# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:59:08 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: L-norleucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N)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
 NLN  NLN  "NORLEUCINE AMIDE"  L-peptide  23  9  .  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_NLN
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
 NLN  N     N  NH2   0  -0.789   1.7973  -0.4701  -0.8406
 NLN  CA    C  CH1   0  -0.218   0.3479  -0.5039  -0.8056
 NLN  C     C  C     0   0.520  -0.1853   0.0738  -2.1102
 NLN  O     O  O     0  -0.494   0.3733   1.0049  -2.6731
 NLN  CB    C  CH2   0  -0.425  -0.3106   0.2579   0.3583
 NLN  CG    C  CH2   0  -0.418   0.1132  -0.2471   1.7314
 NLN  CD    C  CH2   0  -0.419  -0.6096   0.4680   2.8668
 NLN  CE    C  CH3   0  -0.662  -0.1784  -0.0237   4.2414
 NLN  NH2   N  NH2   0  -0.800  -1.3227  -0.4766  -2.5581
 NLN  H     H  HNH2  0   0.353   2.1641  -0.8775   0.0098
 NLN  H2    H  HNH2  0   0.340   2.1152   0.4917  -0.8530
 NLN  HA    H  HCH1  0   0.248   0.0446  -1.5537  -0.7330
 NLN  HB2   H  HCH2  0   0.224  -1.3987   0.1753   0.2691
 NLN  HB3   H  HCH2  0   0.224  -0.0730   1.3236   0.2684
 NLN  HG2   H  HCH2  0   0.209   1.1922  -0.1170   1.8620
 NLN  HG3   H  HCH2  0   0.215  -0.0783  -1.3238   1.8005
 NLN  HD2   H  HCH2  0   0.214  -1.6895   0.3339   2.7505
 NLN  HD3   H  HCH2  0   0.214  -0.4280   1.5442   2.7878
 NLN  HE1   H  HCH3  0   0.227  -0.7012   0.5057   5.0386
 NLN  HE2   H  HCH3  0   0.217  -0.3841  -1.0889   4.3616
 NLN  HE3   H  HCH3  0   0.217   0.8925   0.1228   4.3933
 NLN  HH21  H  HNH2  0   0.399  -1.7978  -0.0917  -3.3587
 NLN  HH22  H  HNH2  0   0.407  -1.7713  -1.2357  -2.0753

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
 NLN  N    CA    single  1.458  0.019  1.458
 NLN  N    H     single  0.860  0.020  0.860
 NLN  N    H2    single  0.890  0.020  1.040
 NLN  CA   C     single  1.525  0.021  1.525
 NLN  CA   CB    single  1.530  0.020  1.530
 NLN  CA   HA    single  0.970  0.020  0.970
 NLN  C    O     double  1.231  0.020  1.231
 NLN  C    NH2   single  1.341  0.020  1.341
 NLN  CB   CG    single  1.523  0.020  1.523
 NLN  CB   HB2   single  0.970  0.020  1.090
 NLN  CB   HB3   single  0.970  0.020  1.090
 NLN  CG   CD    single  1.524  0.020  1.524
 NLN  CG   HG2   single  0.970  0.020  1.090
 NLN  CG   HG3   single  0.970  0.020  1.090
 NLN  CD   CE    single  1.522  0.020  1.522
 NLN  CD   HD2   single  0.970  0.020  1.090
 NLN  CD   HD3   single  0.970  0.020  1.090
 NLN  CE   HE1   single  0.970  0.020  1.090
 NLN  CE   HE2   single  0.970  0.020  1.090
 NLN  CE   HE3   single  0.970  0.020  1.090
 NLN  NH2  HH21  single  0.860  0.020  1.020
 NLN  NH2  HH22  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
 NLN  H2    N    H     106.19  3.000
 NLN  H2    N    CA    109.64  3.000
 NLN  H     N    CA    114.00  3.000
 NLN  HA    CA   CB    109.00  3.000
 NLN  HA    CA   C     109.00  3.000
 NLN  CB    CA   C     110.10  1.900
 NLN  HA    CA   N     110.00  3.000
 NLN  CB    CA   N     110.50  1.700
 NLN  C     CA   N     111.00  2.800
 NLN  NH2   C    O     123.11  3.000
 NLN  NH2   C    CA    115.31  3.000
 NLN  O     C    CA    120.80  1.700
 NLN  HB3   CB   HB2   106.40  3.000
 NLN  HB3   CB   CG    109.64  3.000
 NLN  HB2   CB   CG    108.96  3.000
 NLN  HB3   CB   CA    109.06  3.000
 NLN  HB2   CB   CA    109.04  3.000
 NLN  CG    CB   CA    113.49  3.000
 NLN  HG3   CG   HG2   106.35  3.000
 NLN  HG3   CG   CD    109.34  3.000
 NLN  HG2   CG   CD    108.83  3.000
 NLN  HG3   CG   CB    109.51  3.000
 NLN  HG2   CG   CB    110.03  3.000
 NLN  CD    CG   CB    112.58  3.000
 NLN  HD3   CD   HD2   106.05  3.000
 NLN  HD3   CD   CE    109.63  3.000
 NLN  HD2   CD   CE    109.63  3.000
 NLN  HD3   CD   CG    109.21  3.000
 NLN  HD2   CD   CG    109.35  3.000
 NLN  CE    CD   CG    112.76  3.000
 NLN  HE3   CE   HE2   107.49  3.000
 NLN  HE3   CE   HE1   107.67  3.000
 NLN  HE2   CE   HE1   107.63  3.000
 NLN  HE3   CE   CD    111.12  3.000
 NLN  HE2   CE   CD    111.18  3.000
 NLN  HE1   CE   CD    111.57  3.000
 NLN  HH22  NH2  HH21  117.37  3.000
 NLN  HH22  NH2  C     121.88  3.000
 NLN  HH21  NH2  C     120.59  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
 NLN  CONST_01  HH21  NH2  C   CA   180.00   0.0  0
 NLN  CONST_02  HH22  NH2  C   CA     0.00   0.0  0
 NLN  CONST_03  HH21  NH2  C   O      0.00   0.0  0
 NLN  CONST_04  HH22  NH2  C   O    180.00   0.0  0
 NLN  Var_01    CD    CG   CB  CA  -176.77  30.0  3
 NLN  Var_02    CE    CD   CG  CB  -179.41  30.0  3
 NLN  Var_03    HG2   CG   CB  CA    61.65  30.0  3
 NLN  Var_04    HG3   CG   CB  CA   -54.91  30.0  3
 NLN  Var_05    HD2   CD   CG  CB    58.36  30.0  3
 NLN  Var_06    HD3   CD   CG  CB   -57.28  30.0  3
 NLN  Var_07    HE1   CE   CD  CG   179.56  30.0  3
 NLN  Var_08    HE2   CE   CD  CG   -60.29  30.0  3
 NLN  Var_09    HE3   CE   CD  CG    59.39  30.0  3
 NLN  Var_10    HB2   CB   CG  CD   -55.07  30.0  1
 NLN  Var_11    HB3   CB   CG  CD    61.01  30.0  1
 NLN  Var_12    HG2   CG   CD  CE   -57.15  30.0  1
 NLN  Var_13    HG3   CG   CD  CE    58.63  30.0  1

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
 NLN  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
 NLN  plan-1  CA    0.020
 NLN  plan-1  C     0.020
 NLN  plan-1  O     0.020
 NLN  plan-1  NH2   0.020
 NLN  plan-1  HH21  0.020
 NLN  plan-1  HH22  0.020

