# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 02:33:44 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2S,5R,6R)-6-({[3-(2-chlorophenyl)-5-methylisoxazol-4-yl]carbonyl}amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(c2ccccc2Cl)c1C(=O)N[C@H]3[C@H]4SC(C)(C)[C@@H](N4C3=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
 CXN  CXN  '(2S,5R,6R)-6-({[3-(2-chlorophenyl)-5-methylisoxazol-4-yl]carbonyl}amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid'  ligand  47  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CXN
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
 CXN  C1    C   C     0   0.512   0.0223   1.7576  -1.9199
 CXN  O1    O   O     0  -0.393  -0.7501   2.6145  -1.5949
 CXN  C2    C   C     0  -0.226   1.3055   1.1583  -1.3347
 CXN  C3    C   C     0  -0.214   1.0374   0.0129  -2.3462
 CXN  N7    N   N     0  -0.417   0.0034   0.8489  -2.9500
 CXN  C6    C   CH1   0  -0.152  -1.1823   0.1937  -3.4435
 CXN  C8    C   C     0   0.548  -1.4137   0.4978  -4.9113
 CXN  O81   O   OH1   0  -0.583  -2.6377   0.1517  -5.2776
 CXN  O82   O   O     0  -0.418  -0.5939   0.9834  -5.6423
 CXN  C5    C   CT    0  -0.257  -1.0064  -1.3411  -3.1696
 CXN  C51   C   CH3   0  -0.647  -0.3390  -2.0711  -4.3327
 CXN  C52   C   CH3   0  -0.637  -2.3245  -2.0001  -2.7909
 CXN  S4    S   S2    0   0.087   0.1147  -1.3992  -1.7024
 CXN  N2    N   NH1   0  -0.666   1.2803   0.9039   0.0617
 CXN  C21   C   C     0   0.498   2.3970   0.9329   0.8286
 CXN  O21   O   O     0  -0.465   3.5039   1.1533   0.3661
 CXN  C22   C   CR5   0  -0.322   2.2045   0.7078   2.2688
 CXN  N25   N   N     0  -0.143   1.3501   0.2298   4.2905
 CXN  O24   O   O     0  -0.326   2.6345   0.6690   4.4139
 CXN  C23   C   CR5   0   0.475   3.1506   0.9499   3.2248
 CXN  C26   C   CR5   0   0.286   1.0842   0.2493   3.0200
 CXN  C27   C   CH3   0  -0.751   4.5458   1.4378   3.1816
 CXN  C28   C   CR6   0   0.001  -0.2506  -0.1600   2.5488
 CXN  C29   C   CR6   0  -0.069  -0.4459  -1.3718   1.8893
 CXN  CL    CL  CL    0  -0.099   0.9005  -2.4215   1.6260
 CXN  C30   C   CR16  0  -0.184  -1.6983  -1.7463   1.4322
 CXN  C31   C   CR16  0  -0.256  -2.7774  -0.9006   1.6405
 CXN  C32   C   CR16  0  -0.235  -2.6059   0.3080   2.3008
 CXN  C33   C   CR16  0  -0.263  -1.3479   0.6738   2.7534
 CXN  H2    H   H     0   0.336   2.1964   1.7260  -1.6043
 CXN  H3    H   H     0   0.306   1.8591  -0.2704  -3.0020
 CXN  H6    H   HCH1  0   0.314  -2.0477   0.5554  -2.8790
 CXN  H81   H   HOH1  0   0.490  -2.7688   0.3186  -6.2240
 CXN  H511  H   HCH3  0   0.262  -0.1214  -3.0984  -4.0452
 CXN  H512  H   HCH3  0   0.247  -0.9945  -2.1090  -5.2051
 CXN  H513  H   HCH3  0   0.254   0.5987  -1.6030  -4.6327
 CXN  H521  H   HCH3  0   0.253  -2.1709  -3.0474  -2.5304
 CXN  H522  H   HCH3  0   0.247  -2.7895  -1.5002  -1.9408
 CXN  H523  H   HCH3  0   0.255  -3.0198  -1.9692  -3.6291
 CXN  HN2   H   HNH1  0   0.412   0.3865   0.7205   0.4906
 CXN  H271  H   HCH3  0   0.271   4.9019   1.6840   4.1794
 CXN  H272  H   HCH3  0   0.279   5.1996   0.6758   2.7574
 CXN  H273  H   HCH3  0   0.276   4.6218   2.3191   2.5487
 CXN  H30   H   HCR6  0   0.286  -1.8291  -2.6889   0.9191
 CXN  H31   H   HCR6  0   0.277  -3.7555  -1.1921   1.2824
 CXN  H32   H   HCR6  0   0.273  -3.4488   0.9655   2.4630
 CXN  H33   H   HCR6  0   0.275  -1.2049   1.6178   3.2629

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
 CXN  C1   O1    double    1.199  0.020  1.199
 CXN  C1   C2    single    1.532  0.020  1.532
 CXN  C1   N7    single    1.374  0.020  1.374
 CXN  C2   C3    single    1.551  0.020  1.551
 CXN  C2   N2    single    1.420  0.020  1.420
 CXN  C2   H2    single    0.970  0.020  1.090
 CXN  C3   N7    single    1.460  0.020  1.460
 CXN  C3   S4    single    1.806  0.020  1.806
 CXN  C3   H3    single    0.970  0.020  1.090
 CXN  N7   C6    single    1.442  0.020  1.442
 CXN  C6   C8    single    1.517  0.020  1.517
 CXN  C6   C5    single    1.569  0.020  1.569
 CXN  C6   H6    single    0.970  0.020  1.090
 CXN  C8   O81   single    1.324  0.020  1.324
 CXN  C8   O82   double    1.201  0.020  1.201
 CXN  O81  H81   single    0.850  0.020  0.980
 CXN  C5   C51   single    1.527  0.020  1.527
 CXN  C5   C52   single    1.521  0.020  1.521
 CXN  C5   S4    single    1.847  0.020  1.847
 CXN  C51  H511  single    0.970  0.020  1.090
 CXN  C51  H512  single    0.970  0.020  1.090
 CXN  C51  H513  single    0.970  0.020  1.090
 CXN  C52  H521  single    0.970  0.020  1.090
 CXN  C52  H522  single    0.970  0.020  1.090
 CXN  C52  H523  single    0.970  0.020  1.090
 CXN  N2   C21   single    1.355  0.020  1.355
 CXN  N2   HN2   single    0.860  0.020  1.020
 CXN  C21  O21   double    1.220  0.020  1.220
 CXN  C21  C22   single    1.470  0.020  1.470
 CXN  C22  C23   aromatic  1.367  0.020  1.367
 CXN  C22  C26   aromatic  1.425  0.020  1.425
 CXN  N25  O24   aromatic  1.363  0.020  1.363
 CXN  N25  C26   aromatic  1.298  0.020  1.298
 CXN  O24  C23   aromatic  1.326  0.020  1.326
 CXN  C23  C27   single    1.479  0.020  1.479
 CXN  C26  C28   single    1.473  0.020  1.473
 CXN  C27  H271  single    0.970  0.020  1.090
 CXN  C27  H272  single    0.970  0.020  1.090
 CXN  C27  H273  single    0.970  0.020  1.090
 CXN  C28  C29   aromatic  1.393  0.020  1.393
 CXN  C28  C33   aromatic  1.393  0.020  1.393
 CXN  C29  CL    single    1.727  0.020  1.727
 CXN  C29  C30   aromatic  1.385  0.020  1.385
 CXN  C30  C31   aromatic  1.387  0.020  1.387
 CXN  C30  H30   single    0.930  0.020  1.080
 CXN  C31  C32   aromatic  1.388  0.020  1.388
 CXN  C31  H31   single    0.930  0.020  1.080
 CXN  C32  C33   aromatic  1.386  0.020  1.386
 CXN  C32  H32   single    0.930  0.020  1.080
 CXN  C33  H33   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
 CXN  N7    C1   C2     92.25  3.000
 CXN  N7    C1   O1    131.86  3.000
 CXN  C2    C1   O1    135.70  3.000
 CXN  H2    C2   N2    110.55  3.000
 CXN  H2    C2   C3    111.37  3.000
 CXN  N2    C2   C3    120.40  3.000
 CXN  H2    C2   C1    112.72  3.000
 CXN  N2    C2   C1    115.52  3.000
 CXN  C3    C2   C1     83.98  3.000
 CXN  H3    C3   S4    113.39  3.000
 CXN  H3    C3   N7    115.74  3.000
 CXN  S4    C3   N7    103.49  3.000
 CXN  H3    C3   C2    117.03  3.000
 CXN  S4    C3   C2    115.67  3.000
 CXN  N7    C3   C2     88.24  3.000
 CXN  C6    N7   C3    117.62  3.000
 CXN  C6    N7   C1    124.66  3.000
 CXN  C3    N7   C1     93.38  3.000
 CXN  H6    C6   C5    108.77  3.000
 CXN  H6    C6   C8    108.19  3.000
 CXN  C5    C6   C8    112.47  3.000
 CXN  H6    C6   N7    108.87  3.000
 CXN  C5    C6   N7    107.01  3.000
 CXN  C8    C6   N7    111.45  3.000
 CXN  O82   C8   O81   124.65  3.000
 CXN  O82   C8   C6    124.47  3.000
 CXN  O81   C8   C6    110.88  3.000
 CXN  H81   O81  C8    110.49  3.000
 CXN  S4    C5   C52   108.33  3.000
 CXN  S4    C5   C51   108.95  3.000
 CXN  C52   C5   C51   111.17  3.000
 CXN  S4    C5   C6    103.74  3.000
 CXN  C52   C5   C6    111.72  3.000
 CXN  C51   C5   C6    112.56  3.000
 CXN  H513  C51  H512  108.14  3.000
 CXN  H513  C51  H511  107.81  3.000
 CXN  H512  C51  H511  107.35  3.000
 CXN  H513  C51  C5    112.35  3.000
 CXN  H512  C51  C5    111.27  3.000
 CXN  H511  C51  C5    109.72  3.000
 CXN  H523  C52  H522  108.34  3.000
 CXN  H523  C52  H521  107.51  3.000
 CXN  H522  C52  H521  108.31  3.000
 CXN  H523  C52  C5    110.43  3.000
 CXN  H522  C52  C5    111.41  3.000
 CXN  H521  C52  C5    110.71  3.000
 CXN  C5    S4   C3     90.14  3.000
 CXN  HN2   N2   C21   119.59  3.000
 CXN  HN2   N2   C2    117.82  3.000
 CXN  C21   N2   C2    122.57  3.000
 CXN  C22   C21  O21   121.19  3.000
 CXN  C22   C21  N2    116.31  3.000
 CXN  O21   C21  N2    122.49  3.000
 CXN  C26   C22  C23   103.45  3.000
 CXN  C26   C22  C21   131.97  3.000
 CXN  C23   C22  C21   124.58  3.000
 CXN  C26   N25  O24   106.07  3.000
 CXN  C23   O24  N25   110.72  3.000
 CXN  C27   C23  O24   117.60  3.000
 CXN  C27   C23  C22   133.72  3.000
 CXN  O24   C23  C22   108.68  3.000
 CXN  C28   C26  N25   119.63  3.000
 CXN  C28   C26  C22   129.28  3.000
 CXN  N25   C26  C22   111.09  3.000
 CXN  H273  C27  H272  107.34  3.000
 CXN  H273  C27  H271  109.12  3.000
 CXN  H272  C27  H271  108.60  3.000
 CXN  H273  C27  C23   110.51  3.000
 CXN  H272  C27  C23   110.28  3.000
 CXN  H271  C27  C23   110.90  3.000
 CXN  C33   C28  C29   118.66  3.000
 CXN  C33   C28  C26   120.02  3.000
 CXN  C29   C28  C26   121.32  3.000
 CXN  C30   C29  CL    119.36  3.000
 CXN  C30   C29  C28   121.21  3.000
 CXN  CL    C29  C28   119.43  3.000
 CXN  H30   C30  C31   120.58  3.000
 CXN  H30   C30  C29   120.13  3.000
 CXN  C31   C30  C29   119.29  3.000
 CXN  H31   C31  C32   120.26  3.000
 CXN  H31   C31  C30   119.31  3.000
 CXN  C32   C31  C30   120.42  3.000
 CXN  H32   C32  C33   119.87  3.000
 CXN  H32   C32  C31   120.31  3.000
 CXN  C33   C32  C31   119.82  3.000
 CXN  H33   C33  C32   120.26  3.000
 CXN  H33   C33  C28   119.14  3.000
 CXN  C32   C33  C28   120.59  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
 CXN  CONST_01  N25   O24  C23  C22     0.00   0.0  0
 CXN  CONST_02  O24   N25  C26  C22     0.00   0.0  0
 CXN  CONST_05  C23   C22  C26  N25     0.00   0.0  0
 CXN  CONST_08  C28   C26  N25  O24   180.00   0.0  0
 CXN  CONST_09  C26   C22  C23  O24     0.00   0.0  0
 CXN  CONST_10  C28   C26  C22  C23   180.00   0.0  0
 CXN  CONST_11  C26   N25  O24  C23     0.00   0.0  0
 CXN  CONST_12  C30   C29  C28  C26   180.00   0.0  0
 CXN  CONST_13  C32   C33  C28  C26   180.00   0.0  0
 CXN  CONST_14  C31   C30  C29  C28     0.00   0.0  0
 CXN  CONST_15  C31   C32  C33  C28     0.00   0.0  0
 CXN  CONST_16  C32   C33  C28  C29     0.00   0.0  0
 CXN  CONST_17  C32   C31  C30  C29     0.00   0.0  0
 CXN  CONST_18  C33   C28  C29  C30     0.00   0.0  0
 CXN  CONST_19  C33   C32  C31  C30     0.00   0.0  0
 CXN  CONST_20  C3    N7   C1   C2      0.00   0.0  0
 CXN  CONST_22  O24   C23  C22  C21   180.00   0.0  0
 CXN  CONST_23  N25   C26  C22  C21   180.00   0.0  0
 CXN  CONST_24  C28   C26  C22  C21     0.00   0.0  0
 CXN  CONST_25  C27   C23  O24  N25   180.00   0.0  0
 CXN  CONST_26  C27   C23  C22  C26   180.00   0.0  0
 CXN  CONST_27  CL    C29  C28  C26     0.00   0.0  0
 CXN  CONST_28  C33   C28  C29  CL    180.00   0.0  0
 CXN  CONST_29  C31   C30  C29  CL    180.00   0.0  0
 CXN  CONST_32  H33   C33  C28  C26     0.00   0.0  0
 CXN  CONST_33  H30   C30  C29  C28   180.00   0.0  0
 CXN  CONST_34  H32   C32  C33  C28   180.00   0.0  0
 CXN  CONST_35  H31   C31  C30  C29   180.00   0.0  0
 CXN  CONST_36  C22   C21  N2   C2    180.00   0.0  0
 CXN  CONST_37  O21   C21  N2   C2      0.00   0.0  0
 CXN  CONST_38  HN2   N2   C21  C22     0.00   0.0  0
 CXN  CONST_39  H81   O81  C8   C6    180.00   0.0  0
 CXN  Var_01    C6    C5   S4   C3    -37.51  30.0  1
 CXN  Var_02    C23   C22  C21  N2   -166.85  30.0  2
 CXN  Var_03    H511  C51  C5   C6    172.61  30.0  3
 CXN  Var_04    H521  C52  C5   C6   -175.67  30.0  3
 CXN  Var_05    H271  C27  C23  C22   168.64  30.0  2

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
 CXN  chir_01  C2  C1  C3  N2  positiv
 CXN  chir_02  C3  S4  N7  C2  negativ
 CXN  chir_03  C6  N7  C8  C5  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
 CXN  plan-1  C21  0.020
 CXN  plan-1  C22  0.020
 CXN  plan-1  N25  0.020
 CXN  plan-1  O24  0.020
 CXN  plan-1  C23  0.020
 CXN  plan-1  C26  0.020
 CXN  plan-1  C27  0.020
 CXN  plan-1  C28  0.020
 CXN  plan-2  C26  0.020
 CXN  plan-2  C28  0.020
 CXN  plan-2  C29  0.020
 CXN  plan-2  CL   0.020
 CXN  plan-2  C30  0.020
 CXN  plan-2  C31  0.020
 CXN  plan-2  C32  0.020
 CXN  plan-2  C33  0.020
 CXN  plan-2  H30  0.020
 CXN  plan-2  H31  0.020
 CXN  plan-2  H32  0.020
 CXN  plan-2  H33  0.020
 CXN  plan-3  C2   0.020
 CXN  plan-3  N2   0.020
 CXN  plan-3  C21  0.020
 CXN  plan-3  O21  0.020
 CXN  plan-3  C22  0.020
 CXN  plan-3  HN2  0.020
 CXN  plan-4  C1   0.020
 CXN  plan-4  O1   0.020
 CXN  plan-4  C2   0.020
 CXN  plan-4  C3   0.020
 CXN  plan-4  N7   0.020
 CXN  plan-4  C6   0.020
 CXN  plan-5  C6   0.020
 CXN  plan-5  C8   0.020
 CXN  plan-5  O81  0.020
 CXN  plan-5  O82  0.020
 CXN  plan-5  H81  0.020

