# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:06:47 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  44  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  OC    -1  -0.614  -2.9460  -2.4675   0.9987
 NLH  N    N  NH2    0  -0.794   2.2641  -1.1229  -1.5249
 NLH  CA   C  CH1    0  -0.127   2.1934  -0.4672  -0.2262
 NLH  CB   C  CH2    0  -0.416   3.3414   0.5138   0.0446
 NLH  CG   C  CH2    0  -0.419   4.7129  -0.1518  -0.0011
 NLH  CD   C  CH2    0  -0.416   5.8480   0.8035   0.3474
 NLH  CE   C  CH3    0  -0.662   7.2180   0.1417   0.2917
 NLH  OA   O  OH1    0  -0.679   0.7082   0.7918   1.2121
 NLH  OB   O  OH1    0  -0.687   0.7348   1.2044  -1.0036
 NLH  CZ   C  CH2    0  -0.497  -0.3106  -0.8722  -0.2387
 NLH  CJ   C  CH1    0  -0.313  -1.7123  -0.5394   0.3005
 NLH  CL   C  CH2    0  -0.449  -2.3260   0.7291  -0.2936
 NLH  CX   C  CH2    0  -0.405  -3.7635   0.9921   0.1435
 NLH  CV   C  CH2    0  -0.418  -4.2907   2.3356  -0.3456
 NLH  CY   C  CH3    0  -0.661  -5.7340   2.5940   0.0646
 NLH  C    C  C      0   0.408  -2.6070  -1.7684   0.0224
 NLH  O    O  O      0  -0.618  -2.9024  -1.9797  -1.1727
 NLH  HA   H  HCH1   0   0.219   2.2522  -1.2609   0.5297
 NLH  HB   H  HCH2   0   0.210   3.3134   1.3298  -0.6852
 NLH  HBA  H  HCH2   0   0.212   3.2081   0.9722   1.0278
 NLH  HG   H  HCH2   0   0.206   4.7298  -1.0007   0.6931
 NLH  HGA  H  HCH2   0   0.202   4.8985  -0.5674  -0.9972
 NLH  HD   H  HCH2   0   0.209   5.8277   1.6556  -0.3397
 NLH  HDA  H  HCH2   0   0.210   5.6800   1.2170   1.3465
 NLH  HE   H  HCH3   0   0.215   7.4273  -0.2478  -0.7065
 NLH  HEA  H  HCH3   0   0.225   8.0126   0.8454   0.5438
 NLH  HEB  H  HCH3   0   0.215   7.2834  -0.6945   0.9904
 NLH  HOA  H  HOH1   0   0.447   0.5145   0.1165   1.8710
 NLH  HOB  H  HOH1   0   0.459  -0.1764   1.4976  -1.1031
 NLH  HZ   H  HCH2   0   0.236  -0.3829  -1.1192  -1.2981
 NLH  HZA  H  HCH2   0   0.225   0.0262  -1.7911   0.2547
 NLH  HJ   H  HCH1   0   0.189  -1.6561  -0.4089   1.3864
 NLH  HL   H  HCH2   0   0.203  -1.7360   1.6021   0.0094
 NLH  HLA  H  HCH2   0   0.208  -2.2888   0.6790  -1.3871
 NLH  HX   H  HCH2   0   0.213  -4.4137   0.1955  -0.2293
 NLH  HXA  H  HCH2   0   0.204  -3.8254   0.9552   1.2369
 NLH  HV   H  HCH2   0   0.209  -3.6525   3.1370   0.0398
 NLH  HVA  H  HCH2   0   0.209  -4.2069   2.3811  -1.4361
 NLH  HY   H  HCH3   0   0.215  -6.4009   1.8260  -0.3319
 NLH  HYA  H  HCH3   0   0.215  -5.8426   2.5930   1.1509
 NLH  HYB  H  HCH3   0   0.225  -6.0881   3.5587  -0.3011
 NLH  HN   H  HNH2   0   0.334   2.3488  -0.4235  -2.2533
 NLH  CW   C  CT     0   0.504   0.8004   0.1796  -0.0590
 NLH  HNA  H  HNH2   0   0.349   3.1052  -1.6830  -1.5765

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   deloc   1.248  0.020  1.248
 NLH  N   CA   single  1.457  0.020  1.457
 NLH  N   HN   single  0.890  0.020  1.040
 NLH  N   HNA  single  0.890  0.020  1.040
 NLH  CB  CA   single  1.534  0.020  1.534
 NLH  CA  CW   single  1.545  0.020  1.545
 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  1.414  0.020  1.414
 NLH  CW  OB   single  1.395  0.020  1.395
 NLH  CW  CZ   single  1.540  0.020  1.540
 NLH  OA  HOA  single  0.850  0.020  0.980
 NLH  OB  HOB  single  0.850  0.020  0.980
 NLH  CZ  CJ   single  1.538  0.020  1.538
 NLH  CZ  HZ   single  0.970  0.020  1.090
 NLH  CZ  HZA  single  0.970  0.020  1.090
 NLH  CJ  CL   single  1.529  0.020  1.529
 NLH  CJ  C    single  1.545  0.020  1.545
 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  1.523  0.020  1.523
 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    deloc   1.249  0.020  1.249

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  HNA  N   HN   106.01  3.000
 NLH  HNA  N   CA   109.58  3.000
 NLH  HN   N   CA   109.53  3.000
 NLH  HA   CA  CW   106.05  3.000
 NLH  HA   CA  CB   107.50  3.000
 NLH  CW   CA  CB   112.82  3.000
 NLH  HA   CA  N    106.62  3.000
 NLH  CW   CA  N    109.19  3.000
 NLH  CB   CA  N    114.14  3.000
 NLH  HBA  CB  HB   106.49  3.000
 NLH  HBA  CB  CG   108.64  3.000
 NLH  HB   CB  CG   109.16  3.000
 NLH  HBA  CB  CA   109.62  3.000
 NLH  HB   CB  CA   109.86  3.000
 NLH  CG   CB  CA   112.87  3.000
 NLH  HGA  CG  HG   106.22  3.000
 NLH  HGA  CG  CD   108.64  3.000
 NLH  HG   CG  CD   109.21  3.000
 NLH  HGA  CG  CB   110.20  3.000
 NLH  HG   CG  CB   109.43  3.000
 NLH  CD   CG  CB   112.92  3.000
 NLH  HDA  CD  HD   106.02  3.000
 NLH  HDA  CD  CE   109.62  3.000
 NLH  HD   CD  CE   109.40  3.000
 NLH  HDA  CD  CG   109.35  3.000
 NLH  HD   CD  CG   109.30  3.000
 NLH  CE   CD  CG   112.92  3.000
 NLH  HEB  CE  HEA  107.61  3.000
 NLH  HEB  CE  HE   107.48  3.000
 NLH  HEA  CE  HE   107.57  3.000
 NLH  HEB  CE  CD   111.31  3.000
 NLH  HEA  CE  CD   111.51  3.000
 NLH  HE   CE  CD   111.17  3.000
 NLH  HOA  OA  CW   108.94  3.000
 NLH  HOB  OB  CW   109.77  3.000
 NLH  HZA  CZ  HZ   105.54  3.000
 NLH  HZA  CZ  CJ   107.67  3.000
 NLH  HZ   CZ  CJ   109.22  3.000
 NLH  HZA  CZ  CW   107.36  3.000
 NLH  HZ   CZ  CW   108.41  3.000
 NLH  CJ   CZ  CW   117.94  3.000
 NLH  HJ   CJ  C    107.64  3.000
 NLH  HJ   CJ  CL   107.88  3.000
 NLH  C    CJ  CL   110.94  3.000
 NLH  HJ   CJ  CZ   109.06  3.000
 NLH  C    CJ  CZ   107.00  3.000
 NLH  CL   CJ  CZ   114.14  3.000
 NLH  HLA  CL  HL   107.10  3.000
 NLH  HLA  CL  CX   109.02  3.000
 NLH  HL   CL  CX   106.90  3.000
 NLH  HLA  CL  CJ   109.65  3.000
 NLH  HL   CL  CJ   109.71  3.000
 NLH  CX   CL  CJ   114.19  3.000
 NLH  HXA  CX  HX   106.37  3.000
 NLH  HXA  CX  CV   109.29  3.000
 NLH  HX   CX  CV   109.09  3.000
 NLH  HXA  CX  CL   109.48  3.000
 NLH  HX   CX  CL   109.70  3.000
 NLH  CV   CX  CL   112.71  3.000
 NLH  HVA  CV  HV   106.00  3.000
 NLH  HVA  CV  CY   109.51  3.000
 NLH  HV   CV  CY   109.49  3.000
 NLH  HVA  CV  CX   109.26  3.000
 NLH  HV   CV  CX   109.31  3.000
 NLH  CY   CV  CX   113.02  3.000
 NLH  HYB  CY  HYA  107.58  3.000
 NLH  HYB  CY  HY   107.58  3.000
 NLH  HYA  CY  HY   107.46  3.000
 NLH  HYB  CY  CV   111.56  3.000
 NLH  HYA  CY  CV   111.24  3.000
 NLH  HY   CY  CV   111.21  3.000
 NLH  O    C   CJ   116.34  3.000
 NLH  O    C   OC   126.13  3.000
 NLH  CJ   C   OC   117.52  3.000
 NLH  CZ   CW  OB   112.87  3.000
 NLH  CZ   CW  OA   110.70  3.000
 NLH  OB   CW  OA   106.71  3.000
 NLH  CZ   CW  CA   110.60  3.000
 NLH  OB   CW  CA   106.06  3.000
 NLH  OA   CW  CA   109.72  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  Var_01  CD  CG  CB  CA  -176.66  30.0  1
 NLH  Var_02  CJ  CZ  CW  CA   161.74  30.0  3
 NLH  Var_03  CE  CD  CG  CB  -179.57  30.0  3
 NLH  Var_04  CV  CX  CL  CJ   173.86  30.0  3
 NLH  Var_05  CY  CV  CX  CL   178.92  30.0  3
 NLH  Var_06  HE  CE  CD  CG    59.92  30.0  3
 NLH  Var_07  HY  CY  CV  CX   -59.63  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

