# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:07:47 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 1-[(4S)-4-amino-5-hydroxypentyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)CCCNC(N)=N
#
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
 OAR  OAR  1-[(4S)-4-amino-5-hydroxypentyl]guanidine  peptide  27  11  .  2022-09-22  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_OAR
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
 OAR  O     O  OH1   0  -0.674   4.9154   0.1034  -0.4177
 OAR  N1    N  NH2   0  -0.787   2.7021  -1.3011   0.7946
 OAR  NE    N  NH1   0  -0.647  -2.4300  -0.4067  -0.1110
 OAR  NH1   N  NH2   0  -0.840  -4.6946  -0.7871  -0.2950
 OAR  NH2   N  N     0  -0.719  -3.8667   1.1777   0.7369
 OAR  CA    C  CH1   0  -0.130   2.5581  -0.2161  -0.1654
 OAR  CB    C  CH2   0  -0.426   1.2406   0.5196   0.0582
 OAR  CG    C  CH2   0  -0.449   0.0071  -0.3558  -0.1098
 OAR  CD    C  CH2   0  -0.226  -1.2748   0.4375   0.0891
 OAR  CZ    C  C     0   0.549  -3.6919   0.0686   0.1153
 OAR  C     C  CH2   0  -0.135   3.7097   0.7840  -0.1442
 OAR  HO    H  HOH1  0   0.454   5.6457   0.7103  -0.2700
 OAR  H     H  HNH2  0   0.344   3.6009  -1.7486   0.6642
 OAR  H2    H  HNH2  0   0.331   2.7246  -0.9140   1.7324
 OAR  HE    H  HNH1  0   0.377  -2.3359  -1.0919  -0.8439
 OAR  HH11  H  HNH2  0   0.381  -4.4818  -1.4053  -1.0628
 OAR  HH12  H  HNH2  0   0.384  -5.5990  -0.3577  -0.4055
 OAR  HH2   H  H     0   0.313  -4.8551   1.3599   0.8666
 OAR  HA    H  HCH1  0   0.217   2.5290  -0.6672  -1.1656
 OAR  HB2   H  HCH2  0   0.215   1.2436   0.9648   1.0608
 OAR  HB3   H  HCH2  0   0.223   1.1862   1.3572  -0.6443
 OAR  HG2   H  HCH2  0   0.216   0.0140  -0.7960  -1.1134
 OAR  HG3   H  HCH2  0   0.230   0.0374  -1.1879   0.5963
 OAR  HD2   H  HCH2  0   0.204  -1.2858   1.3012  -0.5894
 OAR  HD3   H  HCH2  0   0.224  -1.3050   0.8415   1.1024
 OAR  HC1   H  HCH2  0   0.184   3.7374   1.2694   0.8423
 OAR  HC2   H  HCH2  0   0.187   3.5203   1.5724  -0.8855

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
 OAR  O    C     single  1.231  0.020  1.231
 OAR  C    CA    single  1.525  0.021  1.525
 OAR  CA   N1    single  1.456  0.020  1.456
 OAR  CA   CB    single  1.530  0.020  1.530
 OAR  CB   CG    single  1.522  0.020  1.522
 OAR  CG   CD    single  1.521  0.020  1.521
 OAR  CD   NE    single  1.445  0.020  1.445
 OAR  NE   CZ    single  1.367  0.020  1.367
 OAR  CZ   NH2   double  1.283  0.020  1.283
 OAR  CZ   NH1   single  1.381  0.020  1.381
 OAR  O    HO    single  0.850  0.020  0.980
 OAR  N1   H     single  0.890  0.020  1.040
 OAR  N1   H2    single  0.890  0.020  1.040
 OAR  NE   HE    single  0.890  0.020  1.040
 OAR  NH1  HH11  single  0.890  0.020  1.040
 OAR  NH1  HH12  single  0.890  0.020  1.040
 OAR  NH2  HH2   single  0.890  0.020  1.040
 OAR  CA   HA    single  0.970  0.020  0.970
 OAR  CB   HB2   single  0.970  0.020  1.090
 OAR  CB   HB3   single  0.970  0.020  1.090
 OAR  CG   HG2   single  0.970  0.020  1.090
 OAR  CG   HG3   single  0.970  0.020  1.090
 OAR  CD   HD2   single  0.970  0.020  1.090
 OAR  CD   HD3   single  0.970  0.020  1.090
 OAR  C    HC1   single  0.970  0.020  1.090
 OAR  C    HC2   single  0.970  0.020  1.090

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
 OAR  HO    O    C     108.36  3.000
 OAR  H2    N1   H     105.54  3.000
 OAR  H2    N1   CA    109.11  3.000
 OAR  H     N1   CA    109.41  3.000
 OAR  HE    NE   CZ    116.29  3.000
 OAR  HE    NE   CD    115.05  3.000
 OAR  CZ    NE   CD    120.79  3.000
 OAR  HH12  NH1  HH11  111.55  3.000
 OAR  HH12  NH1  CZ    114.87  3.000
 OAR  HH11  NH1  CZ    116.93  3.000
 OAR  HH2   NH2  CZ    110.50  3.000
 OAR  HA    CA   C     109.00  3.000
 OAR  HA    CA   CB    109.00  3.000
 OAR  C     CA   CB    110.10  1.900
 OAR  HA    CA   N1    107.29  3.000
 OAR  CB    CA   N1    110.37  3.000
 OAR  C     CA   N1    113.88  3.000
 OAR  HB3   CB   HB2   106.03  3.000
 OAR  HB3   CB   CG    109.21  3.000
 OAR  HB2   CB   CG    109.67  3.000
 OAR  HB3   CB   CA    108.53  3.000
 OAR  HB2   CB   CA    109.11  3.000
 OAR  CG    CB   CA    113.98  3.000
 OAR  HG3   CG   HG2   106.61  3.000
 OAR  HG3   CG   CD    109.66  3.000
 OAR  HG2   CG   CD    109.55  3.000
 OAR  HG3   CG   CB    110.16  3.000
 OAR  HG2   CG   CB    109.09  3.000
 OAR  CD    CG   CB    111.64  3.000
 OAR  HD3   CD   HD2   106.39  3.000
 OAR  HD3   CD   CG    109.75  3.000
 OAR  HD2   CD   CG    109.75  3.000
 OAR  HD3   CD   NE    108.83  3.000
 OAR  HD2   CD   NE    111.47  3.000
 OAR  CG    CD   NE    110.55  3.000
 OAR  NH2   CZ   NH1   125.50  3.000
 OAR  NH1   CZ   NE    113.93  3.000
 OAR  NH2   CZ   NE    120.42  3.000
 OAR  HC2   C    HC1   107.03  3.000
 OAR  HC2   C    CA    109.33  3.000
 OAR  HC1   C    CA    108.71  3.000
 OAR  HC2   C    O     111.26  3.000
 OAR  HC1   C    O     111.42  3.000
 OAR  CA    C    O     120.80  1.700

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
 OAR  CONST_01  CD   NE   CZ  NH1   180.00   0.0  0
 OAR  CONST_02  CD   NE   CZ  NH2     0.00   0.0  0
 OAR  CONST_03  HH2  NH2  CZ  NE    180.00   0.0  0
 OAR  Var_01    CB   CG   CD  NE    178.46  30.0  1
 OAR  Var_02    CD   CG   CB  CA   -178.52  30.0  3
 OAR  Var_03    CZ   NE   CD  CG    175.02  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
 OAR  chir_01  CA  C  N1  CB  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
 OAR  plan-1  NE    0.020
 OAR  plan-1  NH1   0.020
 OAR  plan-1  NH2   0.020
 OAR  plan-1  CD    0.020
 OAR  plan-1  CZ    0.020
 OAR  plan-1  HE    0.020
 OAR  plan-1  HH11  0.020
 OAR  plan-1  HH12  0.020
 OAR  plan-1  HH2   0.020

