# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:11:31 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-(L-arginyl)-1,3-benzothiazole-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=N)C(=O)c1sc2cc(ccc2n1)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
 AR2  AR2  '2-(L-arginyl)-1,3-benzothiazole-6-carboxylic acid'  L-peptide  39  23  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_AR2
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
 AR2  N     N  NH2    0  -0.778  12.4796  23.6319  -2.4093
 AR2  CA    C  CH1    0  -0.217  11.1502  23.0358  -2.4154
 AR2  CB    C  CH2    0  -0.413  11.1849  21.5953  -2.9056
 AR2  CG    C  CH2    0  -0.457  11.6374  21.4850  -4.3550
 AR2  CD    C  CH2    0  -0.226  11.5561  20.0513  -4.8553
 AR2  NE    N  NH1    0  -0.645  11.9961  19.9685  -6.2294
 AR2  CZ    C  C      0   0.547  12.0222  18.7620  -6.8779
 AR2  NH1   N  N      0  -0.714  11.8310  17.6705  -6.2327
 AR2  NH2   N  NH2    0  -0.839  12.2362  18.8748  -8.2374
 AR2  N5    N  N      0  -0.392   9.9588  25.5066  -1.3814
 AR2  S5    S  S2     0   0.271   9.4894  24.6834   1.0235
 AR2  C5    C  CR5    0  -0.071  10.0449  24.4774  -0.6124
 AR2  C61   C  CR56   0   0.351   9.4286  26.5741  -0.7105
 AR2  C62   C  CR56   0  -0.225   9.1053  26.3228   0.6356
 AR2  C63   C  CR16   0  -0.325   8.5629  27.3101   1.4501
 AR2  C64   C  CR6    0  -0.106   8.3348  28.5657   0.9113
 AR2  C65   C  CR16   0  -0.286   8.6528  28.8140  -0.4370
 AR2  C66   C  CR16   0  -0.296   9.1955  27.8430  -1.2480
 AR2  C1    C  C      0   0.409   7.7409  29.6784   1.7791
 AR2  O1    O  O      0  -0.580   7.5076  30.7554   1.2013
 AR2  O2    O  OC    -1  -0.580   7.5486  29.4027   2.9774
 AR2  C     C  C      0   0.398  10.5551  23.1459  -1.0211
 AR2  H     H  HNH2   0   0.362  12.4353  24.6250  -2.2214
 AR2  HN2   H  HNH2   0   0.352  13.0628  23.2109  -1.6961
 AR2  HA    H  HCH1   0   0.262  10.5334  23.6262  -3.0978
 AR2  HB1   H  HCH2   0   0.229  11.8387  20.9971  -2.2643
 AR2  HB2   H  HCH2   0   0.234  10.1821  21.1696  -2.8076
 AR2  HG1   H  HCH2   0   0.221  11.0066  22.1257  -4.9812
 AR2  HG2   H  HCH2   0   0.231  12.6602  21.8511  -4.4614
 AR2  HD1   H  HCH2   0   0.222  12.1927  19.4119  -4.2402
 AR2  HD2   H  HCH2   0   0.205  10.5314  19.6767  -4.7350
 AR2  HE    H  HNH1   0   0.377  11.7493  20.7621  -6.8013
 AR2  HH11  H  H      0   0.315  11.9601  16.8686  -6.8387
 AR2  HH21  H  HNH2   0   0.383  12.5185  18.0242  -8.6980
 AR2  HH22  H  HNH2   0   0.380  12.7906  19.6624  -8.5373
 AR2  H63   H  HCR6   0   0.262   8.3210  27.1115   2.4853
 AR2  H65   H  HCR6   0   0.251   8.4662  29.7997  -0.8398
 AR2  H66   H  HCR6   0   0.262   9.4415  28.0434  -2.2828
 AR2  O     O  O      0  -0.373  10.5329  22.2473  -0.2105

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
 AR2  N    CA    single    1.458  0.019  1.458
 AR2  N    H     single    0.860  0.020  0.860
 AR2  N    HN2   single    0.890  0.020  1.040
 AR2  CA   CB    single    1.530  0.020  1.530
 AR2  CA   C     single    1.525  0.021  1.525
 AR2  CA   HA    single    0.970  0.020  0.970
 AR2  CB   CG    single    1.522  0.020  1.522
 AR2  CB   HB1   single    0.970  0.020  1.090
 AR2  CB   HB2   single    0.970  0.020  1.090
 AR2  CG   CD    single    1.521  0.020  1.521
 AR2  CG   HG1   single    0.970  0.020  1.090
 AR2  CG   HG2   single    0.970  0.020  1.090
 AR2  CD   NE    single    1.445  0.020  1.445
 AR2  CD   HD1   single    0.970  0.020  1.090
 AR2  CD   HD2   single    0.970  0.020  1.090
 AR2  NE   CZ    single    1.370  0.020  1.370
 AR2  NE   HE    single    0.890  0.020  1.040
 AR2  CZ   NH1   double    1.282  0.020  1.282
 AR2  CZ   NH2   single    1.381  0.020  1.381
 AR2  NH1  HH11  single    0.890  0.020  1.040
 AR2  NH2  HH21  single    0.890  0.020  1.040
 AR2  NH2  HH22  single    0.890  0.020  1.040
 AR2  N5   C5    aromatic  1.288  0.020  1.288
 AR2  N5   C61   aromatic  1.368  0.020  1.368
 AR2  S5   C5    aromatic  1.740  0.020  1.740
 AR2  S5   C62   aromatic  1.728  0.020  1.728
 AR2  C5   C     single    1.483  0.020  1.483
 AR2  C61  C62   aromatic  1.407  0.020  1.407
 AR2  C61  C66   aromatic  1.398  0.020  1.398
 AR2  C62  C63   aromatic  1.390  0.020  1.390
 AR2  C63  C64   aromatic  1.385  0.020  1.385
 AR2  C63  H63   single    0.930  0.020  1.080
 AR2  C64  C65   aromatic  1.407  0.020  1.407
 AR2  C64  C1    single    1.531  0.020  1.531
 AR2  C65  C66   aromatic  1.377  0.020  1.377
 AR2  C65  H65   single    0.930  0.020  1.080
 AR2  C66  H66   single    0.930  0.020  1.080
 AR2  C1   O1    deloc     1.244  0.020  1.244
 AR2  C1   O2    deloc     1.244  0.020  1.244
 AR2  O    C     double    1.231  0.020  1.231

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
 AR2  HN2   N    H     107.61  3.000
 AR2  HN2   N    CA    110.99  3.000
 AR2  H     N    CA    114.00  3.000
 AR2  HA    CA   C     109.00  3.000
 AR2  HA    CA   CB    109.00  3.000
 AR2  C     CA   CB    110.10  1.900
 AR2  HA    CA   N     110.00  3.000
 AR2  C     CA   N     111.00  2.800
 AR2  CB    CA   N     110.50  1.700
 AR2  HB2   CB   HB1   106.41  3.000
 AR2  HB2   CB   CG    109.24  3.000
 AR2  HB1   CB   CG    109.93  3.000
 AR2  HB2   CB   CA    108.58  3.000
 AR2  HB1   CB   CA    110.02  3.000
 AR2  CG    CB   CA    112.46  3.000
 AR2  HG2   CG   HG1   106.71  3.000
 AR2  HG2   CG   CD    109.53  3.000
 AR2  HG1   CG   CD    109.42  3.000
 AR2  HG2   CG   CB    110.31  3.000
 AR2  HG1   CG   CB    109.31  3.000
 AR2  CD    CG   CB    111.45  3.000
 AR2  HD2   CD   HD1   106.42  3.000
 AR2  HD2   CD   NE    111.65  3.000
 AR2  HD1   CD   NE    108.94  3.000
 AR2  HD2   CD   CG    109.61  3.000
 AR2  HD1   CD   CG    109.60  3.000
 AR2  NE    CD   CG    110.52  3.000
 AR2  HE    NE   CZ    115.41  3.000
 AR2  HE    NE   CD    114.80  3.000
 AR2  CZ    NE   CD    120.42  3.000
 AR2  NH2   CZ   NH1   126.02  3.000
 AR2  NH2   CZ   NE    113.39  3.000
 AR2  NH1   CZ   NE    120.57  3.000
 AR2  HH11  NH1  CZ    110.71  3.000
 AR2  HH22  NH2  HH21  111.67  3.000
 AR2  HH22  NH2  CZ    116.20  3.000
 AR2  HH21  NH2  CZ    115.12  3.000
 AR2  C61   N5   C5    110.90  3.000
 AR2  C62   S5   C5     88.41  3.000
 AR2  C     C5   S5    118.37  3.000
 AR2  C     C5   N5    125.16  3.000
 AR2  S5    C5   N5    116.46  3.000
 AR2  C66   C61  C62   119.46  3.000
 AR2  C66   C61  N5    125.77  3.000
 AR2  C62   C61  N5    114.77  3.000
 AR2  C63   C62  C61   121.56  3.000
 AR2  C63   C62  S5    128.98  3.000
 AR2  C61   C62  S5    109.46  3.000
 AR2  H63   C63  C64   120.12  3.000
 AR2  H63   C63  C62   121.18  3.000
 AR2  C64   C63  C62   118.70  3.000
 AR2  C1    C64  C65   120.16  3.000
 AR2  C1    C64  C63   120.15  3.000
 AR2  C65   C64  C63   119.69  3.000
 AR2  H65   C65  C66   119.45  3.000
 AR2  H65   C65  C64   118.61  3.000
 AR2  C66   C65  C64   121.94  3.000
 AR2  H66   C66  C65   121.48  3.000
 AR2  H66   C66  C61   119.87  3.000
 AR2  C65   C66  C61   118.65  3.000
 AR2  O2    C1   O1    127.58  3.000
 AR2  O2    C1   C64   116.40  3.000
 AR2  O1    C1   C64   116.01  3.000
 AR2  O     C    C5    118.40  3.000
 AR2  O     C    CA    120.80  1.700
 AR2  C5    C    CA    116.90  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
 AR2  CONST_01  C62   S5   C5   N5      0.00   0.0  0
 AR2  CONST_02  S5    C62  C61  N5      0.00   0.0  0
 AR2  CONST_03  C63   C62  C61  N5    180.00   0.0  0
 AR2  CONST_04  C65   C66  C61  N5    180.00   0.0  0
 AR2  CONST_05  C61   N5   C5   S5      0.00   0.0  0
 AR2  CONST_06  C66   C61  C62  S5    180.00   0.0  0
 AR2  CONST_07  C64   C63  C62  S5    180.00   0.0  0
 AR2  CONST_08  C62   C61  N5   C5      0.00   0.0  0
 AR2  CONST_09  C66   C61  N5   C5    180.00   0.0  0
 AR2  CONST_10  C61   C62  S5   C5      0.00   0.0  0
 AR2  CONST_11  C63   C62  S5   C5    180.00   0.0  0
 AR2  CONST_12  C64   C63  C62  C61     0.00   0.0  0
 AR2  CONST_13  C64   C65  C66  C61     0.00   0.0  0
 AR2  CONST_14  C65   C66  C61  C62     0.00   0.0  0
 AR2  CONST_15  C65   C64  C63  C62     0.00   0.0  0
 AR2  CONST_16  C66   C61  C62  C63     0.00   0.0  0
 AR2  CONST_17  C66   C65  C64  C63     0.00   0.0  0
 AR2  CONST_18  C     C5   N5   C61   180.00   0.0  0
 AR2  CONST_19  C     C5   S5   C62   180.00   0.0  0
 AR2  CONST_20  C1    C64  C63  C62   180.00   0.0  0
 AR2  CONST_21  C1    C64  C65  C66   180.00   0.0  0
 AR2  CONST_22  H66   C66  C61  N5      0.00   0.0  0
 AR2  CONST_23  H63   C63  C62  S5      0.00   0.0  0
 AR2  CONST_24  H65   C65  C66  C61   180.00   0.0  0
 AR2  CONST_25  NH1   CZ   NE   CD      0.00   0.0  0
 AR2  CONST_26  NH2   CZ   NE   CD    180.00   0.0  0
 AR2  CONST_27  HH11  NH1  CZ   NE    180.00   0.0  0
 AR2  Var_01    N5    C5   C    CA      6.52  30.0  2
 AR2  Var_02    O1    C1   C64  C63  -176.63  30.0  2
 AR2  Var_03    CD    CG   CB   CA   -175.39  30.0  3
 AR2  Var_04    NE    CD   CG   CB   -179.71  30.0  3
 AR2  Var_05    CZ    NE   CD   CG    179.12  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
 AR2  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
 AR2  plan-1  N5    0.020
 AR2  plan-1  S5    0.020
 AR2  plan-1  C5    0.020
 AR2  plan-1  C61   0.020
 AR2  plan-1  C62   0.020
 AR2  plan-1  C63   0.020
 AR2  plan-1  C64   0.020
 AR2  plan-1  C65   0.020
 AR2  plan-1  C66   0.020
 AR2  plan-1  C1    0.020
 AR2  plan-1  C     0.020
 AR2  plan-1  H63   0.020
 AR2  plan-1  H65   0.020
 AR2  plan-1  H66   0.020
 AR2  plan-2  CA    0.020
 AR2  plan-2  C5    0.020
 AR2  plan-2  C     0.020
 AR2  plan-2  O     0.020
 AR2  plan-3  CD    0.020
 AR2  plan-3  NE    0.020
 AR2  plan-3  CZ    0.020
 AR2  plan-3  NH1   0.020
 AR2  plan-3  NH2   0.020
 AR2  plan-3  HE    0.020
 AR2  plan-3  HH11  0.020
 AR2  plan-3  HH21  0.020
 AR2  plan-3  HH22  0.020
 AR2  plan-4  C64   0.020
 AR2  plan-4  C1    0.020
 AR2  plan-4  O1    0.020
 AR2  plan-4  O2    0.020

