# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:22:26 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-(4-carbamimidamidophenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(NC(N)=N)cc1)C(O)=O
#
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
 7XC  7XC  '(2~{R})-2-azanyl-3-(4-carbamimidamidophenyl)propanoic acid'  D-peptide  29  16  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_7XC
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
 7XC  CD1  C  CR16   0  -0.311  -28.9041  -16.8774  -2.7398
 7XC  OXT  O  OC    -1  -0.608  -27.4386  -13.7936  -7.1541
 7XC  N3   N  N      0  -0.698  -33.8268  -18.8723  -3.0707
 7XC  CG   C  CR6    0   0.116  -29.0896  -16.6439  -4.1019
 7XC  CB   C  CH2    0  -0.523  -28.0353  -15.9846  -4.9394
 7XC  CA   C  CH1    0  -0.187  -28.1734  -14.4429  -4.9837
 7XC  C    C  C      0   0.399  -27.1010  -13.9041  -5.9593
 7XC  C10  C  C      0   0.560  -33.3551  -18.7791  -1.8848
 7XC  O    O  O      0  -0.607  -25.9720  -13.6855  -5.4746
 7XC  N    N  NH2    0  -0.795  -28.0442  -13.7968  -3.6902
 7XC  CD2  C  CR16   0  -0.298  -30.3282  -16.9864  -4.6354
 7XC  CE2  C  CR16   0  -0.305  -31.3455  -17.5396  -3.8697
 7XC  CZ   C  CR6    0   0.354  -31.1459  -17.7689  -2.5056
 7XC  CE1  C  CR16   0  -0.345  -29.9052  -17.4251  -1.9571
 7XC  N2   N  NH1    0  -0.750  -32.0912  -18.3001  -1.6353
 7XC  N4   N  NH2    0  -0.843  -33.9904  -19.1940  -0.7324
 7XC  HD1  H  HCR6   0   0.246  -27.9539  -16.6363  -2.2781
 7XC  H3   H  H      0   0.327  -34.7748  -19.2288  -3.0459
 7XC  HB1  H  HCH2   0   0.231  -28.0821  -16.3696  -5.9614
 7XC  HB2  H  HCH2   0   0.228  -27.0432  -16.2296  -4.5479
 7XC  HA   H  HCH1   0   0.202  -29.1663  -14.2131  -5.3849
 7XC  H    H  HNH2   0   0.335  -28.6457  -14.2455  -3.0095
 7XC  H2   H  HNH2   0   0.324  -27.0935  -13.9211  -3.3648
 7XC  HD2  H  HCR6   0   0.237  -30.5139  -16.8230  -5.6914
 7XC  HE2  H  HCR6   0   0.278  -32.2871  -17.7979  -4.3256
 7XC  HE1  H  HCR6   0   0.257  -29.7194  -17.5922  -0.9020
 7XC  H4   H  HNH1   0   0.402  -31.7813  -18.3535  -0.6780
 7XC  H6   H  HNH2   0   0.386  -33.7689  -18.7003   0.1191
 7XC  H5   H  HNH2   0   0.389  -34.9831  -19.3360  -0.8293

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
 7XC  O    C    deloc     1.231  0.020  1.231
 7XC  OXT  C    deloc     1.246  0.020  1.246
 7XC  C    CA   single    1.525  0.021  1.525
 7XC  CB   CA   single    1.530  0.020  1.530
 7XC  CB   CG   single    1.499  0.020  1.499
 7XC  CA   N    single    1.458  0.019  1.458
 7XC  CD2  CG   aromatic  1.391  0.020  1.391
 7XC  CD2  CE2  aromatic  1.388  0.020  1.388
 7XC  CG   CD1  aromatic  1.394  0.020  1.394
 7XC  CE2  CZ   aromatic  1.398  0.020  1.398
 7XC  CD1  CE1  aromatic  1.384  0.020  1.384
 7XC  N3   C10  double    1.280  0.020  1.280
 7XC  CZ   CE1  aromatic  1.399  0.020  1.399
 7XC  CZ   N2   single    1.390  0.020  1.390
 7XC  C10  N2   single    1.374  0.020  1.374
 7XC  C10  N4   single    1.380  0.020  1.380
 7XC  CD1  HD1  single    0.930  0.020  1.080
 7XC  N3   H3   single    0.890  0.020  1.040
 7XC  CB   HB1  single    0.970  0.020  1.090
 7XC  CB   HB2  single    0.970  0.020  1.090
 7XC  CA   HA   single    0.970  0.020  0.970
 7XC  N    H    single    0.860  0.020  0.860
 7XC  N    H2   single    0.890  0.020  1.040
 7XC  CD2  HD2  single    0.930  0.020  1.080
 7XC  CE2  HE2  single    0.930  0.020  1.080
 7XC  CE1  HE1  single    0.930  0.020  1.080
 7XC  N2   H4   single    0.860  0.020  1.020
 7XC  N4   H6   single    0.890  0.020  1.040
 7XC  N4   H5   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
 7XC  HD1  CD1  CE1  118.78  3.000
 7XC  HD1  CD1  CG   119.71  3.000
 7XC  CE1  CD1  CG   121.51  3.000
 7XC  H3   N3   C10  110.36  3.000
 7XC  CD2  CG   CB   121.33  3.000
 7XC  CD2  CG   CD1  116.86  3.000
 7XC  CB   CG   CD1  121.72  3.000
 7XC  HB2  CB   HB1  107.13  3.000
 7XC  HB2  CB   CA   108.30  3.000
 7XC  HB1  CB   CA   108.67  3.000
 7XC  HB2  CB   CG   109.83  3.000
 7XC  HB1  CB   CG   109.71  3.000
 7XC  CA   CB   CG   113.02  3.000
 7XC  HA   CA   N    110.00  3.000
 7XC  HA   CA   C    109.00  3.000
 7XC  N    CA   C    111.00  2.800
 7XC  HA   CA   CB   109.00  3.000
 7XC  N    CA   CB   110.50  1.700
 7XC  C    CA   CB   110.10  1.900
 7XC  O    C    CA   120.80  1.700
 7XC  CA   C    OXT  116.60  3.000
 7XC  O    C    OXT  127.00  3.000
 7XC  N4   C10  N2   112.12  3.000
 7XC  N4   C10  N3   125.62  3.000
 7XC  N2   C10  N3   122.18  3.000
 7XC  H2   N    H    106.69  3.000
 7XC  H2   N    CA   108.38  3.000
 7XC  H    N    CA   114.00  3.000
 7XC  HD2  CD2  CE2  118.13  3.000
 7XC  HD2  CD2  CG   119.26  3.000
 7XC  CE2  CD2  CG   122.61  3.000
 7XC  HE2  CE2  CZ   119.90  3.000
 7XC  HE2  CE2  CD2  120.16  3.000
 7XC  CZ   CE2  CD2  119.93  3.000
 7XC  N2   CZ   CE1  116.83  3.000
 7XC  N2   CZ   CE2  125.20  3.000
 7XC  CE1  CZ   CE2  117.96  3.000
 7XC  HE1  CE1  CZ   119.70  3.000
 7XC  HE1  CE1  CD1  119.17  3.000
 7XC  CZ   CE1  CD1  121.13  3.000
 7XC  H4   N2   CZ   113.94  3.000
 7XC  H4   N2   C10  115.90  3.000
 7XC  CZ   N2   C10  130.15  3.000
 7XC  H5   N4   H6   111.50  3.000
 7XC  H5   N4   C10  114.57  3.000
 7XC  H6   N4   C10  117.18  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
 7XC  CONST_01  CE2  CD2  CG   CD1    0.00   0.0  0
 7XC  CONST_02  CE2  CZ   CE1  CD1    0.00   0.0  0
 7XC  CONST_03  CZ   CE2  CD2  CG     0.00   0.0  0
 7XC  CONST_04  CZ   CE1  CD1  CG     0.00   0.0  0
 7XC  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 7XC  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 7XC  CONST_07  N2   CZ   CE1  CD1  180.00   0.0  0
 7XC  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 7XC  CONST_09  CE1  CD1  CG   CB   180.00   0.0  0
 7XC  CONST_10  N2   CZ   CE2  CD2  180.00   0.0  0
 7XC  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 7XC  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 7XC  CONST_13  HE1  CE1  CD1  CG   180.00   0.0  0
 7XC  CONST_14  HD1  CD1  CG   CD2  180.00   0.0  0
 7XC  CONST_15  CE2  CZ   N2   C10    0.00   0.0  0
 7XC  CONST_16  CE1  CZ   N2   C10  180.00   0.0  0
 7XC  CONST_17  H4   N2   CZ   CE2  180.00   0.0  0
 7XC  CONST_18  CZ   N2   C10  N3     0.00   0.0  0
 7XC  CONST_19  N4   C10  N2   CZ   180.00   0.0  0
 7XC  CONST_22  H3   N3   C10  N2   180.00   0.0  0
 7XC  Var_01    CA   CB   CG   CD1  -90.06  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
 7XC  chir_01  CA  C  CB  N  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
 7XC  plan-1  CD1  0.020
 7XC  plan-1  CG   0.020
 7XC  plan-1  CB   0.020
 7XC  plan-1  CD2  0.020
 7XC  plan-1  CE2  0.020
 7XC  plan-1  CZ   0.020
 7XC  plan-1  CE1  0.020
 7XC  plan-1  N2   0.020
 7XC  plan-1  HD1  0.020
 7XC  plan-1  HD2  0.020
 7XC  plan-1  HE2  0.020
 7XC  plan-1  HE1  0.020
 7XC  plan-2  N3   0.020
 7XC  plan-2  C10  0.020
 7XC  plan-2  CZ   0.020
 7XC  plan-2  N2   0.020
 7XC  plan-2  N4   0.020
 7XC  plan-2  H3   0.020
 7XC  plan-2  H4   0.020
 7XC  plan-2  H6   0.020
 7XC  plan-2  H5   0.020
 7XC  plan-3  OXT  0.020
 7XC  plan-3  CA   0.020
 7XC  plan-3  C    0.020
 7XC  plan-3  O    0.020

