# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 07:29:05 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-octanoyl-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)N[C@H](C(C)C)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
 4N3  4N3  'N-octanoyl-D-valine      '  D-peptide  42  17  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4N3
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
 4N3  N     N  NH1   0  -0.637  -1.7948   0.2590  -0.1507
 4N3  CA    C  CH1   0  -0.210  -3.1027  -0.1162   0.3093
 4N3  CB    C  CH1   0  -0.238  -3.5917  -1.4423  -0.3179
 4N3  CG1   C  CH3   0  -0.677  -3.7833  -1.3348  -1.8277
 4N3  CG2   C  CH3   0  -0.655  -2.6344  -2.5740   0.0340
 4N3  C     C  C     0   0.549  -4.0834   1.0147   0.0572
 4N3  O     O  O     0  -0.432  -3.8425   2.0035  -0.5863
 4N3  CO1   C  C     0   0.573  -0.7034   0.3022   0.6407
 4N3  O2    O  O     0  -0.495  -0.7328   0.0207   1.8297
 4N3  CD    C  CH2   0  -0.585   0.5643   0.7510  -0.0522
 4N3  CE    C  CH2   0  -0.414   1.8126   0.0561   0.4763
 4N3  CF    C  CH2   0  -0.415   3.0820   0.5637  -0.1950
 4N3  CH    C  CH2   0  -0.413   4.3399  -0.1198   0.3253
 4N3  CI    C  CH2   0  -0.407   5.6173   0.3917  -0.3284
 4N3  CJ    C  CH2   0  -0.419   6.8762  -0.2850   0.1999
 4N3  CK    C  CH3   0  -0.662   8.1494   0.2402  -0.4487
 4N3  H1    H  HNH1  0   0.400  -1.6870   0.5154  -1.1189
 4N3  HA    H  HCH1  0   0.303  -3.0399  -0.2614   1.3906
 4N3  HB    H  HCH1  0   0.248  -4.5596  -1.6701   0.1360
 4N3  HG13  H  HCH3  0   0.222  -2.8517  -1.0807  -2.3381
 4N3  HG11  H  HCH3  0   0.245  -4.1184  -2.2899  -2.2329
 4N3  HG12  H  HCH3  0   0.237  -4.5307  -0.5888  -2.1028
 4N3  HG22  H  HCH3  0   0.232  -2.5268  -2.6887   1.1134
 4N3  HG23  H  HCH3  0   0.238  -3.0044  -3.5184  -0.3666
 4N3  HG21  H  HCH3  0   0.222  -1.6422  -2.4052  -0.3875
 4N3  OXT   O  OH1   0  -0.589  -5.2544   0.7739   0.6288
 4N3  HD2   H  HCH2  0   0.250   0.4825   0.6068  -1.1326
 4N3  HD1   H  HCH2  0   0.269   0.6531   1.8320   0.1030
 4N3  HE1   H  HCH2  0   0.224   1.8869   0.2074   1.5555
 4N3  HE2   H  HCH2  0   0.222   1.7254  -1.0237   0.3203
 4N3  HF2   H  HCH2  0   0.211   3.0092   0.4168  -1.2781
 4N3  HF1   H  HCH2  0   0.211   3.1654   1.6453  -0.0414
 4N3  HH1   H  HCH2  0   0.208   4.4064   0.0220   1.4097
 4N3  HH2   H  HCH2  0   0.208   4.2582  -1.2007   0.1667
 4N3  HI1   H  HCH2  0   0.207   5.5550   0.2465  -1.4127
 4N3  HI2   H  HCH2  0   0.206   5.6958   1.4736  -0.1734
 4N3  HJ1   H  HCH2  0   0.210   6.9329  -0.1449   1.2839
 4N3  HJ2   H  HCH2  0   0.210   6.8009  -1.3649   0.0389
 4N3  HK3   H  HCH3  0   0.216   8.1384   0.0791  -1.5284
 4N3  HK2   H  HCH3  0   0.215   8.2640   1.3126  -0.2794
 4N3  HK1   H  HCH3  0   0.226   9.0363  -0.2540  -0.0504
 4N3  HXT   H  HOH1  0   0.486  -5.8786   1.4887   0.4313

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
 4N3  C    O     double  1.231  0.020  1.231
 4N3  C    CA    single  1.525  0.021  1.525
 4N3  N    CA    single  1.458  0.019  1.458
 4N3  N    CO1   single  1.349  0.020  1.349
 4N3  CB   CA    single  1.521  0.033  1.521
 4N3  CB   CG2   single  1.523  0.020  1.523
 4N3  CB   CG1   single  1.526  0.020  1.526
 4N3  CD   CO1   single  1.513  0.020  1.513
 4N3  CD   CE    single  1.523  0.020  1.523
 4N3  CF   CE    single  1.523  0.020  1.523
 4N3  CF   CH    single  1.523  0.020  1.523
 4N3  CO1  O2    double  1.222  0.020  1.222
 4N3  CI   CH    single  1.523  0.020  1.523
 4N3  CI   CJ    single  1.524  0.020  1.524
 4N3  CJ   CK    single  1.522  0.020  1.522
 4N3  N    H1    single  0.860  0.020  1.020
 4N3  CA   HA    single  0.970  0.020  0.970
 4N3  CB   HB    single  0.970  0.020  1.090
 4N3  CG1  HG13  single  0.970  0.020  1.090
 4N3  CG1  HG11  single  0.970  0.020  1.090
 4N3  CG1  HG12  single  0.970  0.020  1.090
 4N3  CG2  HG22  single  0.970  0.020  1.090
 4N3  CG2  HG23  single  0.970  0.020  1.090
 4N3  CG2  HG21  single  0.970  0.020  1.090
 4N3  C    OXT   single  1.325  0.020  1.325
 4N3  CD   HD2   single  0.970  0.020  1.090
 4N3  CD   HD1   single  0.970  0.020  1.090
 4N3  CE   HE1   single  0.970  0.020  1.090
 4N3  CE   HE2   single  0.970  0.020  1.090
 4N3  CF   HF2   single  0.970  0.020  1.090
 4N3  CF   HF1   single  0.970  0.020  1.090
 4N3  CH   HH1   single  0.970  0.020  1.090
 4N3  CH   HH2   single  0.970  0.020  1.090
 4N3  CI   HI1   single  0.970  0.020  1.090
 4N3  CI   HI2   single  0.970  0.020  1.090
 4N3  CJ   HJ1   single  0.970  0.020  1.090
 4N3  CJ   HJ2   single  0.970  0.020  1.090
 4N3  CK   HK3   single  0.970  0.020  1.090
 4N3  CK   HK2   single  0.970  0.020  1.090
 4N3  CK   HK1   single  0.970  0.020  1.090
 4N3  OXT  HXT   single  0.850  0.020  0.980

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
 4N3  H1    N    CO1   117.98  3.000
 4N3  H1    N    CA    118.15  3.000
 4N3  CO1   N    CA    123.86  3.000
 4N3  HA    CA   C     110.00  3.000
 4N3  HA    CA   CB    109.00  3.000
 4N3  C     CA   CB    110.50  1.500
 4N3  HA    CA   N     110.00  3.000
 4N3  CB    CA   N     110.40  1.500
 4N3  C     CA   N     111.00  2.800
 4N3  HB    CB   CG2   107.80  3.000
 4N3  HB    CB   CG1   108.33  3.000
 4N3  CG2   CB   CG1   111.09  3.000
 4N3  HB    CB   CA    106.87  3.000
 4N3  CG1   CB   CA    112.38  3.000
 4N3  CG2   CB   CA    110.16  3.000
 4N3  HG12  CG1  HG11  107.14  3.000
 4N3  HG12  CG1  HG13  107.90  3.000
 4N3  HG11  CG1  HG13  106.99  3.000
 4N3  HG12  CG1  CB    112.56  3.000
 4N3  HG11  CG1  CB    110.16  3.000
 4N3  HG13  CG1  CB    111.82  3.000
 4N3  HG21  CG2  HG23  107.49  3.000
 4N3  HG21  CG2  HG22  107.98  3.000
 4N3  HG23  CG2  HG22  107.81  3.000
 4N3  HG21  CG2  CB    111.55  3.000
 4N3  HG23  CG2  CB    110.20  3.000
 4N3  HG22  CG2  CB    111.64  3.000
 4N3  OXT   C    O     123.82  3.000
 4N3  OXT   C    CA    120.80  1.700
 4N3  O     C    CA    120.80  1.700
 4N3  CD    CO1  O2    122.28  3.000
 4N3  O2    CO1  N     122.96  3.000
 4N3  CD    CO1  N     114.76  3.000
 4N3  HD1   CD   HD2   106.04  3.000
 4N3  HD1   CD   CE    109.54  3.000
 4N3  HD2   CD   CE    110.12  3.000
 4N3  HD1   CD   CO1   107.20  3.000
 4N3  HD2   CD   CO1   110.54  3.000
 4N3  CE    CD   CO1   113.11  3.000
 4N3  HE2   CE   HE1   106.44  3.000
 4N3  HE2   CE   CF    109.42  3.000
 4N3  HE1   CE   CF    109.43  3.000
 4N3  HE2   CE   CD    109.59  3.000
 4N3  HE1   CE   CD    109.59  3.000
 4N3  CF    CE   CD    112.21  3.000
 4N3  HF1   CF   HF2   106.03  3.000
 4N3  HF1   CF   CH    109.40  3.000
 4N3  HF2   CF   CH    109.42  3.000
 4N3  HF1   CF   CE    109.31  3.000
 4N3  HF2   CF   CE    109.61  3.000
 4N3  CH    CF   CE    112.84  3.000
 4N3  HH2   CH   HH1   105.99  3.000
 4N3  HH2   CH   CI    109.37  3.000
 4N3  HH1   CH   CI    109.29  3.000
 4N3  HH2   CH   CF    109.37  3.000
 4N3  HH1   CH   CF    109.28  3.000
 4N3  CI    CH   CF    113.28  3.000
 4N3  HI2   CI   HI1   105.95  3.000
 4N3  HI2   CI   CJ    109.28  3.000
 4N3  HI1   CI   CJ    109.34  3.000
 4N3  HI2   CI   CH    109.32  3.000
 4N3  HI1   CI   CH    109.42  3.000
 4N3  CJ    CI   CH    113.26  3.000
 4N3  HJ2   CJ   HJ1   105.99  3.000
 4N3  HJ2   CJ   CK    109.59  3.000
 4N3  HJ1   CJ   CK    109.54  3.000
 4N3  HJ2   CJ   CI    109.29  3.000
 4N3  HJ1   CJ   CI    109.23  3.000
 4N3  CK    CJ   CI    112.96  3.000
 4N3  HK1   CK   HK2   107.65  3.000
 4N3  HK1   CK   HK3   107.61  3.000
 4N3  HK2   CK   HK3   107.42  3.000
 4N3  HK1   CK   CJ    111.60  3.000
 4N3  HK2   CK   CJ    111.14  3.000
 4N3  HK3   CK   CJ    111.22  3.000
 4N3  HXT   OXT  C     110.32  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
 4N3  CONST_01  CD    CO1  N    CA    180.00   0.0  0
 4N3  CONST_02  O2    CO1  N    CA      0.00   0.0  0
 4N3  CONST_03  H1    N    CO1  O2    180.00   0.0  0
 4N3  CONST_04  HXT   OXT  C    CA    180.00   0.0  0
 4N3  Var_01    CE    CD   CO1  N    -145.41  30.0  2
 4N3  Var_02    CF    CE   CD   CO1  -177.66  30.0  3
 4N3  Var_03    CH    CF   CE   CD    179.87  30.0  1
 4N3  Var_04    CI    CH   CF   CE   -179.35  30.0  3
 4N3  Var_05    CJ    CI   CH   CF    179.57  30.0  1
 4N3  Var_06    CK    CJ   CI   CH   -179.47  30.0  3
 4N3  Var_07    HG22  CG2  CB   CA     57.45  30.0  3
 4N3  Var_08    HG13  CG1  CB   CA     60.62  30.0  3
 4N3  Var_09    HK3   CK   CJ   CI    -60.18  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
 4N3  chir_01  CA  C  N  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
 4N3  plan-1  N    0.020
 4N3  plan-1  CA   0.020
 4N3  plan-1  CO1  0.020
 4N3  plan-1  O2   0.020
 4N3  plan-1  CD   0.020
 4N3  plan-1  H1   0.020
 4N3  plan-2  CA   0.020
 4N3  plan-2  C    0.020
 4N3  plan-2  O    0.020
 4N3  plan-2  OXT  0.020
 4N3  plan-2  HXT  0.020

