# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:36:24 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 6-ammonio-L-norleucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC[NH3+])C(N)=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
 LYN  LYN  6-ammonio-L-norleucinamide  L-peptide  26  10  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_LYN
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
 LYN  N     N  NH2   0  -0.789   1.5868   1.7800   0.3923
 LYN  CA    C  CH1   0  -0.218   1.4434   0.3402   0.4758
 LYN  CB    C  CH2   0  -0.429   0.1923  -0.2486  -0.2006
 LYN  CG    C  CH2   0  -0.436  -1.1091   0.2994   0.3686
 LYN  CD    C  CH2   0  -0.448  -2.3298  -0.3492  -0.2730
 LYN  CE    C  CH2   0  -0.303  -3.6096   0.2212   0.3020
 LYN  NZ    N  NT3   1  -0.777  -4.8056  -0.4044  -0.3209
 LYN  C     C  C     0   0.520   2.6687  -0.3103  -0.1543
 LYN  O     O  O     0  -0.493   3.2152   0.1731  -1.1354
 LYN  NT    N  NH2   0  -0.799   3.0614  -1.4589   0.4140
 LYN  H     H  HNH2  0   0.342   1.5617   2.0729  -0.5771
 LYN  H2    H  HNH2  0   0.355   0.8016   2.2278   0.8458
 LYN  HA    H  HCH1  0   0.251   1.4074   0.0731   1.5371
 LYN  HB2   H  HCH2  0   0.232   0.2370  -0.0488  -1.2764
 LYN  HB3   H  HCH2  0   0.231   0.2010  -1.3371  -0.0854
 LYN  HG2   H  HCH2  0   0.233  -1.1347   0.1344   1.4505
 LYN  HG3   H  HCH2  0   0.228  -1.1615   1.3810   0.2154
 LYN  HD2   H  HCH2  0   0.248  -2.3075  -0.1863  -1.3546
 LYN  HD3   H  HCH2  0   0.248  -2.3021  -1.4308  -0.1127
 LYN  HE2   H  HCH2  0   0.291  -3.6857   0.0426   1.3726
 LYN  HE3   H  HCH2  0   0.291  -3.6891   1.2917   0.1243
 LYN  HZ1   H  HNT3  0   0.469  -4.8252  -0.2640  -1.3305
 LYN  HZ2   H  HNT3  0   0.469  -4.8388  -1.4100  -0.1559
 LYN  HZ3   H  HNT3  0   0.478  -5.6703  -0.0131   0.0507
 LYN  HNT1  H  HNH2  0   0.407   2.5914  -1.8411   1.2163
 LYN  HNT2  H  HNH2  0   0.400   3.8041  -2.0051   0.0082

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
 LYN  N   CA    single  1.458  0.019  1.458
 LYN  N   H     single  0.860  0.020  0.860
 LYN  N   H2    single  0.890  0.020  1.040
 LYN  CA  CB    single  1.530  0.020  1.530
 LYN  CA  C     single  1.525  0.021  1.525
 LYN  CA  HA    single  0.970  0.020  0.970
 LYN  CB  CG    single  1.522  0.020  1.522
 LYN  CB  HB2   single  0.970  0.020  1.090
 LYN  CB  HB3   single  0.970  0.020  1.090
 LYN  CG  CD    single  1.524  0.020  1.524
 LYN  CG  HG2   single  0.970  0.020  1.090
 LYN  CG  HG3   single  0.970  0.020  1.090
 LYN  CD  CE    single  1.515  0.020  1.515
 LYN  CD  HD2   single  0.970  0.020  1.090
 LYN  CD  HD3   single  0.970  0.020  1.090
 LYN  CE  NZ    single  1.487  0.020  1.487
 LYN  CE  HE2   single  0.970  0.020  1.090
 LYN  CE  HE3   single  0.970  0.020  1.090
 LYN  NZ  HZ1   single  0.890  0.020  1.040
 LYN  NZ  HZ2   single  0.890  0.020  1.040
 LYN  NZ  HZ3   single  0.890  0.020  1.040
 LYN  C   O     double  1.231  0.020  1.231
 LYN  C   NT    single  1.340  0.020  1.340
 LYN  NT  HNT1  single  0.860  0.020  1.020
 LYN  NT  HNT2  single  0.860  0.020  1.020

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
 LYN  H2    N   H     106.37  3.000
 LYN  H2    N   CA    109.71  3.000
 LYN  H     N   CA    114.00  3.000
 LYN  HA    CA  C     109.00  3.000
 LYN  HA    CA  CB    109.00  3.000
 LYN  C     CA  CB    110.10  1.900
 LYN  HA    CA  N     110.00  3.000
 LYN  C     CA  N     111.00  2.800
 LYN  CB    CA  N     110.50  1.700
 LYN  HB3   CB  HB2   106.53  3.000
 LYN  HB3   CB  CG    108.99  3.000
 LYN  HB2   CB  CG    109.66  3.000
 LYN  HB3   CB  CA    109.13  3.000
 LYN  HB2   CB  CA    109.19  3.000
 LYN  CG    CB  CA    113.12  3.000
 LYN  HG3   CG  HG2   106.64  3.000
 LYN  HG3   CG  CD    108.88  3.000
 LYN  HG2   CG  CD    109.46  3.000
 LYN  HG3   CG  CB    110.16  3.000
 LYN  HG2   CG  CB    109.58  3.000
 LYN  CD    CG  CB    111.97  3.000
 LYN  HD3   CD  HD2   106.95  3.000
 LYN  HD3   CD  CE    109.77  3.000
 LYN  HD2   CD  CE    109.67  3.000
 LYN  HD3   CD  CG    109.81  3.000
 LYN  HD2   CD  CG    109.66  3.000
 LYN  CE    CD  CG    110.90  3.000
 LYN  HE3   CE  HE2   108.49  3.000
 LYN  HE3   CE  NZ    106.67  3.000
 LYN  HE2   CE  NZ    106.67  3.000
 LYN  HE3   CE  CD    111.73  3.000
 LYN  HE2   CE  CD    111.77  3.000
 LYN  NZ    CE  CD    111.24  3.000
 LYN  HZ3   NZ  HZ2   106.98  3.000
 LYN  HZ3   NZ  HZ1   106.97  3.000
 LYN  HZ2   NZ  HZ1   107.19  3.000
 LYN  HZ3   NZ  CE    111.60  3.000
 LYN  HZ2   NZ  CE    111.93  3.000
 LYN  HZ1   NZ  CE    111.86  3.000
 LYN  NT    C   O     123.23  3.000
 LYN  NT    C   CA    115.22  3.000
 LYN  O     C   CA    120.80  1.700
 LYN  HNT2  NT  HNT1  117.39  3.000
 LYN  HNT2  NT  C     120.66  3.000
 LYN  HNT1  NT  C     121.81  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
 LYN  CONST_01  HNT1  NT  C   CA     0.00   0.0  0
 LYN  CONST_02  HNT2  NT  C   CA   180.00   0.0  0
 LYN  Var_01    CD    CG  CB  CA  -177.28  30.0  3
 LYN  Var_02    CE    CD  CG  CB  -179.53  30.0  3
 LYN  Var_03    NZ    CE  CD  CG   179.88  30.0  3
 LYN  Var_04    HZ1   NZ  CE  CD   -59.21  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
 LYN  chir_01  CA  N  CB  C  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
 LYN  plan-1  CA    0.020
 LYN  plan-1  C     0.020
 LYN  plan-1  O     0.020
 LYN  plan-1  NT    0.020
 LYN  plan-1  HNT1  0.020
 LYN  plan-1  HNT2  0.020

