# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 09:02:41 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  50  24  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.456   4.0652  -2.7169   0.9763
 CIL  C2    C  CH1   0  -0.420   4.1194  -1.6306  -0.0603
 CIL  C3    C  CT    0   0.001   2.9842  -2.6433  -0.0459
 CIL  C4    C  CH3   0  -0.676   1.5929  -2.2210   0.3592
 CIL  C5    C  CH3   0  -0.654   3.0017  -3.6589  -1.1638
 CIL  C6    C  C     0   0.583   3.8731  -0.2203   0.3371
 CIL  N7    N  NH1   0  -0.721   4.0606   0.6774  -0.6581
 CIL  C8    C  C     0   0.132   3.8488   2.0560  -0.4513
 CIL  C9    C  C1    0  -0.183   2.7299   2.6585  -0.8614
 CIL  O10   O  O     0  -0.489   3.5035   0.1246   1.4494
 CIL  C11   C  C     0   0.521   4.9472   2.7625   0.2523
 CIL  O12   O  OH1   0  -0.597   4.6871   4.0427   0.4875
 CIL  O13   O  O     0  -0.440   5.9767   2.2231   0.5773
 CIL  C14   C  CH2   0  -0.480   1.5834   1.9642  -1.5107
 CIL  C15   C  CH2   0  -0.423   0.4870   1.6563  -0.4841
 CIL  C16   C  CH2   0  -0.427  -0.6996   0.9437  -1.1215
 CIL  C17   C  CH2   0  -0.549  -1.7737   0.6172  -0.0957
 CIL  C18   C  CH2   0  -0.550  -4.2934  -0.3284   0.5146
 CIL  C19   C  CH1   0  -0.208  -5.4235  -1.3057   0.1875
 CIL  C20   C  C     0   0.526  -6.3937  -1.3470   1.3649
 CIL  O22   O  OH1   0  -0.591  -5.8379  -1.8814   2.4449
 CIL  O23   O  O     0  -0.433  -7.5277  -0.9427   1.3287
 CIL  N21   N  NH2   0  -0.770  -6.0383  -0.9615  -1.0671
 CIL  S     S  S2    0  -0.015  -3.1727  -0.2102  -0.9070
 CIL  H11   H  HCH2  0   0.257   4.7981  -3.5102   0.8991
 CIL  H12A  H  HCH2  0   0.254   3.8339  -2.4139   1.9899
 CIL  H2    H  HCH1  0   0.275   4.8301  -1.7567  -0.8707
 CIL  H41   H  HCH3  0   0.238   1.5849  -1.5012   1.1750
 CIL  H42   H  HCH3  0   0.226   1.0634  -1.7764  -0.4870
 CIL  H43   H  HCH3  0   0.234   1.0185  -3.0919   0.6819
 CIL  H51   H  HCH3  0   0.231   2.4697  -4.5643  -0.8643
 CIL  H52   H  HCH3  0   0.230   2.5132  -3.2672  -2.0581
 CIL  H53   H  HCH3  0   0.230   4.0180  -3.9459  -1.4358
 CIL  H7    H  HNH1  0   0.409   4.3791   0.3610  -1.5608
 CIL  H9    H  H     0   0.277   2.6129   3.7210  -0.6837
 CIL  H12   H  HOH1  0   0.486   5.4434   4.4552   0.9301
 CIL  H141  H  HCH2  0   0.254   1.1724   2.6059  -2.2941
 CIL  H142  H  HCH2  0   0.242   1.9039   1.0355  -1.9849
 CIL  H151  H  HCH2  0   0.235   0.9076   1.0363   0.3121
 CIL  H152  H  HCH2  0   0.235   0.1505   2.5847  -0.0136
 CIL  H161  H  HCH2  0   0.236  -1.1237   1.5700  -1.9111
 CIL  H162  H  HCH2  0   0.231  -0.3570   0.0220  -1.6020
 CIL  H171  H  HCH2  0   0.256  -1.3707  -0.0295   0.6880
 CIL  H172  H  HCH2  0   0.258  -2.1306   1.5338   0.3796
 CIL  H181  H  HCH2  0   0.271  -4.6947   0.6620   0.7467
 CIL  H182  H  HCH2  0   0.282  -3.7320  -0.6765   1.3813
 CIL  H19   H  HCH1  0   0.283  -4.9861  -2.3047   0.0928
 CIL  H22   H  HOH1  0   0.483  -6.4654  -1.8771   3.1836
 CIL  H211  H  HNH2  0   0.360  -6.7559  -1.6323  -1.3087
 CIL  H122  H  HNH2  0   0.349  -6.4927  -0.0584  -1.0078

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  1.502  0.020  1.502
 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  1.521  0.020  1.521
 CIL  C2   C6    single  1.486  0.020  1.486
 CIL  C2   H2    single  0.970  0.020  1.090
 CIL  C3   C4    single  1.509  0.020  1.509
 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  1.353  0.020  1.353
 CIL  C6   O10   double  1.222  0.020  1.222
 CIL  N7   C8    single  1.410  0.020  1.410
 CIL  N7   H7    single  0.860  0.020  1.020
 CIL  C8   C9    double  1.335  0.020  1.335
 CIL  C8   C11   single  1.484  0.020  1.484
 CIL  C9   C14   single  1.489  0.020  1.489
 CIL  C9   H9    single  0.930  0.020  1.080
 CIL  C11  O12   single  1.327  0.020  1.327
 CIL  C11  O13   double  1.207  0.020  1.207
 CIL  O12  H12   single  0.850  0.020  0.980
 CIL  C14  C15   single  1.533  0.020  1.533
 CIL  C14  H141  single  0.970  0.020  1.090
 CIL  C14  H142  single  0.970  0.020  1.090
 CIL  C15  C16   single  1.524  0.020  1.524
 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  1.529  0.020  1.529
 CIL  C18  S     single  1.814  0.020  1.814
 CIL  C18  H181  single  0.970  0.020  1.090
 CIL  C18  H182  single  0.970  0.020  1.090
 CIL  C19  C20   single  1.526  0.020  1.526
 CIL  C19  N21   single  1.439  0.020  1.439
 CIL  C19  H19   single  0.970  0.020  1.090
 CIL  C20  O22   single  1.327  0.020  1.327
 CIL  C20  O23   double  1.204  0.020  1.204
 CIL  O22  H22   single  0.850  0.020  0.980
 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   114.60  3.000
 CIL  H12A  C1   C3    118.26  3.000
 CIL  H11   C1   C3    118.58  3.000
 CIL  H12A  C1   C2    116.82  3.000
 CIL  H11   C1   C2    117.14  3.000
 CIL  C3    C1   C2     61.12  3.000
 CIL  H2    C2   C6    114.75  3.000
 CIL  H2    C2   C3    114.73  3.000
 CIL  C6    C2   C3    120.37  3.000
 CIL  H2    C2   C1    117.06  3.000
 CIL  C6    C2   C1    119.72  3.000
 CIL  C3    C2   C1     59.02  3.000
 CIL  C5    C3   C4    113.42  3.000
 CIL  C5    C3   C2    115.59  3.000
 CIL  C4    C3   C2    120.27  3.000
 CIL  C5    C3   C1    117.79  3.000
 CIL  C4    C3   C1    119.90  3.000
 CIL  C2    C3   C1     59.86  3.000
 CIL  H43   C4   H42   107.37  3.000
 CIL  H43   C4   H41   107.59  3.000
 CIL  H42   C4   H41   107.93  3.000
 CIL  H43   C4   C3    109.94  3.000
 CIL  H42   C4   C3    110.65  3.000
 CIL  H41   C4   C3    113.15  3.000
 CIL  H53   C5   H52   107.88  3.000
 CIL  H53   C5   H51   107.71  3.000
 CIL  H52   C5   H51   107.70  3.000
 CIL  H53   C5   C3    111.86  3.000
 CIL  H52   C5   C3    111.09  3.000
 CIL  H51   C5   C3    110.42  3.000
 CIL  O10   C6   N7    121.61  3.000
 CIL  O10   C6   C2    124.16  3.000
 CIL  N7    C6   C2    114.20  3.000
 CIL  H7    N7   C8    119.05  3.000
 CIL  H7    N7   C6    119.61  3.000
 CIL  C8    N7   C6    121.33  3.000
 CIL  C11   C8   C9    123.45  3.000
 CIL  C11   C8   N7    115.08  3.000
 CIL  C9    C8   N7    121.47  3.000
 CIL  H9    C9   C14   116.46  3.000
 CIL  H9    C9   C8    118.85  3.000
 CIL  C14   C9   C8    124.65  3.000
 CIL  O13   C11  O12   123.40  3.000
 CIL  O13   C11  C8    123.13  3.000
 CIL  O12   C11  C8    113.47  3.000
 CIL  H12   O12  C11   109.80  3.000
 CIL  H142  C14  H141  107.38  3.000
 CIL  H142  C14  C15   109.28  3.000
 CIL  H141  C14  C15   109.21  3.000
 CIL  H142  C14  C9    111.11  3.000
 CIL  H141  C14  C9    109.16  3.000
 CIL  C15   C14  C9    110.62  3.000
 CIL  H152  C15  H151  106.64  3.000
 CIL  H152  C15  C16   109.71  3.000
 CIL  H151  C15  C16   109.82  3.000
 CIL  H152  C15  C14   109.72  3.000
 CIL  H151  C15  C14   109.05  3.000
 CIL  C16   C15  C14   111.76  3.000
 CIL  H162  C16  H161  106.67  3.000
 CIL  H162  C16  C17   109.66  3.000
 CIL  H161  C16  C17   109.64  3.000
 CIL  H162  C16  C15   109.49  3.000
 CIL  H161  C16  C15   109.65  3.000
 CIL  C17   C16  C15   111.61  3.000
 CIL  H172  C17  H171  107.75  3.000
 CIL  H172  C17  S     108.96  3.000
 CIL  H171  C17  S     109.55  3.000
 CIL  H172  C17  C16   110.12  3.000
 CIL  H171  C17  C16   110.51  3.000
 CIL  S     C17  C16   109.91  3.000
 CIL  H182  C18  H181  108.03  3.000
 CIL  H182  C18  S     109.01  3.000
 CIL  H181  C18  S     109.52  3.000
 CIL  H182  C18  C19   110.28  3.000
 CIL  H181  C18  C19   110.67  3.000
 CIL  S     C18  C19   109.30  3.000
 CIL  H19   C19  N21   108.28  3.000
 CIL  H19   C19  C20   107.22  3.000
 CIL  N21   C19  C20   114.05  3.000
 CIL  H19   C19  C18   107.84  3.000
 CIL  N21   C19  C18   110.44  3.000
 CIL  C20   C19  C18   108.78  3.000
 CIL  O23   C20  O22   123.64  3.000
 CIL  O23   C20  C19   124.49  3.000
 CIL  O22   C20  C19   111.87  3.000
 CIL  H22   O22  C20   110.33  3.000
 CIL  H122  N21  H211  106.68  3.000
 CIL  H122  N21  C19   110.73  3.000
 CIL  H211  N21  C19   110.66  3.000
 CIL  C18   S    C17    98.95  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  CONST_04  H12  O12  C11  C8    180.00   0.0  0
 CIL  CONST_05  H22  O22  C20  C19   180.00   0.0  0
 CIL  Var_01    C4   C3   C2   C1    109.18  30.0  1
 CIL  Var_02    N7   C6   C2   C1    174.66  30.0  3
 CIL  Var_03    H41  C4   C3   C1     32.46  30.0  3
 CIL  Var_04    H51  C5   C3   C1     87.35  30.0  3
 CIL  Var_05    C14  C9   C8   N7      2.71   0.0  2
 CIL  Var_06    C9   C8   N7   C6   -100.89  30.0  2
 CIL  Var_07    O12  C11  C8   N7   -176.91  30.0  2
 CIL  Var_08    C15  C14  C9   C8     97.67  30.0  3
 CIL  Var_09    C16  C15  C14  C9   -179.95  30.0  3
 CIL  Var_10    C17  C16  C15  C14   178.95  30.0  3
 CIL  Var_11    S    C17  C16  C15   179.27  30.0  3
 CIL  Var_12    C19  C18  S    C17  -165.89  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-2  H12  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-3  H22  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

