# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 21:55:25 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (5E)-5-[(3aS,4R,5R,6aS)-5-hydroxy-4-[(1E,3S,4R)-3-hydroxy-4-methyloct-1-en-6-yn-1-yl]hexahydropentalen-2(1H)-ylidene]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#CC[C@@H](C)[C@H](O)/C=C/[C@H]1[C@H](O)C[C@@H]2CC(/C[C@H]12)=C\CCCC(O)=O
#
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
 IL2  IL2  '(5E)-5-[(3aS,4R,5R,6aS)-5-hydroxy-4-[(1E,3S,4R)-3-hydroxy-4-methyloct-1-en-6-yn-1-yl]hexahydropentalen-2(1H)-ylidene]pentanoic acid'  ligand  57  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IL2
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
 IL2  C1    C  CH1    0  -0.241  -0.6164  -0.0316   0.7505
 IL2  O1    O  OH1    0  -0.662   2.0344  -2.4940   1.2292
 IL2  C2    C  CH1    0  -0.244  -1.4486  -1.2821   1.1506
 IL2  O2    O  OH1    0  -0.664   4.0382   2.2605   0.7883
 IL2  C3    C  CH1    0  -0.338   0.7776  -0.5861   0.4484
 IL2  C4    C  CH2    0  -0.471  -0.4334  -2.3880   1.4782
 IL2  C5    C  CH1    0   0.090   0.9249  -1.6780   1.5092
 IL2  C6    C  CH2    0  -0.469  -1.3505   0.6318  -0.4276
 IL2  C7    C  CH2    0  -0.488  -2.3580  -1.5384  -0.0565
 IL2  C8    C  C      0   0.114  -2.6289  -0.1578  -0.5848
 IL2  C9    C  C1     0  -0.168   1.8774   0.4182   0.4921
 IL2  C10   C  C1     0  -0.304  -3.7816   0.3395  -1.0279
 IL2  C11   C  C1     0  -0.264   2.8471   0.5099  -0.4101
 IL2  C12   C  CH2    0  -0.478  -5.0874  -0.3813  -1.1575
 IL2  C13   C  CH1    0   0.002   4.0406   1.4176  -0.3389
 IL2  C14   C  CH2    0  -0.402  -6.1882   0.2636  -0.3125
 IL2  C15   C  CH1    0  -0.267   5.3357   0.5882  -0.4525
 IL2  C16   C  CH2    0  -0.582  -7.5281  -0.4364  -0.4641
 IL2  C17   C  CH2    0  -0.588   6.5548   1.5200  -0.5305
 IL2  C18   C  CH3    0  -0.682   5.4721  -0.4295   0.6750
 IL2  C19   C  C      0   0.410  -8.6976   0.1637   0.3367
 IL2  C20   C  CSP    0   0.165   7.7926   0.8107  -0.8357
 IL2  C21   C  CSP    0  -0.087   8.8046   0.2122  -1.0977
 IL2  C22   C  CH3    0  -0.819  10.0264  -0.5148  -1.4132
 IL2  H1    H  HCH1   0   0.242  -0.5411   0.6599   1.5952
 IL2  HO1   H  HOH1   0   0.448   2.1663  -3.0916   1.9711
 IL2  H2    H  HCH1   0   0.244  -2.0751  -1.0544   2.0160
 IL2  H3    H  HCH1   0   0.235   0.7631  -1.0776  -0.5344
 IL2  H4    H  HCH2   0   0.235  -0.6517  -2.9045   2.4147
 IL2  H4A   H  HCH2   0   0.222  -0.4176  -3.1448   0.6878
 IL2  H5    H  HCH1   0   0.191   1.0447  -1.1880   2.4882
 IL2  H6    H  HCH2   0   0.242  -1.5435   1.6934  -0.2661
 IL2  H6A   H  HCH2   0   0.237  -0.7445   0.5614  -1.3379
 IL2  H7    H  HCH2   0   0.232  -1.8117  -2.1215  -0.8091
 IL2  H7A   H  HCH2   0   0.245  -3.2550  -2.1032   0.1975
 IL2  H9    H  H      0   0.227   1.8711   1.0749   1.3599
 IL2  H10   H  H      0   0.216  -3.8021   1.3896  -1.3155
 IL2  H11   H  H      0   0.237   2.8335  -0.1545  -1.2714
 IL2  H12   H  HCH2   0   0.219  -5.4004  -0.3750  -2.2085
 IL2  H12A  H  HCH2   0   0.223  -4.9787  -1.4337  -0.8831
 IL2  H13   H  HCH1   0   0.246   4.0115   2.0924  -1.2038
 IL2  H14   H  HCH2   0   0.206  -5.8795   0.2576   0.7364
 IL2  H14A  H  HCH2   0   0.205  -6.2862   1.3164  -0.5920
 IL2  H15   H  HCH1   0   0.238   5.2731   0.0436  -1.4008
 IL2  H16   H  HCH2   0   0.217  -7.8160  -0.4540  -1.5224
 IL2  H16A  H  HCH2   0   0.216  -7.4252  -1.4913  -0.1844
 IL2  H17   H  HCH2   0   0.263   6.3838   2.2792  -1.3000
 IL2  H17A  H  HCH2   0   0.258   6.6672   2.0603   0.4134
 IL2  H18   H  HCH3   0   0.249   4.6129  -1.0999   0.7104
 IL2  H18A  H  HCH3   0   0.242   6.3667  -1.0385   0.5439
 IL2  H18B  H  HCH3   0   0.212   5.5581   0.0546   1.6514
 IL2  H22   H  HCH3   0   0.262  10.8956   0.1430  -1.3858
 IL2  H22A  H  HCH3   0   0.262  10.2004  -1.3218  -0.7009
 IL2  H22B  H  HCH3   0   0.262   9.9770  -0.9571  -2.4087
 IL2  O3    O  OC    -1  -0.635  -9.7906  -0.4344   0.2385
 IL2  O4    O  O      0  -0.609  -8.4793   1.1897   1.0108
 IL2  HO2   H  HOH1   0   0.446   4.0344   1.7155   1.5828

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
 IL2  C2   C1    single  1.555  0.020  1.555
 IL2  C3   C1    single  1.530  0.020  1.530
 IL2  C1   C6    single  1.538  0.020  1.538
 IL2  C1   H1    single  0.970  0.020  1.090
 IL2  O1   C5    single  1.405  0.020  1.405
 IL2  O1   HO1   single  0.850  0.020  0.980
 IL2  C4   C2    single  1.537  0.020  1.537
 IL2  C7   C2    single  1.533  0.020  1.533
 IL2  C2   H2    single  0.970  0.020  1.090
 IL2  O2   C13   single  1.407  0.020  1.407
 IL2  O2   HO2   single  0.850  0.020  0.980
 IL2  C5   C3    single  1.529  0.020  1.529
 IL2  C3   C9    single  1.490  0.020  1.490
 IL2  C3   H3    single  0.970  0.020  1.090
 IL2  O3   C19   deloc   1.250  0.020  1.250
 IL2  C4   C5    single  1.533  0.020  1.533
 IL2  C4   H4    single  0.970  0.020  1.090
 IL2  C4   H4A   single  0.970  0.020  1.090
 IL2  O4   C19   deloc   1.247  0.020  1.247
 IL2  C5   H5    single  0.970  0.020  1.090
 IL2  C8   C6    single  1.511  0.020  1.511
 IL2  C6   H6    single  0.970  0.020  1.090
 IL2  C6   H6A   single  0.970  0.020  1.090
 IL2  C7   C8    single  1.503  0.020  1.503
 IL2  C7   H7    single  0.970  0.020  1.090
 IL2  C7   H7A   single  0.970  0.020  1.090
 IL2  C8   C10   double  1.331  0.020  1.331
 IL2  C9   C11   double  1.328  0.020  1.328
 IL2  C9   H9    single  0.930  0.020  1.080
 IL2  C12  C10   single  1.497  0.020  1.497
 IL2  C10  H10   single  0.930  0.020  1.080
 IL2  C11  C13   single  1.501  0.020  1.501
 IL2  C11  H11   single  0.930  0.020  1.080
 IL2  C12  C14   single  1.530  0.020  1.530
 IL2  C12  H12   single  0.970  0.020  1.090
 IL2  C12  H12A  single  0.970  0.020  1.090
 IL2  C13  C15   single  1.542  0.020  1.542
 IL2  C13  H13   single  0.970  0.020  1.090
 IL2  C16  C14   single  1.519  0.020  1.519
 IL2  C14  H14   single  0.970  0.020  1.090
 IL2  C14  H14A  single  0.970  0.020  1.090
 IL2  C15  C18   single  1.525  0.020  1.525
 IL2  C15  C17   single  1.536  0.020  1.536
 IL2  C15  H15   single  0.970  0.020  1.090
 IL2  C19  C16   single  1.539  0.020  1.539
 IL2  C16  H16   single  0.970  0.020  1.090
 IL2  C16  H16A  single  0.970  0.020  1.090
 IL2  C17  C20   single  1.459  0.020  1.459
 IL2  C17  H17   single  0.970  0.020  1.090
 IL2  C17  H17A  single  0.970  0.020  1.090
 IL2  C18  H18   single  0.970  0.020  1.090
 IL2  C18  H18A  single  0.970  0.020  1.090
 IL2  C18  H18B  single  0.970  0.020  1.090
 IL2  C20  C21   triple  1.205  0.020  1.205
 IL2  C21  C22   single  1.456  0.020  1.456
 IL2  C22  H22   single  0.970  0.020  1.090
 IL2  C22  H22A  single  0.970  0.020  1.090
 IL2  C22  H22B  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
 IL2  H1    C1   C6    110.58  3.000
 IL2  H1    C1   C3    108.58  3.000
 IL2  C6    C1   C3    116.08  3.000
 IL2  H1    C1   C2    110.27  3.000
 IL2  C6    C1   C2    106.77  3.000
 IL2  C3    C1   C2    104.30  3.000
 IL2  HO1   O1   C5    108.39  3.000
 IL2  H2    C2   C7    108.57  3.000
 IL2  H2    C2   C4    111.10  3.000
 IL2  C7    C2   C4    116.08  3.000
 IL2  H2    C2   C1    110.07  3.000
 IL2  C7    C2   C1    104.44  3.000
 IL2  C4    C2   C1    106.27  3.000
 IL2  HO2   O2   C13   108.76  3.000
 IL2  H3    C3   C9    109.72  3.000
 IL2  H3    C3   C5    107.60  3.000
 IL2  C9    C3   C5    112.94  3.000
 IL2  H3    C3   C1    109.07  3.000
 IL2  C9    C3   C1    114.98  3.000
 IL2  C5    C3   C1    102.09  3.000
 IL2  H4A   C4   H4    107.18  3.000
 IL2  H4A   C4   C5    108.79  3.000
 IL2  H4    C4   C5    112.28  3.000
 IL2  H4A   C4   C2    110.68  3.000
 IL2  H4    C4   C2    113.04  3.000
 IL2  C5    C4   C2    104.86  3.000
 IL2  H5    C5   C4    108.69  3.000
 IL2  H5    C5   C3    108.02  3.000
 IL2  C4    C5   C3    103.37  3.000
 IL2  H5    C5   O1    110.46  3.000
 IL2  C4    C5   O1    115.25  3.000
 IL2  C3    C5   O1    110.63  3.000
 IL2  H6A   C6   H6    106.46  3.000
 IL2  H6A   C6   C8    110.36  3.000
 IL2  H6    C6   C8    111.98  3.000
 IL2  H6A   C6   C1    110.16  3.000
 IL2  H6    C6   C1    112.99  3.000
 IL2  C8    C6   C1    104.95  3.000
 IL2  H7A   C7   H7    107.10  3.000
 IL2  H7A   C7   C8    114.18  3.000
 IL2  H7    C7   C8    109.68  3.000
 IL2  H7A   C7   C2    113.03  3.000
 IL2  H7    C7   C2    109.48  3.000
 IL2  C8    C7   C2    103.31  3.000
 IL2  C10   C8   C7    128.04  3.000
 IL2  C10   C8   C6    124.89  3.000
 IL2  C7    C8   C6    106.92  3.000
 IL2  H9    C9   C11   120.29  3.000
 IL2  H9    C9   C3    115.20  3.000
 IL2  C11   C9   C3    124.45  3.000
 IL2  H10   C10  C12   115.15  3.000
 IL2  H10   C10  C8    117.67  3.000
 IL2  C12   C10  C8    127.17  3.000
 IL2  H11   C11  C13   114.63  3.000
 IL2  H11   C11  C9    119.12  3.000
 IL2  C13   C11  C9    126.17  3.000
 IL2  H12A  C12  H12   105.93  3.000
 IL2  H12A  C12  C14   109.80  3.000
 IL2  H12   C12  C14   108.76  3.000
 IL2  H12A  C12  C10   110.80  3.000
 IL2  H12   C12  C10   109.22  3.000
 IL2  C14   C12  C10   112.13  3.000
 IL2  H13   C13  C15   107.15  3.000
 IL2  H13   C13  C11   108.26  3.000
 IL2  C15   C13  C11   109.82  3.000
 IL2  H13   C13  O2    105.24  3.000
 IL2  C15   C13  O2    112.49  3.000
 IL2  C11   C13  O2    113.50  3.000
 IL2  H14A  C14  H14   106.01  3.000
 IL2  H14A  C14  C16   109.81  3.000
 IL2  H14   C14  C16   110.01  3.000
 IL2  H14A  C14  C12   109.21  3.000
 IL2  H14   C14  C12   108.93  3.000
 IL2  C16   C14  C12   112.65  3.000
 IL2  H15   C15  C18   108.27  3.000
 IL2  H15   C15  C17   107.63  3.000
 IL2  C18   C15  C17   111.79  3.000
 IL2  H15   C15  C13   106.45  3.000
 IL2  C17   C15  C13   110.12  3.000
 IL2  C18   C15  C13   112.31  3.000
 IL2  H16A  C16  H16   104.80  3.000
 IL2  H16A  C16  C19   108.28  3.000
 IL2  H16   C16  C19   107.99  3.000
 IL2  H16A  C16  C14   109.58  3.000
 IL2  H16   C16  C14   109.58  3.000
 IL2  C19   C16  C14   116.01  3.000
 IL2  H17A  C17  H17   106.27  3.000
 IL2  H17A  C17  C20   109.49  3.000
 IL2  H17   C17  C20   108.83  3.000
 IL2  H17A  C17  C15   109.72  3.000
 IL2  H17   C17  C15   109.42  3.000
 IL2  C20   C17  C15   112.90  3.000
 IL2  H18B  C18  H18A  106.88  3.000
 IL2  H18B  C18  H18   107.77  3.000
 IL2  H18A  C18  H18   107.88  3.000
 IL2  H18B  C18  C15   111.83  3.000
 IL2  H18A  C18  C15   110.94  3.000
 IL2  H18   C18  C15   111.33  3.000
 IL2  C16   C19  O4    117.97  3.000
 IL2  C16   C19  O3    115.91  3.000
 IL2  O4    C19  O3    126.11  3.000
 IL2  C21   C20  C17   180.00  3.000
 IL2  C22   C21  C20   180.00  3.000
 IL2  H22B  C22  H22A  107.66  3.000
 IL2  H22B  C22  H22   107.68  3.000
 IL2  H22A  C22  H22   107.63  3.000
 IL2  H22B  C22  C21   111.24  3.000
 IL2  H22A  C22  C21   111.21  3.000
 IL2  H22   C22  C21   111.24  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
 IL2  Var_01  C7   C8   C6   C1    -26.61  30.0  1
 IL2  Var_02  C6   C8   C7   C2     37.54  30.0  1
 IL2  Var_03  C12  C10  C8   C6   -177.65  30.0  2
 IL2  Var_04  C13  C11  C9   C3   -173.92   0.0  2
 IL2  Var_05  C14  C12  C10  C8    119.98  30.0  1
 IL2  Var_06  C14  C16  C19  O3   -178.18  30.0  3
 IL2  Var_07  C16  C14  C12  C10   178.46  30.0  3
 IL2  Var_08  C19  C16  C14  C12  -179.08  30.0  1
 IL2  Var_09  H22  C22  C21  C20  -154.03  30.0  3
 IL2  Var_10  H17  C17  C20  C21   -91.26  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
 IL2  chir_01  C1   C2   C3   C6   negativ
 IL2  chir_02  C2   C7   C4   C1   negativ
 IL2  chir_03  C3   C1   C5   C9   positiv
 IL2  chir_04  C5   O1   C3   C4   negativ
 IL2  chir_05  C13  O2   C11  C15  positiv
 IL2  chir_06  C15  C17  C18  C13  negativ

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
 IL2  plan-1  C16  0.020
 IL2  plan-1  C19  0.020
 IL2  plan-1  O3   0.020
 IL2  plan-1  O4   0.020
 IL2  plan-2  C3   0.020
 IL2  plan-2  C9   0.020
 IL2  plan-2  C11  0.020
 IL2  plan-2  C13  0.020
 IL2  plan-2  H9   0.020
 IL2  plan-2  H11  0.020

