# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:28:05 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2S)-1-[(6-aminopyridin-2-yl)amino]-1-oxopropan-2-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]([NH3+])C(=O)Nc1cccc(N)n1
#
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
 4XF  4XF  (2S)-1-[(6-aminopyridin-2-yl)amino]-1-oxopropan-2-aminium  ligand  26  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4XF
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
 4XF  C1   C  CH3   0  -0.658  -3.4316   0.8143   1.2671
 4XF  C2   C  CH1   0  -0.274  -3.0112   0.3391  -0.1141
 4XF  N4   N  NT3   1  -0.771  -3.9284  -0.7273  -0.5846
 4XF  C8   C  C     0   0.563  -1.6015  -0.2536  -0.0744
 4XF  O9   O  O     0  -0.428  -1.4441  -1.4346   0.1449
 4XF  C11  C  CR6   0   0.522   0.7515   0.5477  -0.1719
 4XF  C12  C  CR16  0  -0.443   1.5179   1.6453  -0.5482
 4XF  C13  C  CR16  0  -0.141   2.8968   1.5053  -0.4618
 4XF  C14  C  CR16  0  -0.401   3.4508   0.3233  -0.0199
 4XF  C15  C  CR6   0   0.457   2.5784  -0.7174   0.3394
 4XF  N10  N  NH1   0  -0.723  -0.6399   0.6791  -0.2526
 4XF  N16  N  NH2   0  -0.834   3.0521  -1.8927   0.8294
 4XF  N17  N  N     0  -0.470   1.2534  -0.5934   0.2594
 4XF  H19  H  HCH3  0   0.275  -4.4485   1.2043   1.2444
 4XF  H18  H  HCH3  0   0.260  -3.3780   0.0082   1.9981
 4XF  H20  H  HCH3  0   0.276  -2.7761   1.6183   1.5951
 4XF  H3   H  HCH1  0   0.336  -3.0891   1.1507  -0.8370
 4XF  H7   H  HNT3  0   0.482  -4.9034  -0.4365  -0.5084
 4XF  H5   H  HNT3  0   0.482  -3.7699  -0.9684  -1.5636
 4XF  H22  H  HCR6  0   0.273   1.0628   2.5617  -0.8982
 4XF  H23  H  HCR6  0   0.271   3.5382   2.3285  -0.7484
 4XF  H24  H  HCR6  0   0.268   4.5224   0.1939   0.0497
 4XF  H21  H  HNH1  0   0.430  -0.9551   1.6018  -0.5146
 4XF  H25  H  HNH2  0   0.394   4.0164  -2.1257   0.6635
 4XF  H26  H  HNH2  0   0.386   2.4202  -2.6759   0.8366
 4XF  H2   H  HNT3  0   0.467  -3.8196  -1.5862  -0.0410

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
 4XF  C14  C13  aromatic  1.378  0.020  1.378
 4XF  C14  C15  aromatic  1.405  0.020  1.405
 4XF  N16  C15  single    1.359  0.020  1.359
 4XF  C13  C12  aromatic  1.389  0.020  1.389
 4XF  C15  N17  aromatic  1.333  0.020  1.333
 4XF  C12  C11  aromatic  1.391  0.020  1.391
 4XF  N17  C11  aromatic  1.319  0.020  1.319
 4XF  C11  N10  single    1.400  0.020  1.400
 4XF  N10  C8   single    1.351  0.020  1.351
 4XF  O9   C8   double    1.211  0.020  1.211
 4XF  C8   C2   single    1.530  0.020  1.530
 4XF  C2   C1   single    1.520  0.020  1.520
 4XF  C2   N4   single    1.483  0.020  1.483
 4XF  C1   H19  single    0.970  0.020  1.090
 4XF  C1   H18  single    0.970  0.020  1.090
 4XF  C1   H20  single    0.970  0.020  1.090
 4XF  C2   H3   single    0.970  0.020  1.090
 4XF  N4   H7   single    0.890  0.020  1.040
 4XF  N4   H5   single    0.890  0.020  1.040
 4XF  C12  H22  single    0.930  0.020  1.080
 4XF  C13  H23  single    0.930  0.020  1.080
 4XF  C14  H24  single    0.930  0.020  1.080
 4XF  N10  H21  single    0.860  0.020  1.020
 4XF  N16  H25  single    0.890  0.020  1.040
 4XF  N16  H26  single    0.890  0.020  1.040
 4XF  N4   H2   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
 4XF  H20  C1   H18  108.35  3.000
 4XF  H20  C1   H19  107.71  3.000
 4XF  H18  C1   H19  108.95  3.000
 4XF  H20  C1   C2   109.77  3.000
 4XF  H18  C1   C2   111.39  3.000
 4XF  H19  C1   C2   110.56  3.000
 4XF  H3   C2   C8   111.82  3.000
 4XF  H3   C2   N4   106.31  3.000
 4XF  C8   C2   N4   107.43  3.000
 4XF  H3   C2   C1   110.50  3.000
 4XF  N4   C2   C1   110.00  3.000
 4XF  C8   C2   C1   110.64  3.000
 4XF  H2   N4   H5   107.16  3.000
 4XF  H2   N4   H7   107.55  3.000
 4XF  H5   N4   H7   106.70  3.000
 4XF  H2   N4   C2   111.69  3.000
 4XF  H5   N4   C2   112.22  3.000
 4XF  H7   N4   C2   111.24  3.000
 4XF  N10  C8   O9   127.17  3.000
 4XF  O9   C8   C2   120.14  3.000
 4XF  N10  C8   C2   112.64  3.000
 4XF  N17  C11  N10  118.57  3.000
 4XF  N10  C11  C12  117.26  3.000
 4XF  N17  C11  C12  124.17  3.000
 4XF  H22  C12  C13  121.56  3.000
 4XF  H22  C12  C11  121.64  3.000
 4XF  C13  C12  C11  116.80  3.000
 4XF  H23  C13  C14  119.93  3.000
 4XF  H23  C13  C12  119.70  3.000
 4XF  C14  C13  C12  120.37  3.000
 4XF  H24  C14  C15  120.67  3.000
 4XF  H24  C14  C13  121.44  3.000
 4XF  C15  C14  C13  117.89  3.000
 4XF  N17  C15  N16  116.65  3.000
 4XF  N17  C15  C14  122.21  3.000
 4XF  N16  C15  C14  121.11  3.000
 4XF  H21  N10  C11  114.27  3.000
 4XF  H21  N10  C8   116.28  3.000
 4XF  C11  N10  C8   129.41  3.000
 4XF  H26  N16  H25  115.02  3.000
 4XF  H26  N16  C15  117.19  3.000
 4XF  H25  N16  C15  118.37  3.000
 4XF  C15  N17  C11  118.57  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
 4XF  CONST_01  C14  C13  C12  C11    0.00  0.0  0
 4XF  CONST_02  C14  C15  N17  C11    0.00  0.0  0
 4XF  CONST_03  C15  C14  C13  C12    0.00  0.0  0
 4XF  CONST_04  C15  N17  C11  C12    0.00  0.0  0
 4XF  CONST_05  N17  C15  C14  C13    0.00  0.0  0
 4XF  CONST_06  N17  C11  C12  C13    0.00  0.0  0
 4XF  CONST_07  N16  C15  N17  C11  180.00  0.0  0
 4XF  CONST_08  N16  C15  C14  C13  180.00  0.0  0
 4XF  CONST_09  N10  C11  C12  C13  180.00  0.0  0
 4XF  CONST_10  N10  C11  N17  C15  180.00  0.0  0
 4XF  CONST_11  H23  C13  C12  C11  180.00  0.0  0
 4XF  CONST_12  H24  C14  C13  C12  180.00  0.0  0
 4XF  CONST_13  H22  C12  C13  C14  180.00  0.0  0
 4XF  CONST_14  C12  C11  N10  C8   180.00  0.0  0
 4XF  CONST_15  N17  C11  N10  C8     0.00  0.0  0
 4XF  CONST_16  H21  N10  C11  C12    0.00  0.0  0
 4XF  CONST_19  C11  N10  C8   C2   180.00  0.0  0
 4XF  CONST_20  C11  N10  C8   O9     0.00  0.0  0

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
 4XF  chir_01  C2  C8  C1  N4  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
 4XF  plan-1  C11  0.020
 4XF  plan-1  C12  0.020
 4XF  plan-1  C13  0.020
 4XF  plan-1  C14  0.020
 4XF  plan-1  C15  0.020
 4XF  plan-1  N10  0.020
 4XF  plan-1  N16  0.020
 4XF  plan-1  N17  0.020
 4XF  plan-1  H22  0.020
 4XF  plan-1  H23  0.020
 4XF  plan-1  H24  0.020
 4XF  plan-2  C2   0.020
 4XF  plan-2  C8   0.020
 4XF  plan-2  O9   0.020
 4XF  plan-2  C11  0.020
 4XF  plan-2  N10  0.020
 4XF  plan-2  H21  0.020
 4XF  plan-3  C15  0.020
 4XF  plan-3  N16  0.020
 4XF  plan-3  H25  0.020
 4XF  plan-3  H26  0.020

