# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 05:49:48 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (1R)-5-({(6R,7R)-3-[(acetyloxy)methyl]-2-carboxy-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-en-7-yl}amino)-1-carboxy-5-oxopentan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OCC1=C(N2[C@H](SC1)[C@H](NC(=O)CCC[C@@H]([NH3+])C(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
 CSC  CSC  (1R)-5-({(6R,7R)-3-[(acetyloxy)methyl]-2-carboxy-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-en-7-yl}amino)-1-carboxy-5-oxopentan-1-aminium  ligand  48  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CSC
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
 CSC  S1    S  S2     0   0.034   -8.6339   -1.6501  -2.8111
 CSC  C2    C  CH2    0  -0.621   -9.4061   -0.0441  -3.1807
 CSC  C3    C  C      0  -0.010   -8.4992    1.1558  -3.0405
 CSC  C3'   C  CH2    0  -0.239   -9.2376    2.4343  -2.7975
 CSC  C4    C  C      0   0.167   -7.1619    1.1083  -3.1500
 CSC  C4'   C  C      0   0.378   -6.1882    2.2848  -3.0283
 CSC  O4A   O  OC    -1  -0.579   -5.2994    2.3042  -3.8925
 CSC  O4B   O  O      0  -0.582   -6.3814    3.0863  -2.0993
 CSC  N5    N  N      0  -0.493   -6.5550   -0.1074  -3.4542
 CSC  C6    C  C      0  -0.194   -7.2156   -1.3238  -3.8742
 CSC  C7    C  C      0  -0.263   -5.9149   -2.0865  -3.5129
 CSC  C8    C  C      0   0.532   -5.4472   -0.7357  -2.9554
 CSC  O9    O  O      0  -0.409   -4.5229   -0.3644  -2.2863
 CSC  N10   N  NH1    0  -0.644   -5.9569   -3.1632  -2.5866
 CSC  C11   C  C      0   0.572   -5.7733   -4.4543  -2.9536
 CSC  O12   O  O      0  -0.482   -5.5702   -4.7822  -4.1102
 CSC  C13   C  CH2    0  -0.579   -5.8390   -5.4577  -1.8267
 CSC  C14   C  CH2    0  -0.429   -4.6694   -6.4357  -1.8695
 CSC  C15   C  CH2    0  -0.453   -4.7682   -7.4766  -0.7618
 CSC  C16   C  CH1    0  -0.257   -3.6461   -8.4966  -0.7904
 CSC  N17   N  NT3    1  -0.798   -2.3215   -7.8594  -0.5374
 CSC  C18   C  C      0   0.470   -3.7972   -9.6549   0.2362
 CSC  O19   O  O      0  -0.594   -2.7507   -9.9710   0.8384
 CSC  O20   O  OC    -1  -0.569   -4.9203  -10.1606   0.3233
 CSC  O1    O  O2     0  -0.454  -10.1596    2.5890  -3.8938
 CSC  C1    C  C      0   0.572  -11.0176    3.6010  -3.8458
 CSC  O2    O  O      0  -0.459  -11.0476    4.4025  -2.9445
 CSC  C20   C  CH3    0  -0.768  -11.9290    3.6066  -5.0372
 CSC  H11   H  HCH2   0   0.295  -10.2370    0.0445  -2.4771
 CSC  H12   H  HCH2   0   0.297   -9.8465   -0.0917  -4.1788
 CSC  H3'1  H  HCH2   0   0.263   -8.5732    3.2921  -2.7427
 CSC  H3'2  H  HCH2   0   0.246   -9.7988    2.3742  -1.8600
 CSC  H6    H  H      0   0.311   -7.5065   -1.3259  -4.9251
 CSC  H7    H  H      0   0.328   -5.3698   -2.3875  -4.4081
 CSC  H10   H  HNH1   0   0.411   -6.1305   -2.9594  -1.6150
 CSC  H131  H  HCH2   0   0.258   -5.8747   -4.9567  -0.8568
 CSC  H132  H  HCH2   0   0.276   -6.7806   -6.0063  -1.9274
 CSC  H141  H  HCH2   0   0.243   -4.6447   -6.9401  -2.8381
 CSC  H142  H  HCH2   0   0.235   -3.7365   -5.8691  -1.7884
 CSC  H151  H  HCH2   0   0.244   -4.7978   -6.9900   0.2193
 CSC  H152  H  HCH2   0   0.261   -5.7046   -8.0269  -0.8595
 CSC  H16   H  HCH1   0   0.302   -3.5797   -8.9421  -1.7867
 CSC  H171  H  HNT3   0   0.464   -1.8181   -7.5945  -1.3808
 CSC  H172  H  HNT3   0   0.454   -1.7793   -8.5650  -0.0131
 CSC  H173  H  HNT3   0   0.458   -2.3883   -7.0342   0.0578
 CSC  H201  H  HCH3   0   0.274  -12.5533    2.7122  -5.0341
 CSC  H202  H  HCH3   0   0.271  -11.3556    3.5968  -5.9641
 CSC  H203  H  HCH3   0   0.261  -12.5688    4.4841  -5.0213

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
 CSC  S1   C2    single  1.820  0.020  1.820
 CSC  S1   C6    single  1.802  0.020  1.802
 CSC  C2   C3    single  1.511  0.020  1.511
 CSC  C2   H11   single  0.970  0.020  1.090
 CSC  C2   H12   single  0.970  0.020  1.090
 CSC  C3   C3'   single  1.496  0.020  1.496
 CSC  C3   C4    double  1.343  0.020  1.343
 CSC  C3'  O1    single  1.441  0.020  1.441
 CSC  C3'  H3'1  single  0.970  0.020  1.090
 CSC  C3'  H3'2  single  0.970  0.020  1.090
 CSC  C4   C4'   single  1.532  0.020  1.532
 CSC  C4   N5    single  1.392  0.020  1.392
 CSC  C4'  O4A   deloc   1.240  0.020  1.240
 CSC  C4'  O4B   deloc   1.242  0.020  1.242
 CSC  N5   C6    single  1.447  0.020  1.447
 CSC  N5   C8    single  1.368  0.020  1.368
 CSC  C6   C7    single  1.550  0.020  1.550
 CSC  C6   H6    single  0.970  0.020  1.090
 CSC  C7   C8    single  1.534  0.020  1.534
 CSC  C7   N10   single  1.421  0.020  1.421
 CSC  C7   H7    single  0.970  0.020  1.090
 CSC  C8   O9    double  1.200  0.020  1.200
 CSC  N10  C11   single  1.355  0.020  1.355
 CSC  N10  H10   single  0.860  0.020  1.020
 CSC  C11  O12   double  1.219  0.020  1.219
 CSC  C11  C13   single  1.510  0.020  1.510
 CSC  C13  C14   single  1.525  0.020  1.525
 CSC  C13  H131  single  0.970  0.020  1.090
 CSC  C13  H132  single  0.970  0.020  1.090
 CSC  C14  C15   single  1.523  0.020  1.523
 CSC  C14  H141  single  0.970  0.020  1.090
 CSC  C14  H142  single  0.970  0.020  1.090
 CSC  C15  C16   single  1.517  0.020  1.517
 CSC  C15  H151  single  0.970  0.020  1.090
 CSC  C15  H152  single  0.970  0.020  1.090
 CSC  C16  N17   single  1.491  0.020  1.491
 CSC  C16  C18   single  1.555  0.020  1.555
 CSC  C16  H16   single  0.970  0.020  1.090
 CSC  N17  H171  single  0.890  0.020  1.040
 CSC  N17  H172  single  0.890  0.020  1.040
 CSC  N17  H173  single  0.890  0.020  1.040
 CSC  C18  O19   deloc   1.248  0.020  1.248
 CSC  C18  O20   deloc   1.235  0.020  1.235
 CSC  O1   C1    single  1.328  0.020  1.328
 CSC  C1   O2    double  1.206  0.020  1.206
 CSC  C1   C20   single  1.500  0.020  1.500
 CSC  C20  H201  single  0.970  0.020  1.090
 CSC  C20  H202  single  0.970  0.020  1.090
 CSC  C20  H203  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
 CSC  C6    S1   C2     93.12  3.000
 CSC  H12   C2   H11   106.59  3.000
 CSC  H12   C2   C3    111.19  3.000
 CSC  H11   C2   C3    109.42  3.000
 CSC  H12   C2   S1    108.56  3.000
 CSC  H11   C2   S1    105.28  3.000
 CSC  C3    C2   S1    115.30  3.000
 CSC  C4    C3   C3'   122.35  3.000
 CSC  C4    C3   C2    124.21  3.000
 CSC  C3'   C3   C2    113.42  3.000
 CSC  H3'2  C3'  H3'1  108.28  3.000
 CSC  H3'2  C3'  O1    109.24  3.000
 CSC  H3'1  C3'  O1    110.18  3.000
 CSC  H3'2  C3'  C3    110.20  3.000
 CSC  H3'1  C3'  C3    112.40  3.000
 CSC  O1    C3'  C3    106.50  3.000
 CSC  N5    C4   C4'   114.25  3.000
 CSC  N5    C4   C3    118.88  3.000
 CSC  C4'   C4   C3    126.82  3.000
 CSC  O4B   C4'  O4A   128.51  3.000
 CSC  O4B   C4'  C4    117.14  3.000
 CSC  O4A   C4'  C4    114.34  3.000
 CSC  C8    N5   C6     95.13  3.000
 CSC  C8    N5   C4    132.41  3.000
 CSC  C6    N5   C4    126.76  3.000
 CSC  H6    C6   C7    116.58  3.000
 CSC  H6    C6   N5    113.78  3.000
 CSC  C7    C6   N5     87.87  3.000
 CSC  H6    C6   S1    110.99  3.000
 CSC  C7    C6   S1    115.70  3.000
 CSC  N5    C6   S1    109.90  3.000
 CSC  H7    C7   N10   109.92  3.000
 CSC  H7    C7   C8    112.88  3.000
 CSC  N10   C7   C8    116.06  3.000
 CSC  H7    C7   C6    111.33  3.000
 CSC  N10   C7   C6    119.99  3.000
 CSC  C8    C7   C6     84.68  3.000
 CSC  O9    C8   C7    135.22  3.000
 CSC  O9    C8   N5    133.24  3.000
 CSC  C7    C8   N5     91.44  3.000
 CSC  H10   N10  C11   118.51  3.000
 CSC  H10   N10  C7    118.70  3.000
 CSC  C11   N10  C7    122.79  3.000
 CSC  C13   C11  O12   122.44  3.000
 CSC  C13   C11  N10   115.16  3.000
 CSC  O12   C11  N10   122.40  3.000
 CSC  H132  C13  H131  106.47  3.000
 CSC  H132  C13  C14   109.62  3.000
 CSC  H131  C13  C14   110.13  3.000
 CSC  H132  C13  C11   107.57  3.000
 CSC  H131  C13  C11   111.05  3.000
 CSC  C14   C13  C11   111.82  3.000
 CSC  H142  C14  H141  106.59  3.000
 CSC  H142  C14  C15   110.80  3.000
 CSC  H141  C14  C15   109.31  3.000
 CSC  H142  C14  C13   108.64  3.000
 CSC  H141  C14  C13   109.77  3.000
 CSC  C15   C14  C13   111.59  3.000
 CSC  H152  C15  H151  106.33  3.000
 CSC  H152  C15  C16   107.11  3.000
 CSC  H151  C15  C16   109.61  3.000
 CSC  H152  C15  C14   109.60  3.000
 CSC  H151  C15  C14   110.46  3.000
 CSC  C16   C15  C14   113.44  3.000
 CSC  H16   C16  C18   107.70  3.000
 CSC  H16   C16  N17   105.95  3.000
 CSC  C18   C16  N17   107.01  3.000
 CSC  H16   C16  C15   109.64  3.000
 CSC  C18   C16  C15   114.62  3.000
 CSC  N17   C16  C15   111.50  3.000
 CSC  H173  N17  H172  106.92  3.000
 CSC  H173  N17  H171  107.79  3.000
 CSC  H172  N17  H171  109.82  3.000
 CSC  H173  N17  C16   112.74  3.000
 CSC  H172  N17  C16   105.10  3.000
 CSC  H171  N17  C16   114.21  3.000
 CSC  O20   C18  O19   128.67  3.000
 CSC  O20   C18  C16   116.10  3.000
 CSC  O19   C18  C16   115.20  3.000
 CSC  C1    O1   C3'   117.90  3.000
 CSC  C20   C1   O2    125.16  3.000
 CSC  C20   C1   O1    111.52  3.000
 CSC  O2    C1   O1    123.33  3.000
 CSC  H203  C20  H202  109.25  3.000
 CSC  H203  C20  H201  108.98  3.000
 CSC  H202  C20  H201  107.22  3.000
 CSC  H203  C20  C1    110.44  3.000
 CSC  H202  C20  C1    110.84  3.000
 CSC  H201  C20  C1    110.03  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
 CSC  CONST_02  C7    C8   N5   C6      0.00   0.0  0
 CSC  CONST_04  O9    C8   N5   C6    180.00   0.0  0
 CSC  CONST_05  O12   C11  N10  C7      0.00   0.0  0
 CSC  CONST_06  C13   C11  N10  C7    180.00   0.0  0
 CSC  CONST_07  H10   N10  C11  O12   180.00   0.0  0
 CSC  Var_01    C4    C3   C2   S1     24.99  30.0  1
 CSC  Var_02    N5    C4   C3   C2      2.16  30.0  1
 CSC  Var_03    C6    N5   C4   C3     10.17  30.0  1
 CSC  Var_04    O1    C3'  C3   C2    -56.75  30.0  3
 CSC  Var_05    O4A   C4'  C4   C3   -135.85  30.0  2
 CSC  Var_06    O2    C1   O1   C3'     1.16  30.0  3
 CSC  Var_07    C14   C13  C11  N10  -132.22  30.0  3
 CSC  Var_08    C15   C14  C13  C11  -177.90  30.0  3
 CSC  Var_09    C16   C15  C14  C13   178.30  30.0  3
 CSC  Var_10    H201  C20  C1   O1     64.18  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
 CSC  chir_01  C6   S1   N5   C7   negativ
 CSC  chir_02  C7   N10  C6   C8   negativ
 CSC  chir_03  C16  C15  N17  C18  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
 CSC  plan-1  C7   0.020
 CSC  plan-1  N10  0.020
 CSC  plan-1  C11  0.020
 CSC  plan-1  O12  0.020
 CSC  plan-1  C13  0.020
 CSC  plan-1  H10  0.020
 CSC  plan-2  O1   0.020
 CSC  plan-2  C1   0.020
 CSC  plan-2  O2   0.020
 CSC  plan-2  C20  0.020
 CSC  plan-3  C4   0.020
 CSC  plan-3  N5   0.020
 CSC  plan-3  C6   0.020
 CSC  plan-3  C7   0.020
 CSC  plan-3  C8   0.020
 CSC  plan-3  O9   0.020
 CSC  plan-4  C4   0.020
 CSC  plan-4  C4'  0.020
 CSC  plan-4  O4A  0.020
 CSC  plan-4  O4B  0.020
 CSC  plan-5  C16  0.020
 CSC  plan-5  C18  0.020
 CSC  plan-5  O19  0.020
 CSC  plan-5  O20  0.020

