# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:01:47 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-amino-1-{[amino(iminio)methyl]amino}-6-[4-(carboxymethyl)pyridinium-1-yl]-1,2,3,4,6-pentadeoxy-D-erythro-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])[C@H](O)C[n+]1ccc(CC(O)=O)cc1
#
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
 AR0  AR0  4-amino-1-{[amino(iminio)methyl]amino}-6-[4-(carboxymethyl)pyridinium-1-yl]-1,2,3,4,6-pentadeoxy-D-erythro-hexitol  peptide  47  22  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AR0
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
 AR0  N    N  NH2   0  -0.793  -1.6839   2.2843  -0.3427
 AR0  C1   C  CH1   0  -0.148  -1.6450   0.9802   0.2980
 AR0  C2   C  CH1   0   0.055  -0.2617   0.3531   0.0729
 AR0  O1   O  OH1   0  -0.649  -0.1026  -0.8671   0.7493
 AR0  C3   C  CH2   0  -0.425  -2.7501   0.0199  -0.1539
 AR0  C4   C  CH2   0  -0.480  -4.1443   0.5031   0.2194
 AR0  C5   C  CH2   0  -0.271  -5.2067  -0.4724  -0.2570
 AR0  N2   N  NH1   0  -0.636  -6.5279  -0.0001   0.1224
 AR0  C6   C  C     0   0.826  -7.6595  -0.6228  -0.1752
 AR0  N3   N  NH2   0  -0.816  -7.6375  -1.7694  -0.8417
 AR0  N4   N  NC2   1  -0.822  -8.8224  -0.0873   0.1752
 AR0  C7   C  CH2   0  -0.373   0.8447   1.3386   0.4635
 AR0  N5   N  NR6   1  -0.402   2.1588   0.7069   0.2908
 AR0  C8   C  CR16  0   0.087   2.7509   0.7489  -0.9125
 AR0  C9   C  CR16  0  -0.373   3.9394   0.1025  -1.1353
 AR0  C10  C  CR6   0   0.275   4.5420  -0.6143  -0.1044
 AR0  C11  C  CR16  0  -0.391   3.9048  -0.6385   1.1288
 AR0  C12  C  CR16  0   0.103   2.7117   0.0245   1.2994
 AR0  C13  C  CH2   0  -0.684   5.8360  -1.3275  -0.3201
 AR0  C    C  C     0   0.566   6.9996  -0.3637  -0.3752
 AR0  O    O  O     0  -0.426   6.8979   0.8339  -0.3239
 AR0  OXT  O  OH1   0  -0.584   8.1465  -1.0114  -0.4939
 AR0  H    H  HNH2  0   0.346  -1.8300   2.1765  -1.3400
 AR0  H1   H  HCH1  0   0.242  -1.7516   1.1515   1.3777
 AR0  H3   H  HCH2  0   0.228  -2.6786  -0.1061  -1.2405
 AR0  H4   H  HCH2  0   0.235  -2.5878  -0.9683   0.2828
 AR0  H5   H  HCH2  0   0.246  -4.2161   0.6145   1.3056
 AR0  H6   H  HCH2  0   0.240  -4.3416   1.4847  -0.2197
 AR0  H7   H  HCH2  0   0.258  -5.1487  -0.5756  -1.3445
 AR0  H8   H  HCH2  0   0.256  -5.0234  -1.4586   0.1802
 AR0  H9   H  HNH1  0   0.427  -6.5902   0.8571   0.6495
 AR0  H10  H  HNH2  0   0.446  -6.7772  -2.2522  -1.0364
 AR0  H11  H  HNH2  0   0.433  -8.4894  -2.2676  -1.0369
 AR0  H12  H  HNC2  0   0.431  -9.6882  -0.5752   0.0223
 AR0  H13  H  HNC2  0   0.433  -8.8677   0.7851   0.6736
 AR0  H14  H  HCH2  0   0.310   0.8124   2.2280  -0.1586
 AR0  H15  H  HCH2  0   0.297   0.7536   1.6493   1.5044
 AR0  H16  H  HCR6  0   0.349   2.2470   1.3156  -1.6812
 AR0  H17  H  HCR6  0   0.313   4.3820   0.1564  -2.1196
 AR0  H18  H  HCR6  0   0.313   4.3259  -1.1738   1.9677
 AR0  H19  H  HCR6  0   0.343   2.1919   0.0366   2.2447
 AR0  H20  H  HCH2  0   0.325   6.0131  -2.0588   0.4707
 AR0  H21  H  HCH2  0   0.332   5.8082  -1.8872  -1.2596
 AR0  HXT  H  HOH1  0   0.488   8.8843  -0.3840  -0.5360
 AR0  H2   H  HNH2  0   0.362  -2.4673   2.8229   0.0015
 AR0  H24  H  HCH1  0   0.252  -0.1489   0.1221  -0.9933
 AR0  H25  H  HOH1  0   0.453  -0.4040  -0.7664   1.6599

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
 AR0  N    C1   single    1.454  0.020  1.454
 AR0  N    H    single    0.860  0.020  0.860
 AR0  N    H2   single    0.890  0.020  1.040
 AR0  C1   C2   single    1.535  0.020  1.535
 AR0  C1   C3   single    1.532  0.020  1.532
 AR0  C1   H1   single    0.970  0.020  1.090
 AR0  C2   O1   single    1.404  0.020  1.404
 AR0  C2   C7   single    1.532  0.020  1.532
 AR0  C3   C4   single    1.522  0.020  1.522
 AR0  C3   H3   single    0.970  0.020  1.090
 AR0  C3   H4   single    0.970  0.020  1.090
 AR0  C4   C5   single    1.519  0.020  1.519
 AR0  C4   H5   single    0.970  0.020  1.090
 AR0  C4   H6   single    0.970  0.020  1.090
 AR0  C5   N2   single    1.453  0.020  1.453
 AR0  C5   H7   single    0.970  0.020  1.090
 AR0  C5   H8   single    0.970  0.020  1.090
 AR0  N2   C6   single    1.325  0.020  1.325
 AR0  N2   H9   single    0.860  0.020  1.020
 AR0  C6   N3   single    1.326  0.020  1.326
 AR0  C6   N4   double    1.327  0.020  1.327
 AR0  N3   H10  single    0.860  0.020  1.020
 AR0  N3   H11  single    0.860  0.020  1.020
 AR0  N4   H12  single    0.860  0.020  1.020
 AR0  N4   H13  single    0.860  0.020  1.020
 AR0  C7   N5   single    1.468  0.020  1.468
 AR0  C7   H14  single    0.970  0.020  1.090
 AR0  C7   H15  single    0.970  0.020  1.090
 AR0  N5   C8   aromatic  1.342  0.020  1.342
 AR0  N5   C12  aromatic  1.337  0.020  1.337
 AR0  C8   C9   aromatic  1.371  0.020  1.371
 AR0  C8   H16  single    0.930  0.020  1.080
 AR0  C9   C10  aromatic  1.393  0.020  1.393
 AR0  C9   H17  single    0.930  0.020  1.080
 AR0  C10  C11  aromatic  1.388  0.020  1.388
 AR0  C10  C13  single    1.493  0.020  1.493
 AR0  C11  C12  aromatic  1.376  0.020  1.376
 AR0  C11  H18  single    0.930  0.020  1.080
 AR0  C12  H19  single    0.930  0.020  1.080
 AR0  C13  C    single    1.512  0.020  1.512
 AR0  C13  H20  single    0.970  0.020  1.090
 AR0  C13  H21  single    0.970  0.020  1.090
 AR0  C    O    double    1.231  0.020  1.231
 AR0  C    OXT  single    1.323  0.020  1.323
 AR0  OXT  HXT  single    0.850  0.020  0.980
 AR0  C2   H24  single    0.970  0.020  1.090
 AR0  O1   H25  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
 AR0  H2   N    H    106.25  3.000
 AR0  H2   N    C1   110.40  3.000
 AR0  H    N    C1   110.01  3.000
 AR0  H1   C1   C3   108.53  3.000
 AR0  H1   C1   C2   107.17  3.000
 AR0  C3   C1   C2   110.52  3.000
 AR0  H1   C1   N    106.90  3.000
 AR0  C3   C1   N    114.40  3.000
 AR0  C2   C1   N    109.02  3.000
 AR0  H24  C2   C7   108.00  3.000
 AR0  H24  C2   O1   105.88  3.000
 AR0  C7   C2   O1   110.75  3.000
 AR0  H24  C2   C1   108.74  3.000
 AR0  C7   C2   C1   110.52  3.000
 AR0  O1   C2   C1   112.73  3.000
 AR0  H25  O1   C2   109.19  3.000
 AR0  H4   C3   H3   106.41  3.000
 AR0  H4   C3   C4   108.97  3.000
 AR0  H3   C3   C4   109.83  3.000
 AR0  H4   C3   C1   109.99  3.000
 AR0  H3   C3   C1   108.51  3.000
 AR0  C4   C3   C1   112.91  3.000
 AR0  H6   C4   H5   107.19  3.000
 AR0  H6   C4   C5   108.93  3.000
 AR0  H5   C4   C5   109.31  3.000
 AR0  H6   C4   C3   110.60  3.000
 AR0  H5   C4   C3   109.63  3.000
 AR0  C5   C4   C3   111.09  3.000
 AR0  H8   C5   H7   107.66  3.000
 AR0  H8   C5   N2   109.93  3.000
 AR0  H7   C5   N2   109.78  3.000
 AR0  H8   C5   C4   109.65  3.000
 AR0  H7   C5   C4   109.59  3.000
 AR0  N2   C5   C4   110.19  3.000
 AR0  H9   N2   C6   117.65  3.000
 AR0  H9   N2   C5   117.97  3.000
 AR0  C6   N2   C5   124.39  3.000
 AR0  N4   C6   N3   119.73  3.000
 AR0  N4   C6   N2   119.95  3.000
 AR0  N3   C6   N2   120.32  3.000
 AR0  H11  N3   H10  116.69  3.000
 AR0  H11  N3   C6   120.77  3.000
 AR0  H10  N3   C6   121.77  3.000
 AR0  H13  N4   H12  117.23  3.000
 AR0  H13  N4   C6   121.34  3.000
 AR0  H12  N4   C6   121.23  3.000
 AR0  H15  C7   H14  108.13  3.000
 AR0  H15  C7   N5   108.05  3.000
 AR0  H14  C7   N5   108.16  3.000
 AR0  H15  C7   C2   111.49  3.000
 AR0  H14  C7   C2   111.05  3.000
 AR0  N5   C7   C2   109.84  3.000
 AR0  C12  N5   C8   120.66  3.000
 AR0  C12  N5   C7   120.05  3.000
 AR0  C8   N5   C7   119.15  3.000
 AR0  H16  C8   C9   122.43  3.000
 AR0  H16  C8   N5   116.67  3.000
 AR0  C9   C8   N5   120.90  3.000
 AR0  H17  C9   C10  121.51  3.000
 AR0  H17  C9   C8   118.66  3.000
 AR0  C10  C9   C8   119.83  3.000
 AR0  C13  C10  C11  121.18  3.000
 AR0  C13  C10  C9   120.92  3.000
 AR0  C11  C10  C9   117.90  3.000
 AR0  H18  C11  C12  118.72  3.000
 AR0  H18  C11  C10  121.29  3.000
 AR0  C12  C11  C10  119.99  3.000
 AR0  H19  C12  C11  122.14  3.000
 AR0  H19  C12  N5   117.12  3.000
 AR0  C11  C12  N5   120.73  3.000
 AR0  H21  C13  H20  106.47  3.000
 AR0  H21  C13  C    108.33  3.000
 AR0  H20  C13  C    109.18  3.000
 AR0  H21  C13  C10  110.27  3.000
 AR0  H20  C13  C10  110.85  3.000
 AR0  C    C13  C10  111.57  3.000
 AR0  OXT  C    O    124.38  3.000
 AR0  OXT  C    C13  111.01  3.000
 AR0  O    C    C13  124.61  3.000
 AR0  HXT  OXT  C    110.30  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
 AR0  CONST_01  C10  C9   C8   N5     0.00   0.0  0
 AR0  CONST_02  C10  C11  C12  N5     0.00   0.0  0
 AR0  CONST_03  C11  C12  N5   C8     0.00   0.0  0
 AR0  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 AR0  CONST_05  C12  N5   C8   C9     0.00   0.0  0
 AR0  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 AR0  CONST_07  C9   C8   N5   C7   180.00   0.0  0
 AR0  CONST_08  C11  C12  N5   C7   180.00   0.0  0
 AR0  CONST_09  C13  C10  C9   C8   180.00   0.0  0
 AR0  CONST_10  C13  C10  C11  C12  180.00   0.0  0
 AR0  CONST_11  H17  C9   C8   N5   180.00   0.0  0
 AR0  CONST_12  H18  C11  C12  N5   180.00   0.0  0
 AR0  CONST_13  H19  C12  N5   C8   180.00   0.0  0
 AR0  CONST_14  H16  C8   C9   C10  180.00   0.0  0
 AR0  CONST_15  N3   C6   N2   C5     0.00   0.0  0
 AR0  CONST_16  N4   C6   N2   C5   180.00   0.0  0
 AR0  CONST_17  H10  N3   C6   N2     0.00   0.0  0
 AR0  CONST_18  H11  N3   C6   N2   180.00   0.0  0
 AR0  CONST_19  H12  N4   C6   N2   180.00   0.0  0
 AR0  CONST_20  H13  N4   C6   N2     0.00   0.0  0
 AR0  CONST_21  H9   N2   C6   N3   180.00   0.0  0
 AR0  CONST_22  HXT  OXT  C    C13  180.00   0.0  0
 AR0  Var_01    C8   N5   C7   C2    86.15  30.0  2
 AR0  Var_02    C    C13  C10  C9    74.66  30.0  2
 AR0  Var_03    O    C    C13  C10   -3.69  30.0  3
 AR0  Var_04    C5   C4   C3   C1   179.55  30.0  3
 AR0  Var_05    N2   C5   C4   C3   179.36  30.0  3
 AR0  Var_06    C6   N2   C5   C4   178.63  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
 AR0  chir_01  C1  N   C2  C3  positiv
 AR0  chir_02  C2  O1  C1  C7  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
 AR0  plan-1  C7   0.020
 AR0  plan-1  N5   0.020
 AR0  plan-1  C8   0.020
 AR0  plan-1  C9   0.020
 AR0  plan-1  C10  0.020
 AR0  plan-1  C11  0.020
 AR0  plan-1  C12  0.020
 AR0  plan-1  C13  0.020
 AR0  plan-1  H16  0.020
 AR0  plan-1  H17  0.020
 AR0  plan-1  H18  0.020
 AR0  plan-1  H19  0.020
 AR0  plan-2  C5   0.020
 AR0  plan-2  N2   0.020
 AR0  plan-2  C6   0.020
 AR0  plan-2  N3   0.020
 AR0  plan-2  N4   0.020
 AR0  plan-2  H9   0.020
 AR0  plan-2  H10  0.020
 AR0  plan-2  H11  0.020
 AR0  plan-2  H12  0.020
 AR0  plan-2  H13  0.020
 AR0  plan-3  C13  0.020
 AR0  plan-3  C    0.020
 AR0  plan-3  O    0.020
 AR0  plan-3  OXT  0.020
 AR0  plan-3  HXT  0.020

