# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 12:01:15 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 5-[(2-amino-1H-benzimidazol-6-yl)amino]-5-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2cc(NC(=O)CCCC(O)=O)ccc2n1
#
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
 BZH  BZH  '5-[(2-amino-1H-benzimidazol-6-yl)amino]-5-oxopentanoic acid'  ligand  33  19  .  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_BZH
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
 BZH  C8    C  CR16  0  -0.402  -2.1290  -0.7815  -4.3618
 BZH  C9    C  CR56  0   0.379  -3.1201  -0.5359  -5.2970
 BZH  N1    N  NR15  0  -0.725  -3.6397  -1.3201  -6.2991
 BZH  C2    C  CR5   0   0.602  -4.6066  -0.5878  -6.9227
 BZH  N10   N  NH2   0  -0.849  -5.3576  -1.1129  -7.9222
 BZH  N3    N  N     0  -0.520  -4.7543   0.6084  -6.4121
 BZH  C4    C  CR56  0   0.143  -3.8361   0.6681  -5.3877
 BZH  C5    C  CR16  0  -0.335  -3.5374   1.6870  -4.4918
 BZH  C6    C  CR16  0  -0.368  -2.5498   1.4673  -3.5462
 BZH  C7    C  CR6   0   0.347  -1.8484   0.2522  -3.4673
 BZH  N11   N  NH1   0  -0.746  -0.8910   0.1622  -2.4449
 BZH  C12   C  C     0   0.559   0.0029  -0.8190  -2.1780
 BZH  O19   O  O     0  -0.479   0.0946  -1.8512  -2.8220
 BZH  C13   C  CH2   0  -0.592   0.9144  -0.5120  -1.0073
 BZH  C14   C  CH2   0  -0.418   1.4237  -1.7648  -0.3089
 BZH  C15   C  CH2   0  -0.582   2.3347  -1.3962   0.8499
 BZH  C16   C  C     0   0.551   2.8650  -2.5865   1.5993
 BZH  O18   O  OH1   0  -0.597   3.6453  -2.2230   2.6130
 BZH  O17   O  O     0  -0.444   2.6272  -3.7388   1.3349
 BZH  H8    H  HCR6  0   0.283  -1.6108  -1.7261  -4.3309
 BZH  HN1   H  HNR5  0   0.416  -3.3772  -2.2676  -6.5173
 BZH  H101  H  HNH2  0   0.398  -4.9347  -1.8276  -8.4927
 BZH  H102  H  HNH2  0   0.396  -5.8835  -0.4395  -8.4550
 BZH  H5    H  HCR6  0   0.251  -4.0610   2.6337  -4.5244
 BZH  H6    H  HCR6  0   0.261  -2.3118   2.2577  -2.8436
 BZH  HN11  H  HNH1  0   0.413  -0.8585   0.9651  -1.8356
 BZH  H131  H  HCH2  0   0.279   1.7595   0.0697  -1.3926
 BZH  H132  H  HCH2  0   0.260   0.4045   0.1372  -0.2907
 BZH  H141  H  HCH2  0   0.240   0.5775  -2.3507   0.0559
 BZH  H142  H  HCH2  0   0.242   1.9606  -2.3929  -1.0202
 BZH  H151  H  HCH2  0   0.279   1.8128  -0.7517   1.5641
 BZH  H152  H  HCH2  0   0.280   3.1885  -0.8086   0.4969
 BZH  HO18  H  HOH1  0   0.479   3.9704  -3.0084   3.0775

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
 BZH  C8   C7    aromatic  1.395  0.020  1.395
 BZH  C8   C9    aromatic  1.385  0.020  1.385
 BZH  C8   H8    single    0.930  0.020  1.080
 BZH  C9   N1    aromatic  1.374  0.020  1.374
 BZH  C9   C4    aromatic  1.404  0.020  1.404
 BZH  N1   C2    aromatic  1.364  0.020  1.364
 BZH  N1   HN1   single    0.860  0.020  1.020
 BZH  C2   N10   single    1.356  0.020  1.356
 BZH  C2   N3    aromatic  1.309  0.020  1.309
 BZH  N10  H101  single    0.890  0.020  1.040
 BZH  N10  H102  single    0.890  0.020  1.040
 BZH  N3   C4    aromatic  1.377  0.020  1.377
 BZH  C4   C5    aromatic  1.389  0.020  1.389
 BZH  C5   C6    aromatic  1.385  0.020  1.385
 BZH  C5   H5    single    0.930  0.020  1.080
 BZH  C6   C7    aromatic  1.405  0.020  1.405
 BZH  C6   H6    single    0.930  0.020  1.080
 BZH  C7   N11   single    1.404  0.020  1.404
 BZH  N11  C12   single    1.354  0.020  1.354
 BZH  N11  HN11  single    0.860  0.020  1.020
 BZH  C12  C13   single    1.515  0.020  1.515
 BZH  C12  O19   double    1.220  0.020  1.220
 BZH  C13  C14   single    1.522  0.020  1.522
 BZH  C13  H131  single    0.970  0.020  1.090
 BZH  C13  H132  single    0.970  0.020  1.090
 BZH  C14  C15   single    1.519  0.020  1.519
 BZH  C14  H141  single    0.970  0.020  1.090
 BZH  C14  H142  single    0.970  0.020  1.090
 BZH  C15  C16   single    1.503  0.020  1.503
 BZH  C15  H151  single    0.970  0.020  1.090
 BZH  C15  H152  single    0.970  0.020  1.090
 BZH  C16  O17   double    1.206  0.020  1.206
 BZH  C16  O18   single    1.330  0.020  1.330
 BZH  O18  HO18  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
 BZH  H8    C8   C7    122.28  3.000
 BZH  H8    C8   C9    121.26  3.000
 BZH  C7    C8   C9    116.45  3.000
 BZH  C4    C9   N1    104.44  3.000
 BZH  C4    C9   C8    124.11  3.000
 BZH  N1    C9   C8    131.44  3.000
 BZH  HN1   N1   C2    126.22  3.000
 BZH  HN1   N1   C9    126.60  3.000
 BZH  C2    N1   C9    107.16  3.000
 BZH  N3    C2   N10   125.37  3.000
 BZH  N3    C2   N1    113.10  3.000
 BZH  N10   C2   N1    121.45  3.000
 BZH  H102  N10  H101  113.21  3.000
 BZH  H102  N10  C2    114.85  3.000
 BZH  H101  N10  C2    117.36  3.000
 BZH  C4    N3   C2    104.74  3.000
 BZH  C5    C4   N3    130.91  3.000
 BZH  C5    C4   C9    118.54  3.000
 BZH  N3    C4   C9    110.55  3.000
 BZH  H5    C5   C6    120.29  3.000
 BZH  H5    C5   C4    121.20  3.000
 BZH  C6    C5   C4    118.51  3.000
 BZH  H6    C6   C7    118.98  3.000
 BZH  H6    C6   C5    118.91  3.000
 BZH  C7    C6   C5    122.11  3.000
 BZH  N11   C7   C6    115.90  3.000
 BZH  N11   C7   C8    123.82  3.000
 BZH  C6    C7   C8    120.28  3.000
 BZH  HN11  N11  C12   115.89  3.000
 BZH  HN11  N11  C7    114.27  3.000
 BZH  C12   N11  C7    129.82  3.000
 BZH  C13   C12  O19   122.28  3.000
 BZH  O19   C12  N11   123.97  3.000
 BZH  C13   C12  N11   113.75  3.000
 BZH  H132  C13  H131  105.96  3.000
 BZH  H132  C13  C14   110.13  3.000
 BZH  H131  C13  C14   109.89  3.000
 BZH  H132  C13  C12   110.26  3.000
 BZH  H131  C13  C12   107.45  3.000
 BZH  C14   C13  C12   112.90  3.000
 BZH  H142  C14  H141  106.89  3.000
 BZH  H142  C14  C15   110.01  3.000
 BZH  H141  C14  C15   109.88  3.000
 BZH  H142  C14  C13   109.85  3.000
 BZH  H141  C14  C13   109.61  3.000
 BZH  C15   C14  C13   110.54  3.000
 BZH  H152  C15  H151  105.43  3.000
 BZH  H152  C15  C16   108.09  3.000
 BZH  H151  C15  C16   108.01  3.000
 BZH  H152  C15  C14   110.60  3.000
 BZH  H151  C15  C14   110.77  3.000
 BZH  C16   C15  C14   113.56  3.000
 BZH  O17   C16  O18   122.96  3.000
 BZH  O18   C16  C15   111.75  3.000
 BZH  O17   C16  C15   125.29  3.000
 BZH  HO18  O18  C16   109.92  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
 BZH  CONST_01  C5    C6   C7   C8     0.00   0.0  0
 BZH  CONST_02  C2    N1   C9   C8   180.00   0.0  0
 BZH  CONST_03  N3    C4   C9   C8   180.00   0.0  0
 BZH  CONST_04  C5    C4   C9   C8     0.00   0.0  0
 BZH  CONST_05  C6    C7   C8   C9     0.00   0.0  0
 BZH  CONST_06  N3    C2   N1   C9     0.00   0.0  0
 BZH  CONST_07  C2    N3   C4   C9     0.00   0.0  0
 BZH  CONST_08  C6    C5   C4   C9     0.00   0.0  0
 BZH  CONST_09  C7    C8   C9   N1   180.00   0.0  0
 BZH  CONST_10  N3    C4   C9   N1     0.00   0.0  0
 BZH  CONST_11  C5    C4   C9   N1   180.00   0.0  0
 BZH  CONST_12  C4    N3   C2   N1     0.00   0.0  0
 BZH  CONST_13  C4    C9   N1   C2     0.00   0.0  0
 BZH  CONST_14  C5    C4   N3   C2   180.00   0.0  0
 BZH  CONST_15  C6    C5   C4   N3   180.00   0.0  0
 BZH  CONST_16  C7    C8   C9   C4     0.00   0.0  0
 BZH  CONST_17  C7    C6   C5   C4     0.00   0.0  0
 BZH  CONST_18  N11   C7   C8   C9   180.00   0.0  0
 BZH  CONST_19  N10   C2   N1   C9   180.00   0.0  0
 BZH  CONST_20  C4    N3   C2   N10  180.00   0.0  0
 BZH  CONST_21  N11   C7   C6   C5   180.00   0.0  0
 BZH  CONST_22  H6    C6   C7   C8   180.00   0.0  0
 BZH  CONST_23  HN1   N1   C9   C8     0.00   0.0  0
 BZH  CONST_24  H5    C5   C4   C9   180.00   0.0  0
 BZH  CONST_25  H8    C8   C9   N1     0.00   0.0  0
 BZH  CONST_26  C12   N11  C7   C8     0.00   0.0  0
 BZH  CONST_27  C12   N11  C7   C6   180.00   0.0  0
 BZH  CONST_28  HN11  N11  C7   C8   180.00   0.0  0
 BZH  CONST_30  H102  N10  C2   N1   180.00   0.0  0
 BZH  CONST_31  C13   C12  N11  C7   180.00   0.0  0
 BZH  CONST_32  O19   C12  N11  C7     0.00   0.0  0
 BZH  CONST_33  HO18  O18  C16  C15  180.00   0.0  0
 BZH  Var_01    C14   C13  C12  N11  152.99  30.0  3
 BZH  Var_02    C15   C14  C13  C12  179.77  30.0  3
 BZH  Var_03    C16   C15  C14  C13  179.33  30.0  3
 BZH  Var_04    O17   C16  C15  C14    0.64  30.0  3

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
 BZH  plan-1  C8    0.020
 BZH  plan-1  C9    0.020
 BZH  plan-1  N1    0.020
 BZH  plan-1  C2    0.020
 BZH  plan-1  N10   0.020
 BZH  plan-1  N3    0.020
 BZH  plan-1  C4    0.020
 BZH  plan-1  C5    0.020
 BZH  plan-1  C6    0.020
 BZH  plan-1  C7    0.020
 BZH  plan-1  N11   0.020
 BZH  plan-1  H8    0.020
 BZH  plan-1  HN1   0.020
 BZH  plan-1  H5    0.020
 BZH  plan-1  H6    0.020
 BZH  plan-2  C7    0.020
 BZH  plan-2  N11   0.020
 BZH  plan-2  C12   0.020
 BZH  plan-2  O19   0.020
 BZH  plan-2  C13   0.020
 BZH  plan-2  HN11  0.020
 BZH  plan-3  C2    0.020
 BZH  plan-3  N10   0.020
 BZH  plan-3  H101  0.020
 BZH  plan-3  H102  0.020
 BZH  plan-4  C15   0.020
 BZH  plan-4  C16   0.020
 BZH  plan-4  O18   0.020
 BZH  plan-4  O17   0.020
 BZH  plan-4  HO18  0.020

