# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:40:22 2021
#   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  42  26  .  2022-03-15  2022-11-17
;
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   0.057  24.4094   8.7063  16.0351
 CLS  C2    C  CH2   0  -0.624  24.9871   9.6556  17.4717
 CLS  C3    C  C     0   0.025  25.5086   8.8324  18.6217
 CLS  C3'   C  CH2   0  -0.267  25.4669   9.5530  19.9387
 CLS  O20   O  O2    0  -0.454  26.2449  10.7541  19.8603
 CLS  C21   C  C     0   0.575  27.5722  10.6258  19.9452
 CLS  O22   O  O     0  -0.439  28.1220   9.5672  20.1101
 CLS  C23   C  CH3   0  -0.770  28.2569  11.9507  19.8038
 CLS  C4    C  C     0   0.234  26.0358   7.6101  18.4603
 CLS  C4'   C  C     0   0.497  26.5706   6.7679  19.5706
 CLS  O4A   O  OH1   0  -0.579  27.6760   6.1461  19.2036
 CLS  O4B   O  O     0  -0.422  26.0552   6.6606  20.6534
 CLS  N5    N  N     0  -0.514  26.1495   7.0479  17.1929
 CLS  C6    C  C     0  -0.203  25.9164   7.7239  15.9331
 CLS  C7    C  C     0  -0.246  25.7338   6.3239  15.2857
 CLS  C8    C  C     0   0.531  25.8081   5.8026  16.7243
 CLS  O9    O  O     0  -0.392  25.6044   4.7617  17.2802
 CLS  N10   N  NH1   0  -0.649  24.5378   6.0255  14.5805
 CLS  C11   C  C     0   0.573  24.4597   6.0992  13.2296
 CLS  O12   O  O     0  -0.456  25.4117   6.3823  12.5310
 CLS  C13   C  CH2   0  -0.684  23.0704   5.8237  12.6795
 CLS  C14   C  CR5   0  -0.116  23.0581   5.5924  11.2101
 CLS  C15   C  CR15  0  -0.238  22.6011   6.4264  10.2350
 CLS  C16   C  CR15  0  -0.183  22.7524   5.8910   8.9256
 CLS  C17   C  CR15  0  -0.470  23.3237   4.6564   8.9309
 CLS  S19   S  S2    0   0.209  23.6801   4.1393  10.5264
 CLS  H21   H  HCH2  0   0.311  25.7364  10.3791  17.1428
 CLS  H22   H  HCH2  0   0.310  24.1232  10.2331  17.8059
 CLS  H3'1  H  HCH2  0   0.280  24.4493   9.8911  20.1355
 CLS  H3'2  H  HCH2  0   0.274  25.7861   8.9457  20.7795
 CLS  H231  H  HCH3  0   0.264  29.3287  11.8400  19.9399
 CLS  H232  H  HCH3  0   0.275  28.0666  12.3676  18.8140
 CLS  H233  H  HCH3  0   0.274  27.8729  12.6634  20.5337
 CLS  HO4   H  HOH1  0   0.493  27.9883   5.5717  19.9195
 CLS  H6    H  H     0   0.323  26.7620   8.3181  15.5882
 CLS  H7    H  H     0   0.339  26.6078   6.0450  14.6950
 CLS  H10   H  HNH1  0   0.418  23.7049   5.8038  15.1041
 CLS  H131  H  HCH2  0   0.301  22.6186   4.9893  13.2227
 CLS  H132  H  HCH2  0   0.316  22.4498   6.6968  12.9012
 CLS  H15   H  HCR5  0   0.264  22.1686   7.3948  10.4474
 CLS  H16   H  HCR5  0   0.266  22.4495   6.4029   8.0237
 CLS  H17   H  HCR5  0   0.294  23.5525   4.0240   8.0871

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    1.816  0.020  1.816
 CLS  S1   C6    single    1.802  0.020  1.802
 CLS  C2   C3    single    1.507  0.020  1.507
 CLS  C2   H21   single    0.970  0.020  1.090
 CLS  C2   H22   single    0.970  0.020  1.090
 CLS  C3   C3'   single    1.502  0.020  1.502
 CLS  C3   C4    double    1.341  0.020  1.341
 CLS  C3'  O20   single    1.433  0.020  1.433
 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    1.336  0.020  1.336
 CLS  C21  O22   double    1.204  0.020  1.204
 CLS  C21  C23   single    1.498  0.020  1.498
 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    1.493  0.020  1.493
 CLS  C4   N5    single    1.391  0.020  1.391
 CLS  C4'  O4A   single    1.320  0.020  1.320
 CLS  C4'  O4B   double    1.204  0.020  1.204
 CLS  O4A  HO4   single    0.850  0.020  0.980
 CLS  N5   C6    single    1.449  0.020  1.449
 CLS  N5   C8    single    1.374  0.020  1.374
 CLS  C6   C7    single    1.553  0.020  1.553
 CLS  C6   H6    single    0.970  0.020  1.090
 CLS  C7   C8    single    1.532  0.020  1.532
 CLS  C7   N10   single    1.420  0.020  1.420
 CLS  C7   H7    single    0.970  0.020  1.090
 CLS  C8   O9    double    1.197  0.020  1.197
 CLS  N10  C11   single    1.355  0.020  1.355
 CLS  N10  H10   single    0.860  0.020  1.020
 CLS  C11  O12   double    1.214  0.020  1.214
 CLS  C11  C13   single    1.519  0.020  1.519
 CLS  C13  C14   single    1.488  0.020  1.488
 CLS  C13  H131  single    0.970  0.020  1.090
 CLS  C13  H132  single    0.970  0.020  1.090
 CLS  C14  C15   aromatic  1.362  0.020  1.362
 CLS  C14  S19   aromatic  1.722  0.020  1.722
 CLS  C15  C16   aromatic  1.423  0.020  1.423
 CLS  C15  H15   single    0.930  0.020  1.080
 CLS  C16  C17   aromatic  1.360  0.020  1.360
 CLS  C16  H16   single    0.930  0.020  1.080
 CLS  C17  S19   aromatic  1.715  0.020  1.715
 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     93.65  3.000
 CLS  H22   C2   H21   106.53  3.000
 CLS  H22   C2   C3    109.22  3.000
 CLS  H21   C2   C3    110.74  3.000
 CLS  H22   C2   S1    105.49  3.000
 CLS  H21   C2   S1    109.04  3.000
 CLS  C3    C2   S1    115.35  3.000
 CLS  C4    C3   C3'   123.63  3.000
 CLS  C4    C3   C2    122.82  3.000
 CLS  C3'   C3   C2    113.42  3.000
 CLS  H3'2  C3'  H3'1  107.96  3.000
 CLS  H3'2  C3'  O20   110.59  3.000
 CLS  H3'1  C3'  O20   104.87  3.000
 CLS  H3'2  C3'  C3    113.76  3.000
 CLS  H3'1  C3'  C3    109.45  3.000
 CLS  O20   C3'  C3    109.81  3.000
 CLS  C21   O20  C3'   117.09  3.000
 CLS  C23   C21  O22   125.57  3.000
 CLS  C23   C21  O20   111.29  3.000
 CLS  O22   C21  O20   123.14  3.000
 CLS  H233  C23  H232  107.24  3.000
 CLS  H233  C23  H231  109.30  3.000
 CLS  H232  C23  H231  108.95  3.000
 CLS  H233  C23  C21   110.73  3.000
 CLS  H232  C23  C21   110.12  3.000
 CLS  H231  C23  C21   110.43  3.000
 CLS  N5    C4   C4'   114.86  3.000
 CLS  N5    C4   C3    120.68  3.000
 CLS  C4'   C4   C3    124.44  3.000
 CLS  O4B   C4'  O4A   124.50  3.000
 CLS  O4B   C4'  C4    124.46  3.000
 CLS  O4A   C4'  C4    111.03  3.000
 CLS  HO4   O4A  C4'   110.09  3.000
 CLS  C8    N5   C6     94.96  3.000
 CLS  C8    N5   C4    131.06  3.000
 CLS  C6    N5   C4    126.20  3.000
 CLS  H6    C6   C7    116.79  3.000
 CLS  H6    C6   N5    113.88  3.000
 CLS  C7    C6   N5     87.75  3.000
 CLS  H6    C6   S1    111.70  3.000
 CLS  C7    C6   S1    114.63  3.000
 CLS  N5    C6   S1    109.87  3.000
 CLS  H7    C7   N10   110.62  3.000
 CLS  H7    C7   C8    112.49  3.000
 CLS  N10   C7   C8    115.83  3.000
 CLS  H7    C7   C6    111.22  3.000
 CLS  N10   C7   C6    119.69  3.000
 CLS  C8    C7   C6     84.81  3.000
 CLS  O9    C8   C7    136.34  3.000
 CLS  O9    C8   N5    132.22  3.000
 CLS  C7    C8   N5     91.37  3.000
 CLS  H10   N10  C11   118.81  3.000
 CLS  H10   N10  C7    118.94  3.000
 CLS  C11   N10  C7    122.15  3.000
 CLS  C13   C11  O12   123.43  3.000
 CLS  C13   C11  N10   113.81  3.000
 CLS  O12   C11  N10   122.75  3.000
 CLS  H132  C13  H131  105.90  3.000
 CLS  H132  C13  C14   108.64  3.000
 CLS  H131  C13  C14   111.63  3.000
 CLS  H132  C13  C11   107.50  3.000
 CLS  H131  C13  C11   109.66  3.000
 CLS  C14   C13  C11   113.17  3.000
 CLS  S19   C14  C15   110.71  3.000
 CLS  S19   C14  C13   121.36  3.000
 CLS  C15   C14  C13   127.93  3.000
 CLS  H15   C15  C16   124.07  3.000
 CLS  H15   C15  C14   122.81  3.000
 CLS  C16   C15  C14   113.12  3.000
 CLS  H16   C16  C17   123.44  3.000
 CLS  H16   C16  C15   124.07  3.000
 CLS  C17   C16  C15   112.50  3.000
 CLS  H17   C17  S19   120.45  3.000
 CLS  H17   C17  C16   128.17  3.000
 CLS  S19   C17  C16   111.39  3.000
 CLS  C17   S19  C14    92.28  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  HO4   O4A  C4'  C4    180.00   0.0  0
 CLS  CONST_18  H10   N10  C11  O12   180.00   0.0  0
 CLS  Var_01    C4    C3   C2   S1     26.68  30.0  1
 CLS  Var_02    N5    C4   C3   C2      1.26  30.0  1
 CLS  Var_03    C6    N5   C4   C3      9.13  30.0  1
 CLS  Var_04    O20   C3'  C3   C2    -58.87  30.0  3
 CLS  Var_05    O4A   C4'  C4   C3   -139.92  30.0  2
 CLS  Var_06    C15   C14  C13  C11  -107.09  30.0  2
 CLS  Var_07    C14   C13  C11  N10  -166.51  30.0  3
 CLS  Var_08    O22   C21  O20  C3'    -1.62  30.0  3
 CLS  Var_09    H231  C23  C21  O20   176.29  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-4  HO4  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

