# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:33:57 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2Z)-7-[(2-amino-2-carboxyethyl)sulfanyl]-2-({[(1S)-2,2-dimethylcyclopropyl]carbonyl}amino)hept-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)C[C@@H]1C(=O)N\C(=C/CCCCSCC(N)C(O)=O)C(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
 CIL  CIL  '(2Z)-7-[(2-amino-2-carboxyethyl)sulfanyl]-2-({[(1S)-2,2-dimethylcyclopropyl]carbonyl}amino)hept-2-enoic acid'  ligand  48  24  .  2022-07-24  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_CIL
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
 CIL  C1    C  CH2    0  -0.458   5.3235  -2.7122   0.4704
 CIL  C2    C  CH1    0  -0.427   4.6908  -1.6563  -0.3925
 CIL  C3    C  CT     0   0.004   3.9088  -2.8858   0.0381
 CIL  C4    C  CH3    0  -0.669   2.8018  -2.7632   1.0573
 CIL  C5    C  CH3    0  -0.656   3.6145  -3.8903  -1.0506
 CIL  C6    C  C      0   0.584   4.3733  -0.3147   0.1715
 CIL  N7    N  NH1    0  -0.714   3.9873   0.5882  -0.7529
 CIL  C8    C  C      0   0.109   3.6757   1.9260  -0.4255
 CIL  C9    C  C1     0  -0.247   2.4809   2.4390  -0.7223
 CIL  O10   O  O      0  -0.499   4.4183  -0.0519   1.3650
 CIL  C11   C  C      0   0.384   4.7955   2.7734   0.1749
 CIL  O12   O  OC    -1  -0.603   4.4570   3.8528   0.6989
 CIL  O13   O  O      0  -0.597   5.9490   2.3254   0.0553
 CIL  C14   C  CH2    0  -0.466   1.3256   1.7191  -1.3358
 CIL  C15   C  CH2    0  -0.411   0.1378   1.6225  -0.3756
 CIL  C16   C  CH2    0  -0.420  -1.0590   0.9294  -1.0171
 CIL  C17   C  CH2    0  -0.545  -2.2380   0.8161  -0.0627
 CIL  C18   C  CH2    0  -0.537  -4.8489   0.0134   0.4546
 CIL  C19   C  CH1    0  -0.218  -5.9985  -0.9347   0.1346
 CIL  C20   C  C      0   0.392  -7.0198  -0.8984   1.3039
 CIL  O22   O  OC    -1  -0.620  -6.5746  -1.2392   2.4193
 CIL  O23   O  O      0  -0.602  -8.1823  -0.5387   1.0418
 CIL  N21   N  NH2    0  -0.780  -6.5252  -0.6360  -1.1846
 CIL  S     S  S2     0  -0.042  -3.6314  -0.0014  -0.8934
 CIL  H11   H  HCH2   0   0.253   6.0891  -3.3310   0.0176
 CIL  H12A  H  HCH2   0   0.251   5.5098  -2.4502   1.5048
 CIL  H2    H  HCH1   0   0.266   4.9800  -1.6497  -1.4387
 CIL  H41   H  HCH3   0   0.237   3.0641  -2.1067   1.8835
 CIL  H42   H  HCH3   0   0.222   1.8878  -2.3798   0.5978
 CIL  H43   H  HCH3   0   0.228   2.5721  -3.7463   1.4730
 CIL  H51   H  HCH3   0   0.229   3.4798  -4.8872  -0.6255
 CIL  H52   H  HCH3   0   0.228   2.6961  -3.6321  -1.5819
 CIL  H53   H  HCH3   0   0.229   4.4194  -3.9486  -1.7844
 CIL  H7    H  HNH1   0   0.397   3.8871   0.2835  -1.7082
 CIL  H9    H  H      0   0.238   2.3277   3.4869  -0.4893
 CIL  H141  H  HCH2   0   0.233   1.0054   2.2527  -2.2373
 CIL  H142  H  HCH2   0   0.224   1.6094   0.7139  -1.6535
 CIL  H151  H  HCH2   0   0.223   0.4444   1.0752   0.5208
 CIL  H152  H  HCH2   0   0.222  -0.1514   2.6247  -0.0447
 CIL  H161  H  HCH2   0   0.226  -1.3620   1.4816  -1.9118
 CIL  H162  H  HCH2   0   0.226  -0.7634  -0.0694  -1.3524
 CIL  H171  H  HCH2   0   0.250  -1.9549   0.2437   0.8244
 CIL  H172  H  HCH2   0   0.250  -2.5510   1.8083   0.2712
 CIL  H181  H  HCH2   0   0.249  -5.2182   1.0340   0.5957
 CIL  H182  H  HCH2   0   0.262  -4.3624  -0.2965   1.3785
 CIL  H19   H  HCH1   0   0.227  -5.5824  -1.9484   0.0985
 CIL  H211  H  HNH2   0   0.339  -7.2677  -1.2914  -1.3951
 CIL  H122  H  HNH2   0   0.327  -6.9855   0.2671  -1.1522

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
 CIL  C1   C2    single  1.503  0.020  1.503
 CIL  C1   C3    single  1.490  0.020  1.490
 CIL  C1   H11   single  0.970  0.020  1.090
 CIL  C1   H12A  single  0.970  0.020  1.090
 CIL  C2   C3    single  1.519  0.020  1.519
 CIL  C2   C6    single  1.490  0.020  1.490
 CIL  C2   H2    single  0.970  0.020  1.090
 CIL  C3   C4    single  1.510  0.020  1.510
 CIL  C3   C5    single  1.510  0.020  1.510
 CIL  C4   H41   single  0.970  0.020  1.090
 CIL  C4   H42   single  0.970  0.020  1.090
 CIL  C4   H43   single  0.970  0.020  1.090
 CIL  C5   H51   single  0.970  0.020  1.090
 CIL  C5   H52   single  0.970  0.020  1.090
 CIL  C5   H53   single  0.970  0.020  1.090
 CIL  C6   N7    single  1.349  0.020  1.349
 CIL  C6   O10   double  1.223  0.020  1.223
 CIL  N7   C8    single  1.412  0.020  1.412
 CIL  N7   H7    single  0.860  0.020  1.020
 CIL  C8   C9    double  1.334  0.020  1.334
 CIL  C8   C11   single  1.527  0.020  1.527
 CIL  C9   C14   single  1.493  0.020  1.493
 CIL  C9   H9    single  0.930  0.020  1.080
 CIL  C11  O12   deloc   1.247  0.020  1.247
 CIL  C11  O13   deloc   1.243  0.020  1.243
 CIL  C14  C15   single  1.530  0.020  1.530
 CIL  C14  H141  single  0.970  0.020  1.090
 CIL  C14  H142  single  0.970  0.020  1.090
 CIL  C15  C16   single  1.525  0.020  1.525
 CIL  C15  H151  single  0.970  0.020  1.090
 CIL  C15  H152  single  0.970  0.020  1.090
 CIL  C16  C17   single  1.521  0.020  1.521
 CIL  C16  H161  single  0.970  0.020  1.090
 CIL  C16  H162  single  0.970  0.020  1.090
 CIL  C17  S     single  1.817  0.020  1.817
 CIL  C17  H171  single  0.970  0.020  1.090
 CIL  C17  H172  single  0.970  0.020  1.090
 CIL  C18  C19   single  1.524  0.020  1.524
 CIL  C18  S     single  1.816  0.020  1.816
 CIL  C18  H181  single  0.970  0.020  1.090
 CIL  C18  H182  single  0.970  0.020  1.090
 CIL  C19  C20   single  1.553  0.020  1.553
 CIL  C19  N21   single  1.452  0.020  1.452
 CIL  C19  H19   single  0.970  0.020  1.090
 CIL  C20  O22   deloc   1.248  0.020  1.248
 CIL  C20  O23   deloc   1.245  0.020  1.245
 CIL  N21  H211  single  0.890  0.020  1.040
 CIL  N21  H122  single  0.890  0.020  1.040

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
 CIL  H12A  C1   H11   114.56  3.000
 CIL  H12A  C1   C3    117.95  3.000
 CIL  H11   C1   C3    118.90  3.000
 CIL  H12A  C1   C2    116.79  3.000
 CIL  H11   C1   C2    117.30  3.000
 CIL  C3    C1   C2     61.02  3.000
 CIL  H2    C2   C6    114.60  3.000
 CIL  H2    C2   C3    114.53  3.000
 CIL  C6    C2   C3    120.78  3.000
 CIL  H2    C2   C1    116.45  3.000
 CIL  C6    C2   C1    120.32  3.000
 CIL  C3    C2   C1     59.04  3.000
 CIL  C5    C3   C4    113.44  3.000
 CIL  C5    C3   C2    115.73  3.000
 CIL  C4    C3   C2    120.20  3.000
 CIL  C5    C3   C1    118.15  3.000
 CIL  C4    C3   C1    119.41  3.000
 CIL  C2    C3   C1     59.94  3.000
 CIL  H43   C4   H42   107.46  3.000
 CIL  H43   C4   H41   107.76  3.000
 CIL  H42   C4   H41   108.03  3.000
 CIL  H43   C4   C3    109.76  3.000
 CIL  H42   C4   C3    110.98  3.000
 CIL  H41   C4   C3    112.65  3.000
 CIL  H53   C5   H52   107.82  3.000
 CIL  H53   C5   H51   107.70  3.000
 CIL  H52   C5   H51   107.55  3.000
 CIL  H53   C5   C3    112.13  3.000
 CIL  H52   C5   C3    110.94  3.000
 CIL  H51   C5   C3    110.52  3.000
 CIL  O10   C6   N7    122.38  3.000
 CIL  O10   C6   C2    123.73  3.000
 CIL  N7    C6   C2    113.85  3.000
 CIL  H7    N7   C8    118.97  3.000
 CIL  H7    N7   C6    118.41  3.000
 CIL  C8    N7   C6    122.58  3.000
 CIL  C11   C8   C9    122.06  3.000
 CIL  C11   C8   N7    117.07  3.000
 CIL  C9    C8   N7    120.70  3.000
 CIL  H9    C9   C14   116.42  3.000
 CIL  H9    C9   C8    116.78  3.000
 CIL  C14   C9   C8    126.81  3.000
 CIL  O13   C11  O12   127.18  3.000
 CIL  O13   C11  C8    116.26  3.000
 CIL  O12   C11  C8    116.52  3.000
 CIL  H142  C14  H141  106.56  3.000
 CIL  H142  C14  C15   109.04  3.000
 CIL  H141  C14  C15   108.67  3.000
 CIL  H142  C14  C9    111.25  3.000
 CIL  H141  C14  C9    109.24  3.000
 CIL  C15   C14  C9    111.91  3.000
 CIL  H152  C15  H151  106.52  3.000
 CIL  H152  C15  C16   109.64  3.000
 CIL  H151  C15  C16   109.71  3.000
 CIL  H152  C15  C14   109.70  3.000
 CIL  H151  C15  C14   109.16  3.000
 CIL  C16   C15  C14   111.96  3.000
 CIL  H162  C16  H161  106.55  3.000
 CIL  H162  C16  C17   109.49  3.000
 CIL  H161  C16  C17   109.63  3.000
 CIL  H162  C16  C15   109.39  3.000
 CIL  H161  C16  C15   109.39  3.000
 CIL  C17   C16  C15   112.23  3.000
 CIL  H172  C17  H171  107.56  3.000
 CIL  H172  C17  S     109.19  3.000
 CIL  H171  C17  S     109.52  3.000
 CIL  H172  C17  C16   110.25  3.000
 CIL  H171  C17  C16   110.33  3.000
 CIL  S     C17  C16   109.95  3.000
 CIL  H182  C18  H181  107.86  3.000
 CIL  H182  C18  S     109.14  3.000
 CIL  H181  C18  S     109.23  3.000
 CIL  H182  C18  C19   109.75  3.000
 CIL  H181  C18  C19   110.65  3.000
 CIL  S     C18  C19   110.16  3.000
 CIL  H19   C19  N21   107.35  3.000
 CIL  H19   C19  C20   107.21  3.000
 CIL  N21   C19  C20   116.16  3.000
 CIL  H19   C19  C18   107.21  3.000
 CIL  N21   C19  C18   109.66  3.000
 CIL  C20   C19  C18   108.87  3.000
 CIL  O23   C20  O22   126.87  3.000
 CIL  O23   C20  C19   117.54  3.000
 CIL  O22   C20  C19   115.58  3.000
 CIL  H122  N21  H211  104.49  3.000
 CIL  H122  N21  C19   108.60  3.000
 CIL  H211  N21  C19   108.77  3.000
 CIL  C18   S    C17    99.85  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
 CIL  CONST_01  C8   N7   C6   C2    180.00   0.0  0
 CIL  CONST_02  H7   N7   C6   C2      0.00   0.0  0
 CIL  CONST_03  O10  C6   N7   C8      0.00   0.0  0
 CIL  Var_01    C4   C3   C2   C1    108.64  30.0  1
 CIL  Var_02    N7   C6   C2   C1    171.13  30.0  3
 CIL  Var_03    H41  C4   C3   C1     28.10  30.0  3
 CIL  Var_04    H51  C5   C3   C1     86.19  30.0  3
 CIL  Var_05    C14  C9   C8   N7      3.51   0.0  2
 CIL  Var_06    C9   C8   N7   C6   -122.71  30.0  2
 CIL  Var_07    O12  C11  C8   N7   -166.41  30.0  2
 CIL  Var_08    C15  C14  C9   C8    114.48  30.0  3
 CIL  Var_09    C16  C15  C14  C9    178.06  30.0  3
 CIL  Var_10    C17  C16  C15  C14   179.36  30.0  3
 CIL  Var_11    S    C17  C16  C15   179.42  30.0  3
 CIL  Var_12    C19  C18  S    C17  -165.53  30.0  1

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
 CIL  chir_02  C19  C18  C20  N21  negativ
 CIL  chir_03  C2   C1   C3   C6   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
 CIL  plan-1  C2   0.020
 CIL  plan-1  C6   0.020
 CIL  plan-1  N7   0.020
 CIL  plan-1  C8   0.020
 CIL  plan-1  O10  0.020
 CIL  plan-1  H7   0.020
 CIL  plan-2  C8   0.020
 CIL  plan-2  C11  0.020
 CIL  plan-2  O12  0.020
 CIL  plan-2  O13  0.020
 CIL  plan-3  C19  0.020
 CIL  plan-3  C20  0.020
 CIL  plan-3  O22  0.020
 CIL  plan-3  O23  0.020
 CIL  plan-4  N7   0.020
 CIL  plan-4  C8   0.020
 CIL  plan-4  C9   0.020
 CIL  plan-4  C11  0.020
 CIL  plan-4  C14  0.020
 CIL  plan-4  H9   0.020

