# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:42:09 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (1S,4S,5S,7R)-7-{[(5S)-5-amino-5-carboxypentanoyl]amino}-3,3-dimethyl-6-oxo-2-thiabicyclo[3.2.0]heptane-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H]2[C@H](NC(=O)CCC[C@H](N)C(O)=O)C(=O)[C@@H]2[C@H]1C(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
 A14  A14  '(1S,4S,5S,7R)-7-{[(5S)-5-amino-5-carboxypentanoyl]amino}-3,3-dimethyl-6-oxo-2-thiabicyclo[3.2.0]heptane-4-carboxylic acid'  ligand  44  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A14
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
 A14  C1    C  C      0   0.407   3.9273  -10.4710  -5.6356
 A14  C2    C  CH1    0  -0.221   2.6456  -10.5939  -4.7792
 A14  C3    C  CH2    0  -0.401   1.8771   -9.2758  -4.6945
 A14  C4    C  CH2    0  -0.410   2.6469   -8.1488  -4.0207
 A14  C7    C  CH2    0  -0.589   1.8101   -6.8821  -3.9116
 A14  C10   C  C      0   0.567   2.5544   -5.7129  -3.3062
 A14  N11   N  NH1    0  -0.644   1.7674   -4.7799  -2.7294
 A14  C12   C  CH1    0  -0.146   2.2626   -3.5718  -2.1642
 A14  C13   C  C      0   0.390   2.4280   -3.4735  -0.6469
 A14  N14   N  NH2    0  -0.805   2.9449  -11.0890  -3.4444
 A14  O15   O  O      0  -0.494   3.7696   -5.5988  -3.3598
 A14  C16   C  CH1    0  -0.408   1.3217   -2.3386  -2.0698
 A14  S17   S  S2     0   0.019  -0.4502   -2.6735  -2.0790
 A14  O18   O  O      0  -0.362   2.8823   -4.2120   0.1799
 A14  O19   O  O      0  -0.609   4.9575  -11.0353  -5.2151
 A14  O20   O  OC    -1  -0.617   3.8124   -9.8482  -6.7104
 A14  C30   C  CH1    0  -0.310   0.5426   -1.9336   0.3320
 A14  C31   C  C      0   0.428   0.2237   -0.4296   0.4896
 A14  C32   C  CT     0  -0.207  -0.6568   -2.7332  -0.2449
 A14  C33   C  CH3    0  -0.623  -0.6540   -4.1881   0.2246
 A14  C37   C  CH3    0  -0.641  -2.0191   -2.1299   0.0860
 A14  O42   O  O      0  -0.586   0.3927    0.2858  -0.5160
 A14  O43   O  OC    -1  -0.608  -0.1813   -0.0644   1.6098
 A14  C15   C  CH1    0  -0.335   1.7359   -2.1229  -0.5961
 A14  H2    H  HCH1   0   0.204   1.9994  -11.2940  -5.3385
 A14  H3C1  H  HCH2   0   0.202   0.9411   -9.4520  -4.1511
 A14  H3C2  H  HCH2   0   0.208   1.5876   -8.9718  -5.7027
 A14  H141  H  HNH2   0   0.332   3.6530  -11.8066  -3.5150
 A14  H142  H  HNH2   0   0.328   2.1213  -11.5198  -3.0450
 A14  H4C1  H  HCH2   0   0.218   3.5532   -7.9321  -4.5897
 A14  H4C2  H  HCH2   0   0.219   2.9681   -8.4728  -3.0287
 A14  H7C1  H  HCH2   0   0.249   0.8953   -7.0790  -3.3451
 A14  H7C2  H  HCH2   0   0.267   1.4785   -6.5697  -4.9088
 A14  H11   H  HNH1   0   0.396   0.7673   -4.9223  -2.6902
 A14  H12   H  HCH1   0   0.312   3.2039   -3.2888  -2.6452
 A14  H16   H  HCH1   0   0.293   1.5475   -1.5412  -2.7729
 A14  H15   H  HCH1   0   0.313   2.4756   -1.3267  -0.4759
 A14  H30   H  HCH1   0   0.248   0.7697   -2.3456   1.3200
 A14  H331  H  HCH3   0   0.230   0.2573   -4.7238  -0.0334
 A14  H332  H  HCH3   0   0.234  -0.7713   -4.2350   1.3098
 A14  H333  H  HCH3   0   0.238  -1.4861   -4.7329  -0.2235
 A14  H371  H  HCH3   0   0.235  -2.8173   -2.7379  -0.3430
 A14  H372  H  HCH3   0   0.238  -2.1655   -2.1060   1.1665
 A14  H373  H  HCH3   0   0.242  -2.1281   -1.1175  -0.2987

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
 A14  C1   C2    single  1.546  0.020  1.546
 A14  C1   O19   deloc   1.248  0.020  1.248
 A14  C1   O20   deloc   1.248  0.020  1.248
 A14  C2   C3    single  1.528  0.020  1.528
 A14  C2   N14   single  1.455  0.020  1.455
 A14  C2   H2    single  0.970  0.020  1.090
 A14  C3   C4    single  1.522  0.020  1.522
 A14  C3   H3C1  single  0.970  0.020  1.090
 A14  C3   H3C2  single  0.970  0.020  1.090
 A14  C4   C7    single  1.522  0.020  1.522
 A14  C4   H4C1  single  0.970  0.020  1.090
 A14  C4   H4C2  single  0.970  0.020  1.090
 A14  C7   C10   single  1.513  0.020  1.513
 A14  C7   H7C1  single  0.970  0.020  1.090
 A14  C7   H7C2  single  0.970  0.020  1.090
 A14  C10  N11   single  1.350  0.020  1.350
 A14  C10  O15   double  1.222  0.020  1.222
 A14  N11  C12   single  1.423  0.020  1.423
 A14  N11  H11   single  0.860  0.020  1.020
 A14  C12  C13   single  1.529  0.020  1.529
 A14  C12  C16   single  1.554  0.020  1.554
 A14  C12  H12   single  0.970  0.020  1.090
 A14  C13  O18   double  1.198  0.020  1.198
 A14  C13  C15   single  1.518  0.020  1.518
 A14  N14  H141  single  0.890  0.020  1.040
 A14  N14  H142  single  0.890  0.020  1.040
 A14  C16  S17   single  1.803  0.020  1.803
 A14  C16  C15   single  1.546  0.020  1.546
 A14  C16  H16   single  0.970  0.020  1.090
 A14  S17  C32   single  1.847  0.020  1.847
 A14  C30  C31   single  1.545  0.020  1.545
 A14  C30  C32   single  1.553  0.020  1.553
 A14  C30  C15   single  1.524  0.020  1.524
 A14  C30  H30   single  0.970  0.020  1.090
 A14  C31  O42   deloc   1.246  0.020  1.246
 A14  C31  O43   deloc   1.246  0.020  1.246
 A14  C32  C33   single  1.529  0.020  1.529
 A14  C32  C37   single  1.526  0.020  1.526
 A14  C33  H331  single  0.970  0.020  1.090
 A14  C33  H332  single  0.970  0.020  1.090
 A14  C33  H333  single  0.970  0.020  1.090
 A14  C37  H371  single  0.970  0.020  1.090
 A14  C37  H372  single  0.970  0.020  1.090
 A14  C37  H373  single  0.970  0.020  1.090
 A14  C15  H15   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
 A14  O20   C1   O19   126.31  3.000
 A14  O20   C1   C2    116.14  3.000
 A14  O19   C1   C2    117.51  3.000
 A14  H2    C2   N14   111.66  3.000
 A14  H2    C2   C3    106.29  3.000
 A14  N14   C2   C3    110.25  3.000
 A14  H2    C2   C1    104.76  3.000
 A14  N14   C2   C1    111.39  3.000
 A14  C3    C2   C1    112.27  3.000
 A14  H3C2  C3   H3C1  106.02  3.000
 A14  H3C2  C3   C4    109.68  3.000
 A14  H3C1  C3   C4    109.35  3.000
 A14  H3C2  C3   C2    108.80  3.000
 A14  H3C1  C3   C2    108.55  3.000
 A14  C4    C3   C2    114.14  3.000
 A14  H4C2  C4   H4C1  106.75  3.000
 A14  H4C2  C4   C7    110.10  3.000
 A14  H4C1  C4   C7    109.18  3.000
 A14  H4C2  C4   C3    109.35  3.000
 A14  H4C1  C4   C3    109.63  3.000
 A14  C7    C4   C3    111.71  3.000
 A14  H7C2  C7   H7C1  105.63  3.000
 A14  H7C2  C7   C10   107.01  3.000
 A14  H7C1  C7   C10   110.08  3.000
 A14  H7C2  C7   C4    109.78  3.000
 A14  H7C1  C7   C4    110.31  3.000
 A14  C10   C7   C4    113.67  3.000
 A14  O15   C10  N11   122.28  3.000
 A14  O15   C10  C7    122.96  3.000
 A14  N11   C10  C7    114.73  3.000
 A14  H11   N11  C12   116.65  3.000
 A14  H11   N11  C10   119.73  3.000
 A14  C12   N11  C10   123.62  3.000
 A14  H12   C12  C16   110.01  3.000
 A14  H12   C12  C13   109.05  3.000
 A14  C16   C12  C13    87.37  3.000
 A14  H12   C12  N11   110.15  3.000
 A14  C16   C12  N11   119.16  3.000
 A14  C13   C12  N11   119.10  3.000
 A14  C15   C13  O18   134.27  3.000
 A14  C15   C13  C12    92.35  3.000
 A14  O18   C13  C12   133.32  3.000
 A14  H142  N14  H141  107.20  3.000
 A14  H142  N14  C2    109.86  3.000
 A14  H141  N14  C2    108.76  3.000
 A14  H16   C16  C15   117.30  3.000
 A14  H16   C16  S17   109.70  3.000
 A14  C15   C16  S17   107.10  3.000
 A14  H16   C16  C12   114.66  3.000
 A14  C15   C16  C12    90.37  3.000
 A14  S17   C16  C12   116.56  3.000
 A14  C32   S17  C16    96.36  3.000
 A14  H30   C30  C15   109.92  3.000
 A14  H30   C30  C32   107.57  3.000
 A14  C15   C30  C32   108.34  3.000
 A14  H30   C30  C31   108.49  3.000
 A14  C15   C30  C31   110.16  3.000
 A14  C32   C30  C31   112.31  3.000
 A14  O43   C31  O42   126.99  3.000
 A14  O43   C31  C30   116.36  3.000
 A14  O42   C31  C30   116.65  3.000
 A14  C37   C32  C33   108.13  3.000
 A14  C37   C32  C30   113.92  3.000
 A14  C33   C32  C30   112.00  3.000
 A14  C37   C32  S17   107.60  3.000
 A14  C33   C32  S17   109.61  3.000
 A14  C30   C32  S17   105.42  3.000
 A14  H333  C33  H332  107.74  3.000
 A14  H333  C33  H331  107.19  3.000
 A14  H332  C33  H331  107.71  3.000
 A14  H333  C33  C32   110.34  3.000
 A14  H332  C33  C32   110.23  3.000
 A14  H331  C33  C32   113.40  3.000
 A14  H373  C37  H372  108.43  3.000
 A14  H373  C37  H371  107.83  3.000
 A14  H372  C37  H371  107.67  3.000
 A14  H373  C37  C32   112.36  3.000
 A14  H372  C37  C32   110.08  3.000
 A14  H371  C37  C32   110.33  3.000
 A14  H15   C15  C30   111.86  3.000
 A14  H15   C15  C16   112.81  3.000
 A14  C30   C15  C16   112.84  3.000
 A14  H15   C15  C13   110.06  3.000
 A14  C30   C15  C13   119.20  3.000
 A14  C16   C15  C13    88.06  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
 A14  CONST_01  C12   N11  C10  C7    180.00   0.0  0
 A14  CONST_02  O15   C10  N11  C12     0.00   0.0  0
 A14  CONST_03  H11   N11  C10  C7      0.00   0.0  0
 A14  Var_01    C30   C32  S17  C16    22.36  30.0  1
 A14  Var_02    H331  C33  C32  S17    58.90  30.0  3
 A14  Var_03    H371  C37  C32  S17    63.73  30.0  3
 A14  Var_04    C7    C4   C3   C2   -177.52  30.0  3
 A14  Var_05    C10   C7   C4   C3   -177.31  30.0  3
 A14  Var_06    N11   C10  C7   C4   -155.72  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
 A14  chir_01  C2   C1   C3   N14  positiv
 A14  chir_02  C12  N11  C13  C16  positiv
 A14  chir_03  C16  S17  C12  C15  positiv
 A14  chir_04  C30  C31  C32  C15  negativ
 A14  chir_05  C15  C13  C16  C30  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
 A14  plan-1  C7   0.020
 A14  plan-1  C10  0.020
 A14  plan-1  N11  0.020
 A14  plan-1  C12  0.020
 A14  plan-1  O15  0.020
 A14  plan-1  H11  0.020
 A14  plan-2  C12  0.020
 A14  plan-2  C13  0.020
 A14  plan-2  O18  0.020
 A14  plan-2  C15  0.020
 A14  plan-3  C1   0.020
 A14  plan-3  C2   0.020
 A14  plan-3  O19  0.020
 A14  plan-3  O20  0.020
 A14  plan-4  C30  0.020
 A14  plan-4  C31  0.020
 A14  plan-4  O42  0.020
 A14  plan-4  O43  0.020

