# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:41:58 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@H](Cl)[C@@H](Cl)C[C@]2(C)[C@@H](C[C@H](O)[C@H]3CC(=O)NC3=O)C(=C)CC[C@@H]12
#
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
 G5B  G5B  (3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione  ligand  55  26  .  2021-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_G5B
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
 G5B  N1   N   NH1   0  -0.677   4.9743   1.2144  -0.0330
 G5B  C2   C   CH1   0  -0.273  -1.4488   2.0332   0.6516
 G5B  C4   C   CT    0  -0.068  -3.4886   0.4744   0.1904
 G5B  C5   C   CT    0  -0.076  -1.0727  -0.5384   0.6022
 G5B  C6   C   CH1   0  -0.250  -0.1130  -1.5541  -0.1147
 G5B  O2   O   O     0  -0.429   6.4881   1.1306  -1.7456
 G5B  C7   C   CH2   0  -0.443  -3.0240  -2.0498   0.0195
 G5B  C8   C   CH2   0  -0.491  -2.0656  -3.0694  -0.5935
 G5B  C1   C   CH2   0  -0.408  -0.5185   0.8735   0.3614
 G5B  C11  C   CH2   0  -0.514   1.3593  -1.4096   0.3091
 G5B  C12  C   CH1   0  -0.172  -2.4517  -0.6409  -0.1102
 G5B  C13  C   CH3   0  -0.666  -1.1027  -0.8921   2.0929
 G5B  C14  C   CH3   0  -0.664  -4.1429   0.3870   1.5805
 G5B  C16  C   CH1   0   0.056   2.2559  -0.9703  -0.8416
 G5B  C17  C   CH1   0  -0.461   3.7086  -0.7128  -0.4095
 G5B  C18  C   C     0   0.595   3.8986   0.5188   0.4605
 G5B  C19  C   C     0   0.548   5.5182   0.6890  -1.1798
 G5B  C20  C   CH2   0  -0.581   4.6646  -0.4835  -1.5821
 G5B  C3   C   CH1   0  -0.246  -2.8322   1.8596   0.0338
 G5B  C9   C   C     0   0.210  -0.6853  -2.9512  -0.0130
 G5B  O1   O   OH1   0  -0.653   2.2334  -1.9146  -1.8901
 G5B  O3   O   O     0  -0.419   3.2630   0.8564   1.4300
 G5B  CL1  CL  CL    0  -0.148  -1.5873   2.3932   2.4269
 G5B  CL2  CL  CL    0  -0.147  -2.5685   2.2601  -1.7314
 G5B  H1   H   HNH1  0   0.423   5.3332   2.0497   0.4125
 G5B  H2   H   HCH1  0   0.322  -1.0049   2.9473   0.2625
 G5B  H3   H   HCH1  0   0.247  -0.1772  -1.2985  -1.1820
 G5B  H4   H   HCH2  0   0.245  -3.9829  -2.1264  -0.4947
 G5B  H5   H   HCH2  0   0.230  -3.2121  -2.3015   1.0661
 G5B  H6   H   HCH2  0   0.239  -2.4492  -4.0826  -0.4598
 G5B  H7   H   HCH2  0   0.231  -2.0136  -2.8882  -1.6741
 G5B  H8   H   HCH2  0   0.248  -0.2777   0.9677  -0.7035
 G5B  H9   H   HCH2  0   0.260   0.4197   1.0458   0.8911
 G5B  H10  H   HCH3  0   0.235  -4.3258   0.1862  -1.8257
 G5B  H11  H   HCH3  0   0.236  -5.3322  -0.4418  -0.5258
 G5B  H12  H   HCH3  0   0.238  -5.2483   1.2863  -0.7981
 G5B  H13  H   HCH2  0   0.263   1.4647  -0.7045   1.1306
 G5B  H14  H   HCH2  0   0.245   1.7594  -2.3480   0.7016
 G5B  H15  H   HCH1  0   0.218  -2.2230  -0.5108  -1.1783
 G5B  H16  H   HCH3  0   0.240  -1.7924  -0.2869   2.6676
 G5B  H17  H   HCH3  0   0.234  -1.3678  -1.9362   2.2531
 G5B  H18  H   HCH3  0   0.229  -0.1179  -0.7410   2.5386
 G5B  H19  H   HCH3  0   0.235  -4.9330   1.1360   1.6660
 G5B  H20  H   HCH3  0   0.239  -4.6107  -0.5905   1.7033
 G5B  H21  H   HCH3  0   0.241  -3.4668   0.5360   2.4145
 G5B  H22  H   H     0   0.232  -0.5978  -4.9679   0.5635
 G5B  H23  H   H     0   0.230   0.8918  -3.9842   0.9830
 G5B  H24  H   HCH1  0   0.244   1.8664  -0.0452  -1.2825
 G5B  H25  H   HCH1  0   0.313   4.0571  -1.5658   0.1863
 G5B  H26  H   HCH2  0   0.299   5.2858  -1.3464  -1.8159
 G5B  H27  H   HCH2  0   0.302   4.1336  -0.2126  -2.4983
 G5B  H28  H   HCH1  0   0.313  -3.5101   2.6387   0.3839
 G5B  H29  H   HOH1  0   0.443   2.4618  -2.7781  -1.5279
 G5B  C10  C   CH3   0  -0.660  -4.6582   0.3679  -0.8045
 G5B  C15  C   C2    0  -0.636  -0.0939  -4.0089   0.5386

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
 G5B  C14  C4   single  1.539  0.020  1.539
 G5B  C10  C4   single  1.539  0.020  1.539
 G5B  C4   C3   single  1.541  0.020  1.541
 G5B  C4   C12  single  1.552  0.020  1.552
 G5B  CL2  C3   single  1.829  0.020  1.829
 G5B  C7   C12  single  1.526  0.020  1.526
 G5B  C7   C8   single  1.528  0.020  1.528
 G5B  C3   C2   single  1.525  0.020  1.525
 G5B  C13  C5   single  1.532  0.020  1.532
 G5B  C12  C5   single  1.556  0.020  1.556
 G5B  C8   C9   single  1.502  0.020  1.502
 G5B  C5   C1   single  1.536  0.020  1.536
 G5B  C5   C6   single  1.571  0.020  1.571
 G5B  C15  C9   double  1.331  0.020  1.331
 G5B  C9   C6   single  1.513  0.020  1.513
 G5B  C2   C1   single  1.515  0.020  1.515
 G5B  C2   CL1  single  1.817  0.020  1.817
 G5B  C6   C11  single  1.539  0.020  1.539
 G5B  C11  C16  single  1.524  0.020  1.524
 G5B  C16  O1   single  1.411  0.020  1.411
 G5B  C16  C17  single  1.537  0.020  1.537
 G5B  C17  C20  single  1.530  0.020  1.530
 G5B  C17  C18  single  1.520  0.020  1.520
 G5B  C20  C19  single  1.505  0.020  1.505
 G5B  O3   C18  double  1.207  0.020  1.207
 G5B  C18  N1   single  1.373  0.020  1.373
 G5B  C19  N1   single  1.374  0.020  1.374
 G5B  C19  O2   double  1.207  0.020  1.207
 G5B  N1   H1   single  0.860  0.020  1.020
 G5B  C2   H2   single  0.970  0.020  1.090
 G5B  C6   H3   single  0.970  0.020  1.090
 G5B  C7   H4   single  0.970  0.020  1.090
 G5B  C7   H5   single  0.970  0.020  1.090
 G5B  C8   H6   single  0.970  0.020  1.090
 G5B  C8   H7   single  0.970  0.020  1.090
 G5B  C1   H8   single  0.970  0.020  1.090
 G5B  C1   H9   single  0.970  0.020  1.090
 G5B  C10  H10  single  0.970  0.020  1.090
 G5B  C10  H11  single  0.970  0.020  1.090
 G5B  C10  H12  single  0.970  0.020  1.090
 G5B  C11  H13  single  0.970  0.020  1.090
 G5B  C11  H14  single  0.970  0.020  1.090
 G5B  C12  H15  single  0.970  0.020  1.090
 G5B  C13  H16  single  0.970  0.020  1.090
 G5B  C13  H17  single  0.970  0.020  1.090
 G5B  C13  H18  single  0.970  0.020  1.090
 G5B  C14  H19  single  0.970  0.020  1.090
 G5B  C14  H20  single  0.970  0.020  1.090
 G5B  C14  H21  single  0.970  0.020  1.090
 G5B  C15  H22  single  0.930  0.020  1.080
 G5B  C15  H23  single  0.930  0.020  1.080
 G5B  C16  H24  single  0.970  0.020  1.090
 G5B  C17  H25  single  0.970  0.020  1.090
 G5B  C20  H26  single  0.970  0.020  1.090
 G5B  C20  H27  single  0.970  0.020  1.090
 G5B  C3   H28  single  0.970  0.020  1.090
 G5B  O1   H29  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
 G5B  H1   N1   C19  122.85  3.000
 G5B  H1   N1   C18  122.53  3.000
 G5B  C19  N1   C18  114.62  3.000
 G5B  H2   C2   CL1  102.36  3.000
 G5B  H2   C2   C3   108.72  3.000
 G5B  CL1  C2   C3   110.44  3.000
 G5B  H2   C2   C1   108.91  3.000
 G5B  CL1  C2   C1   112.69  3.000
 G5B  C3   C2   C1   113.10  3.000
 G5B  C3   C4   C14  108.91  3.000
 G5B  C3   C4   C12  109.98  3.000
 G5B  C14  C4   C12  114.72  3.000
 G5B  C12  C4   C10  109.43  3.000
 G5B  C3   C4   C10  108.67  3.000
 G5B  C14  C4   C10  104.89  3.000
 G5B  C13  C5   C12  114.39  3.000
 G5B  C12  C5   C1   107.98  3.000
 G5B  C13  C5   C1   111.83  3.000
 G5B  C1   C5   C6   107.61  3.000
 G5B  C12  C5   C6   106.86  3.000
 G5B  C13  C5   C6   107.86  3.000
 G5B  H3   C6   C9   104.94  3.000
 G5B  H3   C6   C11  107.54  3.000
 G5B  C9   C6   C11  115.47  3.000
 G5B  H3   C6   C5   104.90  3.000
 G5B  C11  C6   C5   113.47  3.000
 G5B  C9   C6   C5   109.59  3.000
 G5B  H5   C7   H4   106.50  3.000
 G5B  H5   C7   C12  111.01  3.000
 G5B  H4   C7   C12  110.76  3.000
 G5B  H5   C7   C8   109.79  3.000
 G5B  H4   C7   C8   108.39  3.000
 G5B  C12  C7   C8   110.29  3.000
 G5B  H7   C8   H6   106.89  3.000
 G5B  H7   C8   C9   108.92  3.000
 G5B  H6   C8   C9   110.41  3.000
 G5B  H7   C8   C7   108.35  3.000
 G5B  H6   C8   C7   110.48  3.000
 G5B  C9   C8   C7   111.65  3.000
 G5B  H9   C1   H8   105.62  3.000
 G5B  H9   C1   C5   112.30  3.000
 G5B  H8   C1   C5   108.10  3.000
 G5B  H9   C1   C2   108.31  3.000
 G5B  H8   C1   C2   104.79  3.000
 G5B  C5   C1   C2   116.88  3.000
 G5B  H14  C11  H13  104.47  3.000
 G5B  H14  C11  C16  107.66  3.000
 G5B  H13  C11  C16  109.05  3.000
 G5B  H14  C11  C6   111.62  3.000
 G5B  H13  C11  C6   111.20  3.000
 G5B  C16  C11  C6   112.46  3.000
 G5B  H15  C12  C7   105.64  3.000
 G5B  H15  C12  C5   104.63  3.000
 G5B  C7   C12  C5   110.75  3.000
 G5B  H15  C12  C4   104.00  3.000
 G5B  C5   C12  C4   117.14  3.000
 G5B  C7   C12  C4   113.35  3.000
 G5B  H18  C13  H17  107.00  3.000
 G5B  H18  C13  H16  106.30  3.000
 G5B  H17  C13  H16  107.62  3.000
 G5B  H18  C13  C5   110.34  3.000
 G5B  H17  C13  C5   111.66  3.000
 G5B  H16  C13  C5   113.56  3.000
 G5B  H21  C14  H20  107.71  3.000
 G5B  H21  C14  H19  107.26  3.000
 G5B  H20  C14  H19  107.19  3.000
 G5B  H21  C14  C4   114.96  3.000
 G5B  H20  C14  C4   109.57  3.000
 G5B  H19  C14  C4   109.84  3.000
 G5B  H24  C16  O1   105.08  3.000
 G5B  H24  C16  C17  107.90  3.000
 G5B  O1   C16  C17  109.63  3.000
 G5B  H24  C16  C11  109.76  3.000
 G5B  C17  C16  C11  113.08  3.000
 G5B  O1   C16  C11  111.03  3.000
 G5B  H25  C17  C20  109.52  3.000
 G5B  H25  C17  C18  106.23  3.000
 G5B  C20  C17  C18  103.84  3.000
 G5B  H25  C17  C16  108.82  3.000
 G5B  C18  C17  C16  114.51  3.000
 G5B  C20  C17  C16  113.58  3.000
 G5B  O3   C18  C17  128.35  3.000
 G5B  O3   C18  N1   124.02  3.000
 G5B  C17  C18  N1   107.63  3.000
 G5B  C20  C19  O2   128.00  3.000
 G5B  O2   C19  N1   124.74  3.000
 G5B  C20  C19  N1   107.25  3.000
 G5B  H27  C20  H26  107.07  3.000
 G5B  H27  C20  C19  107.85  3.000
 G5B  H26  C20  C19  110.56  3.000
 G5B  H27  C20  C17  112.09  3.000
 G5B  H26  C20  C17  113.72  3.000
 G5B  C19  C20  C17  105.44  3.000
 G5B  H28  C3   CL2  104.07  3.000
 G5B  H28  C3   C4   110.17  3.000
 G5B  CL2  C3   C4   110.88  3.000
 G5B  H28  C3   C2   110.64  3.000
 G5B  CL2  C3   C2   103.60  3.000
 G5B  C4   C3   C2   116.59  3.000
 G5B  C15  C9   C8   120.39  3.000
 G5B  C15  C9   C6   126.39  3.000
 G5B  C8   C9   C6   113.22  3.000
 G5B  H29  O1   C16  108.45  3.000
 G5B  H12  C10  H11  106.81  3.000
 G5B  H12  C10  H10  108.11  3.000
 G5B  H11  C10  H10  107.73  3.000
 G5B  H12  C10  C4   110.41  3.000
 G5B  H11  C10  C4   110.85  3.000
 G5B  H10  C10  C4   112.69  3.000
 G5B  H23  C15  H22  115.76  3.000
 G5B  H23  C15  C9   123.85  3.000
 G5B  H22  C15  C9   120.39  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
 G5B  CONST_01  C19  N1   C18  C17     0.00   0.0  0
 G5B  CONST_02  O3   C18  N1   C19   180.00   0.0  0
 G5B  CONST_03  H1   N1   C18  C17   180.00   0.0  0
 G5B  Var_01    C17  C20  C19  N1     -9.19  30.0  1
 G5B  Var_02    C7   C8   C9   C6    -54.39  30.0  1
 G5B  Var_03    C9   C8   C7   C12    54.01  30.0  1
 G5B  Var_04    C20  C19  N1   C18     3.51  30.0  1
 G5B  Var_05    H22  C15  C9   C6    179.65  30.0  2
 G5B  Var_06    H19  C14  C4   C12  -173.73  30.0  3
 G5B  Var_07    H10  C10  C4   C12   -43.26  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
 G5B  chir_01  C2   C3   C1   CL1  positiv
 G5B  chir_02  C5   C1   C12  C6   negativ
 G5B  chir_03  C6   C5   C9   C11  positiv
 G5B  chir_04  C12  C5   C7   C4   negativ
 G5B  chir_05  C16  O1   C17  C11  positiv
 G5B  chir_06  C17  C16  C20  C18  negativ
 G5B  chir_07  C3   CL2  C2   C4   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
 G5B  plan-1  N1   0.020
 G5B  plan-1  O2   0.020
 G5B  plan-1  C19  0.020
 G5B  plan-1  C20  0.020
 G5B  plan-2  N1   0.020
 G5B  plan-2  C17  0.020
 G5B  plan-2  C18  0.020
 G5B  plan-2  C19  0.020
 G5B  plan-2  O3   0.020
 G5B  plan-2  H1   0.020

