# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 10:10:02 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2R,5S)-5-amino-2-butyl-4,4-dihydroxynonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N)C(O)(O)C[C@@H](CCCC)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
 NLH  NLH  '(2R,5S)-5-amino-2-butyl-4,4-dihydroxynonanoic acid'  ligand  45  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NLH
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
 NLH  OC   O  OH1   0  -0.588  -2.7289  -2.1096   1.6965
 NLH  N    N  NH2   0  -0.830   2.0645   0.0620  -1.7293
 NLH  CA   C  CH1   0  -0.146   2.1439  -0.2480  -0.3010
 NLH  CB   C  CH2   0  -0.439   3.3537   0.4136   0.3545
 NLH  CG   C  CH2   0  -0.414   4.6897  -0.1187  -0.1533
 NLH  CD   C  CH2   0  -0.419   5.8785   0.5354   0.5404
 NLH  CE   C  CH3   0  -0.662   7.2172   0.0100   0.0419
 NLH  OA   O  OH1   0  -0.666   0.8478   0.2946   1.7218
 NLH  OB   O  OH1   0  -0.676   0.5412   1.5195  -0.0781
 NLH  CZ   C  CH2   0  -0.498  -0.3138  -0.7682  -0.1065
 NLH  CJ   C  CH1   0  -0.348  -1.7314  -0.4093   0.3809
 NLH  CL   C  CH2   0  -0.415  -2.4542   0.5928  -0.5215
 NLH  CX   C  CH2   0  -0.421  -3.8270   1.0033   0.0004
 NLH  CV   C  CH2   0  -0.418  -4.4604   2.1117  -0.8321
 NLH  CY   C  CH3   0  -0.663  -5.8279   2.5356  -0.3149
 NLH  C    C  C     0   0.534  -2.5219  -1.6947   0.4510
 NLH  O    O  O     0  -0.451  -2.9071  -2.3092  -0.5146
 NLH  HNA  H  HNH2  0   0.365   2.0292  -0.7720  -2.2967
 NLH  HA   H  HCH1  0   0.224   2.2293  -1.3326  -0.1538
 NLH  HB   H  HCH2  0   0.216   3.3047   1.4974   0.1996
 NLH  HBA  H  HCH2  0   0.230   3.3100   0.2593   1.4342
 NLH  HG   H  HCH2  0   0.212   4.7305  -1.2029   0.0001
 NLH  HGA  H  HCH2  0   0.206   4.7838   0.0354  -1.2332
 NLH  HD   H  HCH2  0   0.212   5.8308   1.6185   0.3912
 NLH  HDA  H  HCH2  0   0.212   5.7995   0.3759   1.6202
 NLH  HE   H  HCH3  0   0.216   7.3352   0.1860  -1.0290
 NLH  HEA  H  HCH3  0   0.226   8.0523   0.4933   0.5501
 NLH  HEB  H  HCH3  0   0.216   7.3064  -1.0652   0.2085
 NLH  HOA  H  HOH1  0   0.451   0.9918  -0.5869   2.0820
 NLH  HOB  H  HOH1  0   0.444   0.7717   1.5260  -1.0221
 NLH  HZ   H  HCH2  0   0.247  -0.3151  -0.8663  -1.1954
 NLH  HZA  H  HCH2  0   0.245  -0.0258  -1.7537   0.2790
 NLH  HJ   H  HCH1  0   0.256  -1.6617   0.0059   1.3894
 NLH  HL   H  HCH2  0   0.242  -1.8301   1.4810  -0.6113
 NLH  HLA  H  HCH2  0   0.217  -2.5470   0.1752  -1.5286
 NLH  HX   H  HCH2  0   0.213  -4.5043   0.1424   0.0188
 NLH  HXA  H  HCH2  0   0.212  -3.7348   1.3405   1.0389
 NLH  HV   H  HCH2  0   0.213  -3.7896   2.9760  -0.8481
 NLH  HVA  H  HCH2  0   0.212  -4.5486   1.7784  -1.8707
 NLH  HY   H  HCH3  0   0.217  -6.5330   1.7029  -0.3351
 NLH  HYA  H  HCH3  0   0.216  -5.7681   2.8905   0.7158
 NLH  HYB  H  HCH3  0   0.227  -6.2506   3.3406  -0.9169
 NLH  HOC  H  HOH1  0   0.476  -3.2093  -2.9518   1.6883
 NLH  CW   C  CT    0   0.533   0.7940   0.2117   0.3259
 NLH  HN   H  HNH2  0   0.363   2.8681   0.5897  -2.0403

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
 NLH  C   OC   single  1.329  0.020  1.329
 NLH  N   CA   single  1.464  0.020  1.464
 NLH  N   HN   single  0.890  0.020  1.040
 NLH  N   HNA  single  0.890  0.020  1.040
 NLH  CB  CA   single  1.527  0.020  1.527
 NLH  CA  CW   single  1.558  0.020  1.558
 NLH  CA  HA   single  0.970  0.020  1.090
 NLH  CG  CB   single  1.525  0.020  1.525
 NLH  CB  HB   single  0.970  0.020  1.090
 NLH  CB  HBA  single  0.970  0.020  1.090
 NLH  CG  CD   single  1.524  0.020  1.524
 NLH  CG  HG   single  0.970  0.020  1.090
 NLH  CG  HGA  single  0.970  0.020  1.090
 NLH  CD  CE   single  1.522  0.020  1.522
 NLH  CD  HD   single  0.970  0.020  1.090
 NLH  CD  HDA  single  0.970  0.020  1.090
 NLH  CE  HE   single  0.970  0.020  1.090
 NLH  CE  HEA  single  0.970  0.020  1.090
 NLH  CE  HEB  single  0.970  0.020  1.090
 NLH  OA  CW   single  1.399  0.020  1.399
 NLH  CW  OB   single  1.392  0.020  1.392
 NLH  CW  CZ   single  1.541  0.020  1.541
 NLH  OA  HOA  single  0.850  0.020  0.980
 NLH  OB  HOB  single  0.850  0.020  0.980
 NLH  CZ  CJ   single  1.541  0.020  1.541
 NLH  CZ  HZ   single  0.970  0.020  1.090
 NLH  CZ  HZA  single  0.970  0.020  1.090
 NLH  CJ  CL   single  1.530  0.020  1.530
 NLH  CJ  C    single  1.511  0.020  1.511
 NLH  CJ  HJ   single  0.970  0.020  1.090
 NLH  CL  CX   single  1.525  0.020  1.525
 NLH  CL  HL   single  0.970  0.020  1.090
 NLH  CL  HLA  single  0.970  0.020  1.090
 NLH  CX  CV   single  1.524  0.020  1.524
 NLH  CX  HX   single  0.970  0.020  1.090
 NLH  CX  HXA  single  0.970  0.020  1.090
 NLH  CV  CY   single  1.522  0.020  1.522
 NLH  CV  HV   single  0.970  0.020  1.090
 NLH  CV  HVA  single  0.970  0.020  1.090
 NLH  CY  HY   single  0.970  0.020  1.090
 NLH  CY  HYA  single  0.970  0.020  1.090
 NLH  CY  HYB  single  0.970  0.020  1.090
 NLH  C   O    double  1.208  0.020  1.208
 NLH  OC  HOC  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
 NLH  HOC  OC  C    109.91  3.000
 NLH  HNA  N   HN   106.63  3.000
 NLH  HNA  N   CA   112.06  3.000
 NLH  HN   N   CA   111.58  3.000
 NLH  HA   CA  CW   107.75  3.000
 NLH  HA   CA  CB   108.00  3.000
 NLH  CW   CA  CB   112.71  3.000
 NLH  HA   CA  N    110.13  3.000
 NLH  CW   CA  N    106.45  3.000
 NLH  CB   CA  N    111.73  3.000
 NLH  HBA  CB  HB   106.13  3.000
 NLH  HBA  CB  CG   108.37  3.000
 NLH  HB   CB  CG   109.71  3.000
 NLH  HBA  CB  CA   109.37  3.000
 NLH  HB   CB  CA   109.42  3.000
 NLH  CG   CB  CA   113.57  3.000
 NLH  HGA  CG  HG   105.91  3.000
 NLH  HGA  CG  CD   108.76  3.000
 NLH  HG   CG  CD   109.38  3.000
 NLH  HGA  CG  CB   110.77  3.000
 NLH  HG   CG  CB   109.35  3.000
 NLH  CD   CG  CB   112.46  3.000
 NLH  HDA  CD  HD   106.00  3.000
 NLH  HDA  CD  CE   109.66  3.000
 NLH  HD   CD  CE   109.59  3.000
 NLH  HDA  CD  CG   109.28  3.000
 NLH  HD   CD  CG   109.19  3.000
 NLH  CE   CD  CG   112.88  3.000
 NLH  HEB  CE  HEA  107.63  3.000
 NLH  HEB  CE  HE   107.44  3.000
 NLH  HEA  CE  HE   107.64  3.000
 NLH  HEB  CE  CD   111.21  3.000
 NLH  HEA  CE  CD   111.58  3.000
 NLH  HE   CE  CD   111.14  3.000
 NLH  HOA  OA  CW   108.94  3.000
 NLH  HOB  OB  CW   104.19  3.000
 NLH  HZA  CZ  HZ   105.65  3.000
 NLH  HZA  CZ  CJ   109.85  3.000
 NLH  HZ   CZ  CJ   109.56  3.000
 NLH  HZA  CZ  CW   106.50  3.000
 NLH  HZ   CZ  CW   109.72  3.000
 NLH  CJ   CZ  CW   115.11  3.000
 NLH  HJ   CJ  C    108.29  3.000
 NLH  HJ   CJ  CL   109.00  3.000
 NLH  C    CJ  CL   109.72  3.000
 NLH  HJ   CJ  CZ   108.76  3.000
 NLH  C    CJ  CZ   107.33  3.000
 NLH  CL   CJ  CZ   113.60  3.000
 NLH  HLA  CL  HL   106.50  3.000
 NLH  HLA  CL  CX   109.96  3.000
 NLH  HL   CL  CX   108.94  3.000
 NLH  HLA  CL  CJ   109.44  3.000
 NLH  HL   CL  CJ   108.18  3.000
 NLH  CX   CL  CJ   113.56  3.000
 NLH  HXA  CX  HX   106.14  3.000
 NLH  HXA  CX  CV   109.20  3.000
 NLH  HX   CX  CV   108.88  3.000
 NLH  HXA  CX  CL   109.36  3.000
 NLH  HX   CX  CL   110.54  3.000
 NLH  CV   CX  CL   112.52  3.000
 NLH  HVA  CV  HV   106.02  3.000
 NLH  HVA  CV  CY   109.57  3.000
 NLH  HV   CV  CY   109.61  3.000
 NLH  HVA  CV  CX   109.30  3.000
 NLH  HV   CV  CX   109.13  3.000
 NLH  CY   CV  CX   112.97  3.000
 NLH  HYB  CY  HYA  107.60  3.000
 NLH  HYB  CY  HY   107.61  3.000
 NLH  HYA  CY  HY   107.51  3.000
 NLH  HYB  CY  CV   111.49  3.000
 NLH  HYA  CY  CV   111.23  3.000
 NLH  HY   CY  CV   111.20  3.000
 NLH  O    C   CJ   124.25  3.000
 NLH  O    C   OC   122.74  3.000
 NLH  CJ   C   OC   112.99  3.000
 NLH  CZ   CW  OB   112.67  3.000
 NLH  CZ   CW  OA   110.20  3.000
 NLH  OB   CW  OA   103.93  3.000
 NLH  CZ   CW  CA   108.81  3.000
 NLH  OB   CW  CA   108.53  3.000
 NLH  OA   CW  CA   112.68  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
 NLH  CONST_01  HOC  OC  C   CJ   180.00   0.0  0
 NLH  Var_01    CD   CG  CB  CA  -178.67  30.0  1
 NLH  Var_02    CJ   CZ  CW  CA  -177.20  30.0  3
 NLH  Var_03    CE   CD  CG  CB   179.93  30.0  3
 NLH  Var_04    CV   CX  CL  CJ   173.77  30.0  3
 NLH  Var_05    CY   CV  CX  CL  -179.64  30.0  3
 NLH  Var_06    HE   CE  CD  CG    59.71  30.0  3
 NLH  Var_07    HY   CY  CV  CX   -60.90  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
 NLH  chir_01  CA  N   CB  CW  negativ
 NLH  chir_02  CJ  CZ  CL  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
 NLH  plan-1  OC   0.020
 NLH  plan-1  CJ   0.020
 NLH  plan-1  C    0.020
 NLH  plan-1  O    0.020
 NLH  plan-1  HOC  0.020

