# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:37:38 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (4~{R},5~{S},6~{S})-4-methyl-6-[(1~{R})-1-oxidanylethyl]-7-oxidanylidene-3-(2-oxidanylidene-2-propan-2-yloxy-ethyl)sulfanyl-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)OC(=O)CSC1=C(N2[C@H]([C@H]1C)[C@@H]([C@@H](C)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
 56X  56X  "(4R,5S,6S)-6-((R)-1-hydroxyethyl)-3-((2-isopropoxy-2-oxoethyl)thio)-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid"  ligand  43  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_56X
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
 56X  C10  C  C      0  -0.451   3.4557   1.4638  70.6467
 56X  C13  C  CH1    0   0.060   2.6847   2.7697  70.4836
 56X  C15  C  C      0   0.173   6.2686   0.3994  72.0883
 56X  C17  C  CH3    0  -0.677   2.4456   3.0920  69.0215
 56X  C20  C  C      0   0.641   8.6040  -2.7715  73.0287
 56X  C21  C  CH1    0   0.009  10.8251  -2.8694  72.1625
 56X  C22  C  CH3    0  -0.668  11.3313  -4.2901  72.3195
 56X  C09  C  C      0  -0.062   4.0260   1.1572  72.0508
 56X  C11  C  CH1    0  -0.270   4.0456  -0.2573  72.6621
 56X  C12  C  C      0   0.498   4.9177   1.4462  70.1983
 56X  C14  C  C      0  -0.182   5.5483  -0.4884  72.7973
 56X  C16  C  CH3    0  -0.660   3.3924  -1.3562  71.8300
 56X  C18  C  C      0   0.376   7.7598   0.5715  71.9266
 56X  C19  C  CH2    0  -0.681   7.1536  -2.7854  72.6172
 56X  C23  C  CH3    0  -0.665  11.4158  -2.1668  70.9575
 56X  N8   N  N      0  -0.487   5.3732   1.3217  71.4961
 56X  O2   O  O      0  -0.413   5.4833   1.4836  69.1381
 56X  O3   O  OH1    0  -0.663   1.4256   2.6782  71.1166
 56X  O4   O  OC    -1  -0.561   8.4763  -0.1531  72.6412
 56X  O5   O  O      0  -0.573   8.1183   1.4393  71.1147
 56X  O6   O  O2     0  -0.461   9.3949  -2.8767  71.9730
 56X  O7   O  O      0  -0.457   8.9759  -2.7814  74.1742
 56X  S1   S  S2     0   0.043   6.0826  -1.8551  73.7464
 56X  H1   H  H      0   0.292   2.8905   0.6428  70.1969
 56X  H2   H  HCH1   0   0.209   3.2796   3.5795  70.9304
 56X  H4   H  HCH3   0   0.238   1.8990   4.0295  68.9175
 56X  H5   H  HCH3   0   0.235   3.3898   3.1947  68.4890
 56X  H6   H  HCH3   0   0.226   1.8697   2.3027  68.5350
 56X  H7   H  HCH1   0   0.234  11.0587  -2.2970  73.0624
 56X  H8   H  HCH3   0   0.239  10.8967  -4.7800  73.1908
 56X  H9   H  HCH3   0   0.228  11.1064  -4.8888  71.4355
 56X  H10  H  HCH3   0   0.234  12.4137  -4.2814  72.4508
 56X  H11  H  H      0   0.262   3.7967   1.9079  72.8122
 56X  H14  H  HCH3   0   0.240   2.3252  -1.1679  71.7056
 56X  H15  H  HCH3   0   0.227   3.8421  -1.4372  70.8390
 56X  H16  H  HCH3   0   0.243   3.5062  -2.3212  72.3232
 56X  H17  H  HCH2   0   0.307   6.8127  -3.8241  72.6526
 56X  H18  H  HCH2   0   0.300   7.0055  -2.4302  71.6002
 56X  H19  H  HCH3   0   0.232  12.4989  -2.1070  71.0642
 56X  H20  H  HCH3   0   0.228  11.1992  -2.7044  70.0334
 56X  H21  H  HCH3   0   0.238  11.0312  -1.1505  70.8675
 56X  H22  H  HOH1   0   0.451   1.5576   2.6579  72.0696
 56X  H3   H  HCH1   0   0.264   3.5678  -0.2367  73.6445

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
 56X  O5   C18  deloc   1.241  0.020  1.241
 56X  O2   C12  double  1.202  0.020  1.202
 56X  C18  O4   deloc   1.245  0.020  1.245
 56X  C18  C15  single  1.510  0.020  1.510
 56X  C12  N8   single  1.381  0.020  1.381
 56X  C12  C10  single  1.529  0.020  1.529
 56X  C15  N8   single  1.415  0.020  1.415
 56X  C15  C14  double  1.345  0.020  1.345
 56X  N8   C09  single  1.466  0.020  1.466
 56X  C16  C11  single  1.525  0.020  1.525
 56X  C17  C13  single  1.516  0.020  1.516
 56X  C10  C09  single  1.546  0.020  1.546
 56X  C10  C13  single  1.525  0.020  1.525
 56X  C14  C11  single  1.526  0.020  1.526
 56X  C14  S1   single  1.748  0.020  1.748
 56X  C09  C11  single  1.541  0.020  1.541
 56X  C13  O3   single  1.412  0.020  1.412
 56X  C23  C21  single  1.515  0.020  1.515
 56X  C19  S1   single  1.813  0.020  1.813
 56X  C19  C20  single  1.508  0.020  1.508
 56X  O6   C21  single  1.443  0.020  1.443
 56X  O6   C20  single  1.323  0.020  1.323
 56X  C21  C22  single  1.516  0.020  1.516
 56X  C20  O7   double  1.204  0.020  1.204
 56X  C10  H1   single  0.970  0.020  1.090
 56X  C13  H2   single  0.970  0.020  1.090
 56X  C17  H4   single  0.970  0.020  1.090
 56X  C17  H5   single  0.970  0.020  1.090
 56X  C17  H6   single  0.970  0.020  1.090
 56X  C21  H7   single  0.970  0.020  1.090
 56X  C22  H8   single  0.970  0.020  1.090
 56X  C22  H9   single  0.970  0.020  1.090
 56X  C22  H10  single  0.970  0.020  1.090
 56X  C09  H11  single  0.970  0.020  1.090
 56X  C16  H14  single  0.970  0.020  1.090
 56X  C16  H15  single  0.970  0.020  1.090
 56X  C16  H16  single  0.970  0.020  1.090
 56X  C19  H17  single  0.970  0.020  1.090
 56X  C19  H18  single  0.970  0.020  1.090
 56X  C23  H19  single  0.970  0.020  1.090
 56X  C23  H20  single  0.970  0.020  1.090
 56X  C23  H21  single  0.970  0.020  1.090
 56X  O3   H22  single  0.850  0.020  0.980
 56X  C11  H3   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
 56X  H1   C10  C12  111.40  3.000
 56X  H1   C10  C09  114.54  3.000
 56X  C12  C10  C09   84.92  3.000
 56X  H1   C10  C13  109.73  3.000
 56X  C09  C10  C13  116.96  3.000
 56X  C12  C10  C13  117.50  3.000
 56X  H2   C13  O3   110.36  3.000
 56X  H2   C13  C17  108.69  3.000
 56X  O3   C13  C17  107.79  3.000
 56X  H2   C13  C10  108.27  3.000
 56X  O3   C13  C10  110.32  3.000
 56X  C17  C13  C10  111.40  3.000
 56X  N8   C15  C18  120.38  3.000
 56X  N8   C15  C14  108.17  3.000
 56X  C18  C15  C14  131.34  3.000
 56X  H6   C17  H5   107.93  3.000
 56X  H6   C17  H4   108.35  3.000
 56X  H5   C17  H4   107.88  3.000
 56X  H6   C17  C13  111.05  3.000
 56X  H5   C17  C13  110.79  3.000
 56X  H4   C17  C13  110.73  3.000
 56X  O7   C20  O6   125.00  3.000
 56X  O7   C20  C19  123.82  3.000
 56X  O6   C20  C19  110.88  3.000
 56X  H7   C21  O6   108.84  3.000
 56X  H7   C21  C23  109.21  3.000
 56X  O6   C21  C23  106.53  3.000
 56X  H7   C21  C22  109.54  3.000
 56X  O6   C21  C22  109.87  3.000
 56X  C23  C21  C22  112.76  3.000
 56X  H10  C22  H9   107.86  3.000
 56X  H10  C22  H8   107.64  3.000
 56X  H9   C22  H8   108.59  3.000
 56X  H10  C22  C21  109.66  3.000
 56X  H9   C22  C21  111.19  3.000
 56X  H8   C22  C21  111.76  3.000
 56X  H11  C09  N8   112.27  3.000
 56X  H11  C09  C11  110.88  3.000
 56X  N8   C09  C11  103.97  3.000
 56X  H11  C09  C10  114.76  3.000
 56X  C11  C09  C10  123.16  3.000
 56X  N8   C09  C10   88.46  3.000
 56X  H3   C11  C16  108.47  3.000
 56X  H3   C11  C14  110.71  3.000
 56X  C16  C11  C14  111.14  3.000
 56X  H3   C11  C09  109.50  3.000
 56X  C14  C11  C09  100.76  3.000
 56X  C16  C11  C09  116.07  3.000
 56X  O2   C12  N8   132.56  3.000
 56X  N8   C12  C10   92.34  3.000
 56X  O2   C12  C10  135.07  3.000
 56X  S1   C14  C11  117.87  3.000
 56X  S1   C14  C15  129.69  3.000
 56X  C11  C14  C15  112.37  3.000
 56X  H16  C16  H15  107.59  3.000
 56X  H16  C16  H14  107.86  3.000
 56X  H15  C16  H14  108.20  3.000
 56X  H16  C16  C11  110.27  3.000
 56X  H15  C16  C11  111.87  3.000
 56X  H14  C16  C11  110.91  3.000
 56X  O5   C18  O4   128.05  3.000
 56X  O4   C18  C15  116.15  3.000
 56X  O5   C18  C15  115.79  3.000
 56X  H18  C19  H17  107.34  3.000
 56X  H18  C19  S1   109.54  3.000
 56X  H17  C19  S1   106.43  3.000
 56X  H18  C19  C20  112.54  3.000
 56X  H17  C19  C20  107.44  3.000
 56X  S1   C19  C20  113.17  3.000
 56X  H21  C23  H20  108.62  3.000
 56X  H21  C23  H19  107.91  3.000
 56X  H20  C23  H19  107.90  3.000
 56X  H21  C23  C21  111.13  3.000
 56X  H20  C23  C21  111.58  3.000
 56X  H19  C23  C21  109.58  3.000
 56X  C12  N8   C09   93.59  3.000
 56X  C09  N8   C15  110.48  3.000
 56X  C12  N8   C15  131.34  3.000
 56X  H22  O3   C13  108.85  3.000
 56X  C21  O6   C20  119.16  3.000
 56X  C19  S1   C14  104.10  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
 56X  CONST_02  C09  N8   C12  C10     0.00   0.0  0
 56X  CONST_04  O2   C12  N8   C09   180.00   0.0  0
 56X  Var_01    C14  C15  N8   C09    10.72  30.0  1
 56X  Var_02    N8   C15  C14  C11     3.24  30.0  1
 56X  Var_03    C14  C15  N8   C12  -103.97  30.0  1
 56X  Var_04    C18  C15  N8   C09  -165.93  30.0  1
 56X  Var_05    C18  C15  C14  C11   179.39  30.0  1
 56X  Var_06    C18  C15  N8   C12    79.39  30.0  1
 56X  Var_07    S1   C14  C15  N8   -179.93  30.0  1
 56X  Var_08    C19  S1   C14  C15   -51.81  30.0  3
 56X  Var_09    C19  S1   C14  C11   124.87  30.0  3
 56X  Var_10    O5   C18  C15  C14   174.95  30.0  2
 56X  Var_11    O4   C18  C15  C14    -6.45  30.0  2
 56X  Var_12    S1   C14  C15  C18    -3.78  30.0  1
 56X  Var_13    O5   C18  C15  N8     -9.30  30.0  2
 56X  Var_14    O4   C18  C15  N8    169.31  30.0  2
 56X  Var_15    C14  S1   C19  C20   112.37  30.0  3
 56X  Var_16    H17  C19  S1   C14  -129.84  30.0  2
 56X  Var_17    H18  C19  S1   C14   -14.10  30.0  2
 56X  Var_18    C23  C21  O6   C20  -145.78  30.0  3
 56X  Var_19    C22  C21  O6   C20    91.80  30.0  3
 56X  Var_20    C19  C20  O6   C21   179.43  30.0  3
 56X  Var_21    O7   C20  O6   C21    -6.66  30.0  3
 56X  Var_22    S1   C19  C20  O6   -150.88  30.0  1
 56X  Var_23    S1   C19  C20  O7     35.11  30.0  1
 56X  Var_24    H7   C21  O6   C20   -28.14  30.0  3
 56X  Var_25    H19  C23  C21  C22   -61.09  30.0  3
 56X  Var_26    H20  C23  C21  C22    58.35  30.0  3
 56X  Var_27    H21  C23  C21  C22   179.75  30.0  3
 56X  Var_28    H8   C22  C21  C23   179.97  30.0  3
 56X  Var_29    H9   C22  C21  C23   -58.50  30.0  3
 56X  Var_30    H10  C22  C21  C23    60.69  30.0  3
 56X  Var_31    H19  C23  C21  O6    178.33  30.0  3
 56X  Var_32    H20  C23  C21  O6    -62.24  30.0  3
 56X  Var_33    H21  C23  C21  O6     59.16  30.0  3
 56X  Var_34    H8   C22  C21  O6    -61.37  30.0  3
 56X  Var_35    H9   C22  C21  O6     60.16  30.0  3
 56X  Var_36    H10  C22  C21  O6    179.35  30.0  3
 56X  Var_37    H17  C19  C20  O6     91.92  30.0  1
 56X  Var_38    H18  C19  C20  O6    -26.03  30.0  1
 56X  Var_39    H17  C19  C20  O7    -82.08  30.0  1
 56X  Var_40    H18  C19  C20  O7    159.97  30.0  1

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
 56X  chir_01  C10  C12  C09  C13  negativ
 56X  chir_02  C13  O3   C10  C17  negativ
 56X  chir_03  C09  N8   C10  C11  negativ
 56X  chir_04  C11  C09  C14  C16  positiv

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
 56X  plan-1  C10  0.020
 56X  plan-1  C15  0.020
 56X  plan-1  C09  0.020
 56X  plan-1  C12  0.020
 56X  plan-1  N8   0.020
 56X  plan-1  O2   0.020
 56X  plan-2  C15  0.020
 56X  plan-2  C18  0.020
 56X  plan-2  O4   0.020
 56X  plan-2  O5   0.020
 56X  plan-3  C20  0.020
 56X  plan-3  C19  0.020
 56X  plan-3  O6   0.020
 56X  plan-3  O7   0.020

