# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 03:34:52 2020
#   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-(naphthalen-2-ylmethyl)-D-glutamic acid'  D-peptide  38  21  .  2022-09-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.301  -3.6300  -4.3152   1.0726
 NHL  C7    C  CR16  0  -0.297  -4.8274  -4.6511   0.5081
 NHL  C3    C  CR66  0   0.096  -5.1269  -4.2858  -0.8265
 NHL  C2    C  CR16  0  -0.310  -6.3527  -4.6244  -1.4446
 NHL  C1    C  CR16  0  -0.261  -6.6066  -4.2575  -2.7388
 NHL  C6    C  CR16  0  -0.259  -5.6448  -3.5330  -3.4739
 NHL  C5    C  CR16  0  -0.316  -4.4492  -3.1930  -2.9007
 NHL  C4    C  CR66  0   0.140  -4.1583  -3.5606  -1.5658
 NHL  C10   C  CR16  0  -0.385  -2.9278  -3.2310  -0.9495
 NHL  C9    C  CR6   0   0.129  -2.6522  -3.5964   0.3420
 NHL  C11   C  CH2   0  -0.502  -1.3463  -3.2354   0.9893
 NHL  CG    C  CH1   0  -0.346  -1.4671  -2.1222   2.0476
 NHL  CD    C  C     0   0.560  -2.0703  -0.9031   1.3937
 NHL  OE2   O  OH1   0  -0.579  -3.3484  -0.7310   1.6957
 NHL  OE1   O  O     0  -0.449  -1.4651  -0.1757   0.6427
 NHL  CB    C  CH2   0  -0.436  -0.0864  -1.8223   2.6270
 NHL  CA    C  CH1   0  -0.221  -0.0774  -0.6819   3.6559
 NHL  N     N  NH2   0  -0.774  -1.1174  -0.8603   4.6366
 NHL  C     C  C     0   0.525   1.3200  -0.5760   4.2543
 NHL  OXT   O  OH1   0  -0.593   2.2134  -0.1599   3.3644
 NHL  O     O  O     0  -0.437   1.5975  -0.8451   5.3960
 NHL  H8    H  HCR6  0   0.250  -3.4185  -4.6075   2.0946
 NHL  H7    H  HCR6  0   0.253  -5.5614  -5.2089   1.0775
 NHL  HC2   H  HCR6  0   0.254  -7.0903  -5.1817  -0.8795
 NHL  H1    H  HCR6  0   0.257  -7.5476  -4.5224  -3.2033
 NHL  H6    H  HCR6  0   0.257  -5.8572  -3.2466  -4.4957
 NHL  H5    H  HCR6  0   0.253  -3.7107  -2.6357  -3.4648
 NHL  H10   H  HCR6  0   0.248  -2.1909  -2.6797  -1.5238
 NHL  H111  H  HCH2  0   0.256  -0.6283  -2.9290   0.2254
 NHL  H112  H  HCH2  0   0.266  -0.9226  -4.1130   1.4843
 NHL  HG    H  HCH1  0   0.274  -2.1271  -2.4607   2.8473
 NHL  HE2   H  HOH1  0   0.476  -3.7032   0.0303   1.2114
 NHL  HB3   H  HCH2  0   0.255   0.2755  -2.7406   3.0999
 NHL  HB2   H  HCH2  0   0.255   0.6109  -1.5919   1.8198
 NHL  H15   H  HCH1  0   0.277  -0.2667   0.2594   3.1306
 NHL  H     H  HNH2  0   0.357  -1.1501  -0.0680   5.2648
 NHL  H2    H  HNH2  0   0.345  -0.9305  -1.6734   5.2109
 NHL  HXT   H  HOH1  0   0.482   3.0954  -0.1296   3.7650

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  1.366  0.020  1.366
 NHL  C8   C9    aromatic  1.417  0.020  1.417
 NHL  C8   H8    single    0.930  0.020  1.080
 NHL  C7   C3    aromatic  1.416  0.020  1.416
 NHL  C7   H7    single    0.930  0.020  1.080
 NHL  C3   C2    aromatic  1.414  0.020  1.414
 NHL  C3   C4    aromatic  1.418  0.020  1.418
 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  1.415  0.020  1.415
 NHL  C5   H5    single    0.930  0.020  1.080
 NHL  C4   C10   aromatic  1.415  0.020  1.415
 NHL  C10  C9    aromatic  1.370  0.020  1.370
 NHL  C10  H10   single    0.930  0.020  1.080
 NHL  C9   C11   single    1.502  0.020  1.502
 NHL  C11  CG    single    1.541  0.020  1.541
 NHL  C11  H111  single    0.970  0.020  1.090
 NHL  C11  H112  single    0.970  0.020  1.090
 NHL  CG   CD    single    1.509  0.020  1.509
 NHL  CG   CB    single    1.527  0.020  1.527
 NHL  CG   HG    single    0.970  0.020  1.090
 NHL  CD   OE1   double    1.208  0.020  1.208
 NHL  CD   OE2   single    1.325  0.020  1.325
 NHL  OE2  HE2   single    0.850  0.020  0.980
 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     double    1.231  0.020  1.231
 NHL  C    OXT   single    1.328  0.020  1.328
 NHL  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
 NHL  H8    C8   C9    119.24  3.000
 NHL  H8    C8   C7    119.64  3.000
 NHL  C9    C8   C7    121.12  3.000
 NHL  H7    C7   C3    119.01  3.000
 NHL  H7    C7   C8    120.22  3.000
 NHL  C3    C7   C8    120.77  3.000
 NHL  C4    C3   C2    119.13  3.000
 NHL  C4    C3   C7    118.62  3.000
 NHL  C2    C3   C7    122.25  3.000
 NHL  HC2   C2   C1    120.31  3.000
 NHL  HC2   C2   C3    119.04  3.000
 NHL  C1    C2   C3    120.65  3.000
 NHL  H1    C1   C6    119.66  3.000
 NHL  H1    C1   C2    120.09  3.000
 NHL  C6    C1   C2    120.25  3.000
 NHL  H6    C6   C5    120.06  3.000
 NHL  H6    C6   C1    119.61  3.000
 NHL  C5    C6   C1    120.33  3.000
 NHL  H5    C5   C4    118.99  3.000
 NHL  H5    C5   C6    120.34  3.000
 NHL  C4    C5   C6    120.67  3.000
 NHL  C10   C4   C5    121.95  3.000
 NHL  C10   C4   C3    119.08  3.000
 NHL  C5    C4   C3    118.97  3.000
 NHL  H10   C10  C9    119.86  3.000
 NHL  H10   C10  C4    118.59  3.000
 NHL  C9    C10  C4    121.56  3.000
 NHL  C11   C9   C10   121.14  3.000
 NHL  C11   C9   C8    120.00  3.000
 NHL  C10   C9   C8    118.86  3.000
 NHL  H112  C11  H111  106.69  3.000
 NHL  H112  C11  CG    107.43  3.000
 NHL  H111  C11  CG    109.22  3.000
 NHL  H112  C11  C9    109.83  3.000
 NHL  H111  C11  C9    109.74  3.000
 NHL  CG    C11  C9    113.68  3.000
 NHL  HG    CG   CB    109.26  3.000
 NHL  HG    CG   CD    109.06  3.000
 NHL  CB    CG   CD    111.54  3.000
 NHL  HG    CG   C11   109.07  3.000
 NHL  CB    CG   C11   109.37  3.000
 NHL  CD    CG   C11   108.51  3.000
 NHL  OE1   CD   OE2   123.16  3.000
 NHL  OE2   CD   CG    113.07  3.000
 NHL  OE1   CD   CG    123.74  3.000
 NHL  HE2   OE2  CD    109.95  3.000
 NHL  HB2   CB   HB3   106.59  3.000
 NHL  HB2   CB   CA    109.57  3.000
 NHL  HB3   CB   CA    109.36  3.000
 NHL  HB2   CB   CG    109.78  3.000
 NHL  HB3   CB   CG    107.35  3.000
 NHL  CA    CB   CG    113.91  3.000
 NHL  H15   CA   C     106.69  3.000
 NHL  H15   CA   N     107.97  3.000
 NHL  C     CA   N     111.00  2.800
 NHL  H15   CA   CB    108.42  3.000
 NHL  C     CA   CB    110.50  1.500
 NHL  N     CA   CB    110.40  1.500
 NHL  H2    N    H     106.42  3.000
 NHL  H2    N    CA    110.62  3.000
 NHL  H     N    CA    114.00  3.000
 NHL  O     C    OXT   123.35  3.000
 NHL  OXT   C    CA    120.80  1.700
 NHL  O     C    CA    120.80  1.700
 NHL  HXT   OXT  C     110.19  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
 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  H7   C7   C3   C2    0.00   0.0  0
 NHL  CONST_27  H6   C6   C1   C2  180.00   0.0  0
 NHL  CONST_28  HE2  OE2  CD   CG  180.00   0.0  0
 NHL  CONST_29  HXT  OXT  C    CA  180.00   0.0  0
 NHL  Var_01    CG   C11  C9   C8  -72.19  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-2  HE2  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
 NHL  plan-3  HXT  0.020

