# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 09:16:55 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)N[C@@H](CCC(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
 9NE  9NE  'N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-glutamic acid'  L-peptide  44  26  .  2012-08-28  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_9NE
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
 9NE  N     N  NC1    0  -0.741  27.8315   7.5940  31.5727
 9NE  CA    C  CH1    0  -0.225  27.2429   6.2714  31.7912
 9NE  C     C  C      0   0.437  26.9991   5.5651  30.4245
 9NE  O     O  O      0  -0.588  25.9380   4.9284  30.2992
 9NE  CB    C  CH2    0  -0.405  26.0138   6.3593  32.6893
 9NE  CG    C  CH2    0  -0.578  26.2871   6.9263  34.0740
 9NE  CD    C  C      0   0.401  27.2485   6.1032  34.9565
 9NE  OE1   O  O      0  -0.619  27.8399   6.7257  35.8626
 9NE  OE2   O  OC    -1  -0.609  27.3292   4.8781  34.7259
 9NE  OXT   O  OC    -1  -0.588  27.9144   5.6581  29.5830
 9NE  S1    S  S      0   1.379  29.2497   8.1014  32.1883
 9NE  O2    O  OS     0  -0.653  29.0738   9.0674  33.2678
 9NE  O3    O  OS     0  -0.664  30.0369   6.9129  32.4954
 9NE  C1    C  CR6    0  -0.278  30.0088   8.9009  30.7682
 9NE  C2    C  CR16   0  -0.222  30.1726   8.0418  29.7086
 9NE  C3    C  CR16   0  -0.259  30.7800   8.4783  28.5263
 9NE  C4    C  CR16   0  -0.290  31.2443   9.7606  28.4325
 9NE  C5    C  CR66   0   0.037  31.1171  10.6655  29.5070
 9NE  C6    C  CR66   0   0.140  30.4457  10.2582  30.7024
 9NE  C7    C  CR16   0  -0.374  30.2178  11.2364  31.7042
 9NE  C8    C  CR16   0  -0.230  30.6306  12.5246  31.5170
 9NE  C9    C  CR16   0  -0.338  31.3377  12.9158  30.3676
 9NE  C10   C  CR6    0   0.295  31.6108  12.0062  29.3766
 9NE  N1    N  NT     0  -0.490  32.3289  12.3416  28.2165
 9NE  C11   C  CH3    0  -0.543  32.2975  13.7334  27.8217
 9NE  C12   C  CH3    0  -0.541  33.6823  11.8066  28.1640
 9NE  H     H  HNC1   0   0.406  27.1871   8.3452  31.3550
 9NE  H111  H  HCH3   0   0.209  32.9023  14.3902  28.4614
 9NE  H112  H  HCH3   0   0.247  32.6870  13.8197  26.8067
 9NE  H113  H  HCH3   0   0.246  31.2733  14.1048  27.8207
 9NE  H121  H  HCH3   0   0.238  34.0683  11.8882  27.1474
 9NE  H122  H  HCH3   0   0.219  34.3649  12.3477  28.8325
 9NE  H123  H  HCH3   0   0.250  33.7050  10.7556  28.4447
 9NE  H2    H  HCR6   0   0.303  29.7715   7.0366  29.7568
 9NE  H3    H  HCR6   0   0.263  30.8649   7.8006  27.6876
 9NE  H4    H  HCR6   0   0.273  31.6874  10.1037  27.5080
 9NE  H7    H  HCR6   0   0.275  29.6966  10.9760  32.6081
 9NE  H8    H  HCR6   0   0.257  30.4298  13.2616  32.2840
 9NE  H9    H  HCR6   0   0.264  31.6786  13.9390  30.2858
 9NE  HA    H  HCH1   0   0.254  27.9907   5.6676  32.3088
 9NE  HB1C  H  HCH2   0   0.201  25.2464   6.9616  32.1907
 9NE  HB2C  H  HCH2   0   0.213  25.5966   5.3581  32.7843
 9NE  HG1C  H  HCH2   0   0.202  26.6436   7.9568  34.0095
 9NE  HG2C  H  HCH2   0   0.225  25.3327   6.9896  34.6114

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
 9NE  S1   O2    double    1.459  0.020  1.459
 9NE  S1   O3    double    1.458  0.020  1.458
 9NE  S1   C1    single    1.798  0.020  1.798
 9NE  S1   N     single    1.627  0.020  1.627
 9NE  OXT  C     deloc     1.247  0.020  1.247
 9NE  N1   C10   single    1.405  0.020  1.405
 9NE  N1   C11   single    1.447  0.020  1.447
 9NE  N1   C12   single    1.456  0.020  1.456
 9NE  C1   C2    aromatic  1.374  0.020  1.374
 9NE  C1   C6    aromatic  1.427  0.020  1.427
 9NE  C2   C3    aromatic  1.399  0.020  1.399
 9NE  C3   C4    aromatic  1.367  0.020  1.367
 9NE  C4   C5    aromatic  1.411  0.020  1.411
 9NE  C5   C6    aromatic  1.430  0.020  1.430
 9NE  C5   C10   aromatic  1.435  0.020  1.435
 9NE  C6   C7    aromatic  1.419  0.020  1.419
 9NE  C7   C8    aromatic  1.366  0.020  1.366
 9NE  C8   C9    aromatic  1.405  0.020  1.405
 9NE  C9   C10   aromatic  1.373  0.020  1.373
 9NE  N    CA    single    1.458  0.019  1.458
 9NE  CA   C     single    1.525  0.021  1.525
 9NE  CA   CB    single    1.530  0.020  1.530
 9NE  C    O     deloc     1.231  0.020  1.231
 9NE  CB   CG    single    1.521  0.020  1.521
 9NE  CG   CD    single    1.543  0.020  1.543
 9NE  CD   OE1   deloc     1.248  0.020  1.248
 9NE  CD   OE2   deloc     1.249  0.020  1.249
 9NE  N    H     single    0.860  0.020  0.860
 9NE  C11  H111  single    0.970  0.020  1.090
 9NE  C11  H112  single    0.970  0.020  1.090
 9NE  C11  H113  single    0.970  0.020  1.090
 9NE  C12  H121  single    0.970  0.020  1.090
 9NE  C12  H122  single    0.970  0.020  1.090
 9NE  C12  H123  single    0.970  0.020  1.090
 9NE  C2   H2    single    0.930  0.020  1.080
 9NE  C3   H3    single    0.930  0.020  1.080
 9NE  C4   H4    single    0.930  0.020  1.080
 9NE  C7   H7    single    0.930  0.020  1.080
 9NE  C8   H8    single    0.930  0.020  1.080
 9NE  C9   H9    single    0.930  0.020  1.080
 9NE  CA   HA    single    0.970  0.020  0.970
 9NE  CB   HB1C  single    0.970  0.020  1.090
 9NE  CB   HB2C  single    0.970  0.020  1.090
 9NE  CG   HG1C  single    0.970  0.020  1.090
 9NE  CG   HG2C  single    0.970  0.020  1.090

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
 9NE  H     N    S1    113.85  3.000
 9NE  H     N    CA    114.00  3.000
 9NE  S1    N    CA    125.14  3.000
 9NE  HA    CA   CB    109.00  3.000
 9NE  HA    CA   C     109.00  3.000
 9NE  CB    CA   C     110.10  1.900
 9NE  HA    CA   N     110.00  3.000
 9NE  CB    CA   N     110.50  1.700
 9NE  C     CA   N     111.00  2.800
 9NE  OXT   C    O     126.62  3.000
 9NE  O     C    CA    120.80  1.700
 9NE  OXT   C    CA    116.33  3.000
 9NE  HB2C  CB   HB1C  106.07  3.000
 9NE  HB2C  CB   CG    109.40  3.000
 9NE  HB1C  CB   CG    109.59  3.000
 9NE  HB2C  CB   CA    107.89  3.000
 9NE  HB1C  CB   CA    109.17  3.000
 9NE  CG    CB   CA    114.39  3.000
 9NE  HG2C  CG   HG1C  104.97  3.000
 9NE  HG2C  CG   CD    107.02  3.000
 9NE  HG1C  CG   CD    109.50  3.000
 9NE  HG2C  CG   CB    108.13  3.000
 9NE  HG1C  CG   CB    110.88  3.000
 9NE  CD    CG   CB    115.71  3.000
 9NE  OE2   CD   OE1   126.33  3.000
 9NE  OE2   CD   CG    117.25  3.000
 9NE  OE1   CD   CG    116.38  3.000
 9NE  C1    S1   O3    107.51  3.000
 9NE  C1    S1   O2    109.93  3.000
 9NE  O3    S1   O2    116.67  3.000
 9NE  C1    S1   N     102.00  3.000
 9NE  O3    S1   N     107.22  3.000
 9NE  O2    S1   N     112.41  3.000
 9NE  C6    C1   C2    121.50  3.000
 9NE  C6    C1   S1    126.05  3.000
 9NE  C2    C1   S1    112.43  3.000
 9NE  H2    C2   C3    119.19  3.000
 9NE  H2    C2   C1    120.12  3.000
 9NE  C3    C2   C1    120.56  3.000
 9NE  H3    C3   C4    120.52  3.000
 9NE  H3    C3   C2    119.60  3.000
 9NE  C4    C3   C2    119.88  3.000
 9NE  H4    C4   C5    119.00  3.000
 9NE  H4    C4   C3    119.71  3.000
 9NE  C5    C4   C3    121.26  3.000
 9NE  C10   C5   C6    120.24  3.000
 9NE  C10   C5   C4    119.95  3.000
 9NE  C6    C5   C4    119.76  3.000
 9NE  C7    C6   C5    117.98  3.000
 9NE  C7    C6   C1    125.03  3.000
 9NE  C5    C6   C1    116.94  3.000
 9NE  H7    C7   C8    119.35  3.000
 9NE  H7    C7   C6    120.29  3.000
 9NE  C8    C7   C6    120.34  3.000
 9NE  H8    C8   C9    118.91  3.000
 9NE  H8    C8   C7    119.28  3.000
 9NE  C9    C8   C7    121.79  3.000
 9NE  H9    C9   C10   120.64  3.000
 9NE  H9    C9   C8    118.93  3.000
 9NE  C10   C9   C8    120.41  3.000
 9NE  N1    C10  C9    122.66  3.000
 9NE  C9    C10  C5    119.03  3.000
 9NE  N1    C10  C5    118.30  3.000
 9NE  C12   N1   C11   111.33  3.000
 9NE  C12   N1   C10   114.65  3.000
 9NE  C11   N1   C10   116.34  3.000
 9NE  H113  C11  H112  107.94  3.000
 9NE  H113  C11  H111  108.32  3.000
 9NE  H112  C11  H111  107.34  3.000
 9NE  H113  C11  N1    110.40  3.000
 9NE  H112  C11  N1    108.80  3.000
 9NE  H111  C11  N1    113.85  3.000
 9NE  H123  C12  H122  107.82  3.000
 9NE  H123  C12  H121  107.78  3.000
 9NE  H122  C12  H121  108.09  3.000
 9NE  H123  C12  N1    111.41  3.000
 9NE  H122  C12  N1    112.01  3.000
 9NE  H121  C12  N1    109.58  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
 9NE  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 9NE  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 9NE  CONST_03  C10   C5   C6   C1   180.00   0.0  0
 9NE  CONST_04  C8    C7   C6   C1   180.00   0.0  0
 9NE  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 9NE  CONST_06  C7    C6   C1   C2   180.00   0.0  0
 9NE  CONST_07  C5    C4   C3   C2     0.00   0.0  0
 9NE  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 9NE  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 9NE  CONST_10  C10   C5   C4   C3   180.00   0.0  0
 9NE  CONST_11  C7    C6   C5   C4   180.00   0.0  0
 9NE  CONST_12  C9    C10  C5   C4   180.00   0.0  0
 9NE  CONST_13  C8    C7   C6   C5     0.00   0.0  0
 9NE  CONST_14  C8    C9   C10  C5     0.00   0.0  0
 9NE  CONST_15  C9    C10  C5   C6     0.00   0.0  0
 9NE  CONST_16  C9    C8   C7   C6     0.00   0.0  0
 9NE  CONST_17  C10   C5   C6   C7     0.00   0.0  0
 9NE  CONST_18  C10   C9   C8   C7     0.00   0.0  0
 9NE  CONST_19  C3    C2   C1   S1   180.00   0.0  0
 9NE  CONST_20  C5    C6   C1   S1   180.00   0.0  0
 9NE  CONST_21  C7    C6   C1   S1     0.00   0.0  0
 9NE  CONST_22  N1    C10  C5   C4     0.00   0.0  0
 9NE  CONST_23  N1    C10  C5   C6   180.00   0.0  0
 9NE  CONST_24  N1    C10  C9   C8   180.00   0.0  0
 9NE  CONST_25  H3    C3   C2   C1   180.00   0.0  0
 9NE  CONST_26  H7    C7   C6   C1     0.00   0.0  0
 9NE  CONST_27  H4    C4   C3   C2   180.00   0.0  0
 9NE  CONST_28  H2    C2   C3   C4   180.00   0.0  0
 9NE  CONST_29  H9    C9   C10  C5   180.00   0.0  0
 9NE  CONST_30  H8    C8   C7   C6   180.00   0.0  0
 9NE  Var_01    C2    C1   S1   N    -59.26  30.0  2
 9NE  Var_02    C1    S1   N    CA   135.42  30.0  1
 9NE  Var_03    H111  C11  N1   C10   73.26  30.0  3
 9NE  Var_04    H121  C12  N1   C10  165.43  30.0  3
 9NE  Var_05    CD    CG   CB   CA   -62.78  30.0  3
 9NE  Var_06    OE1   CD   CG   CB   156.29  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
 9NE  chir_01  CA  N  C  CB  positiv

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
 9NE  plan-1  S1   0.020
 9NE  plan-1  C1   0.020
 9NE  plan-1  C2   0.020
 9NE  plan-1  C3   0.020
 9NE  plan-1  C4   0.020
 9NE  plan-1  C5   0.020
 9NE  plan-1  C6   0.020
 9NE  plan-1  C7   0.020
 9NE  plan-1  C8   0.020
 9NE  plan-1  C9   0.020
 9NE  plan-1  C10  0.020
 9NE  plan-1  N1   0.020
 9NE  plan-1  H2   0.020
 9NE  plan-1  H3   0.020
 9NE  plan-1  H4   0.020
 9NE  plan-1  H7   0.020
 9NE  plan-1  H8   0.020
 9NE  plan-1  H9   0.020
 9NE  plan-2  C10  0.020
 9NE  plan-2  N1   0.020
 9NE  plan-2  C11  0.020
 9NE  plan-2  C12  0.020
 9NE  plan-3  CA   0.020
 9NE  plan-3  C    0.020
 9NE  plan-3  O    0.020
 9NE  plan-3  OXT  0.020
 9NE  plan-4  CG   0.020
 9NE  plan-4  CD   0.020
 9NE  plan-4  OE1  0.020
 9NE  plan-4  OE2  0.020

