# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 02:47:41 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (~{E})-3-(trifluoromethyl)-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]pent-2-en-4-ynoic 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)C(F)(F)F
#
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
 A4K  A4K  '(~{E})-3-(trifluoromethyl)-5-[(1~{S})-2,6,6-trimethyl-1-oxidanyl-4-oxidanylidene-cyclohex-2-en-1-yl]pent-2-en-4-ynoic acid'  ligand  36  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A4K
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
 A4K  C1   C  C      0   0.402   2.5743   2.2244   1.5005
 A4K  C2   C  C1     0  -0.411   2.9841   1.3371   0.3388
 A4K  C4   C  CSP    0   0.121   0.8432   0.1755   0.1083
 A4K  C5   C  CSP    0   0.187  -0.2961  -0.1285   0.3489
 A4K  C6   C  CT     0   1.002   2.6470  -0.3672  -1.4367
 A4K  C8   C  C      0   0.132  -2.4126   0.9356   0.5032
 A4K  C9   C  C1     0  -0.395  -3.1312   1.0847  -0.6172
 A4K  C10  C  C      0   0.409  -3.2663   0.0272  -1.6189
 A4K  C11  C  CH2    0  -0.559  -2.4685  -1.2261  -1.3824
 A4K  C12  C  CT     0  -0.135  -2.3048  -1.5845   0.0967
 A4K  C13  C  CH3    0  -0.750  -2.2511   2.0383   1.4955
 A4K  C14  C  CH3    0  -0.651  -3.6709  -1.9175   0.7061
 A4K  C15  C  CH3    0  -0.647  -1.4014  -2.8105   0.2174
 A4K  O11  O  O      0  -0.565   1.5692   1.8978   2.1526
 A4K  O12  O  OC    -1  -0.594   3.3123   3.2134   1.6690
 A4K  C3   C  C      0  -0.404   2.1869   0.4475  -0.2624
 A4K  F20  F  F      0  -0.298   3.9247  -0.1583  -1.7538
 A4K  F21  F  F      0  -0.309   2.5075  -1.6788  -1.1987
 A4K  F22  F  F      0  -0.310   1.9185  -0.0984  -2.5294
 A4K  C7   C  CT     0   0.093  -1.6679  -0.3652   0.8102
 A4K  O7   O  OH1    0  -0.652  -1.6651  -0.6297   2.1919
 A4K  O10  O  O      0  -0.427  -3.9563   0.1786  -2.6109
 A4K  H1   H  H      0   0.269   3.9927   1.4702  -0.0339
 A4K  H2   H  H      0   0.262  -3.6373   2.0229  -0.8189
 A4K  H3   H  HCH2   0   0.273  -2.9243  -2.0553  -1.9276
 A4K  H4   H  HCH2   0   0.278  -1.4799  -1.0633  -1.8316
 A4K  H5   H  HCH3   0   0.264  -1.1952   2.2148   1.7200
 A4K  H6   H  HCH3   0   0.260  -2.6793   2.9671   1.1249
 A4K  H7   H  HCH3   0   0.264  -2.7441   1.7906   2.4371
 A4K  H8   H  HCH3   0   0.237  -4.1215  -2.7375   0.1443
 A4K  H9   H  HCH3   0   0.244  -3.5803  -2.2416   1.7418
 A4K  H10  H  HCH3   0   0.234  -4.3661  -1.0785   0.6768
 A4K  H11  H  HCH3   0   0.234  -0.4242  -2.6448  -0.2394
 A4K  H12  H  HCH3   0   0.240  -1.2458  -3.0907   1.2588
 A4K  H13  H  HCH3   0   0.236  -1.8620  -3.6606  -0.2882
 A4K  H15  H  HOH1   0   0.463  -1.0159  -0.0630   2.6245

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
 A4K  O10  C10  double  1.218  0.020  1.218
 A4K  C14  C12  single  1.533  0.020  1.533
 A4K  C9   C10  single  1.463  0.020  1.463
 A4K  C9   C8   double  1.339  0.020  1.339
 A4K  C10  C11  single  1.504  0.020  1.504
 A4K  C13  C8   single  1.492  0.020  1.492
 A4K  C8   C7   single  1.530  0.020  1.530
 A4K  C11  C12  single  1.531  0.020  1.531
 A4K  C12  C7   single  1.550  0.020  1.550
 A4K  C12  C15  single  1.528  0.020  1.528
 A4K  O7   C7   single  1.407  0.020  1.407
 A4K  C7   C5   single  1.466  0.020  1.466
 A4K  C5   C4   triple  1.204  0.020  1.204
 A4K  C4   C3   single  1.420  0.020  1.420
 A4K  F21  C6   single  1.340  0.020  1.340
 A4K  O11  C1   deloc   1.242  0.020  1.242
 A4K  C3   C6   single  1.501  0.020  1.501
 A4K  C3   C2   double  1.337  0.020  1.337
 A4K  F22  C6   single  1.341  0.020  1.341
 A4K  C6   F20  single  1.333  0.020  1.333
 A4K  C1   C2   single  1.518  0.020  1.518
 A4K  C1   O12  deloc   1.245  0.020  1.245
 A4K  C2   H1   single  0.930  0.020  1.080
 A4K  C9   H2   single  0.930  0.020  1.080
 A4K  C11  H3   single  0.970  0.020  1.090
 A4K  C11  H4   single  0.970  0.020  1.090
 A4K  C13  H5   single  0.970  0.020  1.090
 A4K  C13  H6   single  0.970  0.020  1.090
 A4K  C13  H7   single  0.970  0.020  1.090
 A4K  C14  H8   single  0.970  0.020  1.090
 A4K  C14  H9   single  0.970  0.020  1.090
 A4K  C14  H10  single  0.970  0.020  1.090
 A4K  C15  H11  single  0.970  0.020  1.090
 A4K  C15  H12  single  0.970  0.020  1.090
 A4K  C15  H13  single  0.970  0.020  1.090
 A4K  O7   H15  single  0.850  0.020  0.980

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
 A4K  O12  C1   O11  128.12  3.000
 A4K  O12  C1   C2   114.06  3.000
 A4K  O11  C1   C2   117.81  3.000
 A4K  H1   C2   C3   118.82  3.000
 A4K  H1   C2   C1   116.28  3.000
 A4K  C3   C2   C1   124.88  3.000
 A4K  C3   C4   C5   180.00  3.000
 A4K  C7   C5   C4   180.00  3.000
 A4K  F22  C6   F21  106.53  3.000
 A4K  F22  C6   F20  107.19  3.000
 A4K  F21  C6   F20  107.18  3.000
 A4K  F20  C6   C3   113.25  3.000
 A4K  F22  C6   C3   111.24  3.000
 A4K  F21  C6   C3   111.11  3.000
 A4K  C7   C8   C13  116.24  3.000
 A4K  C7   C8   C9   121.58  3.000
 A4K  C13  C8   C9   122.15  3.000
 A4K  H2   C9   C10  117.05  3.000
 A4K  H2   C9   C8   120.14  3.000
 A4K  C10  C9   C8   122.81  3.000
 A4K  O10  C10  C11  122.15  3.000
 A4K  C11  C10  C9   116.46  3.000
 A4K  O10  C10  C9   121.35  3.000
 A4K  H4   C11  H3   106.50  3.000
 A4K  H4   C11  C12  109.50  3.000
 A4K  H3   C11  C12  110.44  3.000
 A4K  H4   C11  C10  106.84  3.000
 A4K  H3   C11  C10  109.44  3.000
 A4K  C12  C11  C10  113.81  3.000
 A4K  C7   C12  C15  110.61  3.000
 A4K  C15  C12  C14  108.75  3.000
 A4K  C7   C12  C14  110.74  3.000
 A4K  C15  C12  C11  109.12  3.000
 A4K  C7   C12  C11  107.74  3.000
 A4K  C14  C12  C11  109.86  3.000
 A4K  H7   C13  H6   108.05  3.000
 A4K  H7   C13  H5   107.19  3.000
 A4K  H6   C13  H5   108.19  3.000
 A4K  H7   C13  C8   110.93  3.000
 A4K  H6   C13  C8   111.21  3.000
 A4K  H5   C13  C8   111.12  3.000
 A4K  H10  C14  H9   107.92  3.000
 A4K  H10  C14  H8   107.53  3.000
 A4K  H9   C14  H8   107.47  3.000
 A4K  H10  C14  C12  112.99  3.000
 A4K  H9   C14  C12  111.64  3.000
 A4K  H8   C14  C12  109.06  3.000
 A4K  H13  C15  H12  107.63  3.000
 A4K  H13  C15  H11  107.60  3.000
 A4K  H12  C15  H11  108.13  3.000
 A4K  H13  C15  C12  109.82  3.000
 A4K  H12  C15  C12  111.49  3.000
 A4K  H11  C15  C12  112.00  3.000
 A4K  C6   C3   C4   112.97  3.000
 A4K  C6   C3   C2   121.99  3.000
 A4K  C4   C3   C2   125.03  3.000
 A4K  O7   C7   C12  107.77  3.000
 A4K  O7   C7   C8   110.97  3.000
 A4K  C12  C7   C8   112.12  3.000
 A4K  O7   C7   C5   109.72  3.000
 A4K  C12  C7   C5   111.50  3.000
 A4K  C8   C7   C5   104.77  3.000
 A4K  H15  O7   C7   109.36  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
 A4K  Var_01  C11  C10  C9   C8     -4.33  30.0  1
 A4K  Var_02  C12  C11  C10  C9     33.60  30.0  1
 A4K  Var_03  C7   C8   C9   C10     0.39  30.0  1
 A4K  Var_04  C7   C12  C11  C10   -55.93  30.0  1
 A4K  Var_05  H5   C13  C8   C9   -127.42  30.0  3
 A4K  Var_06  H8   C14  C12  C11    57.58  30.0  3
 A4K  Var_07  H11  C15  C12  C11    57.80  30.0  3
 A4K  Var_08  C4   C3   C2   C1     -1.31   0.0  2
 A4K  Var_09  F21  C6   C3   C2    123.99  30.0  3
 A4K  Var_10  C3   C2   C1   O11    18.46  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
 A4K  chir_01  C7  C12  C8  C5  positiv

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
 A4K  plan-1  C9   0.020
 A4K  plan-1  C10  0.020
 A4K  plan-1  C11  0.020
 A4K  plan-1  O10  0.020
 A4K  plan-2  C1   0.020
 A4K  plan-2  C2   0.020
 A4K  plan-2  O11  0.020
 A4K  plan-2  O12  0.020
 A4K  plan-3  C1   0.020
 A4K  plan-3  C2   0.020
 A4K  plan-3  C4   0.020
 A4K  plan-3  C6   0.020
 A4K  plan-3  C3   0.020
 A4K  plan-3  H1   0.020

