# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 05:15:49 2021
#   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  61  31  .  2022-03-23  2022-11-17
;
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  -0.674   -5.3635   1.5698  20.0817
 R7H  CAI   C  CH2   0  -0.176   -8.6666   1.3675  27.2560
 R7H  CAL   C  CH3   0  -0.677   -9.7380   0.2989  27.3323
 R7H  CAJ   C  CH2   0  -0.337   -7.9448   0.9316  24.3082
 R7H  CAV   C  CR5   0   0.209   -5.8312   1.2773  21.4575
 R7H  C1    C  C     0   0.523    0.2123  -0.7994  14.6732
 R7H  C2    C  CH1   0  -0.067    0.6186  -0.4694  16.0938
 R7H  C3    C  CH2   0  -0.487    1.9812  -1.0711  16.4244
 R7H  C4    C  CH1   0   0.054    2.3498  -0.7383  17.8594
 R7H  C5    C  CH1   0  -0.153    1.2074  -1.1372  18.7988
 R7H  C6    C  CH1   0   0.066   -0.1092  -0.5069  18.3148
 R7H  C10   C  C     0   0.544    1.2493  -1.4645  21.2456
 R7H  C11   C  CH3   0  -0.771    1.7631  -0.9093  22.5463
 R7H  C7    C  CH1   0  -0.016   -1.3108  -0.9030  19.1765
 R7H  C8    C  CH1   0   0.069   -2.6240  -0.3523  18.6180
 R7H  C9    C  CH2   0  -0.597   -3.7967  -0.7184  19.5266
 R7H  N5    N  NH1   0  -0.640    1.5358  -0.7383  20.1503
 R7H  O10   O  O     0  -0.514    0.6490  -2.5358  21.1954
 R7H  O1A   O  O     0  -0.446    0.9463  -0.6075  13.7358
 R7H  O1B   O  OH1   0  -0.572   -1.0125  -1.2758  14.5688
 R7H  O4    O  OH1   0  -0.659    3.5419  -1.4149  18.1670
 R7H  O6    O  O2    0  -0.488   -0.3593  -0.9134  16.9899
 R7H  O7    O  OH1   0  -0.696   -1.4450  -2.2965  19.2933
 R7H  O8    O  OH1   0  -0.671   -2.4685   1.0430  18.5058
 R7H  S9    S  S2    0  -0.034   -5.3342   0.0983  18.9968
 R7H  CAD   C  CR15  0  -0.073   -7.0900   1.3902  21.9918
 R7H  CAG   C  CH2   0  -0.173   -7.8679   2.1972  25.1636
 R7H  NAP   N  N     0  -0.314   -5.0193   0.7960  22.4251
 R7H  NAS   N  N     0  -0.099   -5.7020   0.6096  23.5018
 R7H  NAZ   N  NR5   0  -0.252   -6.9523   0.9583  23.2565
 R7H  OAA   O  O2    0  -0.487   -8.8692   2.2218  26.1407
 R7H  H81   H  HCH2  0   0.302   -6.0278   2.2842  19.5964
 R7H  H71   H  HCH2  0   0.293   -4.3661   2.0056  20.0969
 R7H  H16   H  HCH2  0   0.228   -8.6909   1.9824  28.1614
 R7H  H15   H  HCH2  0   0.213   -7.6746   0.9032  27.2207
 R7H  H14   H  HCH3  0   0.229   -9.6018  -0.2997  28.2335
 R7H  H1    H  HCH3  0   0.231  -10.7338   0.7412  27.3743
 R7H  H13   H  HCH3  0   0.226   -9.7002  -0.3752  26.4757
 R7H  H41   H  HCH2  0   0.279   -7.7681   0.0391  24.9089
 R7H  H51   H  HCH2  0   0.280   -8.9275   0.8421  23.8477
 R7H  H9    H  HCH1  0   0.264    0.7032   0.6298  16.1338
 R7H  H3    H  HCH2  0   0.254    1.9402  -2.1576  16.2989
 R7H  H10   H  HCH2  0   0.267    2.7399  -0.6812  15.7450
 R7H  H4    H  HCH1  0   0.213    2.4860   0.3535  17.9379
 R7H  H5    H  HCH1  0   0.269    1.1200  -2.2260  18.7718
 R7H  H6    H  HCH1  0   0.227   -0.0013   0.5871  18.3651
 R7H  H112  H  HCH3  0   0.268    1.0157  -1.0422  23.3258
 R7H  H111  H  HCH3  0   0.277    2.6496  -1.4738  22.8411
 R7H  H113  H  HCH3  0   0.256    2.0352   0.1426  22.4902
 R7H  H7    H  HCH1  0   0.221   -1.1590  -0.4351  20.1610
 R7H  H8    H  HCH1  0   0.222   -2.8081  -0.8005  17.6335
 R7H  H92   H  HCH2  0   0.284   -3.9780  -1.7917  19.4930
 R7H  H91   H  HCH2  0   0.275   -3.6047  -0.4513  20.5683
 R7H  HN5   H  HNH1  0   0.408    1.9154   0.1873  20.2855
 R7H  H11   H  HOH1  0   0.486   -1.2210  -1.4392  13.6361
 R7H  HO4   H  HOH1  0   0.450    3.8233  -1.1582  19.0511
 R7H  HO7   H  HOH1  0   0.458   -0.7806  -2.5982  19.9342
 R7H  HO8   H  HOH1  0   0.453   -3.2073   1.3795  17.9869
 R7H  H61   H  HCR5  0   0.312   -8.0270   1.7304  21.5844
 R7H  H31   H  HCH2  0   0.219   -6.8668   2.2776  25.6060
 R7H  H2    H  HCH2  0   0.245   -8.0161   3.0732  24.5278

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    1.482  0.020  1.482
 R7H  CAM  S9    single    1.828  0.020  1.828
 R7H  CAI  CAL   single    1.515  0.020  1.515
 R7H  CAI  OAA   single    1.419  0.020  1.419
 R7H  CAJ  CAG   single    1.530  0.020  1.530
 R7H  CAJ  NAZ   single    1.446  0.020  1.446
 R7H  CAV  CAD   aromatic  1.372  0.020  1.372
 R7H  CAV  NAP   aromatic  1.352  0.020  1.352
 R7H  C1   C2    single    1.514  0.020  1.514
 R7H  C1   O1A   double    1.206  0.020  1.206
 R7H  C1   O1B   single    1.318  0.020  1.318
 R7H  C2   C3    single    1.526  0.020  1.526
 R7H  C2   O6    single    1.399  0.020  1.399
 R7H  C3   C4    single    1.519  0.020  1.519
 R7H  C4   C5    single    1.532  0.020  1.532
 R7H  C4   O4    single    1.405  0.020  1.405
 R7H  C5   C6    single    1.538  0.020  1.538
 R7H  C5   N5    single    1.447  0.020  1.447
 R7H  C6   C7    single    1.531  0.020  1.531
 R7H  C6   O6    single    1.408  0.020  1.408
 R7H  C10  C11   single    1.505  0.020  1.505
 R7H  C10  N5    single    1.345  0.020  1.345
 R7H  C10  O10   double    1.229  0.020  1.229
 R7H  C7   C8    single    1.530  0.020  1.530
 R7H  C7   O7    single    1.405  0.020  1.405
 R7H  C8   C9    single    1.528  0.020  1.528
 R7H  C8   O8    single    1.408  0.020  1.408
 R7H  C9   S9    single    1.820  0.020  1.820
 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  O1B  H11   single    0.850  0.020  0.980
 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   107.60  3.000
 R7H  H71   CAM  S9    108.41  3.000
 R7H  H81   CAM  S9    105.86  3.000
 R7H  H71   CAM  CAV   110.79  3.000
 R7H  H81   CAM  CAV   110.51  3.000
 R7H  S9    CAM  CAV   113.39  3.000
 R7H  H15   CAI  H16   106.54  3.000
 R7H  H15   CAI  OAA   111.03  3.000
 R7H  H16   CAI  OAA   107.98  3.000
 R7H  H15   CAI  CAL   110.06  3.000
 R7H  H16   CAI  CAL   109.80  3.000
 R7H  OAA   CAI  CAL   111.29  3.000
 R7H  H13   CAL  H1    108.22  3.000
 R7H  H13   CAL  H14   107.79  3.000
 R7H  H1    CAL  H14   107.76  3.000
 R7H  H13   CAL  CAI   111.83  3.000
 R7H  H1    CAL  CAI   111.20  3.000
 R7H  H14   CAL  CAI   109.90  3.000
 R7H  H51   CAJ  H41   108.17  3.000
 R7H  H51   CAJ  NAZ   108.26  3.000
 R7H  H41   CAJ  NAZ   107.73  3.000
 R7H  H51   CAJ  CAG   110.48  3.000
 R7H  H41   CAJ  CAG   111.17  3.000
 R7H  NAZ   CAJ  CAG   110.91  3.000
 R7H  NAP   CAV  CAD   107.56  3.000
 R7H  NAP   CAV  CAM   123.04  3.000
 R7H  CAD   CAV  CAM   129.39  3.000
 R7H  O1B   C1   O1A   124.15  3.000
 R7H  O1B   C1   C2    113.73  3.000
 R7H  O1A   C1   C2    122.10  3.000
 R7H  H9    C2   O6    110.28  3.000
 R7H  H9    C2   C3    108.45  3.000
 R7H  O6    C2   C3    111.12  3.000
 R7H  H9    C2   C1    105.78  3.000
 R7H  O6    C2   C1    110.14  3.000
 R7H  C3    C2   C1    110.92  3.000
 R7H  H10   C3   H3    108.03  3.000
 R7H  H10   C3   C4    109.98  3.000
 R7H  H3    C3   C4    109.58  3.000
 R7H  H10   C3   C2    110.20  3.000
 R7H  H3    C3   C2    109.46  3.000
 R7H  C4    C3   C2    109.58  3.000
 R7H  H4    C4   O4    110.88  3.000
 R7H  H4    C4   C5    107.83  3.000
 R7H  O4    C4   C5    111.91  3.000
 R7H  H4    C4   C3    108.31  3.000
 R7H  O4    C4   C3    107.90  3.000
 R7H  C5    C4   C3    109.96  3.000
 R7H  H5    C5   N5    108.42  3.000
 R7H  H5    C5   C6    109.40  3.000
 R7H  N5    C5   C6    112.05  3.000
 R7H  H5    C5   C4    107.69  3.000
 R7H  N5    C5   C4    109.38  3.000
 R7H  C6    C5   C4    109.80  3.000
 R7H  H6    C6   O6    110.32  3.000
 R7H  H6    C6   C7    107.97  3.000
 R7H  O6    C6   C7    108.39  3.000
 R7H  H6    C6   C5    108.01  3.000
 R7H  O6    C6   C5    109.26  3.000
 R7H  C7    C6   C5    112.88  3.000
 R7H  O10   C10  N5    122.77  3.000
 R7H  O10   C10  C11   121.58  3.000
 R7H  N5    C10  C11   115.60  3.000
 R7H  H113  C11  H111  108.11  3.000
 R7H  H113  C11  H112  109.08  3.000
 R7H  H111  C11  H112  107.53  3.000
 R7H  H113  C11  C10   113.43  3.000
 R7H  H111  C11  C10   108.66  3.000
 R7H  H112  C11  C10   109.85  3.000
 R7H  H7    C7   O7    111.13  3.000
 R7H  H7    C7   C8    106.98  3.000
 R7H  O7    C7   C8    107.79  3.000
 R7H  H7    C7   C6    106.57  3.000
 R7H  O7    C7   C6    112.24  3.000
 R7H  C8    C7   C6    112.04  3.000
 R7H  H8    C8   O8    110.59  3.000
 R7H  H8    C8   C9    107.87  3.000
 R7H  O8    C8   C9    111.69  3.000
 R7H  H8    C8   C7    108.94  3.000
 R7H  O8    C8   C7    106.92  3.000
 R7H  C9    C8   C7    110.83  3.000
 R7H  H91   C9   H92   107.43  3.000
 R7H  H91   C9   S9    108.44  3.000
 R7H  H92   C9   S9    107.02  3.000
 R7H  H91   C9   C8    111.93  3.000
 R7H  H92   C9   C8    110.22  3.000
 R7H  S9    C9   C8    111.58  3.000
 R7H  HN5   N5   C10   117.78  3.000
 R7H  HN5   N5   C5    117.59  3.000
 R7H  C10   N5   C5    124.30  3.000
 R7H  H11   O1B  C1    109.69  3.000
 R7H  HO4   O4   C4    108.71  3.000
 R7H  C6    O6   C2    112.77  3.000
 R7H  HO7   O7   C7    107.32  3.000
 R7H  HO8   O8   C8    107.71  3.000
 R7H  C9    S9   CAM   101.65  3.000
 R7H  H61   CAD  NAZ   123.15  3.000
 R7H  H61   CAD  CAV   132.60  3.000
 R7H  NAZ   CAD  CAV   104.24  3.000
 R7H  H2    CAG  H31   107.43  3.000
 R7H  H2    CAG  OAA   107.18  3.000
 R7H  H31   CAG  OAA   111.72  3.000
 R7H  H2    CAG  CAJ   109.34  3.000
 R7H  H31   CAG  CAJ   109.38  3.000
 R7H  OAA   CAG  CAJ   111.66  3.000
 R7H  NAS   NAP  CAV   109.35  3.000
 R7H  NAZ   NAS  NAP   107.95  3.000
 R7H  NAS   NAZ  CAD   110.90  3.000
 R7H  NAS   NAZ  CAJ   120.64  3.000
 R7H  CAD   NAZ  CAJ   128.32  3.000
 R7H  CAG   OAA  CAI   115.85  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  H11   O1B  C1   C2    180.00   0.0  0
 R7H  CONST_14  HN5   N5   C10  C11     0.00   0.0  0
 R7H  Var_01    CAD   CAV  CAM  S9    -94.85  30.0  2
 R7H  Var_02    CAG   CAJ  NAZ  CAD   -93.46  30.0  2
 R7H  Var_03    OAA   CAG  CAJ  NAZ   176.74  30.0  3
 R7H  Var_04    C8    C9   S9   CAM   -96.18  30.0  1
 R7H  Var_05    CAJ   CAG  OAA  CAI    75.29  30.0  1
 R7H  Var_06    H112  C11  C10  N5    139.91  30.0  3
 R7H  Var_07    H16   CAI  OAA  CAG   123.20  30.0  1
 R7H  Var_08    H14   CAL  CAI  OAA  -176.04  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
 R7H  plan-3  H11  0.020

