# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:10:58 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 4-carbamimidamidobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NCCCC(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
 ALG  ALG  '4-carbamimidamidobutanoic acid'  peptide  21  10  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_ALG
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
 ALG  C     C  C     0   0.553  -3.1085  -0.1121  -0.1259
 ALG  O     O  O     0  -0.445  -3.2379  -1.3012  -0.2780
 ALG  CA    C  CH2   0  -0.583  -1.7960   0.6071   0.0161
 ALG  CB    C  CH2   0  -0.457  -0.5891  -0.3136  -0.0412
 ALG  CD    C  CH2   0  -0.229   0.7022   0.4771   0.1036
 ALG  NE    N  NH1   0  -0.647   1.8410  -0.4091   0.0420
 ALG  CZ    C  C     0   0.547   3.1121   0.0966  -0.0379
 ALG  NH1   N  N     0  -0.715   3.3082   1.3449  -0.2536
 ALG  NH2   N  NH2   0  -0.840   4.0912  -0.8548   0.1622
 ALG  OXT   O  OH1   0  -0.597  -4.1388   0.7266  -0.0638
 ALG  HA1   H  HCH2  0   0.280  -1.7384   1.3671  -0.7695
 ALG  HA2   H  HCH2  0   0.279  -1.8133   1.1633   0.9592
 ALG  HB1   H  HCH2  0   0.235  -0.6573  -1.0593   0.7557
 ALG  HB2   H  HCH2  0   0.239  -0.5743  -0.8598  -0.9870
 ALG  HD1   H  HCH2  0   0.231   0.7854   1.2049  -0.7046
 ALG  HD2   H  HCH2  0   0.210   0.6851   1.0526   1.0388
 ALG  HNE   H  HNH1  0   0.378   1.7480  -1.2536   0.5863
 ALG  HH1   H  H     0   0.315   4.2970   1.5357  -0.3670
 ALG  HH21  H  HNH2  0   0.382   3.8642  -1.7961  -0.1193
 ALG  HH22  H  HNH2  0   0.384   5.0159  -0.5892  -0.1361
 ALG  HXT   H  HOH1  0   0.479  -4.9696   0.2359  -0.1513

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
 ALG  C    O     double  1.231  0.020  1.231
 ALG  C    CA    single  1.525  0.021  1.525
 ALG  C    OXT   single  1.330  0.020  1.330
 ALG  CA   CB    single  1.521  0.033  1.521
 ALG  CA   HA1   single  0.970  0.020  1.090
 ALG  CA   HA2   single  0.970  0.020  1.090
 ALG  CB   CD    single  1.521  0.020  1.521
 ALG  CB   HB1   single  0.970  0.020  1.090
 ALG  CB   HB2   single  0.970  0.020  1.090
 ALG  CD   NE    single  1.444  0.020  1.444
 ALG  CD   HD1   single  0.970  0.020  1.090
 ALG  CD   HD2   single  0.970  0.020  1.090
 ALG  NE   CZ    single  1.370  0.020  1.370
 ALG  NE   HNE   single  0.890  0.020  1.040
 ALG  CZ   NH1   double  1.282  0.020  1.282
 ALG  CZ   NH2   single  1.380  0.020  1.380
 ALG  NH1  HH1   single  0.890  0.020  1.040
 ALG  NH2  HH21  single  0.890  0.020  1.040
 ALG  NH2  HH22  single  0.890  0.020  1.040
 ALG  OXT  HXT   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
 ALG  OXT   C    CA    120.80  1.700
 ALG  OXT   C    O     123.00  3.000
 ALG  CA    C    O     120.80  1.700
 ALG  HA2   CA   HA1   105.44  3.000
 ALG  HA2   CA   CB    110.67  3.000
 ALG  HA1   CA   CB    110.61  3.000
 ALG  HA2   CA   C     108.09  3.000
 ALG  HA1   CA   C     108.08  3.000
 ALG  CB    CA   C     110.50  1.500
 ALG  HB2   CB   HB1   106.91  3.000
 ALG  HB2   CB   CD    109.32  3.000
 ALG  HB1   CB   CD    109.76  3.000
 ALG  HB2   CB   CA    110.27  3.000
 ALG  HB1   CB   CA    109.65  3.000
 ALG  CD    CB   CA    110.84  3.000
 ALG  HD2   CD   HD1   106.41  3.000
 ALG  HD2   CD   NE    111.72  3.000
 ALG  HD1   CD   NE    108.52  3.000
 ALG  HD2   CD   CB    109.89  3.000
 ALG  HD1   CD   CB    109.94  3.000
 ALG  NE    CD   CB    110.26  3.000
 ALG  HNE   NE   CZ    115.21  3.000
 ALG  HNE   NE   CD    114.70  3.000
 ALG  CZ    NE   CD    120.50  3.000
 ALG  NH2   CZ   NH1   125.97  3.000
 ALG  NH2   CZ   NE    113.29  3.000
 ALG  NH1   CZ   NE    120.73  3.000
 ALG  HH1   NH1  CZ    110.57  3.000
 ALG  HH22  NH2  HH21  111.73  3.000
 ALG  HH22  NH2  CZ    115.25  3.000
 ALG  HH21  NH2  CZ    116.32  3.000
 ALG  HXT   OXT  C     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
 ALG  CONST_01  NH1  CZ   NE  CD     0.00   0.0  0
 ALG  CONST_02  NH2  CZ   NE  CD   180.00   0.0  0
 ALG  CONST_03  HXT  OXT  C   O      0.00   0.0  0
 ALG  CONST_04  HH1  NH1  CZ  NE   180.00   0.0  0
 ALG  Var_01    CD   CB   CA  C    179.81  30.0  3
 ALG  Var_02    CB   CA   C   O     -0.31  30.0  3
 ALG  Var_03    NE   CD   CB  CA  -179.77  30.0  3
 ALG  Var_04    CZ   NE   CD  CB   170.82  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
 ALG  plan-1  CD    0.020
 ALG  plan-1  NE    0.020
 ALG  plan-1  CZ    0.020
 ALG  plan-1  NH1   0.020
 ALG  plan-1  NH2   0.020
 ALG  plan-1  HNE   0.020
 ALG  plan-1  HH1   0.020
 ALG  plan-1  HH21  0.020
 ALG  plan-1  HH22  0.020
 ALG  plan-2  C     0.020
 ALG  plan-2  O     0.020
 ALG  plan-2  CA    0.020
 ALG  plan-2  OXT   0.020
 ALG  plan-2  HXT   0.020

