# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 11:47:44 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: (4S)-4-amino-1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC[C@H](N)CC(=O)N[C@H]1C=C[C@@H](O[C@@H]1C(O)=O)N2C=C[C@@](N)(O)NC2=O)C(N)=N
#
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
 BST  BST  (4S)-4-amino-1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one  ligand  59  31  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BST
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
 BST  O4    O  OH1   0  -0.582  46.7106  17.9874  37.2741
 BST  N1    N  NT    0  -0.572  43.6236  14.6607  38.2615
 BST  C2    C  C     0   0.725  43.7833  13.5053  37.5172
 BST  O2    O  O     0  -0.516  43.5847  13.4743  36.3131
 BST  N3    N  NH1   0  -0.708  44.2010  12.4217  38.2100
 BST  C4    C  CT    0   0.514  44.3027  12.2553  39.6344
 BST  C5    C  C1    0  -0.434  44.3777  13.6128  40.2638
 BST  C6    C  C1    0   0.058  44.0360  14.7021  39.5873
 BST  C1'   C  CH1   0   0.160  43.3062  15.8904  37.5875
 BST  C2'   C  C1    0  -0.303  42.3611  16.7265  38.3965
 BST  C3'   C  C1    0  -0.189  42.5954  18.0064  38.6524
 BST  C4'   C  CH1   0  -0.164  43.8169  18.7135  38.1381
 BST  C5'   C  CH1   0  -0.029  44.3756  17.8974  36.9592
 BST  O5'   O  O2    0  -0.491  44.5270  16.5572  37.3509
 BST  O3    O  O     0  -0.421  45.8547  19.1936  35.5967
 BST  C6'   C  C     0   0.513  45.7219  18.4306  36.5162
 BST  N6    N  NH1   0  -0.652  43.5113  20.0653  37.7501
 BST  C7    C  C     0   0.603  44.2714  21.1281  38.0942
 BST  O7    O  O     0  -0.495  45.2890  21.0195  38.7597
 BST  C8    C  CH2   0  -0.595  43.7319  22.4705  37.6573
 BST  C9    C  CH1   0  -0.086  44.8179  23.3660  37.0696
 BST  N9    N  NH2   0  -0.769  45.3726  22.7007  35.9014
 BST  C10   C  CH2   0  -0.446  44.2950  24.7783  36.7866
 BST  C11   C  CH2   0  -0.312  43.9527  25.5743  38.0430
 BST  N12   N  NT    0  -0.459  43.6031  26.9631  37.7808
 BST  C13   C  CH3   0  -0.559  44.7137  27.8523  37.5194
 BST  C14   C  C     0   0.549  42.3839  27.2872  37.2272
 BST  N14   N  N     0  -0.723  42.1296  28.3101  36.4950
 BST  N15   N  NH2   0  -0.823  41.3619  26.4022  37.5043
 BST  N4    N  NH2   0  -0.794  45.4550  11.4132  39.8674
 BST  O6    O  OH1   0  -0.645  43.1505  11.5660  40.0593
 BST  HO4   H  HOH1  0   0.487  47.5516  18.3688  36.9791
 BST  HN3   H  HNH1  0   0.404  44.3328  11.5847  37.6594
 BST  H5    H  H     0   0.283  44.6939  13.6895  41.2953
 BST  H6    H  H     0   0.302  44.0645  15.6848  40.0377
 BST  H1'   H  HCH1  0   0.281  42.8273  15.6246  36.6390
 BST  H2'   H  H     0   0.285  41.4568  16.2401  38.7418
 BST  H3'   H  H     0   0.277  41.8953  18.5904  39.2385
 BST  H4'   H  HCH1  0   0.293  44.5688  18.7648  38.9304
 BST  H5'   H  HCH1  0   0.267  43.6866  17.9927  36.1094
 BST  HN6   H  HNH1  0   0.402  42.7055  20.2164  37.1635
 BST  H81   H  HCH2  0   0.278  43.2880  22.9346  38.5427
 BST  H82   H  HCH2  0   0.250  42.9208  22.3563  36.9317
 BST  H9    H  HCH1  0   0.228  45.6240  23.4475  37.8061
 BST  HN91  H  HNH2  0   0.333  44.6648  22.6301  35.1788
 BST  HN92  H  HNH2  0   0.342  46.1140  23.2681  35.5086
 BST  H101  H  HCH2  0   0.222  43.4185  24.7266  36.1315
 BST  H102  H  HCH2  0   0.236  45.0719  25.3137  36.2311
 BST  H111  H  HCH2  0   0.244  44.8119  25.5780  38.7174
 BST  H112  H  HCH2  0   0.241  43.1525  25.0880  38.6005
 BST  H131  H  HCH3  0   0.228  45.0569  27.8366  36.4793
 BST  H132  H  HCH3  0   0.249  44.4522  28.8798  37.7733
 BST  H133  H  HCH3  0   0.253  45.5516  27.5646  38.1510
 BST  H14   H  H     0   0.331  42.9687  28.8119  36.2355
 BST  H151  H  HNH2  0   0.380  41.3365  26.0193  38.4362
 BST  H152  H  HNH2  0   0.377  40.4626  26.7653  37.2306
 BST  HN41  H  HNH2  0   0.357  46.3032  11.9278  39.6602
 BST  HN42  H  HNH2  0   0.360  45.5078  11.1537  40.8458
 BST  HO6   H  HOH1  0   0.456  43.0711  11.6411  41.0175

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
 BST  O4   C6'   single  1.322  0.020  1.322
 BST  O4   HO4   single  0.850  0.020  0.980
 BST  N1   C2    single  1.384  0.020  1.384
 BST  N1   C6    single  1.389  0.020  1.389
 BST  N1   C1'   single  1.438  0.020  1.438
 BST  C2   O2    double  1.221  0.020  1.221
 BST  C2   N3    single  1.352  0.020  1.352
 BST  N3   C4    single  1.438  0.020  1.438
 BST  N3   HN3   single  0.860  0.020  1.020
 BST  C4   C5    single  1.498  0.020  1.498
 BST  C4   N4    single  1.446  0.020  1.446
 BST  C4   O6    single  1.408  0.020  1.408
 BST  C5   C6    double  1.327  0.020  1.327
 BST  C5   H5    single  0.930  0.020  1.080
 BST  C6   H6    single  0.930  0.020  1.080
 BST  C1'  C2'   single  1.499  0.020  1.499
 BST  C1'  O5'   single  1.411  0.020  1.411
 BST  C1'  H1'   single  0.970  0.020  1.090
 BST  C2'  C3'   double  1.326  0.020  1.326
 BST  C2'  H2'   single  0.930  0.020  1.080
 BST  C3'  C4'   single  1.502  0.020  1.502
 BST  C3'  H3'   single  0.930  0.020  1.080
 BST  C4'  C5'   single  1.539  0.020  1.539
 BST  C4'  N6    single  1.439  0.020  1.439
 BST  C4'  H4'   single  0.970  0.020  1.090
 BST  C5'  O5'   single  1.404  0.020  1.404
 BST  C5'  C6'   single  1.514  0.020  1.514
 BST  C5'  H5'   single  0.970  0.020  1.090
 BST  O3   C6'   double  1.202  0.020  1.202
 BST  N6   C7    single  1.351  0.020  1.351
 BST  N6   HN6   single  0.860  0.020  1.020
 BST  C7   O7    double  1.221  0.020  1.221
 BST  C7   C8    single  1.511  0.020  1.511
 BST  C8   C9    single  1.525  0.020  1.525
 BST  C8   H81   single  0.970  0.020  1.090
 BST  C8   H82   single  0.970  0.020  1.090
 BST  C9   N9    single  1.454  0.020  1.454
 BST  C9   C10   single  1.532  0.020  1.532
 BST  C9   H9    single  0.970  0.020  1.090
 BST  N9   HN91  single  0.890  0.020  1.040
 BST  N9   HN92  single  0.890  0.020  1.040
 BST  C10  C11   single  1.526  0.020  1.526
 BST  C10  H101  single  0.970  0.020  1.090
 BST  C10  H102  single  0.970  0.020  1.090
 BST  C11  N12   single  1.456  0.020  1.456
 BST  C11  H111  single  0.970  0.020  1.090
 BST  C11  H112  single  0.970  0.020  1.090
 BST  N12  C13   single  1.447  0.020  1.447
 BST  N12  C14   single  1.378  0.020  1.378
 BST  C13  H131  single  0.970  0.020  1.090
 BST  C13  H132  single  0.970  0.020  1.090
 BST  C13  H133  single  0.970  0.020  1.090
 BST  C14  N14   double  1.283  0.020  1.283
 BST  C14  N15   single  1.380  0.020  1.380
 BST  N14  H14   single  0.890  0.020  1.040
 BST  N15  H151  single  0.890  0.020  1.040
 BST  N15  H152  single  0.890  0.020  1.040
 BST  N4   HN41  single  0.890  0.020  1.040
 BST  N4   HN42  single  0.890  0.020  1.040
 BST  O6   HO6   single  0.850  0.020  0.980

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
 BST  HO4   O4   C6'   110.03  3.000
 BST  C1'   N1   C6    119.17  3.000
 BST  C1'   N1   C2    119.18  3.000
 BST  C6    N1   C2    120.27  3.000
 BST  N3    C2   O2    122.36  3.000
 BST  N3    C2   N1    115.42  3.000
 BST  O2    C2   N1    122.21  3.000
 BST  HN3   N3   C4    115.77  3.000
 BST  HN3   N3   C2    115.14  3.000
 BST  C4    N3   C2    128.47  3.000
 BST  O6    C4   N4    108.56  3.000
 BST  O6    C4   C5    110.96  3.000
 BST  N4    C4   C5    114.84  3.000
 BST  O6    C4   N3    107.31  3.000
 BST  N4    C4   N3    106.46  3.000
 BST  C5    C4   N3    108.35  3.000
 BST  H5    C5   C6    120.22  3.000
 BST  H5    C5   C4    118.65  3.000
 BST  C6    C5   C4    121.11  3.000
 BST  H6    C6   C5    121.80  3.000
 BST  H6    C6   N1    115.62  3.000
 BST  C5    C6   N1    122.58  3.000
 BST  H1'   C1'  O5'   110.35  3.000
 BST  H1'   C1'  C2'   109.09  3.000
 BST  O5'   C1'  C2'   111.86  3.000
 BST  H1'   C1'  N1    107.15  3.000
 BST  O5'   C1'  N1    106.97  3.000
 BST  C2'   C1'  N1    111.30  3.000
 BST  H2'   C2'  C3'   121.29  3.000
 BST  H2'   C2'  C1'   116.61  3.000
 BST  C3'   C2'  C1'   122.08  3.000
 BST  H3'   C3'  C4'   117.18  3.000
 BST  H3'   C3'  C2'   120.68  3.000
 BST  C4'   C3'  C2'   122.14  3.000
 BST  H4'   C4'  N6    107.29  3.000
 BST  H4'   C4'  C5'   109.29  3.000
 BST  N6    C4'  C5'   111.64  3.000
 BST  H4'   C4'  C3'   109.46  3.000
 BST  N6    C4'  C3'   111.21  3.000
 BST  C5'   C4'  C3'   107.93  3.000
 BST  H5'   C5'  C6'   107.51  3.000
 BST  H5'   C5'  O5'   111.49  3.000
 BST  C6'   C5'  O5'   108.77  3.000
 BST  H5'   C5'  C4'   108.60  3.000
 BST  C6'   C5'  C4'   111.11  3.000
 BST  O5'   C5'  C4'   109.37  3.000
 BST  C5'   O5'  C1'   113.86  3.000
 BST  O3    C6'  C5'   123.06  3.000
 BST  O3    C6'  O4    124.64  3.000
 BST  C5'   C6'  O4    112.28  3.000
 BST  HN6   N6   C7    118.68  3.000
 BST  HN6   N6   C4'   117.86  3.000
 BST  C7    N6   C4'   123.42  3.000
 BST  C8    C7   O7    122.29  3.000
 BST  C8    C7   N6    115.10  3.000
 BST  O7    C7   N6    122.53  3.000
 BST  H82   C8   H81   106.27  3.000
 BST  H82   C8   C9    109.49  3.000
 BST  H81   C8   C9    110.59  3.000
 BST  H82   C8   C7    111.32  3.000
 BST  H81   C8   C7    106.72  3.000
 BST  C9    C8   C7    112.26  3.000
 BST  H9    C9   C10   107.87  3.000
 BST  H9    C9   N9    107.07  3.000
 BST  C10   C9   N9    113.79  3.000
 BST  H9    C9   C8    107.98  3.000
 BST  C10   C9   C8    111.67  3.000
 BST  N9    C9   C8    108.20  3.000
 BST  HN92  N9   HN91  105.88  3.000
 BST  HN92  N9   C9    109.54  3.000
 BST  HN91  N9   C9    109.76  3.000
 BST  H102  C10  H101  106.71  3.000
 BST  H102  C10  C11   108.77  3.000
 BST  H101  C10  C11   109.73  3.000
 BST  H102  C10  C9    107.59  3.000
 BST  H101  C10  C9    109.87  3.000
 BST  C11   C10  C9    113.90  3.000
 BST  H112  C11  H111  105.26  3.000
 BST  H112  C11  N12   109.97  3.000
 BST  H111  C11  N12   107.26  3.000
 BST  H112  C11  C10   110.68  3.000
 BST  H111  C11  C10   109.49  3.000
 BST  N12   C11  C10   113.77  3.000
 BST  C14   N12  C13   117.53  3.000
 BST  C14   N12  C11   120.61  3.000
 BST  C13   N12  C11   115.76  3.000
 BST  H133  C13  H132  107.38  3.000
 BST  H133  C13  H131  107.82  3.000
 BST  H132  C13  H131  108.05  3.000
 BST  H133  C13  N12   108.90  3.000
 BST  H132  C13  N12   110.68  3.000
 BST  H131  C13  N12   113.79  3.000
 BST  N15   C14  N14   118.62  3.000
 BST  N15   C14  N12   115.08  3.000
 BST  N14   C14  N12   126.30  3.000
 BST  H14   N14  C14   112.17  3.000
 BST  H152  N15  H151  111.44  3.000
 BST  H152  N15  C14   112.04  3.000
 BST  H151  N15  C14   116.62  3.000
 BST  HN42  N4   HN41  106.48  3.000
 BST  HN42  N4   C4    110.25  3.000
 BST  HN41  N4   C4    109.77  3.000
 BST  HO6   O6   C4    109.20  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
 BST  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 BST  CONST_02  C6    N1   C2   N3      0.00   0.0  0
 BST  CONST_03  C1'   N1   C2   N3    180.00   0.0  0
 BST  CONST_04  C6    N1   C2   O2    180.00   0.0  0
 BST  CONST_05  C1'   N1   C2   O2      0.00   0.0  0
 BST  CONST_06  C4    N3   C2   O2    180.00   0.0  0
 BST  CONST_07  HN3   N3   C2   N1    180.00   0.0  0
 BST  CONST_08  O7    C7   N6   C4'     0.00   0.0  0
 BST  CONST_09  C8    C7   N6   C4'   180.00   0.0  0
 BST  CONST_10  HO4   O4   C6'  C5'   180.00   0.0  0
 BST  CONST_13  N14   C14  N12  C13     0.00   0.0  0
 BST  CONST_14  N15   C14  N12  C13   180.00   0.0  0
 BST  CONST_15  HN6   N6   C7   O7    180.00   0.0  0
 BST  CONST_16  H14   N14  C14  N12     0.00   0.0  0
 BST  CONST_18  H152  N15  C14  N12   180.00   0.0  0
 BST  Var_01    C4    C5   C6   N1     -1.58  30.0  1
 BST  Var_02    C5    C6   N1   C2    -11.78  30.0  1
 BST  Var_03    C4'   C3'  C2'  C1'     0.65  30.0  1
 BST  Var_04    C9    C8   C7   N6   -136.06  30.0  3
 BST  Var_05    N12   C11  C10  C9    173.34  30.0  3
 BST  Var_06    C13   N12  C11  C10   -77.70  30.0  3
 BST  Var_07    H131  C13  N12  C11    83.50  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
 BST  chir_01  C4   C5   N3   O6   positiv
 BST  chir_02  C1'  O5'  N1   C2'  negativ
 BST  chir_03  C4'  N6   C5'  C3'  positiv
 BST  chir_04  C5'  O5'  C4'  C6'  negativ
 BST  chir_05  C9   N9   C8   C10  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
 BST  plan-1  C4'   0.020
 BST  plan-1  N6    0.020
 BST  plan-1  C7    0.020
 BST  plan-1  O7    0.020
 BST  plan-1  C8    0.020
 BST  plan-1  HN6   0.020
 BST  plan-2  N1    0.020
 BST  plan-2  C2    0.020
 BST  plan-2  O2    0.020
 BST  plan-2  N3    0.020
 BST  plan-2  C4    0.020
 BST  plan-2  C6    0.020
 BST  plan-2  C1'   0.020
 BST  plan-2  HN3   0.020
 BST  plan-3  C11   0.020
 BST  plan-3  N12   0.020
 BST  plan-3  C13   0.020
 BST  plan-3  C14   0.020
 BST  plan-3  N14   0.020
 BST  plan-3  N15   0.020
 BST  plan-3  H14   0.020
 BST  plan-3  H151  0.020
 BST  plan-3  H152  0.020
 BST  plan-4  O4    0.020
 BST  plan-4  C5'   0.020
 BST  plan-4  O3    0.020
 BST  plan-4  C6'   0.020
 BST  plan-4  HO4   0.020

