# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 02:58:02 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: (2S)-2-{[2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS)C(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H](CC(O)=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
 G5M  G5M  "(2S)-2-{[2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranosyl]oxy}butanedioic acid"  ligand  46  26  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G5M
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
 G5M  C7   C  C      0   0.521  49.7505  123.1350  61.4737
 G5M  C9   C  CH1    0  -0.063  54.5427  121.8997  61.9031
 G5M  C4   C  CH1    0   0.041  51.2203  118.7989  60.3250
 G5M  C6   C  CH2    0  -0.189  53.3262  117.9557  59.1552
 G5M  C1   C  CH1    0   0.296  52.6704  121.2861  60.5340
 G5M  C3   C  CH1    0   0.022  50.7250  119.8712  61.2864
 G5M  C2   C  CH1    0  -0.167  51.1604  121.2485  60.7806
 G5M  C5   C  CH1    0  -0.004  52.7306  118.9455  60.1325
 G5M  C10  C  C      0   0.384  55.7789  121.0150  61.6281
 G5M  C11  C  CH2    0  -0.551  54.5895  122.4331  63.3362
 G5M  C12  C  C      0   0.424  53.3488  123.2952  63.6186
 G5M  C24  C  CH2    0  -0.555  49.0658  123.2240  63.9000
 G5M  C8   C  CH1    0  -0.218  49.4091  124.0422  62.6593
 G5M  N2   N  NH1    0  -0.666  50.7630  122.2819  61.7032
 G5M  N25  N  NH2    0  -0.786  48.2806  124.8790  62.3160
 G5M  O1   O  O2     0  -0.507  53.3030  121.2246  61.7602
 G5M  O13  O  O      0  -0.613  56.8162  121.6518  61.3544
 G5M  O14  O  OC    -1  -0.590  55.6587  119.7831  61.7541
 G5M  O15  O  O      0  -0.596  53.3474  124.4474  63.1476
 G5M  O16  O  OC    -1  -0.614  52.4143  122.7510  64.2568
 G5M  O3   O  OH1    0  -0.679  49.3238  119.7641  61.3649
 G5M  O4   O  OH1    0  -0.673  50.9753  117.5030  60.8175
 G5M  O5   O  O2     0  -0.502  53.0350  120.2509  59.6656
 G5M  O7   O  O      0  -0.480  49.1456  123.2079  60.4155
 G5M  H1   H  HCH1   0   0.194  54.5640  122.7585  61.2187
 G5M  H2   H  HCH1   0   0.204  50.7195  118.9550  59.3575
 G5M  H3   H  HCH2   0   0.205  53.2209  116.9510  59.5792
 G5M  H4   H  HCH2   0   0.208  54.4041  118.1566  59.0882
 G5M  H5   H  HCH1   0   0.228  52.9319  122.2127  60.0059
 G5M  H6   H  HCH1   0   0.205  51.1836  119.6918  62.2708
 G5M  H7   H  HCH1   0   0.262  50.6670  121.4387  59.8250
 G5M  H8   H  HCH1   0   0.227  53.2272  118.7647  61.0935
 G5M  H9   H  HCH2   0   0.206  54.6496  121.5908  64.0310
 G5M  H10  H  HCH2   0   0.218  55.5025  123.0219  63.4449
 G5M  H11  H  HCH2   0   0.288  49.9262  122.6568  64.2441
 G5M  H12  H  HCH2   0   0.279  48.7740  123.8989  64.7055
 G5M  H13  H  HCH1   0   0.258  50.3226  124.6066  62.9073
 G5M  H14  H  HNH1   0   0.426  51.2536  122.3201  62.5951
 G5M  H15  H  HNH2   0   0.351  48.1637  125.5849  63.0317
 G5M  H16  H  HNH2   0   0.351  48.4574  125.3740  61.4520
 G5M  H20  H  HOH1   0   0.444  48.9943  120.3671  62.0468
 G5M  H21  H  HOH1   0   0.448  50.0278  117.4145  60.9635
 G5M  H22  H  HOH1   0   0.454  53.0284  117.3684  57.3347
 G5M  H23  H  HSH1   0   0.230  47.9284  121.2173  64.5233
 G5M  O6   O  OH1    0  -0.669  52.6950  118.0686  57.9020
 G5M  S26  S  S2     0  -0.255  47.6854  122.0828  63.5335

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
 G5M  O6   C6   single  1.408  0.020  1.408
 G5M  C6   C5   single  1.513  0.020  1.513
 G5M  O5   C5   single  1.419  0.020  1.419
 G5M  O5   C1   single  1.399  0.020  1.399
 G5M  C5   C4   single  1.530  0.020  1.530
 G5M  C4   O4   single  1.408  0.020  1.408
 G5M  C4   C3   single  1.523  0.020  1.523
 G5M  O7   C7   double  1.221  0.020  1.221
 G5M  C1   C2   single  1.531  0.020  1.531
 G5M  C1   O1   single  1.381  0.020  1.381
 G5M  C2   C3   single  1.530  0.020  1.530
 G5M  C2   N2   single  1.441  0.020  1.441
 G5M  O3   C3   single  1.407  0.020  1.407
 G5M  O13  C10  deloc   1.248  0.020  1.248
 G5M  C7   N2   single  1.344  0.020  1.344
 G5M  C7   C8   single  1.531  0.020  1.531
 G5M  C10  O14  deloc   1.244  0.020  1.244
 G5M  C10  C9   single  1.545  0.020  1.545
 G5M  O1   C9   single  1.419  0.020  1.419
 G5M  C9   C11  single  1.530  0.020  1.530
 G5M  N25  C8   single  1.446  0.020  1.446
 G5M  C8   C24  single  1.525  0.020  1.525
 G5M  O15  C12  deloc   1.245  0.020  1.245
 G5M  C11  C12  single  1.537  0.020  1.537
 G5M  C24  S26  single  1.828  0.020  1.828
 G5M  C12  O16  deloc   1.256  0.020  1.256
 G5M  C9   H1   single  0.970  0.020  1.090
 G5M  C4   H2   single  0.970  0.020  1.090
 G5M  C6   H3   single  0.970  0.020  1.090
 G5M  C6   H4   single  0.970  0.020  1.090
 G5M  C1   H5   single  0.970  0.020  1.090
 G5M  C3   H6   single  0.970  0.020  1.090
 G5M  C2   H7   single  0.970  0.020  1.090
 G5M  C5   H8   single  0.970  0.020  1.090
 G5M  C11  H9   single  0.970  0.020  1.090
 G5M  C11  H10  single  0.970  0.020  1.090
 G5M  C24  H11  single  0.970  0.020  1.090
 G5M  C24  H12  single  0.970  0.020  1.090
 G5M  C8   H13  single  0.970  0.020  1.090
 G5M  N2   H14  single  0.860  0.020  1.020
 G5M  N25  H15  single  0.890  0.020  1.040
 G5M  N25  H16  single  0.890  0.020  1.040
 G5M  O3   H20  single  0.850  0.020  0.980
 G5M  O4   H21  single  0.850  0.020  0.980
 G5M  O6   H22  single  0.850  0.020  0.980
 G5M  S26  H23  single  1.200  0.020  1.300

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
 G5M  O7   C7   N2   124.00  3.000
 G5M  N2   C7   C8   114.32  3.000
 G5M  O7   C7   C8   121.68  3.000
 G5M  H1   C9   O1   109.03  3.000
 G5M  H1   C9   C11  108.09  3.000
 G5M  O1   C9   C11  106.68  3.000
 G5M  H1   C9   C10  108.75  3.000
 G5M  C11  C9   C10  110.00  3.000
 G5M  O1   C9   C10  114.13  3.000
 G5M  H2   C4   O4   111.03  3.000
 G5M  H2   C4   C5   108.97  3.000
 G5M  O4   C4   C5   107.71  3.000
 G5M  H2   C4   C3   107.88  3.000
 G5M  O4   C4   C3   111.76  3.000
 G5M  C5   C4   C3   109.46  3.000
 G5M  H4   C6   H3   106.60  3.000
 G5M  H4   C6   O6   111.78  3.000
 G5M  H3   C6   O6   112.02  3.000
 G5M  H4   C6   C5   107.82  3.000
 G5M  H3   C6   C5   108.19  3.000
 G5M  O6   C6   C5   110.24  3.000
 G5M  H5   C1   O5   105.29  3.000
 G5M  H5   C1   O1   110.82  3.000
 G5M  O5   C1   O1   113.49  3.000
 G5M  H5   C1   C2   109.46  3.000
 G5M  O1   C1   C2   107.92  3.000
 G5M  O5   C1   C2   109.81  3.000
 G5M  H6   C3   O3   110.64  3.000
 G5M  H6   C3   C2   108.89  3.000
 G5M  O3   C3   C2   111.72  3.000
 G5M  H6   C3   C4   108.31  3.000
 G5M  O3   C3   C4   107.78  3.000
 G5M  C2   C3   C4   109.42  3.000
 G5M  H7   C2   N2   108.10  3.000
 G5M  H7   C2   C3   108.51  3.000
 G5M  N2   C2   C3   110.81  3.000
 G5M  H7   C2   C1   107.48  3.000
 G5M  N2   C2   C1   110.95  3.000
 G5M  C3   C2   C1   110.86  3.000
 G5M  H8   C5   O5   110.04  3.000
 G5M  H8   C5   C6   106.25  3.000
 G5M  O5   C5   C6   107.74  3.000
 G5M  H8   C5   C4   108.72  3.000
 G5M  O5   C5   C4   109.96  3.000
 G5M  C6   C5   C4   114.03  3.000
 G5M  O14  C10  O13  127.44  3.000
 G5M  O14  C10  C9   118.15  3.000
 G5M  O13  C10  C9   114.34  3.000
 G5M  H10  C11  H9   107.83  3.000
 G5M  H10  C11  C12  110.75  3.000
 G5M  H9   C11  C12  111.08  3.000
 G5M  H10  C11  C9   107.87  3.000
 G5M  H9   C11  C9   109.16  3.000
 G5M  C12  C11  C9   110.06  3.000
 G5M  O16  C12  O15  126.35  3.000
 G5M  O16  C12  C11  116.81  3.000
 G5M  O15  C12  C11  116.78  3.000
 G5M  H12  C24  H11  107.52  3.000
 G5M  H12  C24  S26  109.41  3.000
 G5M  H11  C24  S26  109.60  3.000
 G5M  H12  C24  C8   109.21  3.000
 G5M  H11  C24  C8   111.07  3.000
 G5M  S26  C24  C8   109.98  3.000
 G5M  H13  C8   N25  113.82  3.000
 G5M  H13  C8   C24  106.15  3.000
 G5M  N25  C8   C24  109.13  3.000
 G5M  H13  C8   C7   107.03  3.000
 G5M  C24  C8   C7   111.23  3.000
 G5M  N25  C8   C7   109.45  3.000
 G5M  H14  N2   C2   117.04  3.000
 G5M  H14  N2   C7   119.25  3.000
 G5M  C2   N2   C7   123.62  3.000
 G5M  H16  N25  H15  106.44  3.000
 G5M  H16  N25  C8   110.46  3.000
 G5M  H15  N25  C8   109.01  3.000
 G5M  C1   O1   C9   117.94  3.000
 G5M  H20  O3   C3   109.31  3.000
 G5M  H21  O4   C4   108.00  3.000
 G5M  C5   O5   C1   114.85  3.000
 G5M  H22  O6   C6   108.15  3.000
 G5M  H23  S26  C24   96.81  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
 G5M  CONST_01  O7   C7   N2   C2      0.00   0.0  0
 G5M  CONST_02  C8   C7   N2   C2    180.00   0.0  0
 G5M  CONST_03  H14  N2   C7   C8      0.00   0.0  0
 G5M  CONST_04  H14  N2   C7   O7    180.00   0.0  0
 G5M  Var_01    O15  C12  C11  C9    -77.16  30.0  3
 G5M  Var_02    O16  C12  C11  C9    100.14  30.0  3
 G5M  Var_03    H9   C11  C12  O15   161.82  30.0  2
 G5M  Var_04    H10  C11  C12  O15    42.02  30.0  2
 G5M  Var_05    H9   C11  C12  O16   -20.88  30.0  2
 G5M  Var_06    H10  C11  C12  O16  -140.68  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
 G5M  chir_01  C9  C10  O1  C11  negativ
 G5M  chir_02  C4  O4   C5  C3   positiv
 G5M  chir_03  C1  O1   O5  C2   negativ
 G5M  chir_04  C3  O3   C2  C4   positiv
 G5M  chir_05  C2  N2   C3  C1   positiv
 G5M  chir_06  C5  O5   C4  C6   negativ
 G5M  chir_07  C8  N25  C7  C24  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
 G5M  plan-1  C7   0.020
 G5M  plan-1  C2   0.020
 G5M  plan-1  C8   0.020
 G5M  plan-1  N2   0.020
 G5M  plan-1  O7   0.020
 G5M  plan-1  H14  0.020
 G5M  plan-2  C9   0.020
 G5M  plan-2  C10  0.020
 G5M  plan-2  O13  0.020
 G5M  plan-2  O14  0.020
 G5M  plan-3  C11  0.020
 G5M  plan-3  C12  0.020
 G5M  plan-3  O15  0.020
 G5M  plan-3  O16  0.020

