# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:51:55 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: (4S)-4-(naphthalen-2-ylmethyl)-D-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C[C@H](Cc1ccc2ccccc2c1)C(O)=O)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
 NHL  NHL  "(4S)-4-(2-NAPHTHYLMETHYL)-D-GLUTAMIC ACID"  D-peptide  36  21  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_NHL
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
 NHL  C8    C  CR16   0  -0.312  -3.5458  -4.4855   1.0311
 NHL  C7    C  CR16   0  -0.300  -4.7365  -4.8502   0.4679
 NHL  C3    C  CR66   0   0.092  -5.0810  -4.4197  -0.8352
 NHL  C2    C  CR16   0  -0.311  -6.3007  -4.7810  -1.4535
 NHL  C1    C  CR16   0  -0.264  -6.6000  -4.3462  -2.7165
 NHL  C6    C  CR16   0  -0.260  -5.6899  -3.5281  -3.4194
 NHL  C5    C  CR16   0  -0.319  -4.5016  -3.1648  -2.8458
 NHL  C4    C  CR66   0   0.140  -4.1632  -3.6002  -1.5418
 NHL  C10   C  CR16   0  -0.381  -2.9404  -3.2439  -0.9267
 NHL  C9    C  CR6    0   0.143  -2.6174  -3.6716   0.3361
 NHL  C11   C  CH2    0  -0.491  -1.3314  -3.2751   0.9996
 NHL  CG    C  CH1    0  -0.308  -1.4813  -2.0648   1.9316
 NHL  CD    C  C      0   0.424  -1.9426  -0.8302   1.1344
 NHL  OE2   O  OC    -1  -0.618  -2.9941  -0.2644   1.4928
 NHL  OE1   O  O      0  -0.622  -1.2105  -0.4829   0.1814
 NHL  CB    C  CH2    0  -0.412  -0.1447  -1.7921   2.6211
 NHL  CA    C  CH1    0  -0.216  -0.1786  -0.6969   3.6894
 NHL  N     N  NH2    0  -0.784  -1.0938  -1.0715   4.7571
 NHL  C     C  C      0   0.381   1.2706  -0.3929   4.1431
 NHL  OXT   O  OC    -1  -0.625   1.9951   0.1959   3.3126
 NHL  O     O  O      0  -0.612   1.6136  -0.7722   5.2818
 NHL  H8    H  HCR6   0   0.243  -3.2981  -4.8304   2.0286
 NHL  H7    H  HCR6   0   0.249  -5.4289  -5.4797   1.0145
 NHL  HC2   H  HCR6   0   0.252  -6.9979  -5.4093  -0.9118
 NHL  H1    H  HCR6   0   0.254  -7.5363  -4.6281  -3.1807
 NHL  H6    H  HCR6   0   0.255  -5.9364  -3.1882  -4.4169
 NHL  H5    H  HCR6   0   0.251  -3.8041  -2.5354  -3.3859
 NHL  H10   H  HCR6   0   0.237  -2.2496  -2.6091  -1.4700
 NHL  H111  H  HCH2   0   0.226  -0.5776  -3.0471   0.2429
 NHL  H112  H  HCH2   0   0.225  -0.9479  -4.1218   1.5776
 NHL  HG    H  HCH1   0   0.198  -2.2306  -2.2933   2.6939
 NHL  HB3   H  HCH2   0   0.198   0.2160  -2.7196   3.0858
 NHL  HB2   H  HCH2   0   0.211   0.5907  -1.5236   1.8603
 NHL  H15   H  HCH1   0   0.211  -0.5704   0.2155   3.2261
 NHL  H     H  HNH2   0   0.330  -1.1989  -0.2845   5.3870
 NHL  H2    H  HNH2   0   0.318  -0.6368  -1.7799   5.3211

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
 NHL  C8   C7    aromatic  1.367  0.020  1.367
 NHL  C8   C9    aromatic  1.417  0.020  1.417
 NHL  C8   H8    single    0.930  0.020  1.080
 NHL  C7   C3    aromatic  1.415  0.020  1.415
 NHL  C7   H7    single    0.930  0.020  1.080
 NHL  C3   C2    aromatic  1.414  0.020  1.414
 NHL  C3   C4    aromatic  1.419  0.020  1.419
 NHL  C2   C1    aromatic  1.369  0.020  1.369
 NHL  C2   HC2   single    0.930  0.020  1.080
 NHL  C1   C6    aromatic  1.411  0.020  1.411
 NHL  C1   H1    single    0.930  0.020  1.080
 NHL  C6   C5    aromatic  1.369  0.020  1.369
 NHL  C6   H6    single    0.930  0.020  1.080
 NHL  C5   C4    aromatic  1.416  0.020  1.416
 NHL  C5   H5    single    0.930  0.020  1.080
 NHL  C4   C10   aromatic  1.414  0.020  1.414
 NHL  C10  C9    aromatic  1.372  0.020  1.372
 NHL  C10  H10   single    0.930  0.020  1.080
 NHL  C9   C11   single    1.500  0.020  1.500
 NHL  C11  CG    single    1.535  0.020  1.535
 NHL  C11  H111  single    0.970  0.020  1.090
 NHL  C11  H112  single    0.970  0.020  1.090
 NHL  CG   CD    single    1.540  0.020  1.540
 NHL  CG   CB    single    1.528  0.020  1.528
 NHL  CG   HG    single    0.970  0.020  1.090
 NHL  CD   OE1   deloc     1.251  0.020  1.251
 NHL  CD   OE2   deloc     1.247  0.020  1.247
 NHL  CB   CA    single    1.521  0.033  1.521
 NHL  CB   HB3   single    0.970  0.020  1.090
 NHL  CB   HB2   single    0.970  0.020  1.090
 NHL  CA   N     single    1.458  0.019  1.458
 NHL  CA   C     single    1.525  0.021  1.525
 NHL  CA   H15   single    0.970  0.020  1.090
 NHL  N    H     single    0.860  0.020  0.860
 NHL  N    H2    single    0.890  0.020  1.040
 NHL  C    O     deloc     1.231  0.020  1.231
 NHL  C    OXT   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
 NHL  H8    C8   C9    118.97  3.000
 NHL  H8    C8   C7    119.56  3.000
 NHL  C9    C8   C7    121.47  3.000
 NHL  H7    C7   C3    119.06  3.000
 NHL  H7    C7   C8    120.25  3.000
 NHL  C3    C7   C8    120.69  3.000
 NHL  C4    C3   C2    119.19  3.000
 NHL  C4    C3   C7    118.48  3.000
 NHL  C2    C3   C7    122.33  3.000
 NHL  HC2   C2   C1    120.31  3.000
 NHL  HC2   C2   C3    118.98  3.000
 NHL  C1    C2   C3    120.72  3.000
 NHL  H1    C1   C6    119.68  3.000
 NHL  H1    C1   C2    120.14  3.000
 NHL  C6    C1   C2    120.18  3.000
 NHL  H6    C6   C5    120.04  3.000
 NHL  H6    C6   C1    119.62  3.000
 NHL  C5    C6   C1    120.34  3.000
 NHL  H5    C5   C4    118.94  3.000
 NHL  H5    C5   C6    120.28  3.000
 NHL  C4    C5   C6    120.79  3.000
 NHL  C10   C4   C5    121.98  3.000
 NHL  C10   C4   C3    119.22  3.000
 NHL  C5    C4   C3    118.80  3.000
 NHL  H10   C10  C9    119.59  3.000
 NHL  H10   C10  C4    118.72  3.000
 NHL  C9    C10  C4    121.69  3.000
 NHL  C11   C9   C10   121.77  3.000
 NHL  C11   C9   C8    119.77  3.000
 NHL  C10   C9   C8    118.45  3.000
 NHL  H112  C11  H111  106.59  3.000
 NHL  H112  C11  CG    108.88  3.000
 NHL  H111  C11  CG    108.87  3.000
 NHL  H112  C11  C9    109.23  3.000
 NHL  H111  C11  C9    109.90  3.000
 NHL  CG    C11  C9    113.15  3.000
 NHL  HG    CG   CB    108.79  3.000
 NHL  HG    CG   CD    108.86  3.000
 NHL  CB    CG   CD    110.63  3.000
 NHL  HG    CG   C11   109.00  3.000
 NHL  CB    CG   C11   109.22  3.000
 NHL  CD    CG   C11   110.30  3.000
 NHL  OE1   CD   OE2   125.92  3.000
 NHL  OE2   CD   CG    117.87  3.000
 NHL  OE1   CD   CG    116.20  3.000
 NHL  HB2   CB   HB3   106.34  3.000
 NHL  HB2   CB   CA    108.99  3.000
 NHL  HB3   CB   CA    108.44  3.000
 NHL  HB2   CB   CG    108.57  3.000
 NHL  HB3   CB   CG    109.12  3.000
 NHL  CA    CB   CG    115.04  3.000
 NHL  H15   CA   C     107.16  3.000
 NHL  H15   CA   N     107.44  3.000
 NHL  C     CA   N     111.00  2.800
 NHL  H15   CA   CB    107.98  3.000
 NHL  C     CA   CB    110.50  1.500
 NHL  N     CA   CB    110.40  1.500
 NHL  H2    N    H     104.09  3.000
 NHL  H2    N    CA    107.72  3.000
 NHL  H     N    CA    114.00  3.000
 NHL  O     C    OXT   126.17  3.000
 NHL  OXT   C    CA    120.80  1.700
 NHL  O     C    CA    120.80  1.700

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
 NHL  CONST_01  C2    C3   C7   C8    180.00   0.0  0
 NHL  CONST_02  C4    C3   C7   C8      0.00   0.0  0
 NHL  CONST_03  C4    C10  C9   C8      0.00   0.0  0
 NHL  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 NHL  CONST_05  C1    C2   C3   C7    180.00   0.0  0
 NHL  CONST_06  C5    C4   C3   C7    180.00   0.0  0
 NHL  CONST_07  C10   C4   C3   C7      0.00   0.0  0
 NHL  CONST_08  C9    C8   C7   C3      0.00   0.0  0
 NHL  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 NHL  CONST_10  C6    C5   C4   C3      0.00   0.0  0
 NHL  CONST_11  C9    C10  C4   C3      0.00   0.0  0
 NHL  CONST_12  C5    C4   C3   C2      0.00   0.0  0
 NHL  CONST_13  C10   C4   C3   C2    180.00   0.0  0
 NHL  CONST_14  C5    C6   C1   C2      0.00   0.0  0
 NHL  CONST_15  C4    C3   C2   C1      0.00   0.0  0
 NHL  CONST_16  C4    C5   C6   C1      0.00   0.0  0
 NHL  CONST_17  C10   C4   C5   C6    180.00   0.0  0
 NHL  CONST_18  C9    C10  C4   C5    180.00   0.0  0
 NHL  CONST_19  C11   C9   C8   C7    180.00   0.0  0
 NHL  CONST_20  C11   C9   C10  C4    180.00   0.0  0
 NHL  CONST_21  H10   C10  C9   C8    180.00   0.0  0
 NHL  CONST_22  HC2   C2   C3   C7      0.00   0.0  0
 NHL  CONST_23  H8    C8   C7   C3    180.00   0.0  0
 NHL  CONST_24  H1    C1   C2   C3    180.00   0.0  0
 NHL  CONST_25  H5    C5   C4   C3    180.00   0.0  0
 NHL  CONST_26  H10   C10  C4   C3    180.00   0.0  0
 NHL  CONST_27  H7    C7   C3   C2      0.00   0.0  0
 NHL  CONST_28  H6    C6   C1   C2    180.00   0.0  0
 NHL  CONST_29  H5    C5   C6   C1    180.00   0.0  0
 NHL  CONST_30  HC2   C2   C1   C6    180.00   0.0  0
 NHL  CONST_31  H1    C1   C6   C5    180.00   0.0  0
 NHL  CONST_32  H10   C10  C4   C5      0.00   0.0  0
 NHL  CONST_33  H7    C7   C3   C4    180.00   0.0  0
 NHL  CONST_34  HC2   C2   C3   C4    180.00   0.0  0
 NHL  CONST_35  H6    C6   C5   C4    180.00   0.0  0
 NHL  CONST_36  H5    C5   C4   C10     0.00   0.0  0
 NHL  CONST_37  H8    C8   C9   C10   180.00   0.0  0
 NHL  CONST_38  H7    C7   C8   C9    180.00   0.0  0
 NHL  Var_01    CG    C11  C9   C8    -82.51  30.0  2
 NHL  Var_02    CG    C11  C9   C10    96.10  30.0  2
 NHL  Var_03    H111  C11  C9   C8    155.56  30.0  2
 NHL  Var_04    H112  C11  C9   C8     38.95  30.0  2
 NHL  Var_05    H111  C11  C9   C10   -25.83  30.0  2
 NHL  Var_06    H112  C11  C9   C10  -142.44  30.0  2

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
 NHL  chir_01  CG  C11  CD  CB  positiv
 NHL  chir_02  CA  N    C   CB  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
 NHL  plan-1  C8   0.020
 NHL  plan-1  C7   0.020
 NHL  plan-1  C3   0.020
 NHL  plan-1  C2   0.020
 NHL  plan-1  C1   0.020
 NHL  plan-1  C6   0.020
 NHL  plan-1  C5   0.020
 NHL  plan-1  C4   0.020
 NHL  plan-1  C10  0.020
 NHL  plan-1  C9   0.020
 NHL  plan-1  C11  0.020
 NHL  plan-1  H8   0.020
 NHL  plan-1  H7   0.020
 NHL  plan-1  HC2  0.020
 NHL  plan-1  H1   0.020
 NHL  plan-1  H6   0.020
 NHL  plan-1  H5   0.020
 NHL  plan-1  H10  0.020
 NHL  plan-2  CG   0.020
 NHL  plan-2  CD   0.020
 NHL  plan-2  OE2  0.020
 NHL  plan-2  OE1  0.020
 NHL  plan-3  CA   0.020
 NHL  plan-3  C    0.020
 NHL  plan-3  OXT  0.020
 NHL  plan-3  O    0.020

