# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 15:57:00 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: N-dodecanoyl-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=O)N[C@@H](Cc1ccc(O)cc1)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
 NLT  NLT  'N-dodecanoyl-L-tyrosine  '  ligand  59  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NLT
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
 NLT  N     N  NH1   0  -0.639  -2.9355  -1.0110  -0.4676
 NLT  C1    C  C     0   0.576  -1.7799  -1.3453   0.1445
 NLT  OL    O  O     0  -0.494  -1.7648  -1.9317   1.2160
 NLT  C2    C  CH2   0  -0.592  -0.5263  -0.9557  -0.6046
 NLT  C3    C  CH2   0  -0.413   0.6969  -0.7928   0.2840
 NLT  C4    C  CH2   0  -0.415   1.9575  -0.5109  -0.5237
 NLT  C5    C  CH2   0  -0.412   3.1976  -0.3579   0.3473
 NLT  C6    C  CH2   0  -0.412   4.4711  -0.1210  -0.4544
 NLT  C7    C  CH2   0  -0.412   5.7126   0.0121   0.4186
 NLT  C8    C  CH2   0  -0.411   6.9926   0.2277  -0.3788
 NLT  C9    C  CH2   0  -0.411   8.2347   0.3348   0.4971
 NLT  C10   C  CH2   0  -0.406   9.5177   0.5428  -0.2975
 NLT  C11   C  CH2   0  -0.419  10.7630   0.6217   0.5775
 NLT  C12   C  CH3   0  -0.662  12.0374   0.8379  -0.2265
 NLT  CA    C  CH1   0  -0.172  -4.2040  -1.4762   0.0125
 NLT  CB    C  CH2   0  -0.568  -5.3489  -0.7158  -0.6776
 NLT  CG    C  CR6   0   0.133  -5.2987   0.7578  -0.3855
 NLT  CD2   C  CR16  0  -0.288  -5.7313   1.2552   0.8403
 NLT  CE2   C  CR16  0  -0.368  -5.6702   2.6084   1.1340
 NLT  CZ    C  CR6   0   0.340  -5.1682   3.5035   0.1919
 NLT  CE1   C  CR16  0  -0.323  -4.7339   3.0234  -1.0406
 NLT  CD1   C  CR16  0  -0.311  -4.8018   1.6664  -1.3152
 NLT  OH    O  OH1   0  -0.633  -5.0870   4.8305   0.4180
 NLT  C     C  C     0   0.542  -4.3521  -2.9741  -0.2188
 NLT  O     O  OH1   0  -0.591  -5.3593  -3.4704   0.4854
 NLT  O2    O  O     0  -0.429  -3.6628  -3.6232  -0.9604
 NLT  HN    H  HNH1  0   0.400  -2.8905  -0.6323  -1.4006
 NLT  H21   H  HCH2  0   0.255  -0.7039  -0.0446  -1.1827
 NLT  H22   H  HCH2  0   0.271  -0.3432  -1.7443  -1.3437
 NLT  H31   H  HCH2  0   0.223   0.8429  -1.6985   0.8772
 NLT  H32   H  HCH2  0   0.223   0.5304   0.0199   0.9975
 NLT  H41   H  HCH2  0   0.211   1.8179   0.3959  -1.1222
 NLT  H42   H  HCH2  0   0.211   2.1163  -1.3244  -1.2404
 NLT  H51   H  HCH2  0   0.207   3.3201  -1.2569   0.9619
 NLT  H52   H  HCH2  0   0.209   3.0499   0.4696   1.0500
 NLT  H61   H  HCH2  0   0.207   4.3560   0.7814  -1.0654
 NLT  H62   H  HCH2  0   0.207   4.6128  -0.9469  -1.1604
 NLT  H71   H  HCH2  0   0.206   5.8178  -0.8878   1.0354
 NLT  H72   H  HCH2  0   0.207   5.5766   0.8428   1.1201
 NLT  H81   H  HCH2  0   0.206   6.8958   1.1349  -0.9859
 NLT  H82   H  HCH2  0   0.206   7.1212  -0.5973  -1.0884
 NLT  H91   H  HCH2  0   0.205   8.3274  -0.5727   1.1046
 NLT  H92   H  HCH2  0   0.206   8.1087   1.1606   1.2063
 NLT  H101  H  HCH2  0   0.205   9.4338   1.4598  -0.8920
 NLT  H102  H  HCH2  0   0.205   9.6355  -0.2739  -1.0188
 NLT  H111  H  HCH2  0   0.210  10.8493  -0.2981   1.1647
 NLT  H112  H  HCH2  0   0.210  10.6443   1.4330   1.3023
 NLT  H121  H  HCH3  0   0.225  12.9183   0.8771   0.4154
 NLT  H122  H  HCH3  0   0.215  12.1902   0.0324  -0.9478
 NLT  H123  H  HCH3  0   0.215  11.9956   1.7745  -0.7860
 NLT  HA    H  HCH1  0   0.295  -4.2701  -1.2955   1.0890
 NLT  HB1   H  HCH2  0   0.272  -5.2995  -0.8892  -1.7564
 NLT  HB2   H  HCH2  0   0.284  -6.2974  -1.1333  -0.3369
 NLT  HD2   H  HCR6  0   0.254  -6.1318   0.5778   1.5863
 NLT  HE2   H  HCR6  0   0.271  -6.0211   2.9662   2.0956
 NLT  HE1   H  HCR6  0   0.262  -4.3474   3.7122  -1.7817
 NLT  HD1   H  HCR6  0   0.251  -4.4662   1.3137  -2.2836
 NLT  HOH   H  HOH1  0   0.474  -5.4225   5.0437   1.2959
 NLT  HO    H  HOH1  0   0.485  -5.4679  -4.4153   0.2993

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
 NLT  N    C1    single    1.350  0.020  1.350
 NLT  N    CA    single    1.434  0.020  1.434
 NLT  N    HN    single    0.860  0.020  1.020
 NLT  C1   OL    double    1.222  0.020  1.222
 NLT  C1   C2    single    1.511  0.020  1.511
 NLT  C2   C3    single    1.521  0.020  1.521
 NLT  C2   H21   single    0.970  0.020  1.090
 NLT  C2   H22   single    0.970  0.020  1.090
 NLT  C3   C4    single    1.523  0.020  1.523
 NLT  C3   H31   single    0.970  0.020  1.090
 NLT  C3   H32   single    0.970  0.020  1.090
 NLT  C4   C5    single    1.523  0.020  1.523
 NLT  C4   H41   single    0.970  0.020  1.090
 NLT  C4   H42   single    0.970  0.020  1.090
 NLT  C5   C6    single    1.523  0.020  1.523
 NLT  C5   H51   single    0.970  0.020  1.090
 NLT  C5   H52   single    0.970  0.020  1.090
 NLT  C6   C7    single    1.523  0.020  1.523
 NLT  C6   H61   single    0.970  0.020  1.090
 NLT  C6   H62   single    0.970  0.020  1.090
 NLT  C7   C8    single    1.523  0.020  1.523
 NLT  C7   H71   single    0.970  0.020  1.090
 NLT  C7   H72   single    0.970  0.020  1.090
 NLT  C8   C9    single    1.524  0.020  1.524
 NLT  C8   H81   single    0.970  0.020  1.090
 NLT  C8   H82   single    0.970  0.020  1.090
 NLT  C9   C10   single    1.523  0.020  1.523
 NLT  C9   H91   single    0.970  0.020  1.090
 NLT  C9   H92   single    0.970  0.020  1.090
 NLT  C10  C11   single    1.524  0.020  1.524
 NLT  C10  H101  single    0.970  0.020  1.090
 NLT  C10  H102  single    0.970  0.020  1.090
 NLT  C11  C12   single    1.522  0.020  1.522
 NLT  C11  H111  single    0.970  0.020  1.090
 NLT  C11  H112  single    0.970  0.020  1.090
 NLT  C12  H121  single    0.970  0.020  1.090
 NLT  C12  H122  single    0.970  0.020  1.090
 NLT  C12  H123  single    0.970  0.020  1.090
 NLT  CA   CB    single    1.538  0.020  1.538
 NLT  CA   C     single    1.523  0.020  1.523
 NLT  CA   HA    single    0.970  0.020  1.090
 NLT  CB   CG    single    1.503  0.020  1.503
 NLT  CB   HB1   single    0.970  0.020  1.090
 NLT  CB   HB2   single    0.970  0.020  1.090
 NLT  CG   CD2   aromatic  1.392  0.020  1.392
 NLT  CG   CD1   aromatic  1.392  0.020  1.392
 NLT  CD2  CE2   aromatic  1.386  0.020  1.386
 NLT  CD2  HD2   single    0.930  0.020  1.080
 NLT  CE2  CZ    aromatic  1.393  0.020  1.393
 NLT  CE2  HE2   single    0.930  0.020  1.080
 NLT  CZ   CE1   aromatic  1.392  0.020  1.392
 NLT  CZ   OH    single    1.349  0.020  1.349
 NLT  CE1  CD1   aromatic  1.386  0.020  1.386
 NLT  CE1  HE1   single    0.930  0.020  1.080
 NLT  CD1  HD1   single    0.930  0.020  1.080
 NLT  OH   HOH   single    0.850  0.020  0.980
 NLT  C    O     single    1.325  0.020  1.325
 NLT  C    O2    double    1.203  0.020  1.203
 NLT  O    HO    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
 NLT  HN    N    CA    118.12  3.000
 NLT  HN    N    C1    118.33  3.000
 NLT  CA    N    C1    121.68  3.000
 NLT  C2    C1   OL    123.25  3.000
 NLT  C2    C1   N     114.93  3.000
 NLT  OL    C1   N     121.82  3.000
 NLT  H22   C2   H21   105.67  3.000
 NLT  H22   C2   C3    109.68  3.000
 NLT  H21   C2   C3    110.50  3.000
 NLT  H22   C2   C1    106.70  3.000
 NLT  H21   C2   C1    110.00  3.000
 NLT  C3    C2   C1    113.90  3.000
 NLT  H32   C3   H31   106.38  3.000
 NLT  H32   C3   C4    109.53  3.000
 NLT  H31   C3   C4    109.31  3.000
 NLT  H32   C3   C2    109.77  3.000
 NLT  H31   C3   C2    109.63  3.000
 NLT  C4    C3   C2    112.06  3.000
 NLT  H42   C4   H41   106.00  3.000
 NLT  H42   C4   C5    109.31  3.000
 NLT  H41   C4   C5    109.45  3.000
 NLT  H42   C4   C3    109.23  3.000
 NLT  H41   C4   C3    109.72  3.000
 NLT  C5    C4   C3    112.90  3.000
 NLT  H52   C5   H51   105.96  3.000
 NLT  H52   C5   C6    109.43  3.000
 NLT  H51   C5   C6    109.22  3.000
 NLT  H52   C5   C4    109.45  3.000
 NLT  H51   C5   C4    109.23  3.000
 NLT  C6    C5   C4    113.29  3.000
 NLT  H62   C6   H61   105.96  3.000
 NLT  H62   C6   C7    109.25  3.000
 NLT  H61   C6   C7    109.46  3.000
 NLT  H62   C6   C5    109.26  3.000
 NLT  H61   C6   C5    109.49  3.000
 NLT  C7    C6   C5    113.16  3.000
 NLT  H72   C7   H71   105.91  3.000
 NLT  H72   C7   C8    109.39  3.000
 NLT  H71   C7   C8    109.27  3.000
 NLT  H72   C7   C6    109.39  3.000
 NLT  H71   C7   C6    109.21  3.000
 NLT  C8    C7   C6    113.40  3.000
 NLT  H82   C8   H81   105.95  3.000
 NLT  H82   C8   C9    109.24  3.000
 NLT  H81   C8   C9    109.40  3.000
 NLT  H82   C8   C7    109.33  3.000
 NLT  H81   C8   C7    109.44  3.000
 NLT  C9    C8   C7    113.21  3.000
 NLT  H92   C9   H91   105.96  3.000
 NLT  H92   C9   C10   109.37  3.000
 NLT  H91   C9   C10   109.33  3.000
 NLT  H92   C9   C8    109.35  3.000
 NLT  H91   C9   C8    109.23  3.000
 NLT  C10   C9   C8    113.35  3.000
 NLT  H102  C10  H101  105.94  3.000
 NLT  H102  C10  C11   109.18  3.000
 NLT  H101  C10  C11   109.31  3.000
 NLT  H102  C10  C9    109.40  3.000
 NLT  H101  C10  C9    109.43  3.000
 NLT  C11   C10  C9    113.32  3.000
 NLT  H112  C11  H111  106.03  3.000
 NLT  H112  C11  C12   109.59  3.000
 NLT  H111  C11  C12   109.67  3.000
 NLT  H112  C11  C10   109.27  3.000
 NLT  H111  C11  C10   109.20  3.000
 NLT  C12   C11  C10   112.84  3.000
 NLT  H123  C12  H122  107.44  3.000
 NLT  H123  C12  H121  107.56  3.000
 NLT  H122  C12  H121  107.60  3.000
 NLT  H123  C12  C11   111.12  3.000
 NLT  H122  C12  C11   111.18  3.000
 NLT  H121  C12  C11   111.74  3.000
 NLT  HA    CA   C     107.83  3.000
 NLT  HA    CA   CB    108.36  3.000
 NLT  C     CA   CB    110.23  3.000
 NLT  HA    CA   N     109.24  3.000
 NLT  C     CA   N     110.75  3.000
 NLT  CB    CA   N     110.36  3.000
 NLT  HB2   CB   HB1   106.65  3.000
 NLT  HB2   CB   CG    110.09  3.000
 NLT  HB1   CB   CG    110.22  3.000
 NLT  HB2   CB   CA    108.54  3.000
 NLT  HB1   CB   CA    109.31  3.000
 NLT  CG    CB   CA    111.88  3.000
 NLT  CD1   CG   CD2   117.78  3.000
 NLT  CD1   CG   CB    121.48  3.000
 NLT  CD2   CG   CB    120.74  3.000
 NLT  HD2   CD2  CE2   118.71  3.000
 NLT  HD2   CD2  CG    119.83  3.000
 NLT  CE2   CD2  CG    121.46  3.000
 NLT  HE2   CE2  CZ    120.29  3.000
 NLT  HE2   CE2  CD2   119.72  3.000
 NLT  CZ    CE2  CD2   119.99  3.000
 NLT  OH    CZ   CE1   117.97  3.000
 NLT  OH    CZ   CE2   122.72  3.000
 NLT  CE1   CZ   CE2   119.31  3.000
 NLT  HE1   CE1  CD1   120.30  3.000
 NLT  HE1   CE1  CZ    119.86  3.000
 NLT  CD1   CE1  CZ    119.85  3.000
 NLT  HD1   CD1  CE1   118.71  3.000
 NLT  HD1   CD1  CG    119.67  3.000
 NLT  CE1   CD1  CG    121.62  3.000
 NLT  HOH   OH   CZ    110.46  3.000
 NLT  O2    C    O     124.13  3.000
 NLT  O2    C    CA    124.66  3.000
 NLT  O     C    CA    111.19  3.000
 NLT  HO    O    C     110.38  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
 NLT  CONST_01  CZ    CE2  CD2  CG      0.00   0.0  0
 NLT  CONST_02  CZ    CE1  CD1  CG      0.00   0.0  0
 NLT  CONST_03  CE1   CD1  CG   CD2     0.00   0.0  0
 NLT  CONST_04  CE1   CZ   CE2  CD2     0.00   0.0  0
 NLT  CONST_05  CD1   CG   CD2  CE2     0.00   0.0  0
 NLT  CONST_06  CD1   CE1  CZ   CE2     0.00   0.0  0
 NLT  CONST_07  CE2   CD2  CG   CB    180.00   0.0  0
 NLT  CONST_08  CE1   CD1  CG   CB    180.00   0.0  0
 NLT  CONST_09  OH    CZ   CE2  CD2   180.00   0.0  0
 NLT  CONST_10  OH    CZ   CE1  CD1   180.00   0.0  0
 NLT  CONST_11  HE2   CE2  CD2  CG    180.00   0.0  0
 NLT  CONST_12  HE1   CE1  CD1  CG    180.00   0.0  0
 NLT  CONST_13  HD1   CD1  CG   CD2   180.00   0.0  0
 NLT  CONST_14  HD2   CD2  CE2  CZ    180.00   0.0  0
 NLT  CONST_15  CA    N    C1   OL      0.00   0.0  0
 NLT  CONST_16  CA    N    C1   C2    180.00   0.0  0
 NLT  CONST_17  HN    N    C1   OL    180.00   0.0  0
 NLT  CONST_18  HO    O    C    CA    180.00   0.0  0
 NLT  Var_01    CD2   CG   CB   CA    -77.14  30.0  2
 NLT  Var_02    C3    C2   C1   N     155.83  30.0  3
 NLT  Var_03    C4    C3   C2   C1    175.40  30.0  3
 NLT  Var_04    C5    C4   C3   C2   -179.43  30.0  3
 NLT  Var_05    C6    C5   C4   C3    178.12  30.0  3
 NLT  Var_06    C7    C6   C5   C4   -179.19  30.0  3
 NLT  Var_07    C8    C7   C6   C5    179.11  30.0  3
 NLT  Var_08    C9    C8   C7   C6   -178.95  30.0  3
 NLT  Var_09    C10   C9   C8   C7    179.68  30.0  3
 NLT  Var_10    C11   C10  C9   C8   -178.84  30.0  3
 NLT  Var_11    C12   C11  C10  C9   -179.65  30.0  3
 NLT  Var_12    H121  C12  C11  C10  -179.17  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
 NLT  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
 NLT  plan-1  CB   0.020
 NLT  plan-1  CG   0.020
 NLT  plan-1  CD2  0.020
 NLT  plan-1  CE2  0.020
 NLT  plan-1  CZ   0.020
 NLT  plan-1  CE1  0.020
 NLT  plan-1  CD1  0.020
 NLT  plan-1  OH   0.020
 NLT  plan-1  HD2  0.020
 NLT  plan-1  HE2  0.020
 NLT  plan-1  HE1  0.020
 NLT  plan-1  HD1  0.020
 NLT  plan-2  N    0.020
 NLT  plan-2  C1   0.020
 NLT  plan-2  OL   0.020
 NLT  plan-2  C2   0.020
 NLT  plan-2  CA   0.020
 NLT  plan-2  HN   0.020
 NLT  plan-3  CA   0.020
 NLT  plan-3  C    0.020
 NLT  plan-3  O    0.020
 NLT  plan-3  O2   0.020
 NLT  plan-3  HO   0.020

