# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:17:12 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: (6R,7R)-3-[(acetyloxy)methyl]-8-oxo-7-[(thiophen-2-ylacetyl)amino]-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)Cc3sccc3)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
 CLS  CLS  '(6R,7R)-3-[(acetyloxy)methyl]-8-oxo-7-[(thiophen-2-ylacetyl)amino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid'  ligand  41  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_CLS
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
 CLS  S1    S  S2     0   0.037  -1.1802  -0.6601   0.4773
 CLS  C2    C  CH2    0  -0.620  -1.4382  -0.4725   2.2688
 CLS  C3    C  C      0  -0.011  -0.1752  -0.3529   3.0887
 CLS  C3'   C  CH2    0  -0.241  -0.3536  -0.7716   4.5133
 CLS  O20   O  O2     0  -0.454  -1.3852   0.0717   5.0621
 CLS  C21   C  C      0   0.573  -1.8076  -0.1879   6.2938
 CLS  O22   O  O      0  -0.459  -1.3752  -1.0905   6.9673
 CLS  C23   C  CH3    0  -0.768  -2.8609   0.7867   6.7304
 CLS  C4    C  C      0   0.166   0.9942   0.1053   2.6139
 CLS  C4'   C  C      0   0.380   2.3052   0.2616   3.3914
 CLS  O4A   O  OC    -1  -0.581   2.6274  -0.6655   4.1527
 CLS  O4B   O  O      0  -0.578   2.9075   1.3225   3.1707
 CLS  N5    N  N      0  -0.491   1.0537   0.5441   1.2933
 CLS  C6    C  C      0  -0.198  -0.0651   0.7533   0.3995
 CLS  C7    C  C      0  -0.243   0.9451   0.7495  -0.7737
 CLS  C8    C  C      0   0.520   1.9701   0.3600   0.2971
 CLS  O9    O  O      0  -0.408   3.1066  -0.0250   0.2819
 CLS  N10   N  NH1    0  -0.648   0.7904  -0.1989  -1.8259
 CLS  C11   C  C      0   0.575  -0.0194   0.0397  -2.8777
 CLS  O12   O  O      0  -0.465  -0.6413   1.0791  -3.0014
 CLS  C13   C  CH2    0  -0.654  -0.1391  -1.1045  -3.8641
 CLS  C14   C  CR5    0  -0.131  -0.3244  -0.6646  -5.2769
 CLS  C15   C  CR15   0  -0.236   0.3769  -1.0961  -6.3643
 CLS  C16   C  CR15   0  -0.187  -0.0880  -0.5400  -7.5877
 CLS  C17   C  CR15   0  -0.476  -1.1430   0.2997  -7.4062
 CLS  S19   S  S2     0   0.220  -1.5633   0.4364  -5.7497
 CLS  H21   H  HCH2   0   0.295  -1.9856  -1.3648   2.5797
 CLS  H22   H  HCH2   0   0.297  -2.1037   0.3767   2.4382
 CLS  H3'1  H  HCH2   0   0.265   0.5599  -0.6735   5.0930
 CLS  H3'2  H  HCH2   0   0.245  -0.6780  -1.8157   4.5588
 CLS  H231  H  HCH3   0   0.261  -3.2768   0.4930   7.6900
 CLS  H232  H  HCH3   0   0.275  -2.4269   1.7831   6.8266
 CLS  H233  H  HCH3   0   0.269  -3.6615   0.8532   5.9944
 CLS  H6    H  H      0   0.311  -0.6006   1.6863   0.5768
 CLS  H7    H  H      0   0.329   1.1011   1.7556  -1.1682
 CLS  H10   H  HNH1   0   0.418   1.2640  -1.0861  -1.7589
 CLS  H131  H  HCH2   0   0.289   0.7303  -1.7615  -3.8111
 CLS  H132  H  HCH2   0   0.307  -0.9956  -1.7049  -3.5367
 CLS  H15   H  HCR5   0   0.262   1.1972  -1.7969  -6.2919
 CLS  H16   H  HCR5   0   0.263   0.3484  -0.7531  -8.5529
 CLS  H17   H  HCR5   0   0.291  -1.6778   0.8668  -8.1526

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
 CLS  S1   C2    single    1.820  0.020  1.820
 CLS  S1   C6    single    1.802  0.020  1.802
 CLS  C2   C3    single    1.511  0.020  1.511
 CLS  C2   H21   single    0.970  0.020  1.090
 CLS  C2   H22   single    0.970  0.020  1.090
 CLS  C3   C3'   single    1.496  0.020  1.496
 CLS  C3   C4    double    1.343  0.020  1.343
 CLS  C3'  O20   single    1.441  0.020  1.441
 CLS  C3'  H3'1  single    0.970  0.020  1.090
 CLS  C3'  H3'2  single    0.970  0.020  1.090
 CLS  O20  C21   single    1.328  0.020  1.328
 CLS  C21  O22   double    1.206  0.020  1.206
 CLS  C21  C23   single    1.500  0.020  1.500
 CLS  C23  H231  single    0.970  0.020  1.090
 CLS  C23  H232  single    0.970  0.020  1.090
 CLS  C23  H233  single    0.970  0.020  1.090
 CLS  C4   C4'   single    1.532  0.020  1.532
 CLS  C4   N5    single    1.393  0.020  1.393
 CLS  C4'  O4A   deloc     1.242  0.020  1.242
 CLS  C4'  O4B   deloc     1.240  0.020  1.240
 CLS  N5   C6    single    1.447  0.020  1.447
 CLS  N5   C8    single    1.366  0.020  1.366
 CLS  C6   C7    single    1.548  0.020  1.548
 CLS  C6   H6    single    0.970  0.020  1.090
 CLS  C7   C8    single    1.533  0.020  1.533
 CLS  C7   N10   single    1.425  0.020  1.425
 CLS  C7   H7    single    0.970  0.020  1.090
 CLS  C8   O9    double    1.200  0.020  1.200
 CLS  N10  C11   single    1.349  0.020  1.349
 CLS  N10  H10   single    0.860  0.020  1.020
 CLS  C11  O12   double    1.218  0.020  1.218
 CLS  C11  C13   single    1.515  0.020  1.515
 CLS  C13  C14   single    1.491  0.020  1.491
 CLS  C13  H131  single    0.970  0.020  1.090
 CLS  C13  H132  single    0.970  0.020  1.090
 CLS  C14  C15   aromatic  1.364  0.020  1.364
 CLS  C14  S19   aromatic  1.723  0.020  1.723
 CLS  C15  C16   aromatic  1.422  0.020  1.422
 CLS  C15  H15   single    0.930  0.020  1.080
 CLS  C16  C17   aromatic  1.361  0.020  1.361
 CLS  C16  H16   single    0.930  0.020  1.080
 CLS  C17  S19   aromatic  1.714  0.020  1.714
 CLS  C17  H17   single    0.930  0.020  1.080

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
 CLS  C6    S1   C2     92.83  3.000
 CLS  H22   C2   H21   106.60  3.000
 CLS  H22   C2   C3    111.33  3.000
 CLS  H21   C2   C3    109.23  3.000
 CLS  H22   C2   S1    108.62  3.000
 CLS  H21   C2   S1    105.50  3.000
 CLS  C3    C2   S1    115.09  3.000
 CLS  C4    C3   C3'   122.43  3.000
 CLS  C4    C3   C2    124.28  3.000
 CLS  C3'   C3   C2    113.27  3.000
 CLS  H3'2  C3'  H3'1  108.26  3.000
 CLS  H3'2  C3'  O20   109.29  3.000
 CLS  H3'1  C3'  O20   110.23  3.000
 CLS  H3'2  C3'  C3    110.01  3.000
 CLS  H3'1  C3'  C3    112.50  3.000
 CLS  O20   C3'  C3    106.52  3.000
 CLS  C21   O20  C3'   117.82  3.000
 CLS  C23   C21  O22   125.13  3.000
 CLS  C23   C21  O20   111.49  3.000
 CLS  O22   C21  O20   123.38  3.000
 CLS  H233  C23  H232  107.23  3.000
 CLS  H233  C23  H231  109.38  3.000
 CLS  H232  C23  H231  108.74  3.000
 CLS  H233  C23  C21   111.04  3.000
 CLS  H232  C23  C21   109.86  3.000
 CLS  H231  C23  C21   110.50  3.000
 CLS  N5    C4   C4'   114.35  3.000
 CLS  N5    C4   C3    118.68  3.000
 CLS  C4'   C4   C3    126.91  3.000
 CLS  O4B   C4'  O4A   128.45  3.000
 CLS  O4B   C4'  C4    114.37  3.000
 CLS  O4A   C4'  C4    117.18  3.000
 CLS  C8    N5   C6     95.03  3.000
 CLS  C8    N5   C4    132.66  3.000
 CLS  C6    N5   C4    126.73  3.000
 CLS  H6    C6   C7    116.47  3.000
 CLS  H6    C6   N5    113.76  3.000
 CLS  C7    C6   N5     87.89  3.000
 CLS  H6    C6   S1    111.12  3.000
 CLS  C7    C6   S1    115.76  3.000
 CLS  N5    C6   S1    109.78  3.000
 CLS  H7    C7   N10   111.23  3.000
 CLS  H7    C7   C8    113.02  3.000
 CLS  N10   C7   C8    114.79  3.000
 CLS  H7    C7   C6    111.39  3.000
 CLS  N10   C7   C6    119.37  3.000
 CLS  C8    C7   C6     84.70  3.000
 CLS  O9    C8   C7    134.92  3.000
 CLS  O9    C8   N5    133.46  3.000
 CLS  C7    C8   N5     91.52  3.000
 CLS  H10   N10  C11   119.32  3.000
 CLS  H10   N10  C7    119.06  3.000
 CLS  C11   N10  C7    121.55  3.000
 CLS  C13   C11  O12   122.55  3.000
 CLS  C13   C11  N10   114.93  3.000
 CLS  O12   C11  N10   122.48  3.000
 CLS  H132  C13  H131  106.16  3.000
 CLS  H132  C13  C14   110.33  3.000
 CLS  H131  C13  C14   108.82  3.000
 CLS  H132  C13  C11   106.32  3.000
 CLS  H131  C13  C11   111.11  3.000
 CLS  C14   C13  C11   113.82  3.000
 CLS  S19   C14  C15   110.67  3.000
 CLS  S19   C14  C13   122.52  3.000
 CLS  C15   C14  C13   126.74  3.000
 CLS  H15   C15  C16   123.99  3.000
 CLS  H15   C15  C14   122.79  3.000
 CLS  C16   C15  C14   113.21  3.000
 CLS  H16   C16  C17   123.65  3.000
 CLS  H16   C16  C15   124.01  3.000
 CLS  C17   C16  C15   112.34  3.000
 CLS  H17   C17  S19   120.33  3.000
 CLS  H17   C17  C16   128.05  3.000
 CLS  S19   C17  C16   111.60  3.000
 CLS  C17   S19  C14    92.17  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
 CLS  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 CLS  CONST_02  C16   C17  S19  C14     0.00   0.0  0
 CLS  CONST_03  C17   S19  C14  C15     0.00   0.0  0
 CLS  CONST_04  S19   C17  C16  C15     0.00   0.0  0
 CLS  CONST_05  S19   C14  C15  C16     0.00   0.0  0
 CLS  CONST_07  C7    C8   N5   C6      0.00   0.0  0
 CLS  CONST_08  C16   C15  C14  C13   180.00   0.0  0
 CLS  CONST_09  C17   S19  C14  C13   180.00   0.0  0
 CLS  CONST_11  O9    C8   N5   C6    180.00   0.0  0
 CLS  CONST_12  H16   C16  C15  C14   180.00   0.0  0
 CLS  CONST_13  H17   C17  S19  C14   180.00   0.0  0
 CLS  CONST_14  H15   C15  C16  C17   180.00   0.0  0
 CLS  CONST_15  O12   C11  N10  C7      0.00   0.0  0
 CLS  CONST_16  C13   C11  N10  C7    180.00   0.0  0
 CLS  CONST_17  H10   N10  C11  O12   180.00   0.0  0
 CLS  Var_01    C4    C3   C2   S1     25.53  30.0  1
 CLS  Var_02    N5    C4   C3   C2      2.20  30.0  1
 CLS  Var_03    C6    N5   C4   C3      9.89  30.0  1
 CLS  Var_04    O20   C3'  C3   C2    -58.68  30.0  3
 CLS  Var_05    O4A   C4'  C4   C3     43.04  30.0  2
 CLS  Var_06    C15   C14  C13  C11   130.44  30.0  2
 CLS  Var_07    C14   C13  C11  N10  -146.95  30.0  3
 CLS  Var_08    O22   C21  O20  C3'    -0.22  30.0  3
 CLS  Var_09    H231  C23  C21  O20   173.43  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
 CLS  chir_01  C6  S1   N5  C7  negativ
 CLS  chir_02  C7  N10  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
 CLS  plan-1  C13  0.020
 CLS  plan-1  C14  0.020
 CLS  plan-1  C15  0.020
 CLS  plan-1  C16  0.020
 CLS  plan-1  C17  0.020
 CLS  plan-1  S19  0.020
 CLS  plan-1  H15  0.020
 CLS  plan-1  H16  0.020
 CLS  plan-1  H17  0.020
 CLS  plan-2  C7   0.020
 CLS  plan-2  N10  0.020
 CLS  plan-2  C11  0.020
 CLS  plan-2  O12  0.020
 CLS  plan-2  C13  0.020
 CLS  plan-2  H10  0.020
 CLS  plan-3  C4   0.020
 CLS  plan-3  N5   0.020
 CLS  plan-3  C6   0.020
 CLS  plan-3  C7   0.020
 CLS  plan-3  C8   0.020
 CLS  plan-3  O9   0.020
 CLS  plan-4  C4   0.020
 CLS  plan-4  C4'  0.020
 CLS  plan-4  O4A  0.020
 CLS  plan-4  O4B  0.020
 CLS  plan-5  O20  0.020
 CLS  plan-5  C21  0.020
 CLS  plan-5  O22  0.020
 CLS  plan-5  C23  0.020

