# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:28:04 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (6R,7R)-3-[(acetyloxy)methyl]-7-[(4-carboxybutanoyl)amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OCC1=C(N2[C@H](SC1)[C@H](NC(=O)CCCC(O)=O)C2=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
 CEN  CEN  '(6R,7R)-3-[(acetyloxy)methyl]-7-[(4-carboxybutanoyl)amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  42  26  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CEN
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
 CEN  S1    S  S2     0   0.033   0.5575  -1.5427   0.0199
 CEN  C2    C  CH2    0  -0.622   2.3756  -1.6165   0.0301
 CEN  C3    C  C      0  -0.010   3.0698  -0.3151  -0.2936
 CEN  C4    C  C      0   0.169   2.5357   0.8976  -0.0777
 CEN  N5    N  N      0  -0.494   1.2728   0.9858   0.5022
 CEN  C6    C  C      0  -0.195   0.5100  -0.0938   1.0909
 CEN  C7    C  C      0  -0.262  -0.7531   0.7963   0.9516
 CEN  C8    C  C      0   0.531   0.1830   1.7590   0.2083
 CEN  O9    O  O      0  -0.409   0.0357   2.7570  -0.4413
 CEN  C13   C  CH2    0  -0.243   4.4383  -0.4947  -0.8691
 CEN  N14   N  NH1    0  -0.646  -1.8625   0.3204   0.2021
 CEN  C15   C  C      0   0.574  -3.0184  -0.1033   0.7730
 CEN  O16   O  O      0  -0.483  -3.2041  -0.0570   1.9767
 CEN  C17   C  CH2    0  -0.585  -4.0328  -0.6582  -0.1978
 CEN  C1    C  C      0   0.575   6.4063  -1.6690  -0.2645
 CEN  O2    O  O      0  -0.461   6.9008  -1.4305  -1.3393
 CEN  O3    O  O2     0  -0.453   5.1948  -1.2603   0.0890
 CEN  C     C  CH3    0  -0.770   7.0873  -2.4230   0.8392
 CEN  C5    C  CH2    0  -0.407  -5.4724  -0.2926   0.1483
 CEN  C9    C  CH2    0  -0.583  -6.4497  -0.9384  -0.8193
 CEN  C11   C  C      0   0.411  -7.9375  -0.6337  -0.5732
 CEN  O     O  OC    -1  -0.632  -8.7474  -1.2908  -1.2614
 CEN  O1    O  O      0  -0.608  -8.2232   0.2404   0.2679
 CEN  C10   C  C      0   0.378   3.1958   2.2510  -0.3591
 CEN  O4    O  OC    -1  -0.583   3.7695   2.3864  -1.4525
 CEN  O5    O  O      0  -0.579   3.0870   3.0725   0.5626
 CEN  HC21  H  HCH2   0   0.295   2.6375  -2.3679  -0.7180
 CEN  HC22  H  HCH2   0   0.296   2.7026  -2.0102   0.9950
 CEN  HC6   H  H      0   0.311   0.8192  -0.3474   2.1055
 CEN  HC7   H  H      0   0.327  -1.0863   1.1787   1.9166
 CEN  H131  H  HCH2   0   0.264   4.9319   0.4526  -1.0682
 CEN  H132  H  HCH2   0   0.246   4.3786  -1.0524  -1.8086
 CEN  H14   H  HNH1   0   0.409  -1.7652   0.2351  -0.7974
 CEN  H171  H  HCH2   0   0.249  -3.7984  -0.3422  -1.2175
 CEN  H172  H  HCH2   0   0.268  -3.9185  -1.7482  -0.1871
 CEN  HC1   H  HCH3   0   0.279   7.5932  -1.7129   1.4966
 CEN  HC2   H  HCH3   0   0.263   6.3830  -2.9892   1.4444
 CEN  HC3   H  HCH3   0   0.264   7.8394  -3.0920   0.4285
 CEN  HC51  H  HCH2   0   0.219  -5.6933  -0.6088   1.1688
 CEN  HC52  H  HCH2   0   0.220  -5.5895   0.7929   0.1284
 CEN  HC91  H  HCH2   0   0.224  -6.2105  -0.6296  -1.8445
 CEN  HC92  H  HCH2   0   0.217  -6.3126  -2.0255  -0.8131

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
 CEN  S1   C2    single  1.820  0.020  1.820
 CEN  S1   C6    single  1.802  0.020  1.802
 CEN  C2   C3    single  1.510  0.020  1.510
 CEN  C2   HC21  single  0.970  0.020  1.090
 CEN  C2   HC22  single  0.970  0.020  1.090
 CEN  C3   C4    double  1.343  0.020  1.343
 CEN  C3   C13   single  1.495  0.020  1.495
 CEN  C4   N5    single  1.393  0.020  1.393
 CEN  C4   C10   single  1.532  0.020  1.532
 CEN  N5   C6    single  1.447  0.020  1.447
 CEN  N5   C8    single  1.368  0.020  1.368
 CEN  C6   C7    single  1.551  0.020  1.551
 CEN  C6   HC6   single  0.970  0.020  1.090
 CEN  C7   C8    single  1.535  0.020  1.535
 CEN  C7   N14   single  1.421  0.020  1.421
 CEN  C7   HC7   single  0.970  0.020  1.090
 CEN  C8   O9    double  1.200  0.020  1.200
 CEN  C13  O3    single  1.441  0.020  1.441
 CEN  C13  H131  single  0.970  0.020  1.090
 CEN  C13  H132  single  0.970  0.020  1.090
 CEN  N14  C15   single  1.357  0.020  1.357
 CEN  N14  H14   single  0.860  0.020  1.020
 CEN  C15  O16   double  1.219  0.020  1.219
 CEN  C15  C17   single  1.510  0.020  1.510
 CEN  C17  C5    single  1.525  0.020  1.525
 CEN  C17  H171  single  0.970  0.020  1.090
 CEN  C17  H172  single  0.970  0.020  1.090
 CEN  C1   O2    double  1.207  0.020  1.207
 CEN  C1   O3    single  1.327  0.020  1.327
 CEN  C1   C     single  1.500  0.020  1.500
 CEN  C    HC1   single  0.970  0.020  1.090
 CEN  C    HC2   single  0.970  0.020  1.090
 CEN  C    HC3   single  0.970  0.020  1.090
 CEN  C5   C9    single  1.519  0.020  1.519
 CEN  C5   HC51  single  0.970  0.020  1.090
 CEN  C5   HC52  single  0.970  0.020  1.090
 CEN  C9   C11   single  1.538  0.020  1.538
 CEN  C9   HC91  single  0.970  0.020  1.090
 CEN  C9   HC92  single  0.970  0.020  1.090
 CEN  C11  O     deloc   1.250  0.020  1.250
 CEN  C11  O1    deloc   1.246  0.020  1.246
 CEN  C10  O4    deloc   1.242  0.020  1.242
 CEN  C10  O5    deloc   1.240  0.020  1.240

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
 CEN  C6    S1   C2     93.19  3.000
 CEN  HC22  C2   HC21  106.58  3.000
 CEN  HC22  C2   C3    111.25  3.000
 CEN  HC21  C2   C3    109.62  3.000
 CEN  HC22  C2   S1    108.58  3.000
 CEN  HC21  C2   S1    105.28  3.000
 CEN  C3    C2   S1    115.04  3.000
 CEN  C13   C3   C4    122.30  3.000
 CEN  C13   C3   C2    113.56  3.000
 CEN  C4    C3   C2    124.13  3.000
 CEN  C10   C4   N5    114.29  3.000
 CEN  C10   C4   C3    126.66  3.000
 CEN  N5    C4   C3    119.01  3.000
 CEN  C8    N5   C6     95.11  3.000
 CEN  C8    N5   C4    131.97  3.000
 CEN  C6    N5   C4    126.89  3.000
 CEN  HC6   C6   C7    116.60  3.000
 CEN  HC6   C6   N5    113.73  3.000
 CEN  C7    C6   N5     87.97  3.000
 CEN  HC6   C6   S1    111.00  3.000
 CEN  C7    C6   S1    115.42  3.000
 CEN  N5    C6   S1    110.13  3.000
 CEN  HC7   C7   N14   110.23  3.000
 CEN  HC7   C7   C8    113.27  3.000
 CEN  N14   C7   C8    115.52  3.000
 CEN  HC7   C7   C6    111.75  3.000
 CEN  N14   C7   C6    119.40  3.000
 CEN  C8    C7   C6     84.66  3.000
 CEN  O9    C8   C7    135.16  3.000
 CEN  O9    C8   N5    133.17  3.000
 CEN  C7    C8   N5     91.56  3.000
 CEN  H132  C13  H131  108.16  3.000
 CEN  H132  C13  O3    109.19  3.000
 CEN  H131  C13  O3    110.28  3.000
 CEN  H132  C13  C3    109.98  3.000
 CEN  H131  C13  C3    112.43  3.000
 CEN  O3    C13  C3    106.76  3.000
 CEN  H14   N14  C15   118.23  3.000
 CEN  H14   N14  C7    118.43  3.000
 CEN  C15   N14  C7    123.21  3.000
 CEN  C17   C15  O16   123.14  3.000
 CEN  C17   C15  N14   114.62  3.000
 CEN  O16   C15  N14   122.23  3.000
 CEN  H172  C17  H171  105.92  3.000
 CEN  H172  C17  C5    109.55  3.000
 CEN  H171  C17  C5    110.17  3.000
 CEN  H172  C17  C15   106.81  3.000
 CEN  H171  C17  C15   110.46  3.000
 CEN  C5    C17  C15   113.59  3.000
 CEN  C     C1   O3    111.92  3.000
 CEN  C     C1   O2    124.65  3.000
 CEN  O3    C1   O2    123.41  3.000
 CEN  C1    O3   C13   117.77  3.000
 CEN  HC3   C    HC2   109.75  3.000
 CEN  HC3   C    HC1   107.89  3.000
 CEN  HC2   C    HC1   107.67  3.000
 CEN  HC3   C    C1    110.20  3.000
 CEN  HC2   C    C1    112.15  3.000
 CEN  HC1   C    C1    109.05  3.000
 CEN  HC52  C5   HC51  106.47  3.000
 CEN  HC52  C5   C9    109.99  3.000
 CEN  HC51  C5   C9    110.01  3.000
 CEN  HC52  C5   C17   109.60  3.000
 CEN  HC51  C5   C17   109.51  3.000
 CEN  C9    C5   C17   111.15  3.000
 CEN  HC92  C9   HC91  104.91  3.000
 CEN  HC92  C9   C11   108.46  3.000
 CEN  HC91  C9   C11   107.73  3.000
 CEN  HC92  C9   C5    109.73  3.000
 CEN  HC91  C9   C5    109.59  3.000
 CEN  C11   C9   C5    115.85  3.000
 CEN  O1    C11  O     126.30  3.000
 CEN  O1    C11  C9    117.94  3.000
 CEN  O     C11  C9    115.76  3.000
 CEN  O5    C10  O4    128.53  3.000
 CEN  O5    C10  C4    114.28  3.000
 CEN  O4    C10  C4    117.19  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
 CEN  CONST_02  C7   C8   N5   C6      0.00   0.0  0
 CEN  CONST_04  O9   C8   N5   C6    180.00   0.0  0
 CEN  CONST_05  O16  C15  N14  C7      0.00   0.0  0
 CEN  CONST_06  C17  C15  N14  C7    180.00   0.0  0
 CEN  CONST_07  H14  N14  C15  O16   180.00   0.0  0
 CEN  Var_01    C4   C3   C2   S1     26.60  30.0  1
 CEN  Var_02    N5   C4   C3   C2      1.20  30.0  1
 CEN  Var_03    C6   N5   C4   C3      9.49  30.0  1
 CEN  Var_04    O3   C13  C3   C2    -57.28  30.0  3
 CEN  Var_05    O4   C10  C4   C3     45.54  30.0  2
 CEN  Var_06    O2   C1   O3   C13     0.12  30.0  2
 CEN  Var_07    C5   C17  C15  N14  -142.16  30.0  3
 CEN  Var_08    C9   C5   C17  C15  -177.00  30.0  3
 CEN  Var_09    C11  C9   C5   C17  -179.67  30.0  3
 CEN  Var_10    O    C11  C9   C5   -171.54  30.0  3
 CEN  Var_11    HC1  C    C1   O2     92.38  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
 CEN  chir_01  C6  S1   N5  C7  negativ
 CEN  chir_02  C7  N14  C6  C8  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
 CEN  plan-1  C7   0.020
 CEN  plan-1  N14  0.020
 CEN  plan-1  C15  0.020
 CEN  plan-1  O16  0.020
 CEN  plan-1  C17  0.020
 CEN  plan-1  H14  0.020
 CEN  plan-2  C4   0.020
 CEN  plan-2  N5   0.020
 CEN  plan-2  C6   0.020
 CEN  plan-2  C7   0.020
 CEN  plan-2  C8   0.020
 CEN  plan-2  O9   0.020
 CEN  plan-3  C9   0.020
 CEN  plan-3  C11  0.020
 CEN  plan-3  O    0.020
 CEN  plan-3  O1   0.020
 CEN  plan-4  C4   0.020
 CEN  plan-4  C10  0.020
 CEN  plan-4  O4   0.020
 CEN  plan-4  O5   0.020
 CEN  plan-5  C1   0.020
 CEN  plan-5  O2   0.020
 CEN  plan-5  O3   0.020
 CEN  plan-5  C    0.020

