# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:06:07 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (3S,4R,5R)-4-(acetylamino)-3-carbamimidamido-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1CC(=C[C@H](NC(N)=N)[C@H]1NC(C)=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
 1SJ  1SJ  '(3S,4R,5R)-4-(acetylamino)-3-carbamimidamido-5-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid'  ligand  49  23  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1SJ
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
 1SJ  CAA  C  CH3   0  -0.671   4.2762   0.6003   1.4948
 1SJ  CAJ  C  CH2   0  -0.429   4.3307  -0.6095   0.5741
 1SJ  CAT  C  CH1   0   0.050   3.2086  -0.6737  -0.4553
 1SJ  CAK  C  CH2   0  -0.412   3.4014  -1.8641  -1.3906
 1SJ  CAB  C  CH3   0  -0.678   2.3765  -1.9804  -2.5099
 1SJ  OAO  O  O2    0  -0.498   1.9666  -0.7663   0.2304
 1SJ  CAV  C  CH1   0   0.088   0.9292   0.0532  -0.2296
 1SJ  CAL  C  CH2   0  -0.513   1.0660   1.4861   0.2805
 1SJ  CAS  C  C     0  -0.070  -0.1683   2.2922  -0.0034
 1SJ  CAR  C  C     0   0.527  -0.1247   3.7765   0.0685
 1SJ  OAH  O  OH1   0  -0.591   1.0628   4.2255   0.4526
 1SJ  OAG  O  O     0  -0.442  -1.0549   4.5065  -0.1816
 1SJ  CAI  C  C1    0  -0.187  -1.3368   1.7225  -0.2999
 1SJ  CAU  C  CH1   0  -0.148  -1.5606   0.2389  -0.3576
 1SJ  NAM  N  NH1   0  -0.641  -2.7940  -0.1421   0.2834
 1SJ  CAQ  C  C     0   0.552  -4.0164  -0.0517  -0.3387
 1SJ  NAE  N  N     0  -0.714  -4.2474   0.2380  -1.5656
 1SJ  NAD  N  NH2   0  -0.829  -5.0660  -0.3018   0.5146
 1SJ  CAW  C  CH1   0  -0.121  -0.3955  -0.5438   0.2529
 1SJ  NAN  N  NH1   0  -0.623  -0.5227  -1.9360  -0.0823
 1SJ  CAP  C  C     0   0.530  -0.3169  -2.9490   0.7790
 1SJ  OAF  O  O     0  -0.503  -0.0750  -2.7850   1.9658
 1SJ  CAC  C  CH3   0  -0.784  -0.4248  -4.3280   0.1766
 1SJ  H1   H  HCH3  0   0.224   3.3816   0.5945   2.1163
 1SJ  H2   H  HCH3  0   0.232   5.1399   0.6174   2.1602
 1SJ  H3   H  HCH3  0   0.215   4.2819   1.5327   0.9268
 1SJ  H4   H  HCH2  0   0.219   5.2797  -0.6089   0.0311
 1SJ  H5   H  HCH2  0   0.217   4.3205  -1.5302   1.1664
 1SJ  H6   H  HCH1  0   0.202   3.2370   0.2481  -1.0559
 1SJ  H7   H  HCH2  0   0.216   4.3997  -1.7780  -1.8292
 1SJ  H8   H  HCH2  0   0.217   3.4094  -2.7839  -0.7969
 1SJ  H9   H  HCH3  0   0.214   1.3820  -2.2073  -2.1282
 1SJ  H10  H  HCH3  0   0.219   2.3113  -1.0590  -3.0919
 1SJ  H11  H  HCH3  0   0.235   2.6460  -2.7828  -3.1975
 1SJ  H12  H  HCH1  0   0.216   0.9112   0.0773  -1.3306
 1SJ  H13  H  HCH2  0   0.261   1.2624   1.4711   1.3577
 1SJ  H14  H  HCH2  0   0.261   1.9392   1.9520  -0.1812
 1SJ  H16  H  HOH1  0   0.486   1.0558   5.1939   0.4858
 1SJ  H17  H  H     0   0.275  -2.2042   2.3405  -0.5043
 1SJ  H19  H  HCH1  0   0.273  -1.6342  -0.0485  -1.4137
 1SJ  H20  H  HNH1  0   0.390  -2.7995  -0.0524   1.2887
 1SJ  H21  H  H     0   0.329  -3.4108   0.5100  -2.0648
 1SJ  H22  H  HNH2  0   0.382  -4.9041  -0.9813   1.2418
 1SJ  H23  H  HNH2  0   0.380  -5.9433  -0.4476   0.0418
 1SJ  H24  H  HCH1  0   0.269  -0.4391  -0.4588   1.3426
 1SJ  H25  H  HNH1  0   0.398  -0.7187  -2.1623  -1.0442
 1SJ  H26  H  HCH3  0   0.266   0.5171  -4.8579   0.3195
 1SJ  H27  H  HCH3  0   0.266  -1.1964  -4.8931   0.6992
 1SJ  H28  H  HCH3  0   0.246  -0.6587  -4.3268  -0.8866

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
 1SJ  OAF  CAP  double  1.222  0.020  1.222
 1SJ  NAE  CAQ  double  1.282  0.020  1.282
 1SJ  CAJ  CAT  single  1.524  0.020  1.524
 1SJ  CAJ  CAA  single  1.521  0.020  1.521
 1SJ  CAT  CAK  single  1.526  0.020  1.526
 1SJ  CAT  OAO  single  1.422  0.020  1.422
 1SJ  CAK  CAB  single  1.522  0.020  1.522
 1SJ  NAN  CAP  single  1.346  0.020  1.346
 1SJ  NAN  CAW  single  1.438  0.020  1.438
 1SJ  CAP  CAC  single  1.509  0.020  1.509
 1SJ  CAQ  NAD  single  1.376  0.020  1.376
 1SJ  CAQ  NAM  single  1.375  0.020  1.375
 1SJ  CAV  OAO  single  1.400  0.020  1.400
 1SJ  CAV  CAW  single  1.531  0.020  1.531
 1SJ  CAV  CAL  single  1.527  0.020  1.527
 1SJ  CAW  CAU  single  1.531  0.020  1.531
 1SJ  CAU  NAM  single  1.441  0.020  1.441
 1SJ  CAU  CAI  single  1.501  0.020  1.501
 1SJ  CAL  CAS  single  1.501  0.020  1.501
 1SJ  CAI  CAS  double  1.333  0.020  1.333
 1SJ  CAS  CAR  single  1.487  0.020  1.487
 1SJ  OAG  CAR  double  1.209  0.020  1.209
 1SJ  CAR  OAH  single  1.326  0.020  1.326
 1SJ  CAA  H1   single  0.970  0.020  1.090
 1SJ  CAA  H2   single  0.970  0.020  1.090
 1SJ  CAA  H3   single  0.970  0.020  1.090
 1SJ  CAJ  H4   single  0.970  0.020  1.090
 1SJ  CAJ  H5   single  0.970  0.020  1.090
 1SJ  CAT  H6   single  0.970  0.020  1.090
 1SJ  CAK  H7   single  0.970  0.020  1.090
 1SJ  CAK  H8   single  0.970  0.020  1.090
 1SJ  CAB  H9   single  0.970  0.020  1.090
 1SJ  CAB  H10  single  0.970  0.020  1.090
 1SJ  CAB  H11  single  0.970  0.020  1.090
 1SJ  CAV  H12  single  0.970  0.020  1.090
 1SJ  CAL  H13  single  0.970  0.020  1.090
 1SJ  CAL  H14  single  0.970  0.020  1.090
 1SJ  OAH  H16  single  0.850  0.020  0.980
 1SJ  CAI  H17  single  0.930  0.020  1.080
 1SJ  CAU  H19  single  0.970  0.020  1.090
 1SJ  NAM  H20  single  0.890  0.020  1.040
 1SJ  NAE  H21  single  0.890  0.020  1.040
 1SJ  NAD  H22  single  0.890  0.020  1.040
 1SJ  NAD  H23  single  0.890  0.020  1.040
 1SJ  CAW  H24  single  0.970  0.020  1.090
 1SJ  NAN  H25  single  0.860  0.020  1.020
 1SJ  CAC  H26  single  0.970  0.020  1.090
 1SJ  CAC  H27  single  0.970  0.020  1.090
 1SJ  CAC  H28  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
 1SJ  H3   CAA  H2   107.45  3.000
 1SJ  H3   CAA  H1   107.80  3.000
 1SJ  H2   CAA  H1   107.60  3.000
 1SJ  H3   CAA  CAJ  111.35  3.000
 1SJ  H2   CAA  CAJ  110.70  3.000
 1SJ  H1   CAA  CAJ  111.75  3.000
 1SJ  H5   CAJ  H4   106.10  3.000
 1SJ  H5   CAJ  CAT  108.85  3.000
 1SJ  H4   CAJ  CAT  107.67  3.000
 1SJ  H5   CAJ  CAA  109.94  3.000
 1SJ  H4   CAJ  CAA  109.34  3.000
 1SJ  CAT  CAJ  CAA  114.57  3.000
 1SJ  H6   CAT  OAO  109.90  3.000
 1SJ  H6   CAT  CAK  108.40  3.000
 1SJ  OAO  CAT  CAK  110.81  3.000
 1SJ  H6   CAT  CAJ  108.32  3.000
 1SJ  OAO  CAT  CAJ  108.67  3.000
 1SJ  CAK  CAT  CAJ  110.71  3.000
 1SJ  H8   CAK  H7   106.08  3.000
 1SJ  H8   CAK  CAB  109.84  3.000
 1SJ  H7   CAK  CAB  109.01  3.000
 1SJ  H8   CAK  CAT  108.90  3.000
 1SJ  H7   CAK  CAT  107.44  3.000
 1SJ  CAB  CAK  CAT  115.16  3.000
 1SJ  H11  CAB  H10  107.43  3.000
 1SJ  H11  CAB  H9   107.06  3.000
 1SJ  H10  CAB  H9   107.95  3.000
 1SJ  H11  CAB  CAK  110.70  3.000
 1SJ  H10  CAB  CAK  111.57  3.000
 1SJ  H9   CAB  CAK  111.91  3.000
 1SJ  CAV  OAO  CAT  116.79  3.000
 1SJ  H12  CAV  CAW  108.02  3.000
 1SJ  H12  CAV  CAL  108.35  3.000
 1SJ  CAW  CAV  CAL  109.76  3.000
 1SJ  H12  CAV  OAO  110.70  3.000
 1SJ  CAL  CAV  OAO  111.91  3.000
 1SJ  CAW  CAV  OAO  108.02  3.000
 1SJ  H14  CAL  H13  106.16  3.000
 1SJ  H14  CAL  CAS  110.39  3.000
 1SJ  H13  CAL  CAS  109.93  3.000
 1SJ  H14  CAL  CAV  109.31  3.000
 1SJ  H13  CAL  CAV  109.38  3.000
 1SJ  CAS  CAL  CAV  111.53  3.000
 1SJ  CAI  CAS  CAR  117.59  3.000
 1SJ  CAR  CAS  CAL  120.19  3.000
 1SJ  CAI  CAS  CAL  122.21  3.000
 1SJ  OAG  CAR  OAH  122.99  3.000
 1SJ  OAH  CAR  CAS  112.23  3.000
 1SJ  OAG  CAR  CAS  124.78  3.000
 1SJ  H16  OAH  CAR  109.99  3.000
 1SJ  H17  CAI  CAU  115.89  3.000
 1SJ  H17  CAI  CAS  119.95  3.000
 1SJ  CAU  CAI  CAS  124.15  3.000
 1SJ  H19  CAU  CAW  107.52  3.000
 1SJ  H19  CAU  NAM  107.55  3.000
 1SJ  CAW  CAU  NAM  109.80  3.000
 1SJ  H19  CAU  CAI  107.81  3.000
 1SJ  NAM  CAU  CAI  111.82  3.000
 1SJ  CAW  CAU  CAI  112.11  3.000
 1SJ  H20  NAM  CAQ  116.11  3.000
 1SJ  H20  NAM  CAU  115.10  3.000
 1SJ  CAQ  NAM  CAU  122.84  3.000
 1SJ  NAD  CAQ  NAE  119.83  3.000
 1SJ  NAD  CAQ  NAM  112.69  3.000
 1SJ  NAE  CAQ  NAM  127.48  3.000
 1SJ  H21  NAE  CAQ  112.59  3.000
 1SJ  H23  NAD  H22  112.39  3.000
 1SJ  H23  NAD  CAQ  113.56  3.000
 1SJ  H22  NAD  CAQ  116.58  3.000
 1SJ  H24  CAW  NAN  107.70  3.000
 1SJ  H24  CAW  CAU  109.10  3.000
 1SJ  NAN  CAW  CAU  109.56  3.000
 1SJ  H24  CAW  CAV  108.55  3.000
 1SJ  CAU  CAW  CAV  109.48  3.000
 1SJ  NAN  CAW  CAV  112.37  3.000
 1SJ  H25  NAN  CAP  118.16  3.000
 1SJ  H25  NAN  CAW  117.22  3.000
 1SJ  CAP  NAN  CAW  124.49  3.000
 1SJ  CAC  CAP  OAF  121.63  3.000
 1SJ  CAC  CAP  NAN  114.94  3.000
 1SJ  OAF  CAP  NAN  123.43  3.000
 1SJ  H28  CAC  H27  108.47  3.000
 1SJ  H28  CAC  H26  108.31  3.000
 1SJ  H27  CAC  H26  107.27  3.000
 1SJ  H28  CAC  CAP  113.85  3.000
 1SJ  H27  CAC  CAP  109.46  3.000
 1SJ  H26  CAC  CAP  109.28  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
 1SJ  CONST_01  OAF  CAP  NAN  CAW     0.00   0.0  0
 1SJ  CONST_02  CAC  CAP  NAN  CAW   180.00   0.0  0
 1SJ  CONST_03  NAE  CAQ  NAM  CAU     0.00   0.0  0
 1SJ  CONST_04  NAD  CAQ  NAM  CAU   180.00   0.0  0
 1SJ  CONST_05  H16  OAH  CAR  CAS   180.00   0.0  0
 1SJ  CONST_06  H25  NAN  CAP  OAF   180.00   0.0  0
 1SJ  CONST_07  H21  NAE  CAQ  NAM     0.00   0.0  0
 1SJ  CONST_09  H23  NAD  CAQ  NAM   180.00   0.0  0
 1SJ  Var_01    CAI  CAS  CAL  CAV    17.80  30.0  1
 1SJ  Var_02    CAU  CAI  CAS  CAL     1.23  30.0  1
 1SJ  Var_03    OAG  CAR  CAS  CAL   177.70  30.0  2
 1SJ  Var_04    H6   CAT  OAO  CAV    16.70  30.0  2
 1SJ  Var_05    CAK  CAT  CAJ  CAA   176.09  30.0  3
 1SJ  Var_06    CAB  CAK  CAT  CAJ  -176.76  30.0  3
 1SJ  Var_07    H1   CAA  CAJ  CAT    63.75  30.0  3
 1SJ  Var_08    H9   CAB  CAK  CAT   -67.14  30.0  3
 1SJ  Var_09    H26  CAC  CAP  NAN   121.16  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
 1SJ  chir_01  CAV  OAO  CAW  CAL  negativ
 1SJ  chir_02  CAU  NAM  CAI  CAW  negativ
 1SJ  chir_03  CAW  NAN  CAV  CAU  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
 1SJ  plan-1  CAW  0.020
 1SJ  plan-1  NAN  0.020
 1SJ  plan-1  CAP  0.020
 1SJ  plan-1  OAF  0.020
 1SJ  plan-1  CAC  0.020
 1SJ  plan-1  H25  0.020
 1SJ  plan-2  CAU  0.020
 1SJ  plan-2  NAM  0.020
 1SJ  plan-2  CAQ  0.020
 1SJ  plan-2  NAE  0.020
 1SJ  plan-2  NAD  0.020
 1SJ  plan-2  H20  0.020
 1SJ  plan-2  H21  0.020
 1SJ  plan-2  H22  0.020
 1SJ  plan-2  H23  0.020
 1SJ  plan-3  CAS  0.020
 1SJ  plan-3  CAR  0.020
 1SJ  plan-3  OAH  0.020
 1SJ  plan-3  OAG  0.020
 1SJ  plan-3  H16  0.020

