# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:48:25 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-carbamimidoyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccc(c1)C(N)=N)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
 APM  APM  3-carbamimidoyl-L-phenylalanine  L-peptide  27  15  .  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_APM
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
 APM  N     N  NH2    0  -0.791  -4.8046   5.1836  22.6951
 APM  CA    C  CH1    0  -0.200  -4.0453   4.1694  21.9891
 APM  C     C  C      0   0.409  -2.6763   3.9044  22.6608
 APM  O     O  O      0  -0.596  -2.2646   4.7441  23.4831
 APM  CB    C  CH2    0  -0.530  -3.8381   4.4614  20.4827
 APM  CG    C  CR6    0   0.158  -3.1007   5.7410  20.2189
 APM  CD1   C  CR16   0  -0.360  -3.7956   6.9334  20.0330
 APM  CD2   C  CR16   0  -0.298  -1.7083   5.7764  20.1801
 APM  CE1   C  CR6    0   0.026  -3.1308   8.1349  19.7951
 APM  CE2   C  CR16   0  -0.228  -1.0339   6.9671  19.9526
 APM  CZ    C  CR16   0  -0.311  -1.7388   8.1446  19.7561
 APM  CF    C  C      0   0.324  -3.8884   9.3956  19.5550
 APM  NG1   N  N      0  -0.639  -3.5475  10.2985  18.7165
 APM  NG2   N  NH2    0  -0.801  -5.0402   9.5217  20.2752
 APM  OXT   O  OC    -1  -0.614  -2.0889   2.8670  22.2890
 APM  H     H  HNH2   0   0.331  -5.6034   5.4716  22.1422
 APM  H2    H  HNH2   0   0.330  -4.2272   6.0046  22.8233
 APM  HA    H  HCH1   0   0.216  -4.6147   3.2339  22.0324
 APM  HB2   H  HCH2   0   0.236  -3.3057   3.6212  20.0338
 APM  HB3   H  HCH2   0   0.236  -4.8194   4.5073  20.0025
 APM  HD1   H  HCR6   0   0.250  -4.8793   6.9129  20.0383
 APM  HD2   H  HCR6   0   0.244  -1.1478   4.8611  20.3265
 APM  HE2   H  HCR6   0   0.253   0.0482   6.9786  19.9289
 APM  HZ    H  HCR6   0   0.256  -1.2025   9.0707  19.5891
 APM  HG1   H  H      0   0.329  -2.7334  10.0067  18.1890
 APM  HG21  H  HNH2   0   0.382  -5.4974  10.4187  20.2274
 APM  HG22  H  HNH2   0   0.390  -5.0868   9.0816  21.1792

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
 APM  N    CA    single    1.458  0.019  1.458
 APM  N    H     single    0.860  0.020  0.860
 APM  N    H2    single    0.890  0.020  1.040
 APM  CA   C     single    1.525  0.021  1.525
 APM  CA   CB    single    1.521  0.033  1.521
 APM  CA   HA    single    0.970  0.020  0.970
 APM  C    O     deloc     1.231  0.020  1.231
 APM  C    OXT   deloc     1.249  0.020  1.249
 APM  CB   CG    single    1.500  0.020  1.500
 APM  CB   HB2   single    0.970  0.020  1.090
 APM  CB   HB3   single    0.970  0.020  1.090
 APM  CG   CD1   aromatic  1.393  0.020  1.393
 APM  CG   CD2   aromatic  1.393  0.020  1.393
 APM  CD1  CE1   aromatic  1.394  0.020  1.394
 APM  CD1  HD1   single    0.930  0.020  1.080
 APM  CD2  CE2   aromatic  1.387  0.020  1.387
 APM  CD2  HD2   single    0.930  0.020  1.080
 APM  CE1  CZ    aromatic  1.393  0.020  1.393
 APM  CE1  CF    single    1.490  0.020  1.490
 APM  CE2  CZ    aromatic  1.386  0.020  1.386
 APM  CE2  HE2   single    0.930  0.020  1.080
 APM  CZ   HZ    single    0.930  0.020  1.080
 APM  CF   NG1   double    1.279  0.020  1.279
 APM  CF   NG2   single    1.364  0.020  1.364
 APM  NG1  HG1   single    0.890  0.020  1.040
 APM  NG2  HG21  single    0.890  0.020  1.040
 APM  NG2  HG22  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
 APM  H2    N    H     106.76  3.000
 APM  H2    N    CA    109.29  3.000
 APM  H     N    CA    114.00  3.000
 APM  HA    CA   CB    109.00  3.000
 APM  HA    CA   C     110.00  3.000
 APM  CB    CA   C     110.50  1.500
 APM  HA    CA   N     110.00  3.000
 APM  CB    CA   N     110.40  1.500
 APM  C     CA   N     111.00  2.800
 APM  OXT   C    O     126.96  3.000
 APM  OXT   C    CA    120.80  1.700
 APM  O     C    CA    120.80  1.700
 APM  HB3   CB   HB2   106.82  3.000
 APM  HB3   CB   CG    109.15  3.000
 APM  HB2   CB   CG    110.15  3.000
 APM  HB3   CB   CA    108.37  3.000
 APM  HB2   CB   CA    108.69  3.000
 APM  CG    CB   CA    113.44  3.000
 APM  CD2   CG   CD1   118.23  3.000
 APM  CD2   CG   CB    121.18  3.000
 APM  CD1   CG   CB    120.57  3.000
 APM  HD1   CD1  CE1   119.61  3.000
 APM  HD1   CD1  CG    118.81  3.000
 APM  CE1   CD1  CG    121.54  3.000
 APM  HD2   CD2  CE2   119.73  3.000
 APM  HD2   CD2  CG    119.46  3.000
 APM  CE2   CD2  CG    120.81  3.000
 APM  CF    CE1  CZ    119.85  3.000
 APM  CF    CE1  CD1   120.95  3.000
 APM  CZ    CE1  CD1   119.18  3.000
 APM  HE2   CE2  CZ    119.75  3.000
 APM  HE2   CE2  CD2   119.92  3.000
 APM  CZ    CE2  CD2   120.33  3.000
 APM  HZ    CZ   CE2   119.75  3.000
 APM  HZ    CZ   CE1   120.35  3.000
 APM  CE2   CZ   CE1   119.89  3.000
 APM  NG2   CF   NG1   120.40  3.000
 APM  NG2   CF   CE1   114.98  3.000
 APM  NG1   CF   CE1   124.58  3.000
 APM  HG1   NG1  CF    110.63  3.000
 APM  HG22  NG2  HG21  114.26  3.000
 APM  HG22  NG2  CF    118.22  3.000
 APM  HG21  NG2  CF    116.11  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
 APM  CONST_01  CZ    CE1  CD1  CG      0.00   0.0  0
 APM  CONST_02  CZ    CE2  CD2  CG      0.00   0.0  0
 APM  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 APM  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 APM  CONST_05  CE1   CD1  CG   CD2     0.00   0.0  0
 APM  CONST_06  CE1   CZ   CE2  CD2     0.00   0.0  0
 APM  CONST_07  CE1   CD1  CG   CB    180.00   0.0  0
 APM  CONST_08  CE2   CD2  CG   CB    180.00   0.0  0
 APM  CONST_09  CF    CE1  CD1  CG    180.00   0.0  0
 APM  CONST_10  CF    CE1  CZ   CE2   180.00   0.0  0
 APM  CONST_11  HE2   CE2  CD2  CG    180.00   0.0  0
 APM  CONST_12  HD2   CD2  CG   CD1   180.00   0.0  0
 APM  CONST_13  HZ    CZ   CE1  CD1   180.00   0.0  0
 APM  CONST_14  HD1   CD1  CG   CD2   180.00   0.0  0
 APM  CONST_15  HG1   NG1  CF   CE1     0.00   0.0  0
 APM  CONST_16  HG21  NG2  CF   CE1   180.00   0.0  0
 APM  Var_01    CD1   CG   CB   CA    -91.62  30.0  2
 APM  Var_02    NG1   CF   CE1  CD1  -141.96  30.0  2

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
 APM  chir_01  CA  N  C  CB  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
 APM  plan-1  CB    0.020
 APM  plan-1  CG    0.020
 APM  plan-1  CD1   0.020
 APM  plan-1  CD2   0.020
 APM  plan-1  CE1   0.020
 APM  plan-1  CE2   0.020
 APM  plan-1  CZ    0.020
 APM  plan-1  CF    0.020
 APM  plan-1  HD1   0.020
 APM  plan-1  HD2   0.020
 APM  plan-1  HE2   0.020
 APM  plan-1  HZ    0.020
 APM  plan-2  CE1   0.020
 APM  plan-2  CF    0.020
 APM  plan-2  NG1   0.020
 APM  plan-2  NG2   0.020
 APM  plan-2  HG1   0.020
 APM  plan-2  HG21  0.020
 APM  plan-2  HG22  0.020
 APM  plan-3  CA    0.020
 APM  plan-3  C     0.020
 APM  plan-3  O     0.020
 APM  plan-3  OXT   0.020

