# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 11:30:39 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2~{R},3~{R})-2,3-bis(oxidanyl)-~{N},~{N}'-dipropyl-butanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)[C@H](O)[C@@H](O)C(=O)NCCC
#
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
 CJ8  CJ8  (2~{R},3~{R})-2,3-bis(oxidanyl)-~{N},~{N}'-dipropyl-butanediamide  ligand  36  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CJ8
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
 CJ8  CAC  C  CH3   0  -0.665   5.8539   1.8672  -0.4622
 CJ8  CAA  C  CH2   0  -0.477   4.3441   1.8010  -0.2895
 CJ8  CAB  C  CH2   0  -0.234   3.8899   0.4104   0.1226
 CJ8  NAD  N  NH1   0  -0.636   2.4459   0.3618   0.2572
 CJ8  CAE  C  C     0   0.517   1.7912  -0.7164   0.6860
 CJ8  OAN  O  O     0  -0.491   2.3382  -1.7579   1.0236
 CJ8  CAF  C  CH1   0  -0.095   0.2660  -0.6075   0.7190
 CJ8  OAM  O  OH1   0  -0.662  -0.2670  -1.6513   1.4737
 CJ8  CAG  C  CH1   0  -0.095  -0.2713  -0.6347  -0.7278
 CJ8  OAP  O  OH1   0  -0.662   0.2570  -1.7103  -1.4400
 CJ8  CAH  C  C     0   0.518  -1.7966  -0.7393  -0.6872
 CJ8  OAO  O  O     0  -0.491  -2.3457  -1.7898  -0.9922
 CJ8  NAI  N  NH1   0  -0.636  -2.4492   0.3508  -0.2867
 CJ8  CAJ  C  CH2   0  -0.234  -3.8917   0.3984  -0.1354
 CJ8  CAK  C  CH2   0  -0.477  -4.3417   1.7833   0.2991
 CJ8  CAL  C  CH3   0  -0.665  -5.8495   1.8451   0.4917
 CJ8  H1   H  HCH3  0   0.224   6.3707   1.6030   0.4619
 CJ8  H2   H  HCH3  0   0.224   6.1941   1.1812  -1.2395
 CJ8  H3   H  HCH3  0   0.237   6.1716   2.8706  -0.7435
 CJ8  H4   H  HCH2  0   0.234   4.0262   2.5250   0.4658
 CJ8  H5   H  HCH2  0   0.234   3.8512   2.0830  -1.2242
 CJ8  H6   H  HCH2  0   0.235   4.2171  -0.3228  -0.6199
 CJ8  H7   H  HCH2  0   0.236   4.3570   0.1341   1.0713
 CJ8  H8   H  HNH1  0   0.406   1.9238   1.1977   0.0453
 CJ8  H9   H  HCH1  0   0.266  -0.0157   0.3454   1.1828
 CJ8  H10  H  HOH1  0   0.448   0.3842  -2.3671   1.4733
 CJ8  H11  H  HCH1  0   0.266   0.0131   0.2988  -1.2280
 CJ8  H12  H  HOH1  0   0.448  -0.4048  -2.4163  -1.4218
 CJ8  H13  H  HNH1  0   0.406  -1.9266   1.1927  -0.1016
 CJ8  H14  H  HCH2  0   0.235  -4.3711   0.1319  -1.0810
 CJ8  H15  H  HCH2  0   0.235  -4.2086  -0.3434   0.6028
 CJ8  H16  H  HCH2  0   0.234  -3.8381   2.0545   1.2312
 CJ8  H17  H  HCH2  0   0.234  -4.0346   2.5174  -0.4510
 CJ8  H18  H  HCH3  0   0.237  -6.1649   2.8445   0.7898
 CJ8  H19  H  HCH3  0   0.224  -6.3776   1.5919  -0.4290
 CJ8  H20  H  HCH3  0   0.224  -6.1789   1.1487   1.2644

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
 CJ8  OAP  CAG  single  1.394  0.020  1.394
 CJ8  NAI  CAJ  single  1.451  0.020  1.451
 CJ8  NAI  CAH  single  1.332  0.020  1.332
 CJ8  CAG  CAH  single  1.530  0.020  1.530
 CJ8  CAG  CAF  single  1.544  0.020  1.544
 CJ8  CAK  CAJ  single  1.520  0.020  1.520
 CJ8  CAK  CAL  single  1.521  0.020  1.521
 CJ8  OAN  CAE  double  1.224  0.020  1.224
 CJ8  CAH  OAO  double  1.224  0.020  1.224
 CJ8  CAB  NAD  single  1.451  0.020  1.451
 CJ8  CAB  CAA  single  1.520  0.020  1.520
 CJ8  OAM  CAF  single  1.394  0.020  1.394
 CJ8  CAE  NAD  single  1.332  0.020  1.332
 CJ8  CAE  CAF  single  1.529  0.020  1.529
 CJ8  CAC  CAA  single  1.521  0.020  1.521
 CJ8  CAC  H1   single  0.970  0.020  1.090
 CJ8  CAC  H2   single  0.970  0.020  1.090
 CJ8  CAC  H3   single  0.970  0.020  1.090
 CJ8  CAA  H4   single  0.970  0.020  1.090
 CJ8  CAA  H5   single  0.970  0.020  1.090
 CJ8  CAB  H6   single  0.970  0.020  1.090
 CJ8  CAB  H7   single  0.970  0.020  1.090
 CJ8  NAD  H8   single  0.860  0.020  1.020
 CJ8  CAF  H9   single  0.970  0.020  1.090
 CJ8  OAM  H10  single  0.850  0.020  0.980
 CJ8  CAG  H11  single  0.970  0.020  1.090
 CJ8  OAP  H12  single  0.850  0.020  0.980
 CJ8  NAI  H13  single  0.860  0.020  1.020
 CJ8  CAJ  H14  single  0.970  0.020  1.090
 CJ8  CAJ  H15  single  0.970  0.020  1.090
 CJ8  CAK  H16  single  0.970  0.020  1.090
 CJ8  CAK  H17  single  0.970  0.020  1.090
 CJ8  CAL  H18  single  0.970  0.020  1.090
 CJ8  CAL  H19  single  0.970  0.020  1.090
 CJ8  CAL  H20  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
 CJ8  H3   CAC  H2   107.71  3.000
 CJ8  H3   CAC  H1   107.66  3.000
 CJ8  H2   CAC  H1   107.66  3.000
 CJ8  H3   CAC  CAA  111.04  3.000
 CJ8  H2   CAC  CAA  111.28  3.000
 CJ8  H1   CAC  CAA  111.31  3.000
 CJ8  H5   CAA  H4   106.77  3.000
 CJ8  H5   CAA  CAB  109.45  3.000
 CJ8  H4   CAA  CAB  109.37  3.000
 CJ8  H5   CAA  CAC  109.82  3.000
 CJ8  H4   CAA  CAC  109.76  3.000
 CJ8  CAB  CAA  CAC  111.55  3.000
 CJ8  H7   CAB  H6   106.97  3.000
 CJ8  H7   CAB  NAD  109.65  3.000
 CJ8  H6   CAB  NAD  109.77  3.000
 CJ8  H7   CAB  CAA  109.82  3.000
 CJ8  H6   CAB  CAA  109.87  3.000
 CJ8  NAD  CAB  CAA  110.68  3.000
 CJ8  H8   NAD  CAE  118.96  3.000
 CJ8  H8   NAD  CAB  117.91  3.000
 CJ8  CAE  NAD  CAB  123.09  3.000
 CJ8  CAF  CAE  OAN  120.02  3.000
 CJ8  CAF  CAE  NAD  116.07  3.000
 CJ8  OAN  CAE  NAD  123.91  3.000
 CJ8  H9   CAF  CAG  108.81  3.000
 CJ8  H9   CAF  OAM  108.87  3.000
 CJ8  CAG  CAF  OAM  111.18  3.000
 CJ8  H9   CAF  CAE  109.09  3.000
 CJ8  OAM  CAF  CAE  109.86  3.000
 CJ8  CAG  CAF  CAE  109.01  3.000
 CJ8  H10  OAM  CAF  107.24  3.000
 CJ8  H11  CAG  CAH  109.20  3.000
 CJ8  H11  CAG  OAP  109.00  3.000
 CJ8  CAH  CAG  OAP  109.80  3.000
 CJ8  H11  CAG  CAF  108.80  3.000
 CJ8  CAH  CAG  CAF  108.87  3.000
 CJ8  OAP  CAG  CAF  111.14  3.000
 CJ8  H12  OAP  CAG  107.10  3.000
 CJ8  NAI  CAH  OAO  123.89  3.000
 CJ8  OAO  CAH  CAG  119.96  3.000
 CJ8  NAI  CAH  CAG  116.14  3.000
 CJ8  H13  NAI  CAJ  117.96  3.000
 CJ8  H13  NAI  CAH  118.99  3.000
 CJ8  CAJ  NAI  CAH  123.03  3.000
 CJ8  H15  CAJ  H14  106.95  3.000
 CJ8  H15  CAJ  CAK  109.84  3.000
 CJ8  H14  CAJ  CAK  109.85  3.000
 CJ8  H15  CAJ  NAI  109.65  3.000
 CJ8  H14  CAJ  NAI  109.74  3.000
 CJ8  CAK  CAJ  NAI  110.73  3.000
 CJ8  H17  CAK  H16  106.79  3.000
 CJ8  H17  CAK  CAL  109.75  3.000
 CJ8  H16  CAK  CAL  109.78  3.000
 CJ8  H17  CAK  CAJ  109.42  3.000
 CJ8  H16  CAK  CAJ  109.47  3.000
 CJ8  CAL  CAK  CAJ  111.51  3.000
 CJ8  H20  CAL  H19  107.65  3.000
 CJ8  H20  CAL  H18  107.71  3.000
 CJ8  H19  CAL  H18  107.68  3.000
 CJ8  H20  CAL  CAK  111.28  3.000
 CJ8  H19  CAL  CAK  111.31  3.000
 CJ8  H18  CAL  CAK  111.03  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
 CJ8  CONST_01  OAN  CAE  NAD  CAB     0.00   0.0  0
 CJ8  CONST_02  CAF  CAE  NAD  CAB   180.00   0.0  0
 CJ8  CONST_03  CAJ  NAI  CAH  CAG   180.00   0.0  0
 CJ8  CONST_04  CAJ  NAI  CAH  OAO     0.00   0.0  0
 CJ8  CONST_05  H8   NAD  CAE  OAN   180.00   0.0  0
 CJ8  CONST_06  H13  NAI  CAH  CAG     0.00   0.0  0
 CJ8  Var_01    NAD  CAB  CAA  CAC  -178.91  30.0  1
 CJ8  Var_02    CAE  NAD  CAB  CAA  -175.86  30.0  3
 CJ8  Var_03    CAK  CAJ  NAI  CAH  -178.52  30.0  3
 CJ8  Var_04    CAL  CAK  CAJ  NAI  -178.80  30.0  1
 CJ8  Var_05    H1   CAC  CAA  CAB   -59.25  30.0  3
 CJ8  Var_06    H18  CAL  CAK  CAJ  -179.23  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
 CJ8  chir_01  CAF  CAG  OAM  CAE  negativ
 CJ8  chir_02  CAG  OAP  CAF  CAH  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
 CJ8  plan-1  CAB  0.020
 CJ8  plan-1  NAD  0.020
 CJ8  plan-1  CAE  0.020
 CJ8  plan-1  OAN  0.020
 CJ8  plan-1  CAF  0.020
 CJ8  plan-1  H8   0.020
 CJ8  plan-2  CAG  0.020
 CJ8  plan-2  CAH  0.020
 CJ8  plan-2  OAO  0.020
 CJ8  plan-2  NAI  0.020
 CJ8  plan-2  CAJ  0.020
 CJ8  plan-2  H13  0.020

