# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:40:22 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: N~2~-[(2H-1,3-benzodioxol-5-yl)acetyl]-N-[(pyridin-4-yl)methyl]-L-cysteinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SC[C@H](NC(=O)Cc1ccc2OCOc2c1)C(=O)NCc3ccncc3
#
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
 R74  R74  N~2~-[(2H-1,3-benzodioxol-5-yl)acetyl]-N-[(pyridin-4-yl)methyl]-L-cysteinamide  ligand  45  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R74
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
 R74  OB   O  O     0  -0.479  -2.6080   -9.5936  -31.2417
 R74  CAA  C  CR56  0   0.288  -4.8283   -3.6032  -25.1614
 R74  CAB  C  CR16  0  -0.331  -4.9731   -4.9545  -24.9683
 R74  CAC  C  CR16  0  -0.296  -5.4203   -5.7044  -26.0620
 R74  CAD  C  CR6   0   0.111  -5.7084   -5.1153  -27.2866
 R74  CAE  C  CR16  0  -0.393  -5.5463   -3.7332  -27.4618
 R74  CAF  C  CR56  0   0.312  -5.1097   -3.0090  -26.3805
 R74  CAH  C  CH2   0   0.070  -4.6011   -1.4062  -24.9295
 R74  CAJ  C  CH2   0  -0.667  -6.1422   -5.9707  -28.4487
 R74  CAK  C  C     0   0.548  -4.9180   -6.6006  -29.0822
 R74  CAS  C  CH2   0  -0.339  -4.9163   -9.5154  -32.7673
 R74  CAT  C  CR6   0   0.188  -4.8570  -11.0154  -32.9065
 R74  CAU  C  CR16  0  -0.370  -4.3576  -11.5958  -34.0658
 R74  CAV  C  CR16  0  -0.061  -4.3555  -12.9769  -34.1839
 R74  CAX  C  CR16  0  -0.059  -5.2824  -13.2386  -32.1326
 R74  CAY  C  CR16  0  -0.358  -5.3313  -11.8699  -31.9190
 R74  CBB  C  CH2   0  -0.581  -3.4611   -9.8987  -28.3938
 R74  CBC  C  CH1   0  -0.171  -3.6314   -8.6758  -29.2895
 R74  CBD  C  C     0   0.554  -3.6283   -9.1408  -30.7481
 R74  NAQ  N  NH1   0  -0.633  -4.7881   -9.0536  -31.4087
 R74  NAW  N  N     0  -0.411  -4.8061  -13.7959  -33.2404
 R74  NBE  N  NH1   0  -0.653  -4.8042   -7.9353  -28.9001
 R74  OAG  O  O     0  -0.487  -4.8640   -1.6787  -26.2999
 R74  OAI  O  O     0  -0.486  -4.4022   -2.6583  -24.2870
 R74  OAM  O  O     0  -0.467  -4.0810   -5.9465  -29.6783
 R74  SAZ  S  S2    0  -0.230  -3.3619   -9.3508  -26.6564
 R74  H2   H  HCR6  0   0.249  -5.5439   -6.7740  -25.9429
 R74  H3   H  HCR6  0   0.269  -5.7653   -3.2583  -28.4093
 R74  H4   H  HCH2  0   0.245  -3.7010   -0.7978  -24.8400
 R74  H5   H  HCH2  0   0.233  -5.4577   -0.8905  -24.4824
 R74  H6   H  HCH2  0   0.294  -6.6436   -5.3643  -29.2041
 R74  H7   H  HCH2  0   0.283  -6.8533   -6.7306  -28.1211
 R74  H8   H  HCH2  0   0.268  -4.1493   -9.0589  -33.3955
 R74  H9   H  HCH2  0   0.292  -5.8781   -9.1622  -33.1412
 R74  H10  H  HCR6  0   0.266  -3.9652  -10.9873  -34.8707
 R74  H11  H  HCR6  0   0.264  -3.9639  -13.4405  -35.0827
 R74  H12  H  HCR6  0   0.263  -5.6466  -13.9158  -31.3676
 R74  H13  H  HCR6  0   0.257  -5.7344  -11.4897  -30.9894
 R74  H14  H  HCH2  0   0.281  -4.2977  -10.5888  -28.5198
 R74  H15  H  HCH2  0   0.305  -2.5430  -10.4147  -28.6637
 R74  H16  H  HCH1  0   0.300  -2.7563   -8.0315  -29.1740
 R74  H17  H  HNH1  0   0.413  -5.5980   -8.6750  -30.9464
 R74  H18  H  HNH1  0   0.415  -5.5337   -8.4190  -28.3989
 R74  H19  H  HSH1  0   0.234  -2.9868  -10.5288  -26.1472
 R74  H1   H  HCR6  0   0.274  -4.7508   -5.4229  -24.0191

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
 R74  CAU  CAV  aromatic  1.386  0.020  1.386
 R74  CAU  CAT  aromatic  1.389  0.020  1.389
 R74  CAV  NAW  aromatic  1.328  0.020  1.328
 R74  CAS  CAT  single    1.508  0.020  1.508
 R74  CAS  NAQ  single    1.441  0.020  1.441
 R74  CAT  CAY  aromatic  1.389  0.020  1.389
 R74  NAW  CAX  aromatic  1.328  0.020  1.328
 R74  CAY  CAX  aromatic  1.386  0.020  1.386
 R74  OB   CBD  double    1.220  0.020  1.220
 R74  NAQ  CBD  single    1.338  0.020  1.338
 R74  CBD  CBC  single    1.531  0.020  1.531
 R74  CBC  NBE  single    1.441  0.020  1.441
 R74  CBC  CBB  single    1.525  0.020  1.525
 R74  NBE  CAK  single    1.352  0.020  1.352
 R74  CAK  OAM  double    1.218  0.020  1.218
 R74  CAK  CAJ  single    1.515  0.020  1.515
 R74  CBB  SAZ  single    1.824  0.020  1.824
 R74  CAJ  CAD  single    1.507  0.020  1.507
 R74  CAE  CAD  aromatic  1.403  0.020  1.403
 R74  CAE  CAF  aromatic  1.373  0.020  1.373
 R74  CAD  CAC  aromatic  1.389  0.020  1.389
 R74  CAF  OAG  single    1.355  0.020  1.355
 R74  CAF  CAA  aromatic  1.385  0.020  1.385
 R74  OAG  CAH  single    1.422  0.020  1.422
 R74  CAC  CAB  aromatic  1.399  0.020  1.399
 R74  CAA  CAB  aromatic  1.373  0.020  1.373
 R74  CAA  OAI  single    1.356  0.020  1.356
 R74  CAH  OAI  single    1.421  0.020  1.421
 R74  CAB  H1   single    0.930  0.020  1.080
 R74  CAC  H2   single    0.930  0.020  1.080
 R74  CAE  H3   single    0.930  0.020  1.080
 R74  CAH  H4   single    0.970  0.020  1.090
 R74  CAH  H5   single    0.970  0.020  1.090
 R74  CAJ  H6   single    0.970  0.020  1.090
 R74  CAJ  H7   single    0.970  0.020  1.090
 R74  CAS  H8   single    0.970  0.020  1.090
 R74  CAS  H9   single    0.970  0.020  1.090
 R74  CAU  H10  single    0.930  0.020  1.080
 R74  CAV  H11  single    0.930  0.020  1.080
 R74  CAX  H12  single    0.930  0.020  1.080
 R74  CAY  H13  single    0.930  0.020  1.080
 R74  CBB  H14  single    0.970  0.020  1.090
 R74  CBB  H15  single    0.970  0.020  1.090
 R74  CBC  H16  single    0.970  0.020  1.090
 R74  NAQ  H17  single    0.860  0.020  1.020
 R74  NBE  H18  single    0.860  0.020  1.020
 R74  SAZ  H19  single    1.200  0.020  1.300

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
 R74  OAI  CAA  CAF  109.41  3.000
 R74  OAI  CAA  CAB  128.93  3.000
 R74  CAF  CAA  CAB  121.65  3.000
 R74  H1   CAB  CAC  121.30  3.000
 R74  H1   CAB  CAA  121.88  3.000
 R74  CAC  CAB  CAA  116.82  3.000
 R74  H2   CAC  CAD  119.47  3.000
 R74  H2   CAC  CAB  118.66  3.000
 R74  CAD  CAC  CAB  121.87  3.000
 R74  CAJ  CAD  CAE  119.76  3.000
 R74  CAE  CAD  CAC  120.27  3.000
 R74  CAJ  CAD  CAC  119.92  3.000
 R74  H3   CAE  CAF  121.50  3.000
 R74  H3   CAE  CAD  121.22  3.000
 R74  CAF  CAE  CAD  117.27  3.000
 R74  OAG  CAF  CAE  128.49  3.000
 R74  OAG  CAF  CAA  109.38  3.000
 R74  CAE  CAF  CAA  122.12  3.000
 R74  H5   CAH  H4   110.46  3.000
 R74  H5   CAH  OAI  109.86  3.000
 R74  H4   CAH  OAI  109.81  3.000
 R74  H5   CAH  OAG  109.82  3.000
 R74  H4   CAH  OAG  109.81  3.000
 R74  OAI  CAH  OAG  107.02  3.000
 R74  H7   CAJ  H6   107.19  3.000
 R74  H7   CAJ  CAK  111.25  3.000
 R74  H6   CAJ  CAK  108.23  3.000
 R74  H7   CAJ  CAD  110.58  3.000
 R74  H6   CAJ  CAD  110.54  3.000
 R74  CAK  CAJ  CAD  109.02  3.000
 R74  OAM  CAK  NBE  122.56  3.000
 R74  OAM  CAK  CAJ  122.44  3.000
 R74  NBE  CAK  CAJ  114.97  3.000
 R74  H9   CAS  H8   106.67  3.000
 R74  H9   CAS  NAQ  107.34  3.000
 R74  H8   CAS  NAQ  110.26  3.000
 R74  H9   CAS  CAT  108.98  3.000
 R74  H8   CAS  CAT  109.59  3.000
 R74  NAQ  CAS  CAT  113.73  3.000
 R74  CAY  CAT  CAU  117.32  3.000
 R74  CAY  CAT  CAS  122.19  3.000
 R74  CAU  CAT  CAS  120.46  3.000
 R74  H10  CAU  CAV  119.74  3.000
 R74  H10  CAU  CAT  121.05  3.000
 R74  CAV  CAU  CAT  119.20  3.000
 R74  H11  CAV  NAW  116.60  3.000
 R74  H11  CAV  CAU  119.80  3.000
 R74  NAW  CAV  CAU  123.60  3.000
 R74  H12  CAX  NAW  116.53  3.000
 R74  H12  CAX  CAY  119.73  3.000
 R74  NAW  CAX  CAY  123.74  3.000
 R74  H13  CAY  CAX  119.50  3.000
 R74  H13  CAY  CAT  121.44  3.000
 R74  CAX  CAY  CAT  119.05  3.000
 R74  H15  CBB  H14  108.57  3.000
 R74  H15  CBB  SAZ  109.45  3.000
 R74  H14  CBB  SAZ  109.96  3.000
 R74  H15  CBB  CBC  109.21  3.000
 R74  H14  CBB  CBC  110.70  3.000
 R74  SAZ  CBB  CBC  108.94  3.000
 R74  H16  CBC  NBE  108.68  3.000
 R74  H16  CBC  CBD  106.15  3.000
 R74  NBE  CBC  CBD  114.54  3.000
 R74  H16  CBC  CBB  108.73  3.000
 R74  NBE  CBC  CBB  110.14  3.000
 R74  CBD  CBC  CBB  108.40  3.000
 R74  NAQ  CBD  CBC  116.68  3.000
 R74  CBC  CBD  OB   119.98  3.000
 R74  NAQ  CBD  OB   123.32  3.000
 R74  H17  NAQ  CBD  119.70  3.000
 R74  H17  NAQ  CAS  118.83  3.000
 R74  CBD  NAQ  CAS  121.47  3.000
 R74  CAX  NAW  CAV  117.09  3.000
 R74  H18  NBE  CBC  118.46  3.000
 R74  H18  NBE  CAK  118.65  3.000
 R74  CBC  NBE  CAK  122.66  3.000
 R74  CAH  OAG  CAF  106.21  3.000
 R74  CAH  OAI  CAA  106.17  3.000
 R74  H19  SAZ  CBB   96.51  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
 R74  CONST_01  CAD  CAE  CAF  CAA     0.00   0.0  0
 R74  CONST_02  CAD  CAC  CAB  CAA     0.00   0.0  0
 R74  CONST_03  CAE  CAD  CAC  CAB     0.00   0.0  0
 R74  CONST_04  CAE  CAF  CAA  CAB     0.00   0.0  0
 R74  CONST_05  CAF  CAE  CAD  CAC     0.00   0.0  0
 R74  CONST_06  CAF  CAA  CAB  CAC     0.00   0.0  0
 R74  CONST_07  NAW  CAV  CAU  CAT     0.00   0.0  0
 R74  CONST_08  NAW  CAX  CAY  CAT     0.00   0.0  0
 R74  CONST_09  CAX  NAW  CAV  CAU     0.00   0.0  0
 R74  CONST_10  CAX  CAY  CAT  CAU     0.00   0.0  0
 R74  CONST_11  CAY  CAT  CAU  CAV     0.00   0.0  0
 R74  CONST_12  CAY  CAX  NAW  CAV     0.00   0.0  0
 R74  CONST_13  CAJ  CAD  CAC  CAB   180.00   0.0  0
 R74  CONST_14  CAJ  CAD  CAE  CAF   180.00   0.0  0
 R74  CONST_15  CAV  CAU  CAT  CAS   180.00   0.0  0
 R74  CONST_16  CAX  CAY  CAT  CAS   180.00   0.0  0
 R74  CONST_17  H3   CAE  CAF  CAA   180.00   0.0  0
 R74  CONST_18  H2   CAC  CAB  CAA   180.00   0.0  0
 R74  CONST_19  H1   CAB  CAC  CAD   180.00   0.0  0
 R74  CONST_20  H11  CAV  CAU  CAT   180.00   0.0  0
 R74  CONST_21  H12  CAX  CAY  CAT   180.00   0.0  0
 R74  CONST_22  H13  CAY  CAT  CAU   180.00   0.0  0
 R74  CONST_23  H10  CAU  CAT  CAY   180.00   0.0  0
 R74  CONST_24  CAS  NAQ  CBD  OB      0.00   0.0  0
 R74  CONST_25  CBC  NBE  CAK  CAJ   180.00   0.0  0
 R74  CONST_26  CBC  CBD  NAQ  CAS   180.00   0.0  0
 R74  CONST_27  OAM  CAK  NBE  CBC     0.00   0.0  0
 R74  CONST_28  H17  NAQ  CBD  OB    180.00   0.0  0
 R74  CONST_29  H18  NBE  CAK  CAJ     0.00   0.0  0
 R74  Var_01    OAG  CAH  OAI  CAA   -13.06  30.0  1
 R74  Var_02    OAI  CAH  OAG  CAF    13.14  30.0  1
 R74  Var_03    CAK  CAJ  CAD  CAC   -80.32  30.0  2
 R74  Var_04    NAQ  CAS  CAT  CAU  -150.21  30.0  2
 R74  Var_05    NBE  CAK  CAJ  CAD   110.12  30.0  2
 R74  Var_06    CBD  NAQ  CAS  CAT    70.28  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
 R74  chir_01  CBC  CBD  NBE  CBB  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
 R74  plan-1  CAS  0.020
 R74  plan-1  CAT  0.020
 R74  plan-1  CAU  0.020
 R74  plan-1  CAV  0.020
 R74  plan-1  CAX  0.020
 R74  plan-1  CAY  0.020
 R74  plan-1  NAW  0.020
 R74  plan-1  H10  0.020
 R74  plan-1  H11  0.020
 R74  plan-1  H12  0.020
 R74  plan-1  H13  0.020
 R74  plan-2  CAA  0.020
 R74  plan-2  CAB  0.020
 R74  plan-2  CAC  0.020
 R74  plan-2  CAD  0.020
 R74  plan-2  CAE  0.020
 R74  plan-2  CAF  0.020
 R74  plan-2  CAJ  0.020
 R74  plan-2  OAG  0.020
 R74  plan-2  OAI  0.020
 R74  plan-2  H2   0.020
 R74  plan-2  H3   0.020
 R74  plan-2  H1   0.020
 R74  plan-3  CAJ  0.020
 R74  plan-3  CAK  0.020
 R74  plan-3  CBC  0.020
 R74  plan-3  NBE  0.020
 R74  plan-3  OAM  0.020
 R74  plan-3  H18  0.020
 R74  plan-4  OB   0.020
 R74  plan-4  CAS  0.020
 R74  plan-4  CBC  0.020
 R74  plan-4  CBD  0.020
 R74  plan-4  NAQ  0.020
 R74  plan-4  H17  0.020

