# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 28 07:48:12 2020
#   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  58  31  .  2021-08-06  2021-08-06  
;
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  OC    -1  -0.603   -0.8461  -1.9375   0.5963
 BST  N1    N  NR6    0  -0.579    4.5573   0.2299   0.5466
 BST  C2    C  CR6    0   0.708    4.7630   0.9673  -0.6052
 BST  O2    O  O      0  -0.501    3.8903   1.6660  -1.0905
 BST  N3    N  NR16   0  -0.713    6.0154   0.9005  -1.1174
 BST  C4    C  CR6    0   0.512    7.0695  -0.0657  -0.8272
 BST  C5    C  CR16   0  -0.401    6.7662  -0.6869   0.4942
 BST  C6    C  CR16   0   0.045    5.5782  -0.5450   1.0699
 BST  C1'   C  CR16   0   0.187    3.2538   0.1958   1.1617
 BST  C2'   C  CR16   0  -0.247    2.6677   1.5479   1.4364
 BST  C3'   C  CR16   0  -0.220    1.3879   1.8084   1.2152
 BST  C4'   C  CR16   0  -0.112    0.4753   0.7851   0.5968
 BST  C5'   C  CR16   0  -0.110    1.0833  -0.6113   0.8178
 BST  O5'   O  O      0  -0.483    2.4164  -0.5996   0.3690
 BST  O3    O  O      0  -0.574    0.7908  -2.2608  -0.8884
 BST  C6'   C  C      0   0.412    0.2824  -1.7158   0.0981
 BST  N6    N  NH1    0  -0.641   -0.8573   0.8108   1.1672
 BST  C7    C  C      0   0.519   -1.7627   1.7522   0.8568
 BST  O7    O  O      0  -0.507   -1.4776   2.7920   0.2732
 BST  C8    C  CH2    0  -0.570   -3.1874   1.4083   1.2199
 BST  C9    C  CH1    0  -0.093   -3.9955   1.0911  -0.0549
 BST  N9    N  NH2    0  -0.794   -3.3891   0.0857  -0.9154
 BST  C10   C  CH2    0  -0.422   -5.4101   0.6709   0.3276
 BST  C11   C  CH2    0  -0.282   -6.3349   0.5291  -0.8771
 BST  N12   N  NT     0  -0.458   -7.7129   0.2491  -0.5204
 BST  C13   C  CH3    0  -0.537   -8.4547   1.3462   0.0671
 BST  C14   C  C      0   0.562   -8.0697  -1.0514  -0.2695
 BST  N14   N  N      0  -0.722   -7.2364  -2.0091  -0.4760
 BST  N15   N  NH2    0  -0.842   -9.3391  -1.2200   0.2475
 BST  N4    N  NH2    0  -0.803    8.3700   0.5554  -0.8026
 BST  O6    O  OH1    0  -0.649    7.0669  -1.0966  -1.7805
 BST  HN3   H  HNR6   0   0.398    6.1411   1.4628  -1.9484
 BST  H5    H  HCR6   0   0.276    7.5278  -1.2954   0.9588
 BST  H6    H  HCR6   0   0.299    5.3480  -1.0318   2.0076
 BST  H1'   H  HCR6   0   0.249    3.4104  -0.2866   2.1389
 BST  H2'   H  HCR6   0   0.263    3.3200   2.2767   1.9036
 BST  H3'   H  HCR6   0   0.257    0.9773   2.7798   1.4603
 BST  H4'   H  HCR6   0   0.255    0.4093   0.9733  -0.4839
 BST  H5'   H  HCR6   0   0.224    1.0508  -0.8198   1.8998
 BST  HN6   H  HNH1   0   0.396   -1.2101  -0.0995   1.4385
 BST  H81   H  HCH2   0   0.259   -3.6394   2.2573   1.7382
 BST  H82   H  HCH2   0   0.244   -3.2305   0.5509   1.8970
 BST  H9    H  HCH1   0   0.230   -4.0590   2.0135  -0.6421
 BST  HN91  H  HNH2   0   0.347   -2.5329   0.4357  -1.3274
 BST  HN92  H  HNH2   0   0.334   -3.1244  -0.7350  -0.3811
 BST  H101  H  HCH2   0   0.225   -5.8203   1.4127   1.0193
 BST  H102  H  HCH2   0   0.222   -5.3764  -0.2786   0.8714
 BST  H111  H  HCH2   0   0.248   -5.9711  -0.2599  -1.5286
 BST  H112  H  HCH2   0   0.226   -6.3258   1.4572  -1.4567
 BST  H131  H  HCH3   0   0.251   -8.0237   2.2812  -0.2840
 BST  H132  H  HCH3   0   0.238   -9.4995   1.3546  -0.2459
 BST  H133  H  HCH3   0   0.231   -8.4278   1.3556   1.1606
 BST  H14   H  H      0   0.311   -7.6858  -2.9038  -0.3198
 BST  H151  H  HNH2   0   0.383  -10.0557  -0.5802  -0.0566
 BST  H152  H  HNH2   0   0.384   -9.6695  -2.1716   0.2290
 BST  HN41  H  HNH2   0   0.358    8.5708   1.0199  -1.6831
 BST  HN42  H  HNH2   0   0.358    8.3895   1.2755  -0.0911
 BST  HO6   H  HOH1   0   0.451    7.4120  -0.7670  -2.6198

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'   deloc   1.253  0.020  1.253
 BST  N1   C2    single  1.383  0.020  1.383
 BST  N1   C6    single  1.384  0.020  1.384
 BST  N1   C1'   single  1.442  0.020  1.442
 BST  C2   O2    double  1.219  0.020  1.219
 BST  C2   N3    single  1.355  0.020  1.355
 BST  N3   C4    single  1.459  0.020  1.459
 BST  N3   HN3   single  0.860  0.020  1.020
 BST  C4   C5    single  1.491  0.020  1.491
 BST  C4   N4    single  1.441  0.020  1.441
 BST  C4   O6    single  1.404  0.020  1.404
 BST  C5   C6    double  1.328  0.020  1.328
 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  1.401  0.020  1.401
 BST  C1'  H1'   single  0.970  0.020  1.090
 BST  C2'  C3'   double  1.325  0.020  1.325
 BST  C2'  H2'   single  0.930  0.020  1.080
 BST  C3'  C4'   single  1.504  0.020  1.504
 BST  C3'  H3'   single  0.930  0.020  1.080
 BST  C4'  C5'   single  1.539  0.020  1.539
 BST  C4'  N6    single  1.450  0.020  1.450
 BST  C4'  H4'   single  0.970  0.020  1.090
 BST  C5'  O5'   single  1.407  0.020  1.407
 BST  C5'  C6'   single  1.542  0.020  1.542
 BST  C5'  H5'   single  0.970  0.020  1.090
 BST  O3   C6'   deloc   1.236  0.020  1.236
 BST  N6   C7    single  1.343  0.020  1.343
 BST  N6   HN6   single  0.890  0.020  1.040
 BST  C7   O7    double  1.226  0.020  1.226
 BST  C7   C8    single  1.510  0.020  1.510
 BST  C8   C9    single  1.542  0.020  1.542
 BST  C8   H81   single  0.970  0.020  1.090
 BST  C8   H82   single  0.970  0.020  1.090
 BST  C9   N9    single  1.456  0.020  1.456
 BST  C9   C10   single  1.524  0.020  1.524
 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  1.525  0.020  1.525
 BST  C10  H101  single  0.970  0.020  1.090
 BST  C10  H102  single  0.970  0.020  1.090
 BST  C11  N12   single  1.451  0.020  1.451
 BST  C11  H111  single  0.970  0.020  1.090
 BST  C11  H112  single  0.970  0.020  1.090
 BST  N12  C13   single  1.449  0.020  1.449
 BST  N12  C14   single  1.372  0.020  1.372
 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  1.286  0.020  1.286
 BST  C14  N15   single  1.381  0.020  1.381
 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  C1'   N1   C6    119.48  3.000
 BST  C1'   N1   C2    120.16  3.000
 BST  C6    N1   C2    120.24  3.000
 BST  N3    C2   O2    122.66  3.000
 BST  N3    C2   N1    115.22  3.000
 BST  O2    C2   N1    122.06  3.000
 BST  HN3   N3   C4    116.22  3.000
 BST  HN3   N3   C2    113.47  3.000
 BST  C4    N3   C2    128.71  3.000
 BST  O6    C4   N4    109.25  3.000
 BST  O6    C4   C5    107.18  3.000
 BST  N4    C4   C5    110.36  3.000
 BST  O6    C4   N3    110.48  3.000
 BST  N4    C4   N3    111.71  3.000
 BST  C5    C4   N3    107.76  3.000
 BST  H5    C5   C6    120.31  3.000
 BST  H5    C5   C4    118.19  3.000
 BST  C6    C5   C4    121.45  3.000
 BST  H6    C6   C5    121.23  3.000
 BST  H6    C6   N1    115.01  3.000
 BST  C5    C6   N1    123.75  3.000
 BST  H1'   C1'  O5'   109.78  3.000
 BST  H1'   C1'  C2'   106.75  3.000
 BST  O5'   C1'  C2'   112.47  3.000
 BST  H1'   C1'  N1    105.09  3.000
 BST  O5'   C1'  N1    108.21  3.000
 BST  C2'   C1'  N1    114.23  3.000
 BST  H2'   C2'  C3'   121.41  3.000
 BST  H2'   C2'  C1'   116.75  3.000
 BST  C3'   C2'  C1'   121.64  3.000
 BST  H3'   C3'  C4'   118.25  3.000
 BST  H3'   C3'  C2'   120.33  3.000
 BST  C4'   C3'  C2'   121.40  3.000
 BST  H4'   C4'  N6    109.19  3.000
 BST  H4'   C4'  C5'   108.68  3.000
 BST  N6    C4'  C5'   108.83  3.000
 BST  H4'   C4'  C3'   108.92  3.000
 BST  N6    C4'  C3'   112.57  3.000
 BST  C5'   C4'  C3'   108.58  3.000
 BST  H5'   C5'  C6'   107.89  3.000
 BST  H5'   C5'  O5'   110.04  3.000
 BST  C6'   C5'  O5'   110.44  3.000
 BST  H5'   C5'  C4'   107.51  3.000
 BST  C6'   C5'  C4'   112.18  3.000
 BST  O5'   C5'  C4'   108.73  3.000
 BST  C5'   O5'  C1'   113.00  3.000
 BST  O3    C6'  C5'   118.32  3.000
 BST  O3    C6'  O4    127.55  3.000
 BST  C5'   C6'  O4    114.12  3.000
 BST  HN6   N6   C7    117.19  3.000
 BST  HN6   N6   C4'   114.17  3.000
 BST  C7    N6   C4'   122.78  3.000
 BST  C8    C7   O7    121.81  3.000
 BST  C8    C7   N6    114.90  3.000
 BST  O7    C7   N6    123.22  3.000
 BST  H82   C8   H81   107.41  3.000
 BST  H82   C8   C9    109.27  3.000
 BST  H81   C8   C9    109.58  3.000
 BST  H82   C8   C7    111.39  3.000
 BST  H81   C8   C7    109.12  3.000
 BST  C9    C8   C7    110.03  3.000
 BST  H9    C9   C10   108.23  3.000
 BST  H9    C9   N9    106.79  3.000
 BST  C10   C9   N9    110.15  3.000
 BST  H9    C9   C8    107.48  3.000
 BST  C10   C9   C8    109.60  3.000
 BST  N9    C9   C8    114.35  3.000
 BST  HN92  N9   HN91  105.86  3.000
 BST  HN92  N9   C9    110.86  3.000
 BST  HN91  N9   C9    110.73  3.000
 BST  H102  C10  H101  106.60  3.000
 BST  H102  C10  C11   109.29  3.000
 BST  H101  C10  C11   109.58  3.000
 BST  H102  C10  C9    109.58  3.000
 BST  H101  C10  C9    108.64  3.000
 BST  C11   C10  C9    112.96  3.000
 BST  H112  C11  H111  107.20  3.000
 BST  H112  C11  N12   107.57  3.000
 BST  H111  C11  N12   108.99  3.000
 BST  H112  C11  C10   109.54  3.000
 BST  H111  C11  C10   109.77  3.000
 BST  N12   C11  C10   113.55  3.000
 BST  C14   N12  C13   120.71  3.000
 BST  C14   N12  C11   118.36  3.000
 BST  C13   N12  C11   116.10  3.000
 BST  H133  C13  H132  108.08  3.000
 BST  H133  C13  H131  107.79  3.000
 BST  H132  C13  H131  106.28  3.000
 BST  H133  C13  N12   113.53  3.000
 BST  H132  C13  N12   112.33  3.000
 BST  H131  C13  N12   108.49  3.000
 BST  N15   C14  N14   124.39  3.000
 BST  N15   C14  N12   115.04  3.000
 BST  N14   C14  N12   120.54  3.000
 BST  H14   N14  C14   110.21  3.000
 BST  H152  N15  H151  111.16  3.000
 BST  H152  N15  C14   114.19  3.000
 BST  H151  N15  C14   117.59  3.000
 BST  HN42  N4   HN41  106.27  3.000
 BST  HN42  N4   C4    109.62  3.000
 BST  HN41  N4   C4    111.14  3.000
 BST  HO6   O6   C4    109.80  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_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_10  N14   C14  N12  C11     0.00   0.0  0
 BST  CONST_11  N15   C14  N12  C11   180.00   0.0  0
 BST  CONST_14  HN6   N6   C7   O7    180.00   0.0  0
 BST  CONST_15  H14   N14  C14  N12   180.00   0.0  0
 BST  CONST_17  H152  N15  C14  N12   180.00   0.0  0
 BST  Var_01    C4    C5   C6   N1     -3.42  30.0  1
 BST  Var_02    C5    C6   N1   C2     -3.31  30.0  1
 BST  Var_03    C4'   C3'  C2'  C1'    -3.83  30.0  1
 BST  Var_04    C9    C8   C7   N6   -107.49  30.0  3
 BST  Var_05    N12   C11  C10  C9   -174.70  30.0  3
 BST  Var_06    C13   N12  C11  C10    71.88  30.0  3
 BST  Var_07    H131  C13  N12  C11    26.65  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

