# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:19:23 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]-4-hydroxypyrimidin-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=CC(=NC2=O)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
 BLO  BLO  1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]-4-hydroxypyrimidin-2(1H)-one  ligand  54  30  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BLO
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
 BLO  O7    O  O      0  -0.510  -1.0886   2.7756   0.1669
 BLO  C7    C  C      0   0.553  -1.4302   1.7564   0.7531
 BLO  C8    C  CH2    0  -0.578  -2.8673   1.5025   1.1480
 BLO  C9    C  CH1    0  -0.083  -3.7261   1.2577  -0.0967
 BLO  C10   C  CH2    0  -0.440  -5.1346   0.8361   0.3291
 BLO  C11   C  CH2    0  -0.344  -6.1293   0.8034  -0.8292
 BLO  N12   N  NT     0  -0.445  -7.4479   0.3326  -0.4615
 BLO  C14   C  C      0   0.562  -7.7513  -0.9989  -0.3662
 BLO  N15   N  N      0  -0.729  -8.8896  -1.3569   0.1127
 BLO  N14   N  NH2    0  -0.845  -6.8131  -1.8734  -0.8872
 BLO  C13   C  CH3    0  -0.506  -8.3293   1.2699   0.1979
 BLO  N9    N  NH2    0  -0.794  -3.0405   0.3121  -0.9656
 BLO  N6    N  NH1    0  -0.652  -0.5766   0.7744   1.0909
 BLO  C4'   C  CR16   0  -0.107   0.7499   0.6594   0.5203
 BLO  C3'   C  CR16   0  -0.212   1.7076   1.6800   1.0723
 BLO  C2'   C  CR16   0  -0.254   2.9779   1.3816   1.2993
 BLO  C5'   C  CR16   0  -0.116   1.2992  -0.7425   0.8396
 BLO  C6'   C  C      0   0.417   0.4497  -1.8696   0.2173
 BLO  O3    O  OC    -1  -0.604  -0.6904  -1.9869   0.7262
 BLO  O4    O  O      0  -0.570   0.9387  -2.5382  -0.6987
 BLO  O5'   O  O      0  -0.478   2.6286  -0.8254   0.3811
 BLO  C1'   C  CR16   0   0.181   3.5020  -0.0061   1.0922
 BLO  N1    N  NR6    0  -0.558   4.7853  -0.0406   0.4058
 BLO  C6    C  CR16   0   0.119   5.8057  -0.7410   0.9522
 BLO  C5    C  CR16   0  -0.486   7.0093  -0.8366   0.3471
 BLO  C4    C  CR6    0   0.528   7.1181  -0.1584  -0.8928
 BLO  O1    O  OH1    0  -0.586   8.2834  -0.2166  -1.5074
 BLO  N3    N  N      0  -0.539   6.1447   0.5031  -1.4437
 BLO  C2    C  CR6    0   0.619   4.9251   0.5810  -0.8471
 BLO  O2    O  OC     0  -0.475   3.9834   1.1601  -1.3507
 BLO  H81   H  HCH2   0   0.268  -3.2529   2.3679   1.6904
 BLO  H82   H  HCH2   0   0.244  -2.9465   0.6432   1.8199
 BLO  H9    H  HCH1   0   0.232  -3.7956   2.2032  -0.6458
 BLO  H101  H  HCH2   0   0.236  -5.5095   1.5215   1.0955
 BLO  H102  H  HCH2   0   0.221  -5.0747  -0.1513   0.8029
 BLO  H111  H  HCH2   0   0.238  -5.7508   0.2013  -1.6581
 BLO  H112  H  HCH2   0   0.260  -6.2378   1.8111  -1.2363
 BLO  H15   H  H      0   0.313  -8.9740  -2.3663   0.1059
 BLO  H141  H  HNH2   0   0.385  -6.9897  -2.8385  -0.6579
 BLO  H142  H  HNH2   0   0.384  -5.8386  -1.6522  -0.7570
 BLO  H131  H  HCH3   0   0.234  -8.0308   2.2811  -0.0716
 BLO  H132  H  HCH3   0   0.240  -9.3604   1.1242  -0.1179
 BLO  H133  H  HCH3   0   0.220  -8.3008   1.1855   1.2880
 BLO  HN91  H  HNH2   0   0.336  -2.9208  -0.5816  -0.5020
 BLO  HN92  H  HNH2   0   0.354  -3.5738   0.1374  -1.8075
 BLO  HN6   H  HNH1   0   0.397  -0.9804  -0.1230   1.3413
 BLO  H4'   H  HCR6   0   0.256   0.6941   0.7777  -0.5709
 BLO  H3'   H  HCR6   0   0.261   1.3380   2.6779   1.2703
 BLO  H2'   H  HCR6   0   0.268   3.6661   2.1052   1.7211
 BLO  H5'   H  HCR6   0   0.228   1.2706  -0.8662   1.9344
 BLO  H1'   H  HCR6   0   0.257   3.6980  -0.4316   2.0887
 BLO  H6    H  HCR6   0   0.326   5.6073  -1.2175   1.9019
 BLO  H5    H  HCR6   0   0.296   7.8237  -1.3924   0.7839
 BLO  HO1   H  HOH1   0   0.481   8.2339   0.2785  -2.3383

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
 BLO  O7   C7    double    1.224  0.020  1.224
 BLO  C7   C8    single    1.512  0.020  1.512
 BLO  C7   N6    single    1.344  0.020  1.344
 BLO  C8   C9    single    1.532  0.020  1.532
 BLO  C8   H81   single    0.970  0.020  1.090
 BLO  C8   H82   single    0.970  0.020  1.090
 BLO  C9   C10   single    1.531  0.020  1.531
 BLO  C9   N9    single    1.456  0.020  1.456
 BLO  C9   H9    single    0.970  0.020  1.090
 BLO  C10  C11   single    1.527  0.020  1.527
 BLO  C10  H101  single    0.970  0.020  1.090
 BLO  C10  H102  single    0.970  0.020  1.090
 BLO  C11  N12   single    1.448  0.020  1.448
 BLO  C11  H111  single    0.970  0.020  1.090
 BLO  C11  H112  single    0.970  0.020  1.090
 BLO  N12  C14   single    1.369  0.020  1.369
 BLO  N12  C13   single    1.446  0.020  1.446
 BLO  C14  N15   double    1.286  0.020  1.286
 BLO  C14  N14   single    1.384  0.020  1.384
 BLO  N15  H15   single    0.890  0.020  1.040
 BLO  N14  H141  single    0.890  0.020  1.040
 BLO  N14  H142  single    0.890  0.020  1.040
 BLO  C13  H131  single    0.970  0.020  1.090
 BLO  C13  H132  single    0.970  0.020  1.090
 BLO  C13  H133  single    0.970  0.020  1.090
 BLO  N9   HN91  single    0.890  0.020  1.040
 BLO  N9   HN92  single    0.890  0.020  1.040
 BLO  N6   C4'   single    1.449  0.020  1.449
 BLO  N6   HN6   single    0.890  0.020  1.040
 BLO  C4'  C3'   single    1.504  0.020  1.504
 BLO  C4'  C5'   single    1.539  0.020  1.539
 BLO  C4'  H4'   single    0.970  0.020  1.090
 BLO  C3'  C2'   double    1.325  0.020  1.325
 BLO  C3'  H3'   single    0.930  0.020  1.080
 BLO  C2'  C1'   single    1.498  0.020  1.498
 BLO  C2'  H2'   single    0.930  0.020  1.080
 BLO  C5'  C6'   single    1.542  0.020  1.542
 BLO  C5'  O5'   single    1.409  0.020  1.409
 BLO  C5'  H5'   single    0.970  0.020  1.090
 BLO  C6'  O3    deloc     1.254  0.020  1.254
 BLO  C6'  O4    deloc     1.235  0.020  1.235
 BLO  O5'  C1'   single    1.393  0.020  1.393
 BLO  C1'  N1    single    1.456  0.020  1.456
 BLO  C1'  H1'   single    0.970  0.020  1.090
 BLO  N1   C6    aromatic  1.353  0.020  1.353
 BLO  N1   C2    aromatic  1.406  0.020  1.406
 BLO  C6   C5    aromatic  1.351  0.020  1.351
 BLO  C6   H6    single    0.930  0.020  1.080
 BLO  C5   C4    aromatic  1.417  0.020  1.417
 BLO  C5   H5    single    0.930  0.020  1.080
 BLO  C4   O1    single    1.319  0.020  1.319
 BLO  C4   N3    aromatic  1.299  0.020  1.299
 BLO  O1   HO1   single    0.850  0.020  0.980
 BLO  N3   C2    aromatic  1.360  0.020  1.360
 BLO  C2   O2    double    1.215  0.020  1.215

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
 BLO  N6    C7   C8    114.54  3.000
 BLO  N6    C7   O7    123.45  3.000
 BLO  C8    C7   O7    122.01  3.000
 BLO  H82   C8   H81   106.98  3.000
 BLO  H82   C8   C9    109.45  3.000
 BLO  H81   C8   C9    109.42  3.000
 BLO  H82   C8   C7    111.17  3.000
 BLO  H81   C8   C7    109.41  3.000
 BLO  C9    C8   C7    110.33  3.000
 BLO  H9    C9   N9    106.94  3.000
 BLO  H9    C9   C10   108.59  3.000
 BLO  N9    C9   C10   114.87  3.000
 BLO  H9    C9   C8    107.75  3.000
 BLO  N9    C9   C8    108.95  3.000
 BLO  C10   C9   C8    109.50  3.000
 BLO  H102  C10  H101  106.26  3.000
 BLO  H102  C10  C11   110.12  3.000
 BLO  H101  C10  C11   108.75  3.000
 BLO  H102  C10  C9    108.53  3.000
 BLO  H101  C10  C9    109.73  3.000
 BLO  C11   C10  C9    113.22  3.000
 BLO  H112  C11  H111  105.08  3.000
 BLO  H112  C11  N12   107.71  3.000
 BLO  H111  C11  N12   109.22  3.000
 BLO  H112  C11  C10   109.13  3.000
 BLO  H111  C11  C10   111.21  3.000
 BLO  N12   C11  C10   114.05  3.000
 BLO  C13   N12  C14   117.63  3.000
 BLO  C13   N12  C11   117.41  3.000
 BLO  C14   N12  C11   122.40  3.000
 BLO  N14   C14  N15   124.35  3.000
 BLO  N14   C14  N12   115.98  3.000
 BLO  N15   C14  N12   119.53  3.000
 BLO  H15   N15  C14   110.41  3.000
 BLO  H142  N14  H141  110.51  3.000
 BLO  H142  N14  C14   117.91  3.000
 BLO  H141  N14  C14   113.62  3.000
 BLO  H133  C13  H132  107.68  3.000
 BLO  H133  C13  H131  108.14  3.000
 BLO  H132  C13  H131  108.21  3.000
 BLO  H133  C13  N12   112.87  3.000
 BLO  H132  C13  N12   111.01  3.000
 BLO  H131  C13  N12   108.80  3.000
 BLO  HN92  N9   HN91  106.89  3.000
 BLO  HN92  N9   C9    111.14  3.000
 BLO  HN91  N9   C9    110.81  3.000
 BLO  HN6   N6   C4'   113.02  3.000
 BLO  HN6   N6   C7    117.08  3.000
 BLO  C4'   N6   C7    122.72  3.000
 BLO  H4'   C4'  C5'   108.79  3.000
 BLO  H4'   C4'  C3'   108.88  3.000
 BLO  C5'   C4'  C3'   108.34  3.000
 BLO  H4'   C4'  N6    109.64  3.000
 BLO  C5'   C4'  N6    108.51  3.000
 BLO  C3'   C4'  N6    112.62  3.000
 BLO  H3'   C3'  C2'   120.25  3.000
 BLO  H3'   C3'  C4'   118.37  3.000
 BLO  C2'   C3'  C4'   121.37  3.000
 BLO  H2'   C2'  C1'   116.75  3.000
 BLO  H2'   C2'  C3'   121.68  3.000
 BLO  C1'   C2'  C3'   121.37  3.000
 BLO  H5'   C5'  O5'   109.95  3.000
 BLO  H5'   C5'  C6'   107.73  3.000
 BLO  O5'   C5'  C6'   110.21  3.000
 BLO  H5'   C5'  C4'   107.40  3.000
 BLO  O5'   C5'  C4'   108.84  3.000
 BLO  C6'   C5'  C4'   112.66  3.000
 BLO  O4    C6'  O3    127.61  3.000
 BLO  O4    C6'  C5'   118.47  3.000
 BLO  O3    C6'  C5'   113.91  3.000
 BLO  C1'   O5'  C5'   113.02  3.000
 BLO  H1'   C1'  N1    105.11  3.000
 BLO  H1'   C1'  O5'   110.27  3.000
 BLO  N1    C1'  O5'   107.35  3.000
 BLO  H1'   C1'  C2'   107.17  3.000
 BLO  N1    C1'  C2'   113.30  3.000
 BLO  O5'   C1'  C2'   113.34  3.000
 BLO  C2    N1   C6    120.93  3.000
 BLO  C2    N1   C1'   119.83  3.000
 BLO  C6    N1   C1'   119.13  3.000
 BLO  H6    C6   C5    121.74  3.000
 BLO  H6    C6   N1    116.40  3.000
 BLO  C5    C6   N1    121.86  3.000
 BLO  H5    C5   C4    122.88  3.000
 BLO  H5    C5   C6    121.88  3.000
 BLO  C4    C5   C6    115.24  3.000
 BLO  N3    C4   O1    119.14  3.000
 BLO  N3    C4   C5    123.84  3.000
 BLO  O1    C4   C5    117.03  3.000
 BLO  HO1   O1   C4    109.39  3.000
 BLO  C2    N3   C4    121.00  3.000
 BLO  O2    C2   N3    122.72  3.000
 BLO  O2    C2   N1    120.22  3.000
 BLO  N3    C2   N1    117.06  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
 BLO  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 BLO  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 BLO  CONST_03  N3    C2   N1   C6     0.00   0.0  0
 BLO  CONST_04  N3    C4   C5   C6     0.00   0.0  0
 BLO  CONST_05  C2    N1   C6   C5     0.00   0.0  0
 BLO  CONST_06  C2    N3   C4   C5     0.00   0.0  0
 BLO  CONST_07  C5    C6   N1   C1'  180.00   0.0  0
 BLO  CONST_08  N3    C2   N1   C1'  180.00   0.0  0
 BLO  CONST_09  O2    C2   N1   C1'    0.00   0.0  0
 BLO  CONST_10  O2    C2   N1   C6   180.00   0.0  0
 BLO  CONST_11  O1    C4   C5   C6   180.00   0.0  0
 BLO  CONST_12  O2    C2   N3   C4   180.00   0.0  0
 BLO  CONST_13  C2    N3   C4   O1   180.00   0.0  0
 BLO  CONST_14  H6    C6   N1   C1'    0.00   0.0  0
 BLO  CONST_15  H5    C5   C6   N1   180.00   0.0  0
 BLO  CONST_18  N15   C14  N12  C11  180.00   0.0  0
 BLO  CONST_19  N14   C14  N12  C11    0.00   0.0  0
 BLO  CONST_20  C13   N12  C14  N15    0.00   0.0  0
 BLO  CONST_21  C13   N12  C14  N14  180.00   0.0  0
 BLO  CONST_23  H15   N15  C14  N12  180.00   0.0  0
 BLO  CONST_24  H141  N14  C14  N12  180.00   0.0  0
 BLO  Var_01    C1'   C2'  C3'  C4'   -3.58  30.0  1
 BLO  Var_02    C9    C8   C7   O7    69.09  30.0  3
 BLO  Var_03    N12   C11  C10  C9   176.61  30.0  3
 BLO  Var_04    C14   N12  C11  C10  -82.10  30.0  3
 BLO  Var_05    H131  C13  N12  C11   24.73  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
 BLO  chir_01  C9   C8   C10  N9   positiv
 BLO  chir_02  C4'  N6   C3'  C5'  negativ
 BLO  chir_03  C5'  O5'  C4'  C6'  negativ
 BLO  chir_04  C1'  O5'  N1   C2'  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
 BLO  plan-1  C1'   0.020
 BLO  plan-1  N1    0.020
 BLO  plan-1  C6    0.020
 BLO  plan-1  C5    0.020
 BLO  plan-1  C4    0.020
 BLO  plan-1  O1    0.020
 BLO  plan-1  N3    0.020
 BLO  plan-1  C2    0.020
 BLO  plan-1  O2    0.020
 BLO  plan-1  H6    0.020
 BLO  plan-1  H5    0.020
 BLO  plan-2  O7    0.020
 BLO  plan-2  C7    0.020
 BLO  plan-2  C8    0.020
 BLO  plan-2  N6    0.020
 BLO  plan-2  C4'   0.020
 BLO  plan-2  HN6   0.020
 BLO  plan-3  C11   0.020
 BLO  plan-3  N12   0.020
 BLO  plan-3  C14   0.020
 BLO  plan-3  N15   0.020
 BLO  plan-3  N14   0.020
 BLO  plan-3  C13   0.020
 BLO  plan-3  H15   0.020
 BLO  plan-3  H141  0.020
 BLO  plan-3  H142  0.020
 BLO  plan-4  C5'   0.020
 BLO  plan-4  C6'   0.020
 BLO  plan-4  O3    0.020
 BLO  plan-4  O4    0.020

