# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 20 10:51:28 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (3~{R},5~{R},6~{S},7~{S},8~{R},13~{S})-5-(hydroxymethyl)-7-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-oxidanyl-11-oxidanylidene-2,4-dioxa-9-thia-12-azatricyclo[8.4.0.0^{3,8}]tetradec-1(10)-ene-13-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@H]3OC4=C(S[C@H]23)C(=O)N[C@@H](C4)C(O)=O)[C@H](O)[C@@H](O)[C@H]1O
#
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
 EGZ  EGZ  '(3~{R},5~{R},6~{S},7~{S},8~{R},13~{S})-5-(hydroxymethyl)-7-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-oxidanyl-11-oxidanylidene-2,4-dioxa-9-thia-12-azatricyclo[8.4.0.0^{3,8}]tetradec-1(10)-ene-13-carboxylic acid'  ligand  57  33  .  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_EGZ
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
 EGZ  C01   C  CH2    0  -0.588  -5.0611   0.7077   0.0966
 EGZ  C02   C  CH1    0  -0.261  -5.7005  -0.5167  -0.5403
 EGZ  C04   C  C      0   0.467  -4.0530  -1.9506   0.5013
 EGZ  C06   C  C      0  -0.323  -3.1411  -0.7931   0.4818
 EGZ  C07   C  C      0   0.528  -3.6093   0.4569   0.3347
 EGZ  C09   C  CH1    0   0.337  -1.5599   1.5074   0.8928
 EGZ  C10   C  CH1    0  -0.503  -0.7653   0.3771   0.2470
 EGZ  C12   C  CH1    0   0.014   0.6749   0.4751   0.7185
 EGZ  C13   C  CH1    0   0.034   1.2390   1.8657   0.3889
 EGZ  C14   C  CH1    0  -0.063   0.3033   2.9039   1.0077
 EGZ  C16   C  CH2    0  -0.139   0.7341   4.3217   0.7018
 EGZ  C20   C  CH1    0   0.297   2.7092  -0.7055   0.4310
 EGZ  C21   C  CH1    0  -0.116   3.1391  -2.1687   0.3747
 EGZ  C22   C  CH1    0   0.030   4.6448  -2.2330   0.6192
 EGZ  C23   C  CH1    0  -0.018   5.3947  -1.3340  -0.3649
 EGZ  C24   C  CH1    0   0.028   4.8086   0.0701  -0.2878
 EGZ  C26   C  CH2    0  -0.094   5.4222   1.0370  -1.2771
 EGZ  C31   C  C      0   0.370  -5.3122  -0.6345  -2.0436
 EGZ  N03   N  NH1    0  -0.472  -5.3462  -1.6911   0.2290
 EGZ  O05   O  O      0  -0.614  -3.6287  -3.0576   0.8172
 EGZ  O15   O  O2     0  -0.509  -1.0278   2.7384   0.5492
 EGZ  O17   O  OH1    0  -0.660  -0.0384   5.2008   1.4808
 EGZ  O18   O  OH1    0  -0.653   1.3586   2.0833  -0.9878
 EGZ  O19   O  O2     0  -0.555   1.3649  -0.6022   0.1254
 EGZ  O25   O  O2     0  -0.450   3.4154   0.0357  -0.5276
 EGZ  O27   O  OH1    0  -0.663   4.9014   2.3177  -1.0120
 EGZ  O28   O  OH1    0  -0.686   5.2910  -1.7978  -1.6865
 EGZ  O29   O  OH1    0  -0.693   5.1525  -3.5350   0.4882
 EGZ  O30   O  OH1    0  -0.700   2.5088  -2.9227   1.3794
 EGZ  O32   O  O      0  -0.466  -4.8171  -1.7062  -2.4253
 EGZ  O33   O  OC    -1  -0.681  -5.5615   0.3775  -2.7268
 EGZ  S11   S  S2     0   0.070  -1.4542  -1.2242   0.7267
 EGZ  H012  H  HCH2   0   0.265  -5.1934   1.5685  -0.5582
 EGZ  H011  H  HCH2   0   0.259  -5.5391   0.9533   1.0514
 EGZ  H021  H  HCH1   0   0.277  -6.7855  -0.4046  -0.4839
 EGZ  H3    H  HCH1   0   0.315  -1.5694   1.3703   1.9868
 EGZ  H101  H  HCH1   0   0.339  -0.8102   0.4885  -0.8408
 EGZ  H121  H  HCH1   0   0.282   0.7020   0.3698   1.8157
 EGZ  H131  H  HCH1   0   0.255   2.2063   1.9803   0.8975
 EGZ  H141  H  HCH1   0   0.221   0.3384   2.7531   2.1007
 EGZ  H162  H  HCH2   0   0.227   1.8042   4.4034   0.9328
 EGZ  H161  H  HCH2   0   0.145   0.6212   4.5145  -0.3705
 EGZ  H201  H  HCH1   0   0.238   2.9139  -0.3096   1.4439
 EGZ  H211  H  HCH1   0   0.294   2.9150  -2.5601  -0.6267
 EGZ  H221  H  HCH1   0   0.283   4.8347  -1.8387   1.6310
 EGZ  H231  H  HCH1   0   0.266   6.4450  -1.2736  -0.0423
 EGZ  H241  H  HCH1   0   0.188   5.0054   0.4469   0.7289
 EGZ  H261  H  HCH2   0   0.168   6.5128   1.0033  -1.1529
 EGZ  H262  H  HCH2   0   0.129   5.2019   0.7134  -2.2996
 EGZ  H031  H  HNH1   0   0.350  -5.9294  -2.5057   0.1050
 EGZ  H171  H  HOH1   0   0.463   0.1872   6.1012   1.2295
 EGZ  H181  H  HOH1   0   0.457   2.1833   1.6689  -1.2694
 EGZ  H271  H  HOH1   0   0.480   5.1212   2.8939  -1.7501
 EGZ  H281  H  HOH1   0   0.452   5.5919  -2.7128  -1.7119
 EGZ  H291  H  HOH1   0   0.455   4.6457  -4.1252   1.0573
 EGZ  H301  H  HOH1   0   0.438   1.6142  -3.1345   1.0950
 EGZ  O08   O  O2     0  -0.514  -2.8790   1.5784   0.4207

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
 EGZ  C01  C02   single  1.521  0.020  1.521
 EGZ  C01  C07   single  1.492  0.020  1.492
 EGZ  C02  C31   single  1.557  0.020  1.557
 EGZ  C02  N03   single  1.448  0.020  1.448
 EGZ  C04  C06   single  1.474  0.020  1.474
 EGZ  C04  N03   single  1.347  0.020  1.347
 EGZ  C04  O05   double  1.227  0.020  1.227
 EGZ  C06  C07   double  1.343  0.020  1.343
 EGZ  C06  S11   single  1.758  0.020  1.758
 EGZ  C07  O08   single  1.341  0.020  1.341
 EGZ  C09  C10   single  1.525  0.020  1.525
 EGZ  C09  O15   single  1.384  0.020  1.384
 EGZ  C10  C12   single  1.519  0.020  1.519
 EGZ  C10  S11   single  1.808  0.020  1.808
 EGZ  C12  C13   single  1.536  0.020  1.536
 EGZ  C12  O19   single  1.410  0.020  1.410
 EGZ  C13  C14   single  1.528  0.020  1.528
 EGZ  C13  O18   single  1.399  0.020  1.399
 EGZ  C14  C16   single  1.513  0.020  1.513
 EGZ  C14  O15   single  1.418  0.020  1.418
 EGZ  C16  O17   single  1.406  0.020  1.406
 EGZ  C20  C21   single  1.526  0.020  1.526
 EGZ  C20  O19   single  1.382  0.020  1.382
 EGZ  C20  O25   single  1.403  0.020  1.403
 EGZ  C21  C22   single  1.527  0.020  1.527
 EGZ  C21  O30   single  1.405  0.020  1.405
 EGZ  C22  C23   single  1.529  0.020  1.529
 EGZ  C22  O29   single  1.404  0.020  1.404
 EGZ  C23  C24   single  1.524  0.020  1.524
 EGZ  C23  O28   single  1.404  0.020  1.404
 EGZ  C24  C26   single  1.513  0.020  1.513
 EGZ  C24  O25   single  1.414  0.020  1.414
 EGZ  C26  O27   single  1.408  0.020  1.408
 EGZ  C31  O32   deloc   1.241  0.020  1.241
 EGZ  C31  O33   deloc   1.246  0.020  1.246
 EGZ  C01  H012  single  0.970  0.020  1.090
 EGZ  C01  H011  single  0.970  0.020  1.090
 EGZ  C02  H021  single  0.970  0.020  1.090
 EGZ  C09  H3    single  0.970  0.020  1.090
 EGZ  C10  H101  single  0.970  0.020  1.090
 EGZ  C12  H121  single  0.970  0.020  1.090
 EGZ  C13  H131  single  0.970  0.020  1.090
 EGZ  C14  H141  single  0.970  0.020  1.090
 EGZ  C16  H162  single  0.970  0.020  1.090
 EGZ  C16  H161  single  0.970  0.020  1.090
 EGZ  C20  H201  single  0.970  0.020  1.090
 EGZ  C21  H211  single  0.970  0.020  1.090
 EGZ  C22  H221  single  0.970  0.020  1.090
 EGZ  C23  H231  single  0.970  0.020  1.090
 EGZ  C24  H241  single  0.970  0.020  1.090
 EGZ  C26  H261  single  0.970  0.020  1.090
 EGZ  C26  H262  single  0.970  0.020  1.090
 EGZ  N03  H031  single  0.890  0.020  1.040
 EGZ  O17  H171  single  0.850  0.020  0.980
 EGZ  O18  H181  single  0.850  0.020  0.980
 EGZ  O27  H271  single  0.850  0.020  0.980
 EGZ  O28  H281  single  0.850  0.020  0.980
 EGZ  O29  H291  single  0.850  0.020  0.980
 EGZ  O30  H301  single  0.850  0.020  0.980
 EGZ  C09  O08   single  1.403  0.020  1.403

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
 EGZ  H011  C01  H012  107.07  3.000
 EGZ  H011  C01  C07   108.85  3.000
 EGZ  H012  C01  C07   110.29  3.000
 EGZ  H011  C01  C02   111.22  3.000
 EGZ  H012  C01  C02   109.47  3.000
 EGZ  C07   C01  C02   109.90  3.000
 EGZ  H021  C02  N03   107.39  3.000
 EGZ  H021  C02  C31   107.78  3.000
 EGZ  N03   C02  C31   112.99  3.000
 EGZ  H021  C02  C01   108.26  3.000
 EGZ  N03   C02  C01   109.12  3.000
 EGZ  C31   C02  C01   111.12  3.000
 EGZ  O05   C04  N03   123.91  3.000
 EGZ  O05   C04  C06   119.88  3.000
 EGZ  N03   C04  C06   116.12  3.000
 EGZ  S11   C06  C07   125.31  3.000
 EGZ  S11   C06  C04   113.53  3.000
 EGZ  C07   C06  C04   121.12  3.000
 EGZ  O08   C07  C06   125.55  3.000
 EGZ  O08   C07  C01   113.54  3.000
 EGZ  C06   C07  C01   120.87  3.000
 EGZ  O08   C09  H3    109.40  3.000
 EGZ  O08   C09  O15   103.47  3.000
 EGZ  H3    C09  O15   111.11  3.000
 EGZ  O08   C09  C10   112.64  3.000
 EGZ  H3    C09  C10   109.42  3.000
 EGZ  O15   C09  C10   110.71  3.000
 EGZ  H101  C10  S11   109.77  3.000
 EGZ  H101  C10  C12   109.94  3.000
 EGZ  S11   C10  C12   109.64  3.000
 EGZ  H101  C10  C09   108.91  3.000
 EGZ  S11   C10  C09   110.21  3.000
 EGZ  C12   C10  C09   108.35  3.000
 EGZ  H121  C12  O19   109.48  3.000
 EGZ  H121  C12  C13   106.91  3.000
 EGZ  O19   C12  C13   114.93  3.000
 EGZ  H121  C12  C10   109.04  3.000
 EGZ  O19   C12  C10   106.51  3.000
 EGZ  C13   C12  C10   109.88  3.000
 EGZ  H131  C13  O18   111.35  3.000
 EGZ  H131  C13  C14   106.30  3.000
 EGZ  O18   C13  C14   110.19  3.000
 EGZ  H131  C13  C12   108.56  3.000
 EGZ  O18   C13  C12   112.54  3.000
 EGZ  C14   C13  C12   107.65  3.000
 EGZ  H141  C14  O15   109.52  3.000
 EGZ  H141  C14  C16   108.61  3.000
 EGZ  O15   C14  C16   108.14  3.000
 EGZ  H141  C14  C13   106.77  3.000
 EGZ  O15   C14  C13   111.38  3.000
 EGZ  C16   C14  C13   112.35  3.000
 EGZ  H161  C16  H162  107.06  3.000
 EGZ  H161  C16  O17   112.07  3.000
 EGZ  H162  C16  O17   111.87  3.000
 EGZ  H161  C16  C14   109.49  3.000
 EGZ  H162  C16  C14   107.74  3.000
 EGZ  O17   C16  C14   108.51  3.000
 EGZ  H201  C20  O25   110.08  3.000
 EGZ  H201  C20  O19   110.82  3.000
 EGZ  O25   C20  O19   107.40  3.000
 EGZ  H201  C20  C21   108.94  3.000
 EGZ  O25   C20  C21   109.85  3.000
 EGZ  O19   C20  C21   109.72  3.000
 EGZ  H211  C21  O30   111.66  3.000
 EGZ  H211  C21  C22   109.40  3.000
 EGZ  O30   C21  C22   107.77  3.000
 EGZ  H211  C21  C20   108.53  3.000
 EGZ  O30   C21  C20   111.20  3.000
 EGZ  C22   C21  C20   108.20  3.000
 EGZ  H221  C22  O29   110.80  3.000
 EGZ  H221  C22  C23   107.21  3.000
 EGZ  O29   C22  C23   107.93  3.000
 EGZ  H221  C22  C21   107.57  3.000
 EGZ  O29   C22  C21   112.39  3.000
 EGZ  C23   C22  C21   110.84  3.000
 EGZ  H231  C23  O28   111.38  3.000
 EGZ  H231  C23  C24   107.56  3.000
 EGZ  O28   C23  C24   108.88  3.000
 EGZ  H231  C23  C22   108.16  3.000
 EGZ  O28   C23  C22   112.03  3.000
 EGZ  C24   C23  C22   108.69  3.000
 EGZ  H241  C24  O25   109.92  3.000
 EGZ  H241  C24  C26   108.20  3.000
 EGZ  O25   C24  C26   107.71  3.000
 EGZ  H241  C24  C23   107.04  3.000
 EGZ  O25   C24  C23   110.37  3.000
 EGZ  C26   C24  C23   113.56  3.000
 EGZ  H262  C26  H261  107.24  3.000
 EGZ  H262  C26  O27   111.73  3.000
 EGZ  H261  C26  O27   111.96  3.000
 EGZ  H262  C26  C24   109.88  3.000
 EGZ  H261  C26  C24   108.01  3.000
 EGZ  O27   C26  C24   107.95  3.000
 EGZ  O33   C31  O32   127.78  3.000
 EGZ  O33   C31  C02   114.71  3.000
 EGZ  O32   C31  C02   117.51  3.000
 EGZ  H031  N03  C04   115.09  3.000
 EGZ  H031  N03  C02   116.61  3.000
 EGZ  C04   N03  C02   119.91  3.000
 EGZ  C14   O15  C09   112.61  3.000
 EGZ  H171  O17  C16   108.17  3.000
 EGZ  H181  O18  C13   107.06  3.000
 EGZ  C20   O19  C12   116.10  3.000
 EGZ  C24   O25  C20   113.14  3.000
 EGZ  H271  O27  C26   108.42  3.000
 EGZ  H281  O28  C23   108.38  3.000
 EGZ  H291  O29  C22   108.83  3.000
 EGZ  H301  O30  C21   108.89  3.000
 EGZ  C10   S11  C06    96.40  3.000
 EGZ  C09   O08  C07   119.43  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
 EGZ  CONST_03  H031  N03  C04  C06  180.00   0.0  0
 EGZ  Var_01    C04   C06  C07  C01   -4.04  30.0  1
 EGZ  Var_02    C06   C07  C01  C02  -24.99  30.0  1
 EGZ  Var_03    N03   C04  C06  C07    6.50  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
 EGZ  chir_01  C02  C01  C31  N03  negativ
 EGZ  chir_02  C09  O08  O15  C10  positiv
 EGZ  chir_03  C10  S11  C12  C09  positiv
 EGZ  chir_04  C12  O19  C13  C10  negativ
 EGZ  chir_05  C13  O18  C14  C12  negativ
 EGZ  chir_06  C14  O15  C13  C16  negativ
 EGZ  chir_07  C20  O25  O19  C21  negativ
 EGZ  chir_08  C21  O30  C20  C22  negativ
 EGZ  chir_09  C22  O29  C21  C23  positiv
 EGZ  chir_10  C23  O28  C24  C22  negativ
 EGZ  chir_11  C24  O25  C23  C26  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
 EGZ  plan-1  C02   0.020
 EGZ  plan-1  C04   0.020
 EGZ  plan-1  C06   0.020
 EGZ  plan-1  N03   0.020
 EGZ  plan-1  O05   0.020
 EGZ  plan-1  H031  0.020
 EGZ  plan-2  C02   0.020
 EGZ  plan-2  C31   0.020
 EGZ  plan-2  O32   0.020
 EGZ  plan-2  O33   0.020

