# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:34:37 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: 5-amino-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)CC[C@H](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
 XFW  XFW  '5-amino-L-ornithine      '  peptide  22  10  .  2016-04-26  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_XFW
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
 XFW  C     C  C      0   0.400   -6.6968   0.2611  15.6740
 XFW  O     O  O      0  -0.585   -7.5722   1.1370  15.5610
 XFW  CA    C  CH1    0  -0.158   -6.4411  -0.3028  17.0984
 XFW  CB    C  CH2    0  -0.442   -7.7211  -0.7164  17.8237
 XFW  CG    C  CH2    0  -0.443   -8.2423  -2.1299  17.5688
 XFW  CD    C  CH1    0   0.058   -8.6076  -2.4995  16.1240
 XFW  NE1   N  NH2    0  -0.800   -9.5275  -3.6289  16.1680
 XFW  NE2   N  NH2    0  -0.819   -7.4998  -2.9027  15.2777
 XFW  N     N  NH2    0  -0.816   -5.8010   0.7657  17.8723
 XFW  HA    H  HCH1   0   0.173   -5.7880  -1.1849  17.0100
 XFW  HB2   H  HCH2   0   0.211   -7.5414  -0.6429  18.9021
 XFW  HB3   H  HCH2   0   0.213   -8.5019   0.0170  17.6048
 XFW  HG2   H  HCH2   0   0.214   -9.1322  -2.2525  18.1953
 XFW  HG3   H  HCH2   0   0.208   -7.5175  -2.8662  17.9352
 XFW  HD2   H  HCH1   0   0.186   -9.0565  -1.6138  15.6465
 XFW  HE12  H  HNH2   0   0.335  -10.3705  -3.3680  16.6642
 XFW  HE13  H  HNH2   0   0.334   -9.8114  -3.8559  15.2227
 XFW  HE22  H  HNH2   0   0.352   -6.8996  -2.1144  15.0637
 XFW  HE23  H  HNH2   0   0.324   -6.9295  -3.5813  15.7705
 XFW  H     H  HNH2   0   0.333   -5.5289   0.3959  18.7758
 XFW  OXT   O  OC    -1  -0.611   -5.9735  -0.1916  14.7559
 XFW  H2    H  HNH2   0   0.334   -4.9340   1.0382  17.4240

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
 XFW  NE2  CD    single  1.451  0.020  1.451
 XFW  O    C     deloc   1.231  0.020  1.231
 XFW  C    CA    single  1.525  0.021  1.525
 XFW  CD   NE1   single  1.457  0.020  1.457
 XFW  CD   CG    single  1.535  0.020  1.535
 XFW  CA   CB    single  1.521  0.033  1.521
 XFW  CA   N     single  1.458  0.019  1.458
 XFW  CG   CB    single  1.528  0.020  1.528
 XFW  CA   HA    single  0.970  0.020  0.970
 XFW  CB   HB2   single  0.970  0.020  1.090
 XFW  CB   HB3   single  0.970  0.020  1.090
 XFW  CG   HG2   single  0.970  0.020  1.090
 XFW  CG   HG3   single  0.970  0.020  1.090
 XFW  CD   HD2   single  0.970  0.020  1.090
 XFW  NE1  HE12  single  0.890  0.020  1.040
 XFW  NE1  HE13  single  0.890  0.020  1.040
 XFW  NE2  HE22  single  0.890  0.020  1.040
 XFW  NE2  HE23  single  0.890  0.020  1.040
 XFW  N    H     single  0.860  0.020  0.860
 XFW  C    OXT   deloc   1.253  0.020  1.253
 XFW  N    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
 XFW  OXT   C    CA    120.80  1.700
 XFW  OXT   C    O     126.45  3.000
 XFW  CA    C    O     120.80  1.700
 XFW  HA    CA   N     110.00  3.000
 XFW  HA    CA   CB    109.00  3.000
 XFW  N     CA   CB    110.40  1.500
 XFW  HA    CA   C     110.00  3.000
 XFW  N     CA   C     111.00  2.800
 XFW  CB    CA   C     110.50  1.500
 XFW  HB3   CB   HB2   105.61  3.000
 XFW  HB3   CB   CG    110.09  3.000
 XFW  HB2   CB   CG    106.39  3.000
 XFW  HB3   CB   CA    108.76  3.000
 XFW  HB2   CB   CA    108.16  3.000
 XFW  CG    CB   CA    117.18  3.000
 XFW  HG3   CG   HG2   105.72  3.000
 XFW  HG3   CG   CD    108.07  3.000
 XFW  HG2   CG   CD    108.54  3.000
 XFW  HG3   CG   CB    109.88  3.000
 XFW  HG2   CG   CB    106.57  3.000
 XFW  CD    CG   CB    117.44  3.000
 XFW  HD2   CD   NE2   106.35  3.000
 XFW  HD2   CD   NE1   112.26  3.000
 XFW  NE2   CD   NE1   106.51  3.000
 XFW  HD2   CD   CG    108.14  3.000
 XFW  NE1   CD   CG    107.96  3.000
 XFW  NE2   CD   CG    115.72  3.000
 XFW  HE13  NE1  HE12  106.37  3.000
 XFW  HE13  NE1  CD    108.81  3.000
 XFW  HE12  NE1  CD    109.92  3.000
 XFW  HE23  NE2  HE22  106.85  3.000
 XFW  HE23  NE2  CD    109.38  3.000
 XFW  HE22  NE2  CD    111.04  3.000
 XFW  H2    N    H     105.23  3.000
 XFW  H2    N    CA    109.63  3.000
 XFW  H     N    CA    114.00  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
 XFW  Var_01  CD    CG   CB  CA  -60.17  30.0  1
 XFW  Var_02  NE2   CD   CG  CB   82.38  30.0  1
 XFW  Var_03  HE22  NE2  CD  CG  -70.16  30.0  3
 XFW  Var_04  HE12  NE1  CD  CG   61.25  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
 XFW  chir_01  CA  C  CB  N  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
 XFW  plan-1  C    0.020
 XFW  plan-1  O    0.020
 XFW  plan-1  CA   0.020
 XFW  plan-1  OXT  0.020

