# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 15:14:58 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (1S)-4-carbamimidamido-1-carboxybutan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCC[C@H]([NH3+])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
 GND  GND  (1S)-4-carbamimidamido-1-carboxybutan-1-aminium  L-peptide  26  12  .  2012-08-28  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_GND
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
 GND  CA    C  CH1    0  -0.249  55.9711   0.2234  -2.6010
 GND  CB    C  CH2    0  -0.455  56.7187   1.1444  -3.5471
 GND  CG    C  CH2    0  -0.432  58.1846   1.3456  -3.1825
 GND  CD    C  CH2    0  -0.294  58.8654   2.3228  -4.1360
 GND  NE    N  NH1    0  -0.640  60.2800   2.5178  -3.8874
 GND  CZ    C  C      0   0.517  60.7805   3.1436  -2.7712
 GND  NH1   N  N      0  -0.711  61.9358   2.9339  -2.2535
 GND  NH2   N  NH2    0  -0.810  59.9373   4.0672  -2.1951
 GND  C     C  C      0   0.471  54.4470   0.0955  -2.8944
 GND  OXT   O  OC    -1  -0.559  53.8395   1.1488  -3.1007
 GND  O     O  O      0  -0.590  54.0030  -1.0721  -2.8578
 GND  N     N  NT3    1  -0.804  56.5192  -1.1646  -2.6265
 GND  HA    H  HCH1   0   0.296  56.0886   0.5791  -1.5741
 GND  HB1   H  HCH2   0   0.257  56.2034   2.1056  -3.5304
 GND  HB2   H  HCH2   0   0.241  56.6317   0.7647  -4.5712
 GND  HG1   H  HCH2   0   0.226  58.7286   0.3960  -3.2116
 GND  HG2   H  HCH2   0   0.232  58.2588   1.7210  -2.1580
 GND  HD1   H  HCH2   0   0.235  58.3430   3.2817  -4.1210
 GND  HD2   H  HCH2   0   0.249  58.7726   1.9577  -5.1605
 GND  HE    H  HNH1   0   0.381  60.8594   1.7639  -4.2224
 GND  HH11  H  H      0   0.311  62.3999   2.1553  -2.7078
 GND  HH21  H  HNH2   0   0.383  59.3601   4.6092  -2.8190
 GND  HH22  H  HNH2   0   0.379  60.3978   4.6460  -1.5108
 GND  HN1   H  HNT3   0   0.461  57.1538  -1.3791  -1.8605
 GND  HN2   H  HNT3   0   0.457  56.9992  -1.3875  -3.4981
 GND  HN3   H  HNT3   0   0.450  55.6699  -1.7615  -2.5739

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
 GND  CA   CB    single  1.521  0.033  1.521
 GND  CA   C     single  1.525  0.021  1.525
 GND  CA   N     single  1.458  0.019  1.458
 GND  CA   HA    single  0.970  0.020  0.970
 GND  CB   CG    single  1.524  0.020  1.524
 GND  CB   HB1   single  0.970  0.020  1.090
 GND  CB   HB2   single  0.970  0.020  1.090
 GND  CG   CD    single  1.526  0.020  1.526
 GND  CG   HG1   single  0.970  0.020  1.090
 GND  CG   HG2   single  0.970  0.020  1.090
 GND  CD   NE    single  1.449  0.020  1.449
 GND  CD   HD1   single  0.970  0.020  1.090
 GND  CD   HD2   single  0.970  0.020  1.090
 GND  NE   CZ    single  1.374  0.020  1.374
 GND  NE   HE    single  0.890  0.020  1.040
 GND  CZ   NH1   double  1.283  0.020  1.283
 GND  CZ   NH2   single  1.377  0.020  1.377
 GND  NH1  HH11  single  0.890  0.020  1.040
 GND  NH2  HH21  single  0.890  0.020  1.040
 GND  NH2  HH22  single  0.890  0.020  1.040
 GND  C    OXT   deloc   1.233  0.020  1.233
 GND  C    O     deloc   1.231  0.020  1.231
 GND  N    HN1   single  0.890  0.020  1.040
 GND  N    HN2   single  0.890  0.020  1.040
 GND  N    HN3   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
 GND  HA    CA   N     110.00  3.000
 GND  HA    CA   C     110.00  3.000
 GND  N     CA   C     111.00  2.800
 GND  HA    CA   CB    109.00  3.000
 GND  N     CA   CB    110.40  1.500
 GND  C     CA   CB    110.50  1.500
 GND  HB2   CB   HB1   106.39  3.000
 GND  HB2   CB   CG    110.23  3.000
 GND  HB1   CB   CG    109.54  3.000
 GND  HB2   CB   CA    109.47  3.000
 GND  HB1   CB   CA    107.02  3.000
 GND  CG    CB   CA    113.88  3.000
 GND  HG2   CG   HG1   106.80  3.000
 GND  HG2   CG   CD    109.59  3.000
 GND  HG1   CG   CD    108.50  3.000
 GND  HG2   CG   CB    109.56  3.000
 GND  HG1   CG   CB    110.92  3.000
 GND  CD    CG   CB    111.36  3.000
 GND  HD2   CD   HD1   105.42  3.000
 GND  HD2   CD   NE    106.79  3.000
 GND  HD1   CD   NE    110.26  3.000
 GND  HD2   CD   CG    109.54  3.000
 GND  HD1   CD   CG    109.90  3.000
 GND  NE    CD   CG    114.49  3.000
 GND  HE    NE   CZ    113.65  3.000
 GND  HE    NE   CD    113.78  3.000
 GND  CZ    NE   CD    123.79  3.000
 GND  NH2   CZ   NH1   119.48  3.000
 GND  NH2   CZ   NE    114.98  3.000
 GND  NH1   CZ   NE    125.54  3.000
 GND  HH11  NH1  CZ    110.91  3.000
 GND  HH22  NH2  HH21  111.92  3.000
 GND  HH22  NH2  CZ    112.93  3.000
 GND  HH21  NH2  CZ    116.89  3.000
 GND  O     C    OXT   128.88  3.000
 GND  O     C    CA    120.80  1.700
 GND  OXT   C    CA    120.80  1.700
 GND  HN3   N    HN2   107.60  3.000
 GND  HN3   N    HN1   110.51  3.000
 GND  HN2   N    HN1   107.69  3.000
 GND  HN3   N    CA    103.48  3.000
 GND  HN2   N    CA    113.00  3.000
 GND  HN1   N    CA    114.34  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
 GND  CONST_03  HH11  NH1  CZ  NE      0.00   0.0  0
 GND  CONST_05  HH22  NH2  CZ  NE    180.00   0.0  0
 GND  CONST_06  HE    NE   CZ  NH1     0.00   0.0  0
 GND  Var_01    CD    CG   CB  CA   -177.72  30.0  3
 GND  Var_02    NE    CD   CG  CB   -177.35  30.0  3
 GND  Var_03    CZ    NE   CD  CG    -67.95  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
 GND  chir_01  CA  CB  C  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
 GND  plan-1  CD    0.020
 GND  plan-1  NE    0.020
 GND  plan-1  CZ    0.020
 GND  plan-1  NH1   0.020
 GND  plan-1  NH2   0.020
 GND  plan-1  HE    0.020
 GND  plan-1  HH11  0.020
 GND  plan-1  HH21  0.020
 GND  plan-1  HH22  0.020
 GND  plan-2  CA    0.020
 GND  plan-2  C     0.020
 GND  plan-2  OXT   0.020
 GND  plan-2  O     0.020

