6   single  1.506  0.020  1.506
 A4H  C24  C23  single  1.490  0.020  1.490
 A4H  C3   C6   single  1.488  0.020  1.488
 A4H  C3   C2   double  1.340  0.020  1.340
 A4H  O11  C1   deloc   1.248  0.020  1.248
 A4H  C6   C23  single  1.505  0.020  1.505
 A4H  C2   C1   single  1.504  0.020  1.504
 A4H  C1   O12  deloc   1.251  0.020  1.251
 A4H  C2   H1   single  0.930  0.020  1.080
 A4H  C5   H2   single  0.930  0.020  1.080
 A4H  C6   H3   single  0.970  0.020  1.090
 A4H  C13  H4   single  0.970  0.020  1.090
 A4H  C13  H5   single  0.970  0.020  1.090
 A4H  C13  H6   single  0.970  0.020  1.090
 A4H  C15  H7   single  0.970  0.020  1.090
 A4H  C15  H8   single  0.970  0.020  1.090
 A4H  C15  H9   single  0.970  0.020  1.090
 A4H  C24  H10  single  0.970  0.020  1.090
 A4H  C24  H11  single  0.970  0.020  1.090
 A4H  C23  H13  single  0.970  0.020  1.090
 A4H  C23  H14  single  0.970  0.020  1.090
 A4H  C4   H15  single  0.930  0.020  1.080
 A4H  O7   H16  single  0.850  0.020  0.980
 A4H  C14  H17  single  0.970  0.020  1.090
 A4H  C14  H18  single  0.970  0.020  1.090
 A4H  C14  H19  single  0.970  0.020  1.090
 A4H  C9   H20  single  0.930  0.020  1.080
 A4H  C11  H21  single  0.970  0.020  1.090
 A4H  C11  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
 A4H  O12  C1   O11  126.21  3.000
 A4H  O12  C1   C2   115.36  3.000
 A4H  O11  C1   C2   118.42  3.000
 A4H  H1   C2   C3   117.21  3.000
 A4H  H1   C2   C1   115.52  3.000
 A4H  C3   C2   C1   127.26  3.000
 A4H  C4   C3   C6   118.16  3.000
 A4H  C6   C3   C2   118.71  3.000
 A4H  C4   C3   C2   123.06  3.000
 A4H  H2   C5   C7   115.04  3.000
 A4H  H2   C5   C4   119.79  3.000
 A4H  C7   C5   C4   125.12  3.000
 A4H  H3   C6   C23  114.81  3.000
 A4H  H3   C6   C24  113.97  3.000
 A4H  C23  C6   C24   59.32  3.000
 A4H  H3   C6   C3   112.95  3.000
 A4H  C23  C6   C3   122.14  3.000
 A4H  C24  C6   C3   123.65  3.000
 A4H  H11  C24  H10  114.07  3.000
 A4H  H11  C24  C23  118.20  3.000
 A4H  H10  C24  C23  118.70  3.000
 A4H  H11  C24  C6   118.60  3.000
 A4H  H10  C24  C6   116.74  3.000
 A4H  C23  C24  C6    60.31  3.000
 A4H  H14  C23  H13  114.40  3.000
 A4H  H14  C23  C24  118.77  3.000
 A4H  H13  C23  C24  117.51  3.000
 A4H  H14  C23  C6   117.56  3.000
 A4H  H13  C23  C6   117.85  3.000
 A4H  C24  C23  C6    60.37  3.000
 A4H  H15  C4   C5   119.52  3.000
 A4H  H15  C4   C3   115.96  3.000
 A4H  C5   C4   C3   124.50  3.000
 A4H  C8   C7   C12  111.55  3.000
 A4H  C12  C7   O7   107.02  3.000
 A4H  C8   C7   O7   106.66  3.000
 A4H  O7   C7   C5   112.09  3.000
 A4H  C12  C7   C5   110.09  3.000
 A4H  C8   C7   C5   109.39  3.000
 A4H  H16  O7   C7   109.07  3.000
 A4H  C11  C12  C14  108.74  3.000
 A4H  C11  C12  C7   109.32  3.000
 A4H  C14  C12  C7   110.80  3.000
 A4H  C7   C12  C15  110.91  3.000
 A4H  C11  C12  C15  108.99  3.000
 A4H  C14  C12  C15  108.04  3.000
 A4H  H19  C14  H18  108.27  3.000
 A4H  H19  C14  H17  108.09  3.000
 A4H  H18  C14  H17  107.27  3.000
 A4H  H19  C14  C12  111.60  3.000
 A4H  H18  C14  C12  109.31  3.000
 A4H  H17  C14  C12  112.14  3.000
 A4H  C9   C8   C7   122.46  3.000
 A4H  C7   C8   C13  117.02  3.000
 A4H  C9   C8   C13  120.42  3.000
 A4H  H20  C9   C10  116.74  3.000
 A4H  H20  C9   C8   120.05  3.000
 A4H  C10  C9   C8   123.19  3.000
 A4H  C11  C10  O10  122.72  3.000
 A4H  C11  C10  C9   115.85  3.000
 A4H  O10  C10  C9   121.36  3.000
 A4H  H22  C11  H21  106.55  3.000
 A4H  H22  C11  C10  106.86  3.000
 A4H  H21  C11  C10  109.72  3.000
 A4H  H22  C11  C12  109.90  3.000
 A4H  H21  C11  C12  110.30  3.000
 A4H  C10  C11  C12  113.24  3.000
 A4H  H6   C13  H5   107.98  3.000
 A4H  H6   C13  H4   105.98  3.000
 A4H  H5   C13  H4   108.40  3.000
 A4H  H6   C13  C8   111.24  3.000
 A4H  H5   C13  C8   111.59  3.000
 A4H  H4   C13  C8   111.42  3.000
 A4H  H9   C15  H8   107.51  3.000
 A4H  H9   C15  H7   107.62  3.000
 A4H  H8   C15  H7   107.21  3.000
 A4H  H9   C15  C12  113.46  3.000
 A4H  H8   C15  C12  109.47  3.000
 A4H  H7   C15  C12  111.31  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
 A4H  Var_01  C10  C9   C8   C7      0.18  30.0  1
 A4H  Var_02  C10  C11  C12  C7     56.46  30.0  1
 A4H  Var_03  C9   C10  C11  C12   -37.15  30.0  1
 A4H  Var_04  C11  C10  C9   C8      7.99  30.0  1
 A4H  Var_05  C23  C24  C6   C3    110.38  30.0  1
 A4H  Var_06  H13  C23  C24  C6   -108.04  30.0  1
 A4H  Var_07  C24  C6   C3   C2    135.34  30.0  3
 A4H  Var_08  H4   C13  C8   C7     67.11  30.0  3
 A4H  Var_09  H17  C14  C12  C7     66.44  30.0  3
 A4H  Var_10  H7   C15  C12  C7     71.62  30.0  3
 A4H  Var_11  C6   C3   C2   C1    178.29   0.0  2
 A4H  Var_12  C7   C5   C4   C3   -179.16   0.0  2
 A4H  Var_13  O11  C1   C2   C3    -17.62  30.0  2

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
 A4H  chir_02  C7  C12  C8  C5   positiv
 A4H  chir_03  C6  C24  C3  C23  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
 A4H  plan-1  C9   0.020
 A4H  plan-1  C10  0.020
 A4H  plan-1  O10  0.020
 A4H  plan-1  C11  0.020
 A4H  plan-2  C1   0.020
 A4H  plan-2  C2   0.020
 A4H  plan-2  O11  0.020
 A4H  plan-2  O12  0.020
 A4H  plan-3  C3   0.020
 A4H  plan-3  C5   0.020
 A4H  plan-3  C4   0.020
 A4H  plan-3  C7   0.020
 A4H  plan-3  H2   0.020
 A4H  plan-3  H15  0.020
 A4H  plan-4  C1   0.020
 A4H  plan-4  C2   0.020
 A4H  plan-4  C3   0.020
 A4H  plan-4  C6   0.020
 A4H  plan-4  C4   0.020
 A4H  plan-4  H1   0.020

