# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:07:28 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-arginine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1cccc2c1cccc2[S](=O)(=O)N[C@@H](CCCNC(N)=N)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
 9NR  9NR  N~2~-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-arginine  L-peptide  52  28  .  2012-08-28  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_9NR
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
 9NR  N     N  NC1    0  -0.743  28.9756   7.3243  32.4689
 9NR  CA    C  CH1    0  -0.253  27.8733   7.0242  31.5558
 9NR  C     C  C      0   0.436  26.7067   8.0010  31.8870
 9NR  O     O  O      0  -0.586  26.9352   8.8674  32.7560
 9NR  CB    C  CH2    0  -0.392  27.4420   5.5638  31.6299
 9NR  CG    C  CH2    0  -0.463  26.9386   5.1271  32.9976
 9NR  CD    C  CH2    0  -0.223  26.5259   3.6635  32.9892
 9NR  NE    N  NH1    0  -0.647  26.0471   3.2578  34.2893
 9NR  CZ    C  C      0   0.553  25.4706   2.0340  34.4811
 9NR  NH1   N  N      0  -0.722  25.1766   1.2888  33.4770
 9NR  NH2   N  NH2    0  -0.839  25.1668   1.7522  35.7986
 9NR  OXT   O  OC    -1  -0.581  25.6642   7.8258  31.2406
 9NR  S1    S  S      0   1.370  30.5125   7.2883  31.9269
 9NR  O2    O  OS     0  -0.663  31.3659   7.7836  32.9973
 9NR  O3    O  OS     0  -0.651  30.7627   5.9536  31.4015
 9NR  N1    N  NT     0  -0.490  30.5359  12.8295  28.4872
 9NR  C1    C  CR6    0  -0.281  30.6120   8.4169  30.5453
 9NR  C2    C  CR16   0  -0.242  30.8129   7.8608  29.3096
 9NR  C3    C  CR16   0  -0.247  30.8427   8.6730  28.1653
 9NR  C4    C  CR16   0  -0.291  30.6926  10.0250  28.2839
 9NR  C5    C  CR66   0   0.045  30.5221  10.6372  29.5466
 9NR  C6    C  CR66   0   0.183  30.4477   9.8247  30.7142
 9NR  C7    C  CR16   0  -0.374  30.1767  10.4499  31.9551
 9NR  C8    C  CR16   0  -0.230  29.9709  11.7997  32.0136
 9NR  C9    C  CR16   0  -0.336  30.0755  12.6096  30.8717
 9NR  C10   C  CR6    0   0.292  30.3801  12.0589  29.6503
 9NR  C11   C  CH3    0  -0.543  29.8349  14.0955  28.4559
 9NR  C12   C  CH3    0  -0.541  31.9155  12.9779  28.0448
 9NR  H     H  HNC1   0   0.407  28.7267   8.1544  33.0140
 9NR  H111  H  HCH3   0   0.210  30.2838  14.8675  29.0950
 9NR  H112  H  HCH3   0   0.248  29.8425  14.4745  27.4335
 9NR  H113  H  HCH3   0   0.247  28.7965  13.9621  28.7569
 9NR  H121  H  HCH3   0   0.240  31.9318  13.3665  27.0261
 9NR  H122  H  HCH3   0   0.220  32.4788  13.6707  28.6837
 9NR  H123  H  HCH3   0   0.251  32.4388  12.0238  28.0457
 9NR  H2    H  HCR6   0   0.285  30.9288   6.7920  29.2009
 9NR  H3    H  HCR6   0   0.267  30.9656   8.2176  27.1923
 9NR  H4    H  HCR6   0   0.275  30.6777  10.6423  27.3966
 9NR  H7    H  HCR6   0   0.250  30.1449   9.8871  32.8741
 9NR  H8    H  HCR6   0   0.263  29.7492  12.2629  32.9663
 9NR  H9    H  HCR6   0   0.267  29.9409  13.6778  30.9761
 9NR  HA    H  HCH1   0   0.261  28.1648   7.2377  30.5182
 9NR  HB1C  H  HCH2   0   0.221  26.6591   5.4098  30.8848
 9NR  HB2C  H  HCH2   0   0.225  28.2773   4.9278  31.3266
 9NR  HG1C  H  HCH2   0   0.221  27.7185   5.2874  33.7480
 9NR  HG2C  H  HCH2   0   0.226  26.0794   5.7335  33.2982
 9NR  HD1C  H  HCH2   0   0.222  25.7281   3.5139  32.2600
 9NR  HD2C  H  HCH2   0   0.205  27.3692   3.0441  32.6562
 9NR  HH11  H  H      0   0.312  24.6959   0.4518  33.7856
 9NR  HH21  H  HNH2   0   0.379  25.7075   2.2198  36.5100
 9NR  HH22  H  HNH2   0   0.383  25.0472   0.7739  36.0056
 9NR  HE    H  HNH1   0   0.378  26.5297   3.6663  35.0738

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
 9NR  S1   O2    double    1.456  0.020  1.456
 9NR  S1   O3    double    1.456  0.020  1.456
 9NR  S1   C1    single    1.787  0.020  1.787
 9NR  S1   N     single    1.630  0.020  1.630
 9NR  OXT  C     deloc     1.239  0.020  1.239
 9NR  N1   C10   single    1.404  0.020  1.404
 9NR  N1   C11   single    1.448  0.020  1.448
 9NR  N1   C12   single    1.456  0.020  1.456
 9NR  C1   C2    aromatic  1.370  0.020  1.370
 9NR  C1   C6    aromatic  1.427  0.020  1.427
 9NR  C2   C3    aromatic  1.404  0.020  1.404
 9NR  C3   C4    aromatic  1.365  0.020  1.365
 9NR  C4   C5    aromatic  1.414  0.020  1.414
 9NR  C5   C6    aromatic  1.424  0.020  1.424
 9NR  C5   C10   aromatic  1.432  0.020  1.432
 9NR  C6   C7    aromatic  1.416  0.020  1.416
 9NR  C7   C8    aromatic  1.367  0.020  1.367
 9NR  C8   C9    aromatic  1.404  0.020  1.404
 9NR  C9   C10   aromatic  1.374  0.020  1.374
 9NR  N    CA    single    1.458  0.019  1.458
 9NR  CA   C     single    1.525  0.021  1.525
 9NR  CA   CB    single    1.530  0.020  1.530
 9NR  C    O     deloc     1.231  0.020  1.231
 9NR  CB   CG    single    1.521  0.020  1.521
 9NR  CG   CD    single    1.521  0.020  1.521
 9NR  CD   NE    single    1.444  0.020  1.444
 9NR  NE   CZ    single    1.366  0.020  1.366
 9NR  CZ   NH1   double    1.285  0.020  1.285
 9NR  CZ   NH2   single    1.381  0.020  1.381
 9NR  N    H     single    0.860  0.020  0.860
 9NR  C11  H111  single    0.970  0.020  1.090
 9NR  C11  H112  single    0.970  0.020  1.090
 9NR  C11  H113  single    0.970  0.020  1.090
 9NR  C12  H121  single    0.970  0.020  1.090
 9NR  C12  H122  single    0.970  0.020  1.090
 9NR  C12  H123  single    0.970  0.020  1.090
 9NR  C2   H2    single    0.930  0.020  1.080
 9NR  C3   H3    single    0.930  0.020  1.080
 9NR  C4   H4    single    0.930  0.020  1.080
 9NR  C7   H7    single    0.930  0.020  1.080
 9NR  C8   H8    single    0.930  0.020  1.080
 9NR  C9   H9    single    0.930  0.020  1.080
 9NR  CA   HA    single    0.970  0.020  0.970
 9NR  CB   HB1C  single    0.970  0.020  1.090
 9NR  CB   HB2C  single    0.970  0.020  1.090
 9NR  CG   HG1C  single    0.970  0.020  1.090
 9NR  CG   HG2C  single    0.970  0.020  1.090
 9NR  CD   HD1C  single    0.970  0.020  1.090
 9NR  CD   HD2C  single    0.970  0.020  1.090
 9NR  NH1  HH11  single    0.890  0.020  1.040
 9NR  NH2  HH21  single    0.890  0.020  1.040
 9NR  NH2  HH22  single    0.890  0.020  1.040
 9NR  NE   HE    single    0.890  0.020  1.040

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
 9NR  H     N    S1    115.09  3.000
 9NR  H     N    CA    114.00  3.000
 9NR  S1    N    CA    119.90  3.000
 9NR  HA    CA   CB    109.00  3.000
 9NR  HA    CA   C     109.00  3.000
 9NR  CB    CA   C     110.10  1.900
 9NR  HA    CA   N     110.00  3.000
 9NR  CB    CA   N     110.50  1.700
 9NR  C     CA   N     111.00  2.800
 9NR  OXT   C    O     127.98  3.000
 9NR  O     C    CA    120.80  1.700
 9NR  OXT   C    CA    115.51  3.000
 9NR  HB2C  CB   HB1C  106.06  3.000
 9NR  HB2C  CB   CG    109.60  3.000
 9NR  HB1C  CB   CG    109.62  3.000
 9NR  HB2C  CB   CA    109.13  3.000
 9NR  HB1C  CB   CA    107.75  3.000
 9NR  CG    CB   CA    114.35  3.000
 9NR  HG2C  CG   HG1C  106.87  3.000
 9NR  HG2C  CG   CD    108.78  3.000
 9NR  HG1C  CG   CD    109.77  3.000
 9NR  HG2C  CG   CB    110.36  3.000
 9NR  HG1C  CG   CB    109.79  3.000
 9NR  CD    CG   CB    111.17  3.000
 9NR  HD2C  CD   HD1C  106.36  3.000
 9NR  HD2C  CD   NE    111.67  3.000
 9NR  HD1C  CD   NE    108.71  3.000
 9NR  HD2C  CD   CG    109.65  3.000
 9NR  HD1C  CD   CG    109.52  3.000
 9NR  NE    CD   CG    110.82  3.000
 9NR  HE    NE   CZ    117.12  3.000
 9NR  HE    NE   CD    115.37  3.000
 9NR  CZ    NE   CD    121.20  3.000
 9NR  NH2   CZ   NH1   125.24  3.000
 9NR  NH2   CZ   NE    114.17  3.000
 9NR  NH1   CZ   NE    120.43  3.000
 9NR  HH11  NH1  CZ    110.47  3.000
 9NR  HH22  NH2  HH21  111.66  3.000
 9NR  HH22  NH2  CZ    114.86  3.000
 9NR  HH21  NH2  CZ    117.41  3.000
 9NR  C1    S1   O3    106.88  3.000
 9NR  C1    S1   O2    108.72  3.000
 9NR  O3    S1   O2    118.46  3.000
 9NR  C1    S1   N     107.20  3.000
 9NR  O3    S1   N     107.59  3.000
 9NR  O2    S1   N     107.50  3.000
 9NR  C12   N1   C11   111.28  3.000
 9NR  C12   N1   C10   114.38  3.000
 9NR  C11   N1   C10   116.38  3.000
 9NR  C6    C1   C2    121.60  3.000
 9NR  C6    C1   S1    121.67  3.000
 9NR  C2    C1   S1    116.70  3.000
 9NR  H2    C2   C3    119.22  3.000
 9NR  H2    C2   C1    120.53  3.000
 9NR  C3    C2   C1    120.24  3.000
 9NR  H3    C3   C4    120.51  3.000
 9NR  H3    C3   C2    119.49  3.000
 9NR  C4    C3   C2    119.99  3.000
 9NR  H4    C4   C5    118.96  3.000
 9NR  H4    C4   C3    119.71  3.000
 9NR  C5    C4   C3    121.31  3.000
 9NR  C10   C5   C6    120.11  3.000
 9NR  C10   C5   C4    120.42  3.000
 9NR  C6    C5   C4    119.44  3.000
 9NR  C7    C6   C5    118.46  3.000
 9NR  C7    C6   C1    124.15  3.000
 9NR  C5    C6   C1    117.36  3.000
 9NR  H7    C7   C8    118.33  3.000
 9NR  H7    C7   C6    121.49  3.000
 9NR  C8    C7   C6    120.17  3.000
 9NR  H8    C8   C9    118.97  3.000
 9NR  H8    C8   C7    119.42  3.000
 9NR  C9    C8   C7    121.58  3.000
 9NR  H9    C9   C10   120.60  3.000
 9NR  H9    C9   C8    118.81  3.000
 9NR  C10   C9   C8    120.56  3.000
 9NR  C9    C10  C5    118.95  3.000
 9NR  C9    C10  N1    122.76  3.000
 9NR  C5    C10  N1    118.29  3.000
 9NR  H113  C11  H112  107.96  3.000
 9NR  H113  C11  H111  108.36  3.000
 9NR  H112  C11  H111  107.37  3.000
 9NR  H113  C11  N1    110.39  3.000
 9NR  H112  C11  N1    108.72  3.000
 9NR  H111  C11  N1    113.84  3.000
 9NR  H123  C12  H122  107.82  3.000
 9NR  H123  C12  H121  107.82  3.000
 9NR  H122  C12  H121  108.13  3.000
 9NR  H123  C12  N1    111.46  3.000
 9NR  H122  C12  N1    111.93  3.000
 9NR  H121  C12  N1    109.53  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
 9NR  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 9NR  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 9NR  CONST_03  C10   C5   C6   C1    180.00   0.0  0
 9NR  CONST_04  C8    C7   C6   C1    180.00   0.0  0
 9NR  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 9NR  CONST_06  C7    C6   C1   C2    180.00   0.0  0
 9NR  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 9NR  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 9NR  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 9NR  CONST_10  C10   C5   C4   C3    180.00   0.0  0
 9NR  CONST_11  C7    C6   C5   C4    180.00   0.0  0
 9NR  CONST_12  C9    C10  C5   C4    180.00   0.0  0
 9NR  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 9NR  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 9NR  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 9NR  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 9NR  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 9NR  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 9NR  CONST_19  C3    C2   C1   S1    180.00   0.0  0
 9NR  CONST_20  C5    C6   C1   S1    180.00   0.0  0
 9NR  CONST_21  C7    C6   C1   S1      0.00   0.0  0
 9NR  CONST_22  C4    C5   C10  N1      0.00   0.0  0
 9NR  CONST_23  C6    C5   C10  N1    180.00   0.0  0
 9NR  CONST_24  C8    C9   C10  N1    180.00   0.0  0
 9NR  CONST_25  H3    C3   C2   C1    180.00   0.0  0
 9NR  CONST_26  H7    C7   C6   C1      0.00   0.0  0
 9NR  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 9NR  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 9NR  CONST_29  H9    C9   C10  C5    180.00   0.0  0
 9NR  CONST_30  H8    C8   C7   C6    180.00   0.0  0
 9NR  CONST_35  NH1   CZ   NE   CD      0.00   0.0  0
 9NR  CONST_36  NH2   CZ   NE   CD    180.00   0.0  0
 9NR  CONST_37  HH11  NH1  CZ   NE    180.00   0.0  0
 9NR  Var_01    C2    C1   S1   N    -111.61  30.0  2
 9NR  Var_02    C1    S1   N    CA     56.37  30.0  1
 9NR  Var_03    H111  C11  N1   C10    73.66  30.0  3
 9NR  Var_04    H121  C12  N1   C10   166.09  30.0  3
 9NR  Var_05    CD    CG   CB   CA    179.87  30.0  3
 9NR  Var_06    NE    CD   CG   CB   -179.89  30.0  3
 9NR  Var_07    CZ    NE   CD   CG    171.97  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
 9NR  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
 9NR  plan-1  S1    0.020
 9NR  plan-1  N1    0.020
 9NR  plan-1  C1    0.020
 9NR  plan-1  C2    0.020
 9NR  plan-1  C3    0.020
 9NR  plan-1  C4    0.020
 9NR  plan-1  C5    0.020
 9NR  plan-1  C6    0.020
 9NR  plan-1  C7    0.020
 9NR  plan-1  C8    0.020
 9NR  plan-1  C9    0.020
 9NR  plan-1  C10   0.020
 9NR  plan-1  H2    0.020
 9NR  plan-1  H3    0.020
 9NR  plan-1  H4    0.020
 9NR  plan-1  H7    0.020
 9NR  plan-1  H8    0.020
 9NR  plan-1  H9    0.020
 9NR  plan-2  N1    0.020
 9NR  plan-2  C10   0.020
 9NR  plan-2  C11   0.020
 9NR  plan-2  C12   0.020
 9NR  plan-3  CD    0.020
 9NR  plan-3  NE    0.020
 9NR  plan-3  CZ    0.020
 9NR  plan-3  NH1   0.020
 9NR  plan-3  NH2   0.020
 9NR  plan-3  HH11  0.020
 9NR  plan-3  HH21  0.020
 9NR  plan-3  HH22  0.020
 9NR  plan-3  HE    0.020
 9NR  plan-4  CA    0.020
 9NR  plan-4  C     0.020
 9NR  plan-4  O     0.020
 9NR  plan-4  OXT   0.020

