# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:49:51 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-amino-1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]pyrimidin-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)N)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
 BLS  BLS  4-amino-1-[4-({(3S)-3-amino-5-[carbamimidoyl(methyl)amino]pentanoyl}amino)-2,3,4-trideoxy-beta-D-erythro-hex-2-enopyranuronosyl]pyrimidin-2(1H)-one  ligand  56  30  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BLS
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
 BLS  O4    O  OH1   0  -0.587  -0.1861  -1.9063  -0.5957
 BLS  N1    N  NR6   0  -0.565   5.0277   0.1374   0.7291
 BLS  C2    C  CR6   0   0.602   5.4105   1.0722  -0.2538
 BLS  O2    O  OC    0  -0.496   4.5636   1.8034  -0.7382
 BLS  N3    N  N     0  -0.542   6.7110   1.1169  -0.6095
 BLS  C4    C  CR6   0   0.515   7.5935   0.2921  -0.0840
 BLS  N4    N  NH2   0  -0.807   8.8619   0.3868  -0.4772
 BLS  C5    C  CR16  0  -0.479   7.2312  -0.6936   0.8879
 BLS  C6    C  CR16  0   0.107   5.9364  -0.7253   1.2513
 BLS  C1'   C  CH1   0   0.184   3.6405   0.0283   1.1225
 BLS  C2'   C  C1    0  -0.257   3.0392   1.3258   1.5683
 BLS  C3'   C  C1    0  -0.201   1.8241   1.6925   1.1924
 BLS  C4'   C  CH1   0  -0.163   1.0037   0.8717   0.2401
 BLS  C5'   C  CH1   0  -0.021   1.5586  -0.5688   0.2334
 BLS  O5'   O  O2    0  -0.481   2.9472  -0.5530   0.0531
 BLS  O3    O  O     0  -0.420   1.5232  -1.5042  -1.9795
 BLS  C6'   C  C     0   0.507   0.9846  -1.3761  -0.9133
 BLS  N6    N  NH1   0  -0.648  -0.3877   0.8913   0.6095
 BLS  C7    C  C     0   0.583  -1.3967   1.0148  -0.2778
 BLS  O7    O  O     0  -0.494  -1.2043   1.1607  -1.4760
 BLS  C8    C  CH2   0  -0.592  -2.7804   0.9950   0.3323
 BLS  C9    C  CH1   0  -0.090  -3.8642   0.4990  -0.6302
 BLS  N9    N  NH2   0  -0.791  -3.6509  -0.8502  -1.1315
 BLS  C10   C  CH2   0  -0.423  -5.2267   0.5835   0.0531
 BLS  C11   C  CH2   0  -0.305  -6.3842   0.2485  -0.8830
 BLS  N12   N  NT    0  -0.455  -7.6963   0.3640  -0.2647
 BLS  C13   C  CH3   0  -0.507  -8.2282   1.7052  -0.1692
 BLS  C14   C  C     0   0.550  -8.1046  -0.5387   0.6884
 BLS  N14   N  N     0  -0.718  -8.9557  -0.1882   1.5845
 BLS  N15   N  NH2   0  -0.835  -7.5120  -1.7830   0.6121
 BLS  HO4   H  HOH1  0   0.486  -0.5474  -2.3913  -1.3533
 BLS  HN41  H  HNH2  0   0.415   9.5685  -0.2380  -0.1309
 BLS  HN42  H  HNH2  0   0.404   9.1275   1.0628  -1.1733
 BLS  H5    H  HCR6  0   0.290   7.9487  -1.3785   1.3129
 BLS  H6    H  HCR6  0   0.318   5.5650  -1.4337   1.9790
 BLS  H1'   H  HCH1  0   0.268   3.6300  -0.6518   1.9871
 BLS  H2'   H  H     0   0.278   3.6165   1.9129   2.2723
 BLS  H3'   H  H     0   0.271   1.3860   2.6169   1.5503
 BLS  H4'   H  HCH1  0   0.289   1.0881   1.2934  -0.7650
 BLS  H5'   H  HCH1  0   0.269   1.2833  -1.0466   1.1849
 BLS  HN6   H  HNH1  0   0.403  -0.6155   0.7223   1.5772
 BLS  H81   H  HCH2  0   0.277  -3.0110   2.0174   0.6514
 BLS  H82   H  HCH2  0   0.253  -2.7816   0.3832   1.2399
 BLS  H9    H  HCH1  0   0.229  -3.8751   1.1657  -1.4980
 BLS  HN91  H  HNH2  0   0.344  -2.7824  -0.8952  -1.6482
 BLS  HN92  H  HNH2  0   0.335  -3.5646  -1.4975  -0.3560
 BLS  H101  H  HCH2  0   0.231  -5.3608   1.5920   0.4552
 BLS  H102  H  HCH2  0   0.223  -5.2420  -0.1001   0.9090
 BLS  H111  H  HCH2  0   0.242  -6.2395  -0.7446  -1.3060
 BLS  H112  H  HCH2  0   0.240  -6.3734   0.9312  -1.7357
 BLS  H131  H  HCH3  0   0.231  -8.0072   2.2346  -1.0949
 BLS  H132  H  HCH3  0   0.241  -9.3073   1.6786  -0.0399
 BLS  H133  H  HCH3  0   0.214  -7.8089   2.2818   0.6621
 BLS  HN14  H  H     0   0.313  -9.2238  -0.9876   2.1470
 BLS  H151  H  HNH2  0   0.384  -7.9493  -2.4882   1.1833
 BLS  H152  H  HNH2  0   0.384  -7.2941  -2.1358  -0.3061

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
 BLS  O4   C6'   single    1.324  0.020  1.324
 BLS  O4   HO4   single    0.850  0.020  0.980
 BLS  N1   C2    aromatic  1.409  0.020  1.409
 BLS  N1   C6    aromatic  1.357  0.020  1.357
 BLS  N1   C1'   single    1.446  0.020  1.446
 BLS  C2   O2    double    1.219  0.020  1.219
 BLS  C2   N3    aromatic  1.349  0.020  1.349
 BLS  N3   C4    aromatic  1.317  0.020  1.317
 BLS  C4   N4    single    1.331  0.020  1.331
 BLS  C4   C5    aromatic  1.431  0.020  1.431
 BLS  N4   HN41  single    0.860  0.020  1.020
 BLS  N4   HN42  single    0.860  0.020  1.020
 BLS  C5   C6    aromatic  1.345  0.020  1.345
 BLS  C5   H5    single    0.930  0.020  1.080
 BLS  C6   H6    single    0.930  0.020  1.080
 BLS  C1'  C2'   single    1.498  0.020  1.498
 BLS  C1'  O5'   single    1.401  0.020  1.401
 BLS  C1'  H1'   single    0.970  0.020  1.090
 BLS  C2'  C3'   double    1.324  0.020  1.324
 BLS  C2'  H2'   single    0.930  0.020  1.080
 BLS  C3'  C4'   single    1.501  0.020  1.501
 BLS  C3'  H3'   single    0.930  0.020  1.080
 BLS  C4'  C5'   single    1.544  0.020  1.544
 BLS  C4'  N6    single    1.440  0.020  1.440
 BLS  C4'  H4'   single    0.970  0.020  1.090
 BLS  C5'  O5'   single    1.400  0.020  1.400
 BLS  C5'  C6'   single    1.515  0.020  1.515
 BLS  C5'  H5'   single    0.970  0.020  1.090
 BLS  O3   C6'   double    1.201  0.020  1.201
 BLS  N6   C7    single    1.349  0.020  1.349
 BLS  N6   HN6   single    0.860  0.020  1.020
 BLS  C7   O7    double    1.222  0.020  1.222
 BLS  C7   C8    single    1.512  0.020  1.512
 BLS  C8   C9    single    1.532  0.020  1.532
 BLS  C8   H81   single    0.970  0.020  1.090
 BLS  C8   H82   single    0.970  0.020  1.090
 BLS  C9   N9    single    1.455  0.020  1.455
 BLS  C9   C10   single    1.526  0.020  1.526
 BLS  C9   H9    single    0.970  0.020  1.090
 BLS  N9   HN91  single    0.890  0.020  1.040
 BLS  N9   HN92  single    0.890  0.020  1.040
 BLS  C10  C11   single    1.526  0.020  1.526
 BLS  C10  H101  single    0.970  0.020  1.090
 BLS  C10  H102  single    0.970  0.020  1.090
 BLS  C11  N12   single    1.455  0.020  1.455
 BLS  C11  H111  single    0.970  0.020  1.090
 BLS  C11  H112  single    0.970  0.020  1.090
 BLS  N12  C13   single    1.446  0.020  1.446
 BLS  N12  C14   single    1.375  0.020  1.375
 BLS  C13  H131  single    0.970  0.020  1.090
 BLS  C13  H132  single    0.970  0.020  1.090
 BLS  C13  H133  single    0.970  0.020  1.090
 BLS  C14  N14   double    1.285  0.020  1.285
 BLS  C14  N15   single    1.380  0.020  1.380
 BLS  N14  HN14  single    0.890  0.020  1.040
 BLS  N15  H151  single    0.890  0.020  1.040
 BLS  N15  H152  single    0.890  0.020  1.040

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
 BLS  HO4   O4   C6'   110.03  3.000
 BLS  C1'   N1   C6    119.31  3.000
 BLS  C1'   N1   C2    120.02  3.000
 BLS  C6    N1   C2    120.53  3.000
 BLS  N3    C2   O2    123.03  3.000
 BLS  N3    C2   N1    117.88  3.000
 BLS  O2    C2   N1    119.09  3.000
 BLS  C4    N3   C2    121.33  3.000
 BLS  C5    C4   N4    119.40  3.000
 BLS  C5    C4   N3    122.18  3.000
 BLS  N4    C4   N3    118.42  3.000
 BLS  HN42  N4   HN41  118.08  3.000
 BLS  HN42  N4   C4    120.24  3.000
 BLS  HN41  N4   C4    121.60  3.000
 BLS  H5    C5   C6    121.24  3.000
 BLS  H5    C5   C4    122.43  3.000
 BLS  C6    C5   C4    116.33  3.000
 BLS  H6    C6   C5    121.86  3.000
 BLS  H6    C6   N1    116.44  3.000
 BLS  C5    C6   N1    121.70  3.000
 BLS  H1'   C1'  O5'   109.80  3.000
 BLS  H1'   C1'  C2'   107.32  3.000
 BLS  O5'   C1'  C2'   112.83  3.000
 BLS  H1'   C1'  N1    105.64  3.000
 BLS  O5'   C1'  N1    107.36  3.000
 BLS  C2'   C1'  N1    113.62  3.000
 BLS  H2'   C2'  C3'   121.57  3.000
 BLS  H2'   C2'  C1'   116.68  3.000
 BLS  C3'   C2'  C1'   121.60  3.000
 BLS  H3'   C3'  C4'   117.06  3.000
 BLS  H3'   C3'  C2'   120.90  3.000
 BLS  C4'   C3'  C2'   122.02  3.000
 BLS  H4'   C4'  N6    107.78  3.000
 BLS  H4'   C4'  C5'   109.16  3.000
 BLS  N6    C4'  C5'   111.17  3.000
 BLS  H4'   C4'  C3'   109.28  3.000
 BLS  N6    C4'  C3'   110.97  3.000
 BLS  C5'   C4'  C3'   108.45  3.000
 BLS  H5'   C5'  C6'   109.18  3.000
 BLS  H5'   C5'  O5'   111.38  3.000
 BLS  C6'   C5'  O5'   106.51  3.000
 BLS  H5'   C5'  C4'   108.16  3.000
 BLS  C6'   C5'  C4'   111.36  3.000
 BLS  O5'   C5'  C4'   110.27  3.000
 BLS  C5'   O5'  C1'   113.40  3.000
 BLS  O3    C6'  C5'   123.96  3.000
 BLS  O3    C6'  O4    124.52  3.000
 BLS  C5'   C6'  O4    111.52  3.000
 BLS  HN6   N6   C7    118.52  3.000
 BLS  HN6   N6   C4'   117.53  3.000
 BLS  C7    N6   C4'   123.73  3.000
 BLS  C8    C7   O7    122.75  3.000
 BLS  C8    C7   N6    114.69  3.000
 BLS  O7    C7   N6    122.53  3.000
 BLS  H82   C8   H81   106.25  3.000
 BLS  H82   C8   C9    109.83  3.000
 BLS  H81   C8   C9    109.65  3.000
 BLS  H82   C8   C7    110.04  3.000
 BLS  H81   C8   C7    107.33  3.000
 BLS  C9    C8   C7    113.46  3.000
 BLS  H9    C9   C10   108.20  3.000
 BLS  H9    C9   N9    107.05  3.000
 BLS  C10   C9   N9    109.66  3.000
 BLS  H9    C9   C8    107.93  3.000
 BLS  C10   C9   C8    109.41  3.000
 BLS  N9    C9   C8    114.39  3.000
 BLS  HN92  N9   HN91  106.82  3.000
 BLS  HN92  N9   C9    109.93  3.000
 BLS  HN91  N9   C9    110.06  3.000
 BLS  H102  C10  H101  106.64  3.000
 BLS  H102  C10  C11   109.37  3.000
 BLS  H101  C10  C11   109.57  3.000
 BLS  H102  C10  C9    109.13  3.000
 BLS  H101  C10  C9    108.97  3.000
 BLS  C11   C10  C9    112.97  3.000
 BLS  H112  C11  H111  105.39  3.000
 BLS  H112  C11  N12   106.92  3.000
 BLS  H111  C11  N12   110.93  3.000
 BLS  H112  C11  C10   109.52  3.000
 BLS  H111  C11  C10   109.74  3.000
 BLS  N12   C11  C10   113.95  3.000
 BLS  C14   N12  C13   117.00  3.000
 BLS  C14   N12  C11   120.68  3.000
 BLS  C13   N12  C11   115.68  3.000
 BLS  H133  C13  H132  107.61  3.000
 BLS  H133  C13  H131  108.16  3.000
 BLS  H132  C13  H131  108.33  3.000
 BLS  H133  C13  N12   113.43  3.000
 BLS  H132  C13  N12   110.51  3.000
 BLS  H131  C13  N12   108.67  3.000
 BLS  N15   C14  N14   124.68  3.000
 BLS  N15   C14  N12   115.22  3.000
 BLS  N14   C14  N12   120.08  3.000
 BLS  HN14  N14  C14   110.32  3.000
 BLS  H152  N15  H151  111.44  3.000
 BLS  H152  N15  C14   117.31  3.000
 BLS  H151  N15  C14   114.41  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
 BLS  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 BLS  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 BLS  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 BLS  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 BLS  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 BLS  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 BLS  CONST_07  C1'   N1   C2   N3    180.00   0.0  0
 BLS  CONST_08  C1'   N1   C6   C5    180.00   0.0  0
 BLS  CONST_09  N4    C4   N3   C2    180.00   0.0  0
 BLS  CONST_10  C6    N1   C2   O2    180.00   0.0  0
 BLS  CONST_11  C1'   N1   C2   O2      0.00   0.0  0
 BLS  CONST_12  C4    N3   C2   O2    180.00   0.0  0
 BLS  CONST_13  C6    C5   C4   N4    180.00   0.0  0
 BLS  CONST_14  H5    C5   C6   N1    180.00   0.0  0
 BLS  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 BLS  CONST_16  HN41  N4   C4   N3    180.00   0.0  0
 BLS  CONST_17  HN42  N4   C4   N3      0.00   0.0  0
 BLS  CONST_18  O7    C7   N6   C4'     0.00   0.0  0
 BLS  CONST_19  C8    C7   N6   C4'   180.00   0.0  0
 BLS  CONST_20  HO4   O4   C6'  C5'   180.00   0.0  0
 BLS  CONST_23  N14   C14  N12  C13     0.00   0.0  0
 BLS  CONST_24  N15   C14  N12  C13   180.00   0.0  0
 BLS  CONST_25  HN6   N6   C7   O7    180.00   0.0  0
 BLS  CONST_26  HN14  N14  C14  N12   180.00   0.0  0
 BLS  CONST_27  H151  N15  C14  N12   180.00   0.0  0
 BLS  Var_01    C4'   C3'  C2'  C1'    -3.39  30.0  1
 BLS  Var_02    C9    C8   C7   N6   -153.55  30.0  3
 BLS  Var_03    N12   C11  C10  C9   -178.14  30.0  3
 BLS  Var_04    C13   N12  C11  C10    80.14  30.0  3
 BLS  Var_05    H131  C13  N12  C11    41.00  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
 BLS  chir_01  C1'  N1   C2'  O5'  negativ
 BLS  chir_02  C4'  N6   C5'  C3'  positiv
 BLS  chir_03  C5'  O5'  C4'  C6'  negativ
 BLS  chir_04  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
 BLS  plan-1  N1    0.020
 BLS  plan-1  C2    0.020
 BLS  plan-1  O2    0.020
 BLS  plan-1  N3    0.020
 BLS  plan-1  C4    0.020
 BLS  plan-1  N4    0.020
 BLS  plan-1  C5    0.020
 BLS  plan-1  C6    0.020
 BLS  plan-1  C1'   0.020
 BLS  plan-1  H5    0.020
 BLS  plan-1  H6    0.020
 BLS  plan-2  C4'   0.020
 BLS  plan-2  N6    0.020
 BLS  plan-2  C7    0.020
 BLS  plan-2  O7    0.020
 BLS  plan-2  C8    0.020
 BLS  plan-2  HN6   0.020
 BLS  plan-3  C4    0.020
 BLS  plan-3  N4    0.020
 BLS  plan-3  HN41  0.020
 BLS  plan-3  HN42  0.020
 BLS  plan-4  C11   0.020
 BLS  plan-4  N12   0.020
 BLS  plan-4  C13   0.020
 BLS  plan-4  C14   0.020
 BLS  plan-4  N14   0.020
 BLS  plan-4  N15   0.020
 BLS  plan-4  HN14  0.020
 BLS  plan-4  H151  0.020
 BLS  plan-4  H152  0.020
 BLS  plan-5  O4    0.020
 BLS  plan-5  C5'   0.020
 BLS  plan-5  O3    0.020
 BLS  plan-5  C6'   0.020
 BLS  plan-5  HO4   0.020

