# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 16:28:05 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: (4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCCn1cc(CSC[C@@H](O)[C@@H](O)[C@@H]2O[C@@H](C[C@H](O)[C@H]2NC(C)=O)C(O)=O)nn1
#
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
 R7H  R7H  '(4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{S})-3-[[1-(2-ethoxyethyl)-1,2,3-triazol-4-yl]methylsulfanyl]-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid'  ligand  60  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R7H
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
 R7H  CAM   C  CH2    0  -0.671   -5.1391   2.5800  20.5416
 R7H  CAI   C  CH2    0  -0.153   -9.4607   0.0702  26.6729
 R7H  CAL   C  CH3    0  -0.685  -10.7301  -0.0845  27.4788
 R7H  CAJ   C  CH2    0  -0.336   -8.3094   0.5807  23.8455
 R7H  CAV   C  CR5    0   0.204   -5.7959   1.8603  21.6605
 R7H  C1    C  C      0   0.385   -0.3597  -1.7690  14.8026
 R7H  C2    C  CH1    0  -0.094    0.4348  -1.2116  16.0053
 R7H  C3    C  CH2    0  -0.471    1.6544  -2.0585  16.3465
 R7H  C4    C  CH1    0   0.059    2.3939  -1.4660  17.5322
 R7H  C5    C  CH1    0  -0.153    1.4258  -1.2345  18.6964
 R7H  C6    C  CH1    0   0.081    0.2014  -0.4371  18.2105
 R7H  C10   C  C      0   0.545    1.9356  -0.8158  21.0788
 R7H  C11   C  CH3    0  -0.771    2.8075  -0.0417  22.0306
 R7H  C7    C  CH1    0  -0.006   -0.8477  -0.2361  19.3116
 R7H  C8    C  CH1    0   0.050   -2.1134   0.4382  18.7705
 R7H  C9    C  CH2    0  -0.568   -3.0910   0.7443  19.9035
 R7H  N5    N  NH1    0  -0.637    2.1223  -0.5620  19.7741
 R7H  O10   O  O      0  -0.513    1.1140  -1.6331  21.4913
 R7H  O1A   O  O      0  -0.610    0.3285  -1.9916  13.7866
 R7H  O1B   O  OC    -1  -0.587   -1.5835  -1.9228  14.9387
 R7H  O4    O  OH1    0  -0.660    3.4402  -2.3377  17.8875
 R7H  O6    O  O2     0  -0.491   -0.4017  -1.1023  17.1354
 R7H  O7    O  OH1    0  -0.694   -1.2327  -1.4494  19.9078
 R7H  O8    O  OH1    0  -0.670   -1.7125   1.6198  18.1197
 R7H  S9    S  S2     0  -0.032   -4.5999   1.4839  19.1907
 R7H  CAD   C  CR15   0  -0.075   -7.1296   1.7661  21.9676
 R7H  CAG   C  CH2    0  -0.161   -8.4558   1.4917  25.0672
 R7H  NAP   N  N      0  -0.306   -5.1143   1.1296  22.5704
 R7H  NAS   N  N      0  -0.098   -5.9453   0.6009  23.4009
 R7H  NAZ   N  NR5    0  -0.252   -7.1643   0.9698  23.0495
 R7H  OAA   O  O2     0  -0.478   -9.5985   1.1864  25.8142
 R7H  H81   H  HCH2   0   0.304   -5.8349   3.2864  20.0894
 R7H  H71   H  HCH2   0   0.296   -4.2749   3.1477  20.8888
 R7H  H16   H  HCH2   0   0.203   -8.6012   0.2134  27.3410
 R7H  H15   H  HCH2   0   0.205   -9.2712  -0.8490  26.1050
 R7H  H14   H  HCH3   0   0.231  -10.6357  -0.9352  28.1531
 R7H  H1    H  HCH3   0   0.229  -10.9288   0.8017  28.0823
 R7H  H13   H  HCH3   0   0.229  -11.5911  -0.2630  26.8340
 R7H  H41   H  HCH2   0   0.281   -8.1760  -0.4619  24.1317
 R7H  H51   H  HCH2   0   0.277   -9.1939   0.6469  23.2138
 R7H  H9    H  HCH1   0   0.198    0.7910  -0.2050  15.7217
 R7H  H3    H  HCH2   0   0.225    1.3398  -3.0802  16.5857
 R7H  H10   H  HCH2   0   0.241    2.3204  -2.1111  15.4853
 R7H  H4    H  HCH1   0   0.198    2.7929  -0.4826  17.2291
 R7H  H5    H  HCH1   0   0.257    1.1008  -2.2141  19.0552
 R7H  H6    H  HCH1   0   0.205    0.5599   0.5576  17.8991
 R7H  H112  H  HCH3   0   0.270    3.3978  -0.7406  22.6231
 R7H  H111  H  HCH3   0   0.253    3.4865   0.6509  21.5372
 R7H  H113  H  HCH3   0   0.268    2.1794   0.5190  22.7224
 R7H  H7    H  HCH1   0   0.213   -0.4109   0.4508  20.0519
 R7H  H8    H  HCH1   0   0.212   -2.6011  -0.2535  18.0688
 R7H  H92   H  HCH2   0   0.275   -3.3461  -0.1555  20.4581
 R7H  H91   H  HCH2   0   0.264   -2.6474   1.4645  20.5951
 R7H  HN5   H  HNH1   0   0.406    2.7398   0.1968  19.5244
 R7H  HO4   H  HOH1   0   0.445    3.9439  -1.9390  18.6051
 R7H  HO7   H  HOH1   0   0.456   -0.5299  -1.6995  20.5300
 R7H  HO8   H  HOH1   0   0.441   -2.5093   2.1211  17.9061
 R7H  H61   H  HCR5   0   0.310   -8.0136   2.1815  21.5136
 R7H  H31   H  HCH2   0   0.214   -7.5446   1.4326  25.6771
 R7H  H2    H  HCH2   0   0.244   -8.5564   2.5251  24.7264

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
 R7H  CAM  CAV   single    1.484  0.020  1.484
 R7H  CAM  S9    single    1.821  0.020  1.821
 R7H  CAI  CAL   single    1.512  0.020  1.512
 R7H  CAI  OAA   single    1.415  0.020  1.415
 R7H  CAJ  CAG   single    1.531  0.020  1.531
 R7H  CAJ  NAZ   single    1.448  0.020  1.448
 R7H  CAV  CAD   aromatic  1.372  0.020  1.372
 R7H  CAV  NAP   aromatic  1.351  0.020  1.351
 R7H  C1   C2    single    1.545  0.020  1.545
 R7H  C1   O1A   deloc     1.247  0.020  1.247
 R7H  C1   O1B   deloc     1.241  0.020  1.241
 R7H  C2   C3    single    1.523  0.020  1.523
 R7H  C2   O6    single    1.410  0.020  1.410
 R7H  C3   C4    single    1.518  0.020  1.518
 R7H  C4   C5    single    1.532  0.020  1.532
 R7H  C4   O4    single    1.407  0.020  1.407
 R7H  C5   C6    single    1.540  0.020  1.540
 R7H  C5   N5    single    1.449  0.020  1.449
 R7H  C6   C7    single    1.534  0.020  1.534
 R7H  C6   O6    single    1.401  0.020  1.401
 R7H  C10  C11   single    1.505  0.020  1.505
 R7H  C10  N5    single    1.342  0.020  1.342
 R7H  C10  O10   double    1.230  0.020  1.230
 R7H  C7   C8    single    1.533  0.020  1.533
 R7H  C7   O7    single    1.406  0.020  1.406
 R7H  C8   C9    single    1.528  0.020  1.528
 R7H  C8   O8    single    1.407  0.020  1.407
 R7H  C9   S9    single    1.825  0.020  1.825
 R7H  CAD  NAZ   aromatic  1.344  0.020  1.344
 R7H  CAG  OAA   single    1.399  0.020  1.399
 R7H  NAP  NAS   aromatic  1.288  0.020  1.288
 R7H  NAS  NAZ   aromatic  1.321  0.020  1.321
 R7H  CAM  H81   single    0.970  0.020  1.090
 R7H  CAM  H71   single    0.970  0.020  1.090
 R7H  CAI  H16   single    0.970  0.020  1.090
 R7H  CAI  H15   single    0.970  0.020  1.090
 R7H  CAL  H14   single    0.970  0.020  1.090
 R7H  CAL  H1    single    0.970  0.020  1.090
 R7H  CAL  H13   single    0.970  0.020  1.090
 R7H  CAJ  H41   single    0.970  0.020  1.090
 R7H  CAJ  H51   single    0.970  0.020  1.090
 R7H  C2   H9    single    0.970  0.020  1.090
 R7H  C3   H3    single    0.970  0.020  1.090
 R7H  C3   H10   single    0.970  0.020  1.090
 R7H  C4   H4    single    0.970  0.020  1.090
 R7H  C5   H5    single    0.970  0.020  1.090
 R7H  C6   H6    single    0.970  0.020  1.090
 R7H  C11  H112  single    0.970  0.020  1.090
 R7H  C11  H111  single    0.970  0.020  1.090
 R7H  C11  H113  single    0.970  0.020  1.090
 R7H  C7   H7    single    0.970  0.020  1.090
 R7H  C8   H8    single    0.970  0.020  1.090
 R7H  C9   H92   single    0.970  0.020  1.090
 R7H  C9   H91   single    0.970  0.020  1.090
 R7H  N5   HN5   single    0.860  0.020  1.020
 R7H  O4   HO4   single    0.850  0.020  0.980
 R7H  O7   HO7   single    0.850  0.020  0.980
 R7H  O8   HO8   single    0.850  0.020  0.980
 R7H  CAD  H61   single    0.930  0.020  1.080
 R7H  CAG  H31   single    0.970  0.020  1.090
 R7H  CAG  H2    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
 R7H  H71   CAM  H81   107.49  3.000
 R7H  H71   CAM  S9    108.35  3.000
 R7H  H81   CAM  S9    105.75  3.000
 R7H  H71   CAM  CAV   111.29  3.000
 R7H  H81   CAM  CAV   110.16  3.000
 R7H  S9    CAM  CAV   113.48  3.000
 R7H  H15   CAI  H16   106.80  3.000
 R7H  H15   CAI  OAA   111.33  3.000
 R7H  H16   CAI  OAA   110.04  3.000
 R7H  H15   CAI  CAL   109.59  3.000
 R7H  H16   CAI  CAL   110.26  3.000
 R7H  OAA   CAI  CAL   108.81  3.000
 R7H  H13   CAL  H1    108.45  3.000
 R7H  H13   CAL  H14   107.85  3.000
 R7H  H1    CAL  H14   107.92  3.000
 R7H  H13   CAL  CAI   111.38  3.000
 R7H  H1    CAL  CAI   111.40  3.000
 R7H  H14   CAL  CAI   109.70  3.000
 R7H  H51   CAJ  H41   108.06  3.000
 R7H  H51   CAJ  NAZ   107.89  3.000
 R7H  H41   CAJ  NAZ   107.74  3.000
 R7H  H51   CAJ  CAG   110.43  3.000
 R7H  H41   CAJ  CAG   111.81  3.000
 R7H  NAZ   CAJ  CAG   110.76  3.000
 R7H  NAP   CAV  CAD   107.61  3.000
 R7H  NAP   CAV  CAM   123.14  3.000
 R7H  CAD   CAV  CAM   129.24  3.000
 R7H  O1B   C1   O1A   127.69  3.000
 R7H  O1B   C1   C2    117.80  3.000
 R7H  O1A   C1   C2    114.50  3.000
 R7H  H9    C2   O6    109.05  3.000
 R7H  H9    C2   C3    107.81  3.000
 R7H  O6    C2   C3    109.78  3.000
 R7H  H9    C2   C1    107.13  3.000
 R7H  O6    C2   C1    110.28  3.000
 R7H  C3    C2   C1    112.66  3.000
 R7H  H10   C3   H3    107.64  3.000
 R7H  H10   C3   C4    109.77  3.000
 R7H  H3    C3   C4    109.47  3.000
 R7H  H10   C3   C2    109.82  3.000
 R7H  H3    C3   C2    109.72  3.000
 R7H  C4    C3   C2    110.37  3.000
 R7H  H4    C4   O4    110.64  3.000
 R7H  H4    C4   C5    107.61  3.000
 R7H  O4    C4   C5    111.81  3.000
 R7H  H4    C4   C3    108.02  3.000
 R7H  O4    C4   C3    108.52  3.000
 R7H  C5    C4   C3    110.17  3.000
 R7H  H5    C5   N5    108.35  3.000
 R7H  H5    C5   C6    109.35  3.000
 R7H  N5    C5   C6    112.12  3.000
 R7H  H5    C5   C4    107.59  3.000
 R7H  N5    C5   C4    109.37  3.000
 R7H  C6    C5   C4    109.94  3.000
 R7H  H6    C6   O6    110.60  3.000
 R7H  H6    C6   C7    107.87  3.000
 R7H  O6    C6   C7    108.59  3.000
 R7H  H6    C6   C5    107.33  3.000
 R7H  O6    C6   C5    109.79  3.000
 R7H  C7    C6   C5    112.65  3.000
 R7H  O10   C10  N5    122.99  3.000
 R7H  O10   C10  C11   121.10  3.000
 R7H  N5    C10  C11   115.90  3.000
 R7H  H113  C11  H111  108.67  3.000
 R7H  H113  C11  H112  107.28  3.000
 R7H  H111  C11  H112  108.46  3.000
 R7H  H113  C11  C10   109.40  3.000
 R7H  H111  C11  C10   113.71  3.000
 R7H  H112  C11  C10   109.13  3.000
 R7H  H7    C7   O7    111.24  3.000
 R7H  H7    C7   C8    106.90  3.000
 R7H  O7    C7   C8    107.65  3.000
 R7H  H7    C7   C6    107.06  3.000
 R7H  O7    C7   C6    112.25  3.000
 R7H  C8    C7   C6    111.65  3.000
 R7H  H8    C8   O8    111.07  3.000
 R7H  H8    C8   C9    108.40  3.000
 R7H  O8    C8   C9    110.92  3.000
 R7H  H8    C8   C7    108.35  3.000
 R7H  O8    C8   C7    107.30  3.000
 R7H  C9    C8   C7    110.78  3.000
 R7H  H91   C9   H92   108.54  3.000
 R7H  H91   C9   S9    108.41  3.000
 R7H  H92   C9   S9    109.91  3.000
 R7H  H91   C9   C8    109.98  3.000
 R7H  H92   C9   C8    111.26  3.000
 R7H  S9    C9   C8    108.70  3.000
 R7H  HN5   N5   C10   117.87  3.000
 R7H  HN5   N5   C5    117.32  3.000
 R7H  C10   N5   C5    124.65  3.000
 R7H  HO4   O4   C4    108.69  3.000
 R7H  C6    O6   C2    113.36  3.000
 R7H  HO7   O7   C7    107.20  3.000
 R7H  HO8   O8   C8    107.66  3.000
 R7H  C9    S9   CAM   101.47  3.000
 R7H  H61   CAD  NAZ   123.14  3.000
 R7H  H61   CAD  CAV   132.61  3.000
 R7H  NAZ   CAD  CAV   104.24  3.000
 R7H  H2    CAG  H31   107.49  3.000
 R7H  H2    CAG  OAA   107.32  3.000
 R7H  H31   CAG  OAA   111.69  3.000
 R7H  H2    CAG  CAJ   108.82  3.000
 R7H  H31   CAG  CAJ   109.38  3.000
 R7H  OAA   CAG  CAJ   111.99  3.000
 R7H  NAS   NAP  CAV   109.31  3.000
 R7H  NAZ   NAS  NAP   108.00  3.000
 R7H  NAS   NAZ  CAD   110.84  3.000
 R7H  NAS   NAZ  CAJ   120.56  3.000
 R7H  CAD   NAZ  CAJ   128.49  3.000
 R7H  CAG   OAA  CAI   114.62  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
 R7H  CONST_01  NAS   NAZ  CAD  CAV     0.00   0.0  0
 R7H  CONST_02  NAZ   NAS  NAP  CAV     0.00   0.0  0
 R7H  CONST_03  NAS   NAP  CAV  CAD     0.00   0.0  0
 R7H  CONST_04  NAP   NAS  NAZ  CAD     0.00   0.0  0
 R7H  CONST_05  NAZ   CAD  CAV  NAP     0.00   0.0  0
 R7H  CONST_06  NAZ   CAD  CAV  CAM   180.00   0.0  0
 R7H  CONST_07  NAS   NAP  CAV  CAM   180.00   0.0  0
 R7H  CONST_08  CAV   CAD  NAZ  CAJ   180.00   0.0  0
 R7H  CONST_09  NAP   NAS  NAZ  CAJ   180.00   0.0  0
 R7H  CONST_10  H61   CAD  CAV  NAP   180.00   0.0  0
 R7H  CONST_11  C11   C10  N5   C5    180.00   0.0  0
 R7H  CONST_12  O10   C10  N5   C5      0.00   0.0  0
 R7H  CONST_13  HN5   N5   C10  C11     0.00   0.0  0
 R7H  Var_01    CAD   CAV  CAM  S9   -103.06  30.0  2
 R7H  Var_02    CAG   CAJ  NAZ  CAD   -95.62  30.0  2
 R7H  Var_03    OAA   CAG  CAJ  NAZ   176.62  30.0  3
 R7H  Var_04    C8    C9   S9   CAM  -149.10  30.0  1
 R7H  Var_05    CAJ   CAG  OAA  CAI    79.72  30.0  1
 R7H  Var_06    H112  C11  C10  N5   -120.48  30.0  3
 R7H  Var_07    H16   CAI  OAA  CAG    55.34  30.0  1
 R7H  Var_08    H14   CAL  CAI  OAA  -179.44  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
 R7H  chir_01  C2  C1  C3  O6  positiv
 R7H  chir_02  C4  O4  C5  C3  positiv
 R7H  chir_03  C5  N5  C6  C4  negativ
 R7H  chir_04  C6  O6  C5  C7  positiv
 R7H  chir_05  C7  O7  C6  C8  negativ
 R7H  chir_06  C8  O8  C7  C9  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
 R7H  plan-1  CAM  0.020
 R7H  plan-1  CAJ  0.020
 R7H  plan-1  CAV  0.020
 R7H  plan-1  CAD  0.020
 R7H  plan-1  NAP  0.020
 R7H  plan-1  NAS  0.020
 R7H  plan-1  NAZ  0.020
 R7H  plan-1  H61  0.020
 R7H  plan-2  C5   0.020
 R7H  plan-2  C10  0.020
 R7H  plan-2  C11  0.020
 R7H  plan-2  N5   0.020
 R7H  plan-2  O10  0.020
 R7H  plan-2  HN5  0.020
 R7H  plan-3  C1   0.020
 R7H  plan-3  C2   0.020
 R7H  plan-3  O1A  0.020
 R7H  plan-3  O1B  0.020

