# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun 27 19:26:27 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 2-{[(4S,5R)-4-{[2-(acetylamino)-2-deoxy-4-O-sulfo-beta-D-glucopyranosyl]oxy}-5-(hydroxymethyl)-L-prolyl]amino}ethanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O[S](O)(=O)=O)[C@@H](CO)O[C@H]1O[C@H]2C[C@H](N[C@@H]2CO)C(=O)NCC[S](O)(=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
 BUL  BUL  '2-{[(4S,5R)-4-{[2-(acetylamino)-2-deoxy-4-O-sulfo-beta-D-glucopyranosyl]oxy}-5-(hydroxymethyl)-L-prolyl]amino}ethanesulfonic acid'  ligand  62  35  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BUL
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
 BUL  O1    O  O2     0  -0.486  -0.3775   0.0275  -1.4787
 BUL  C2    C  CH1    0   0.332   0.9110   0.2602  -1.9816
 BUL  C3    C  CH1    0  -0.162   1.0532  -0.4144  -3.3440
 BUL  C4    C  CH1    0   0.072  -0.0203   0.1144  -4.2966
 BUL  C5    C  CH1    0  -0.045  -1.4045   0.0541  -3.6432
 BUL  C6    C  CH1    0  -0.010  -1.3846   0.6565  -2.2353
 BUL  N7    N  NH1    0  -0.625   3.3166   0.1258   2.0609
 BUL  C8    C  CH1    0  -0.196   1.9786   0.5380   2.4279
 BUL  C9    C  CH2    0  -0.470   1.1332   0.0953   1.2328
 BUL  C10   C  CH1    0   0.019   2.0609   0.4297   0.0714
 BUL  C11   C  CH1    0  -0.074   3.4555   0.0898   0.6087
 BUL  C12   C  CH2    0  -0.156  -2.6996   0.4613  -1.5109
 BUL  O13   O  OH1    0  -0.665  -2.6144   1.1002  -0.2595
 BUL  O14   O  OC2    0  -0.623  -2.3156   0.8323  -4.4202
 BUL  O15   O  OH1    0  -0.691   0.0673  -0.6219  -5.4840
 BUL  N16   N  NH1    0  -0.623   2.3646  -0.1941  -3.8907
 BUL  C17   C  C      0   0.511   3.3496  -1.1156  -3.9042
 BUL  O18   O  O      0  -0.495   3.1901  -2.2746  -3.5550
 BUL  C19   C  CH3    0  -0.790   4.6730  -0.5903  -4.4074
 BUL  O20   O  O2     0  -0.490   1.8284  -0.2865  -1.1194
 BUL  C21   C  CH2    0  -0.166   4.5006   1.0390   0.0594
 BUL  O22   O  OH1    0  -0.671   5.7652   0.6559   0.5503
 BUL  C26   C  CH2    0  -0.244   0.0030   0.1090   5.6326
 BUL  C27   C  CH2    0  -0.670  -1.2277   0.9427   5.9417
 BUL  S28   S  S      0   1.399  -2.1047   0.3422   7.3984
 BUL  O29   O  OS     0  -0.767  -2.5091  -1.0399   7.0721
 BUL  O30   O  OS     0  -0.766  -1.1326   0.4126   8.5065
 BUL  O31   O  OS    -1  -0.761  -3.2474   1.2593   7.5643
 BUL  S32   S  S      0   1.588  -3.4006   0.0622  -5.3831
 BUL  O33   O  OS     0  -0.714  -4.0866   1.1937  -5.9911
 BUL  O34   O  OS     0  -0.742  -2.5756  -0.7238  -6.3211
 BUL  O35   O  OS    -1  -0.719  -4.2147  -0.7682  -4.4988
 BUL  H2    H  HCH1   0   0.187   1.0686   1.3511  -2.0898
 BUL  H3    H  HCH1   0   0.272   0.9131  -1.4896  -3.2092
 BUL  H4    H  HCH1   0   0.202   0.1896   1.1831  -4.4811
 BUL  H5    H  HCH1   0   0.251  -1.7305  -0.9922  -3.5729
 BUL  H6    H  HCH1   0   0.229  -1.1797   1.7365  -2.3188
 BUL  H7    H  HNH1   0   0.356   4.0362   0.6669   2.5178
 BUL  H8    H  HCH1   0   0.243   1.8829   1.6282   2.5440
 BUL  H91   H  HCH2   0   0.263   0.1691   0.5982   1.1813
 BUL  H92   H  HCH2   0   0.244   0.9613  -0.9836   1.2689
 BUL  H10   H  HCH1   0   0.222   1.9991   1.5098  -0.1305
 BUL  H11   H  HCH1   0   0.226   3.7138  -0.9262   0.2792
 BUL  H121  H  HCH2   0   0.213  -3.5030   0.8793  -2.1250
 BUL  H122  H  HCH2   0   0.198  -2.8952  -0.6152  -1.4094
 BUL  H13   H  HOH1   0   0.457  -3.4882   1.0850   0.1408
 BUL  H15   H  HOH1   0   0.453  -0.7992  -0.6352  -5.9275
 BUL  H16   H  HNH1   0   0.399   2.5948   0.7460  -4.1750
 BUL  H191  H  HCH3   0   0.261   5.4235  -1.3758  -4.3942
 BUL  H192  H  HCH3   0   0.267   4.5789  -0.2111  -5.4258
 BUL  H193  H  HCH3   0   0.260   5.0219   0.2366  -3.7868
 BUL  H211  H  HCH2   0   0.200   4.4630   1.0014  -1.0386
 BUL  H212  H  HCH2   0   0.198   4.2464   2.0661   0.3548
 BUL  H22   H  HOH1   0   0.457   6.4081   1.3159   0.2759
 BUL  H25   H  HNH1   0   0.400   0.4846   1.5543   4.1617
 BUL  H261  H  HCH2   0   0.245  -0.2846  -0.9323   5.4868
 BUL  H262  H  HCH2   0   0.241   0.6971   0.1428   6.4763
 BUL  H271  H  HCH2   0   0.270  -0.9596   1.9848   6.1311
 BUL  H272  H  HCH2   0   0.272  -1.9300   0.9194   5.1059
 BUL  C23   C  C      0   0.550   1.5003  -0.1399   3.7055
 BUL  O24   O  O      0  -0.491   1.8299  -1.2736   4.0161
 BUL  N25   N  NH1    0  -0.646   0.6379   0.5943   4.4264

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
 BUL  O1   C2    single  1.403  0.020  1.403
 BUL  O1   C6    single  1.408  0.020  1.408
 BUL  C2   C3    single  1.527  0.020  1.527
 BUL  C2   O20   single  1.373  0.020  1.373
 BUL  C2   H2    single  0.970  0.020  1.090
 BUL  C3   C4    single  1.530  0.020  1.530
 BUL  C3   N16   single  1.438  0.020  1.438
 BUL  C3   H3    single  0.970  0.020  1.090
 BUL  C4   C5    single  1.532  0.020  1.532
 BUL  C4   O15   single  1.400  0.020  1.400
 BUL  C4   H4    single  0.970  0.020  1.090
 BUL  C5   C6    single  1.531  0.020  1.531
 BUL  C5   O14   single  1.428  0.020  1.428
 BUL  C5   H5    single  0.970  0.020  1.090
 BUL  C6   C12   single  1.514  0.020  1.514
 BUL  C6   H6    single  0.970  0.020  1.090
 BUL  N7   C8    single  1.447  0.020  1.447
 BUL  N7   C11   single  1.459  0.020  1.459
 BUL  N7   H7    single  0.890  0.020  1.040
 BUL  C8   C9    single  1.529  0.020  1.529
 BUL  C8   C23   single  1.523  0.020  1.523
 BUL  C8   H8    single  0.970  0.020  1.090
 BUL  C9   C10   single  1.524  0.020  1.524
 BUL  C9   H91   single  0.970  0.020  1.090
 BUL  C9   H92   single  0.970  0.020  1.090
 BUL  C10  C11   single  1.533  0.020  1.533
 BUL  C10  O20   single  1.409  0.020  1.409
 BUL  C10  H10   single  0.970  0.020  1.090
 BUL  C11  C21   single  1.515  0.020  1.515
 BUL  C11  H11   single  0.970  0.020  1.090
 BUL  C12  O13   single  1.408  0.020  1.408
 BUL  C12  H121  single  0.970  0.020  1.090
 BUL  C12  H122  single  0.970  0.020  1.090
 BUL  O13  H13   single  0.850  0.020  0.980
 BUL  O14  S32   single  1.642  0.020  1.642
 BUL  O15  H15   single  0.850  0.020  0.980
 BUL  N16  C17   single  1.349  0.020  1.349
 BUL  N16  H16   single  0.860  0.020  1.020
 BUL  C17  O18   double  1.221  0.020  1.221
 BUL  C17  C19   single  1.510  0.020  1.510
 BUL  C19  H191  single  0.970  0.020  1.090
 BUL  C19  H192  single  0.970  0.020  1.090
 BUL  C19  H193  single  0.970  0.020  1.090
 BUL  C21  O22   single  1.410  0.020  1.410
 BUL  C21  H211  single  0.970  0.020  1.090
 BUL  C21  H212  single  0.970  0.020  1.090
 BUL  O22  H22   single  0.850  0.020  0.980
 BUL  C23  O24   double  1.221  0.020  1.221
 BUL  C23  N25   single  1.343  0.020  1.343
 BUL  N25  C26   single  1.447  0.020  1.447
 BUL  N25  H25   single  0.860  0.020  1.020
 BUL  C26  C27   single  1.518  0.020  1.518
 BUL  C26  H261  single  0.970  0.020  1.090
 BUL  C26  H262  single  0.970  0.020  1.090
 BUL  C27  S28   single  1.803  0.020  1.803
 BUL  C27  H271  single  0.970  0.020  1.090
 BUL  C27  H272  single  0.970  0.020  1.090
 BUL  S28  O29   deloc   1.476  0.020  1.476
 BUL  S28  O30   deloc   1.476  0.020  1.476
 BUL  S28  O31   deloc   1.475  0.020  1.475
 BUL  S32  O33   deloc   1.456  0.020  1.456
 BUL  S32  O34   deloc   1.476  0.020  1.476
 BUL  S32  O35   deloc   1.461  0.020  1.461

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
 BUL  C6    O1   C2    112.97  3.000
 BUL  H2    C2   O20   111.02  3.000
 BUL  H2    C2   C3    109.56  3.000
 BUL  O20   C2   C3    108.80  3.000
 BUL  H2    C2   O1    109.22  3.000
 BUL  O20   C2   O1    108.82  3.000
 BUL  C3    C2   O1    109.40  3.000
 BUL  H3    C3   N16   108.34  3.000
 BUL  H3    C3   C4    109.09  3.000
 BUL  N16   C3   C4    110.51  3.000
 BUL  H3    C3   C2    108.23  3.000
 BUL  N16   C3   C2    110.88  3.000
 BUL  C4    C3   C2    109.73  3.000
 BUL  H4    C4   O15   110.81  3.000
 BUL  H4    C4   C5    106.32  3.000
 BUL  O15   C4   C5    113.43  3.000
 BUL  H4    C4   C3    107.77  3.000
 BUL  O15   C4   C3    107.61  3.000
 BUL  C5    C4   C3    110.79  3.000
 BUL  H5    C5   O14   111.39  3.000
 BUL  H5    C5   C6    108.65  3.000
 BUL  O14   C5   C6    107.10  3.000
 BUL  H5    C5   C4    109.46  3.000
 BUL  O14   C5   C4    108.84  3.000
 BUL  C6    C5   C4    111.40  3.000
 BUL  H6    C6   C12   108.90  3.000
 BUL  H6    C6   C5    108.55  3.000
 BUL  C12   C6   C5    112.20  3.000
 BUL  H6    C6   O1    110.21  3.000
 BUL  C12   C6   O1    107.85  3.000
 BUL  C5    C6   O1    109.12  3.000
 BUL  H7    N7   C11   113.31  3.000
 BUL  H7    N7   C8    113.05  3.000
 BUL  C11   N7   C8    110.33  3.000
 BUL  H8    C8   C23   108.96  3.000
 BUL  H8    C8   C9    108.73  3.000
 BUL  C23   C8   C9    110.67  3.000
 BUL  H8    C8   N7    112.91  3.000
 BUL  C23   C8   N7    112.10  3.000
 BUL  C9    C8   N7    103.32  3.000
 BUL  H92   C9   H91   108.56  3.000
 BUL  H92   C9   C10   109.72  3.000
 BUL  H91   C9   C10   113.69  3.000
 BUL  H92   C9   C8    110.29  3.000
 BUL  H91   C9   C8    113.13  3.000
 BUL  C10   C9   C8    101.28  3.000
 BUL  H10   C10  O20   109.55  3.000
 BUL  H10   C10  C11   109.45  3.000
 BUL  O20   C10  C11   109.49  3.000
 BUL  H10   C10  C9    108.72  3.000
 BUL  O20   C10  C9    115.61  3.000
 BUL  C11   C10  C9    103.78  3.000
 BUL  H11   C11  C21   107.96  3.000
 BUL  H11   C11  C10   108.29  3.000
 BUL  C21   C11  C10   111.21  3.000
 BUL  H11   C11  N7    110.09  3.000
 BUL  C21   C11  N7    114.27  3.000
 BUL  C10   C11  N7    104.88  3.000
 BUL  H122  C12  H121  107.18  3.000
 BUL  H122  C12  O13   111.92  3.000
 BUL  H121  C12  O13   111.72  3.000
 BUL  H122  C12  C6    108.97  3.000
 BUL  H121  C12  C6    108.66  3.000
 BUL  O13   C12  C6    108.32  3.000
 BUL  H13   O13  C12   107.94  3.000
 BUL  S32   O14  C5    119.01  3.000
 BUL  H15   O15  C4    109.75  3.000
 BUL  H16   N16  C17   117.85  3.000
 BUL  H16   N16  C3    117.27  3.000
 BUL  C17   N16  C3    124.41  3.000
 BUL  C19   C17  O18   122.68  3.000
 BUL  C19   C17  N16   113.93  3.000
 BUL  O18   C17  N16   123.38  3.000
 BUL  H193  C19  H192  107.17  3.000
 BUL  H193  C19  H191  108.67  3.000
 BUL  H192  C19  H191  108.80  3.000
 BUL  H193  C19  C17   110.75  3.000
 BUL  H192  C19  C17   110.88  3.000
 BUL  H191  C19  C17   110.48  3.000
 BUL  C10   O20  C2    116.02  3.000
 BUL  H212  C21  H211  107.01  3.000
 BUL  H212  C21  O22   111.59  3.000
 BUL  H211  C21  O22   111.67  3.000
 BUL  H212  C21  C11   109.19  3.000
 BUL  H211  C21  C11   108.49  3.000
 BUL  O22   C21  C11   108.81  3.000
 BUL  H22   O22  C21   108.30  3.000
 BUL  H262  C26  H261  107.48  3.000
 BUL  H262  C26  C27   109.92  3.000
 BUL  H261  C26  C27   109.75  3.000
 BUL  H262  C26  N25   110.76  3.000
 BUL  H261  C26  N25   108.94  3.000
 BUL  C27   C26  N25   109.95  3.000
 BUL  H272  C27  H271  108.11  3.000
 BUL  H272  C27  S28   107.36  3.000
 BUL  H271  C27  S28   107.27  3.000
 BUL  H272  C27  C26   110.72  3.000
 BUL  H271  C27  C26   111.11  3.000
 BUL  S28   C27  C26   112.07  3.000
 BUL  O31   S28  O30   113.35  3.000
 BUL  O31   S28  O29   113.26  3.000
 BUL  O30   S28  O29   113.02  3.000
 BUL  O31   S28  C27   105.10  3.000
 BUL  O30   S28  C27   105.68  3.000
 BUL  O29   S28  C27   105.45  3.000
 BUL  O35   S32  O34   113.17  3.000
 BUL  O35   S32  O33   115.59  3.000
 BUL  O34   S32  O33   114.32  3.000
 BUL  O35   S32  O14   106.24  3.000
 BUL  O34   S32  O14   104.66  3.000
 BUL  O33   S32  O14   101.05  3.000
 BUL  N25   C23  O24   123.01  3.000
 BUL  N25   C23  C8    114.12  3.000
 BUL  O24   C23  C8    122.80  3.000
 BUL  H25   N25  C26   118.15  3.000
 BUL  H25   N25  C23   118.54  3.000
 BUL  C26   N25  C23   123.09  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
 BUL  CONST_01  O18   C17  N16  C3      0.00   0.0  0
 BUL  CONST_02  C19   C17  N16  C3    180.00   0.0  0
 BUL  CONST_03  C26   N25  C23  C8    180.00   0.0  0
 BUL  CONST_04  H25   N25  C23  C8      0.00   0.0  0
 BUL  CONST_05  C26   N25  C23  O24     0.00   0.0  0
 BUL  CONST_06  H16   N16  C17  O18   180.00   0.0  0
 BUL  Var_01    O33   S32  O14  C5   -178.94  30.0  3
 BUL  Var_02    C27   C26  N25  C23  -160.87  30.0  3
 BUL  Var_03    S28   C27  C26  N25   177.58  30.0  3
 BUL  Var_04    O29   S28  C27  C26   -60.70  30.0  3
 BUL  Var_05    H191  C19  C17  N16   179.97  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
 BUL  chir_01  C2   O1   C3   O20  positiv
 BUL  chir_02  C3   N16  C4   C2   positiv
 BUL  chir_03  C4   O15  C3   C5   positiv
 BUL  chir_04  C5   O14  C4   C6   negativ
 BUL  chir_05  C6   O1   C5   C12  negativ
 BUL  chir_06  C8   N7   C9   C23  negativ
 BUL  chir_07  C10  O20  C9   C11  negativ
 BUL  chir_08  C11  N7   C10  C21  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
 BUL  plan-1  C3   0.020
 BUL  plan-1  N16  0.020
 BUL  plan-1  C17  0.020
 BUL  plan-1  O18  0.020
 BUL  plan-1  C19  0.020
 BUL  plan-1  H16  0.020
 BUL  plan-2  C8   0.020
 BUL  plan-2  C26  0.020
 BUL  plan-2  H25  0.020
 BUL  plan-2  C23  0.020
 BUL  plan-2  O24  0.020
 BUL  plan-2  N25  0.020

