# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 17:17:58 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CNC(=O)c2[nH]c3ccccc3c2)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 ZX7  ZX7  N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}-1H-indole-2-carboxamide  ligand  44  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZX7
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
 ZX7  OAD   O  OH1   0  -0.679   3.7332   2.1793   0.9269
 ZX7  CAV   C  CH1   0   0.079   3.6453   0.9802   0.1940
 ZX7  CAW   C  CH1   0  -0.034   4.5453  -0.1009   0.7842
 ZX7  OAE   O  OH1   0  -0.675   5.8794   0.3585   0.6742
 ZX7  CAU   C  CH1   0   0.027   4.3611  -1.4417   0.0715
 ZX7  OAC   O  OH1   0  -0.674   4.8127  -1.3742  -1.2617
 ZX7  CAS   C  CH1   0  -0.122   2.8806  -1.8307   0.0735
 ZX7  CAA   C  CH3   0  -0.663   2.6179  -3.1385  -0.6546
 ZX7  NAM   N  NH1   0  -0.589   2.0360  -0.7752  -0.4682
 ZX7  CAT   C  CH1   0  -0.167   2.1990   0.4895   0.2291
 ZX7  CAK   C  CH2   0  -0.248   1.2261   1.5070  -0.3527
 ZX7  NAL   N  NH1   0  -0.658  -0.1088   0.9596  -0.2824
 ZX7  CAO   C  C     0   0.518  -1.2179   1.7127  -0.3260
 ZX7  OAB   O  O     0  -0.489  -1.2057   2.9293  -0.4662
 ZX7  CAP   C  CR5   0   0.219  -2.4975   0.9884  -0.1801
 ZX7  CAJ   C  CR15  0  -0.400  -3.7357   1.4386  -0.5489
 ZX7  CAQ   C  CR56  0   0.066  -4.6659   0.4112  -0.2219
 ZX7  CAH   C  CR16  0  -0.338  -6.0558   0.2767  -0.3502
 ZX7  CAF   C  CR16  0  -0.270  -6.6559  -0.8776   0.1050
 ZX7  CAG   C  CR16  0  -0.278  -5.8969  -1.9091   0.6893
 ZX7  CAI   C  CR16  0  -0.310  -4.5279  -1.8095   0.8242
 ZX7  CAR   C  CR56  0   0.347  -3.9229  -0.6415   0.3571
 ZX7  NAN   N  NR15  0  -0.740  -2.6117  -0.2718   0.3550
 ZX7  HOAD  H  HOH1  0   0.450   4.6587   2.4438   0.9558
 ZX7  HAV   H  HCH1  0   0.200   3.9292   1.1451  -0.8579
 ZX7  HAW   H  HCH1  0   0.222   4.2644  -0.2367   1.8389
 ZX7  HOAE  H  HOH1  0   0.460   6.4293  -0.1320   1.2936
 ZX7  HAU   H  HCH1  0   0.211   4.9214  -2.2066   0.6337
 ZX7  HOAC  H  HOH1  0   0.447   5.6581  -0.9109  -1.2586
 ZX7  HAS   H  HCH1  0   0.237   2.5947  -1.9618   1.1239
 ZX7  HAA   H  HCH3  0   0.229   3.2272  -3.9424  -0.2402
 ZX7  HAAA  H  HCH3  0   0.235   1.5709  -3.4239  -0.5535
 ZX7  HAAB  H  HCH3  0   0.227   2.8458  -3.0597  -1.7180
 ZX7  HNAM  H  HNH1  0   0.343   2.2559  -0.6471  -1.4525
 ZX7  HAT   H  HCH1  0   0.244   1.9232   0.3194   1.2788
 ZX7  HAK   H  HCH2  0   0.259   1.2649   2.4372   0.2108
 ZX7  HAKA  H  HCH2  0   0.234   1.5049   1.7376  -1.3885
 ZX7  HNAL  H  HNH1  0   0.393  -0.1614  -0.0448  -0.3817
 ZX7  HAJ   H  HCR5  0   0.258  -3.9495   2.3858  -1.0177
 ZX7  HAH   H  HCR6  0   0.251  -6.6452   1.0686  -0.7953
 ZX7  HAF   H  HCR6  0   0.251  -7.7278  -0.9976   0.0165
 ZX7  HAG   H  HCR6  0   0.255  -6.3994  -2.8006   1.0413
 ZX7  HAI   H  HCR6  0   0.263  -3.9479  -2.6058   1.2728
 ZX7  HNAN  H  HNR5  0   0.410  -1.8796  -0.7803   0.8237

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
 ZX7  OAD  CAV   single    1.408  0.020  1.408
 ZX7  CAV  CAW   single    1.525  0.020  1.525
 ZX7  CAV  CAT   single    1.528  0.020  1.528
 ZX7  CAW  OAE   single    1.415  0.020  1.415
 ZX7  CAW  CAU   single    1.530  0.020  1.530
 ZX7  CAU  OAC   single    1.409  0.020  1.409
 ZX7  CAU  CAS   single    1.531  0.020  1.531
 ZX7  CAS  CAA   single    1.520  0.020  1.520
 ZX7  CAS  NAM   single    1.456  0.020  1.456
 ZX7  NAM  CAT   single    1.453  0.020  1.453
 ZX7  CAT  CAK   single    1.523  0.020  1.523
 ZX7  CAK  NAL   single    1.444  0.020  1.444
 ZX7  NAL  CAO   single    1.341  0.020  1.341
 ZX7  CAO  OAB   double    1.225  0.020  1.225
 ZX7  CAO  CAP   single    1.478  0.020  1.478
 ZX7  CAP  CAJ   aromatic  1.368  0.020  1.368
 ZX7  CAP  NAN   aromatic  1.374  0.020  1.374
 ZX7  CAJ  CAQ   aromatic  1.424  0.020  1.424
 ZX7  CAQ  CAH   aromatic  1.402  0.020  1.402
 ZX7  CAQ  CAR   aromatic  1.413  0.020  1.413
 ZX7  CAH  CAF   aromatic  1.378  0.020  1.378
 ZX7  CAF  CAG   aromatic  1.408  0.020  1.408
 ZX7  CAG  CAI   aromatic  1.379  0.020  1.379
 ZX7  CAI  CAR   aromatic  1.396  0.020  1.396
 ZX7  CAR  NAN   aromatic  1.362  0.020  1.362
 ZX7  OAD  HOAD  single    0.850  0.020  0.980
 ZX7  CAV  HAV   single    0.970  0.020  1.090
 ZX7  CAW  HAW   single    0.970  0.020  1.090
 ZX7  OAE  HOAE  single    0.850  0.020  0.980
 ZX7  CAU  HAU   single    0.970  0.020  1.090
 ZX7  OAC  HOAC  single    0.850  0.020  0.980
 ZX7  CAS  HAS   single    0.970  0.020  1.090
 ZX7  CAA  HAA   single    0.970  0.020  1.090
 ZX7  CAA  HAAA  single    0.970  0.020  1.090
 ZX7  CAA  HAAB  single    0.970  0.020  1.090
 ZX7  NAM  HNAM  single    0.890  0.020  1.040
 ZX7  CAT  HAT   single    0.970  0.020  1.090
 ZX7  CAK  HAK   single    0.970  0.020  1.090
 ZX7  CAK  HAKA  single    0.970  0.020  1.090
 ZX7  NAL  HNAL  single    0.860  0.020  1.020
 ZX7  CAJ  HAJ   single    0.930  0.020  1.080
 ZX7  CAH  HAH   single    0.930  0.020  1.080
 ZX7  CAF  HAF   single    0.930  0.020  1.080
 ZX7  CAG  HAG   single    0.930  0.020  1.080
 ZX7  CAI  HAI   single    0.930  0.020  1.080
 ZX7  NAN  HNAN  single    0.860  0.020  1.020

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
 ZX7  HOAD  OAD  CAV   108.03  3.000
 ZX7  HAV   CAV  CAT   108.29  3.000
 ZX7  HAV   CAV  CAW   108.87  3.000
 ZX7  CAT   CAV  CAW   108.78  3.000
 ZX7  HAV   CAV  OAD   110.69  3.000
 ZX7  CAT   CAV  OAD   108.70  3.000
 ZX7  CAW   CAV  OAD   111.43  3.000
 ZX7  HAW   CAW  CAU   107.93  3.000
 ZX7  HAW   CAW  OAE   110.81  3.000
 ZX7  CAU   CAW  OAE   111.22  3.000
 ZX7  HAW   CAW  CAV   107.93  3.000
 ZX7  CAU   CAW  CAV   111.71  3.000
 ZX7  OAE   CAW  CAV   107.22  3.000
 ZX7  HOAE  OAE  CAW   108.86  3.000
 ZX7  HAU   CAU  CAS   108.34  3.000
 ZX7  HAU   CAU  OAC   110.67  3.000
 ZX7  CAS   CAU  OAC   108.87  3.000
 ZX7  HAU   CAU  CAW   108.02  3.000
 ZX7  CAS   CAU  CAW   109.79  3.000
 ZX7  OAC   CAU  CAW   111.11  3.000
 ZX7  HOAC  OAC  CAU   107.52  3.000
 ZX7  HAS   CAS  NAM   106.97  3.000
 ZX7  HAS   CAS  CAA   108.12  3.000
 ZX7  NAM   CAS  CAA   110.20  3.000
 ZX7  HAS   CAS  CAU   106.49  3.000
 ZX7  NAM   CAS  CAU   112.10  3.000
 ZX7  CAA   CAS  CAU   112.66  3.000
 ZX7  HAAB  CAA  HAAA  108.07  3.000
 ZX7  HAAB  CAA  HAA   107.88  3.000
 ZX7  HAAA  CAA  HAA   107.96  3.000
 ZX7  HAAB  CAA  CAS   111.65  3.000
 ZX7  HAAA  CAA  CAS   110.30  3.000
 ZX7  HAA   CAA  CAS   110.84  3.000
 ZX7  HNAM  NAM  CAT   109.31  3.000
 ZX7  HNAM  NAM  CAS   109.03  3.000
 ZX7  CAT   NAM  CAS   112.78  3.000
 ZX7  HAT   CAT  CAK   107.94  3.000
 ZX7  HAT   CAT  NAM   107.20  3.000
 ZX7  CAK   CAT  NAM   109.05  3.000
 ZX7  HAT   CAT  CAV   108.01  3.000
 ZX7  CAK   CAT  CAV   112.41  3.000
 ZX7  NAM   CAT  CAV   112.00  3.000
 ZX7  HAKA  CAK  HAK   107.47  3.000
 ZX7  HAKA  CAK  NAL   111.12  3.000
 ZX7  HAK   CAK  NAL   109.37  3.000
 ZX7  HAKA  CAK  CAT   109.80  3.000
 ZX7  HAK   CAK  CAT   110.52  3.000
 ZX7  NAL   CAK  CAT   108.57  3.000
 ZX7  HNAL  NAL  CAO   120.78  3.000
 ZX7  HNAL  NAL  CAK   114.83  3.000
 ZX7  CAO   NAL  CAK   123.36  3.000
 ZX7  CAP   CAO  OAB   120.46  3.000
 ZX7  CAP   CAO  NAL   115.95  3.000
 ZX7  OAB   CAO  NAL   123.59  3.000
 ZX7  NAN   CAP  CAJ   109.36  3.000
 ZX7  NAN   CAP  CAO   124.06  3.000
 ZX7  CAJ   CAP  CAO   126.57  3.000
 ZX7  HAJ   CAJ  CAQ   127.17  3.000
 ZX7  HAJ   CAJ  CAP   125.85  3.000
 ZX7  CAQ   CAJ  CAP   106.97  3.000
 ZX7  CAR   CAQ  CAH   119.17  3.000
 ZX7  CAR   CAQ  CAJ   106.75  3.000
 ZX7  CAH   CAQ  CAJ   134.08  3.000
 ZX7  HAH   CAH  CAF   120.75  3.000
 ZX7  HAH   CAH  CAQ   120.46  3.000
 ZX7  CAF   CAH  CAQ   118.79  3.000
 ZX7  HAF   CAF  CAG   119.13  3.000
 ZX7  HAF   CAF  CAH   119.81  3.000
 ZX7  CAG   CAF  CAH   121.07  3.000
 ZX7  HAG   CAG  CAI   119.25  3.000
 ZX7  HAG   CAG  CAF   119.23  3.000
 ZX7  CAI   CAG  CAF   121.52  3.000
 ZX7  HAI   CAI  CAR   121.46  3.000
 ZX7  HAI   CAI  CAG   121.28  3.000
 ZX7  CAR   CAI  CAG   117.26  3.000
 ZX7  NAN   CAR  CAI   130.15  3.000
 ZX7  NAN   CAR  CAQ   107.66  3.000
 ZX7  CAI   CAR  CAQ   122.19  3.000
 ZX7  HNAN  NAN  CAR   124.19  3.000
 ZX7  HNAN  NAN  CAP   125.73  3.000
 ZX7  CAR   NAN  CAP   109.24  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
 ZX7  CONST_01  CAH   CAQ  CAJ  CAP   180.00   0.0  0
 ZX7  CONST_02  CAR   CAQ  CAJ  CAP     0.00   0.0  0
 ZX7  CONST_03  CAQ   CAR  NAN  CAP     0.00   0.0  0
 ZX7  CONST_04  CAI   CAR  NAN  CAP   180.00   0.0  0
 ZX7  CONST_05  CAR   NAN  CAP  CAJ     0.00   0.0  0
 ZX7  CONST_06  CAF   CAH  CAQ  CAJ   180.00   0.0  0
 ZX7  CONST_07  CAI   CAR  CAQ  CAJ   180.00   0.0  0
 ZX7  CONST_08  NAN   CAR  CAQ  CAJ     0.00   0.0  0
 ZX7  CONST_09  NAN   CAP  CAJ  CAQ     0.00   0.0  0
 ZX7  CONST_10  CAG   CAF  CAH  CAQ     0.00   0.0  0
 ZX7  CONST_11  CAG   CAI  CAR  CAQ     0.00   0.0  0
 ZX7  CONST_12  CAI   CAR  CAQ  CAH     0.00   0.0  0
 ZX7  CONST_13  NAN   CAR  CAQ  CAH   180.00   0.0  0
 ZX7  CONST_14  CAI   CAG  CAF  CAH     0.00   0.0  0
 ZX7  CONST_15  CAR   CAQ  CAH  CAF     0.00   0.0  0
 ZX7  CONST_16  CAR   CAI  CAG  CAF     0.00   0.0  0
 ZX7  CONST_17  NAN   CAR  CAI  CAG   180.00   0.0  0
 ZX7  CONST_18  CAQ   CAJ  CAP  CAO   180.00   0.0  0
 ZX7  CONST_19  CAR   NAN  CAP  CAO   180.00   0.0  0
 ZX7  CONST_20  HNAN  NAN  CAP  CAJ   180.00   0.0  0
 ZX7  CONST_21  HAH   CAH  CAQ  CAJ     0.00   0.0  0
 ZX7  CONST_22  HAF   CAF  CAH  CAQ   180.00   0.0  0
 ZX7  CONST_23  HAI   CAI  CAR  CAQ   180.00   0.0  0
 ZX7  CONST_24  HAJ   CAJ  CAQ  CAH     0.00   0.0  0
 ZX7  CONST_25  HAG   CAG  CAF  CAH   180.00   0.0  0
 ZX7  CONST_26  CAP   CAO  NAL  CAK   180.00   0.0  0
 ZX7  CONST_27  HNAL  NAL  CAO  CAP     0.00   0.0  0
 ZX7  CONST_28  OAB   CAO  NAL  CAK     0.00   0.0  0
 ZX7  Var_01    CAJ   CAP  CAO  NAL  -160.59  30.0  2
 ZX7  Var_02    CAO   NAL  CAK  CAT   159.25  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
 ZX7  chir_01  CAV  OAD  CAW  CAT  negativ
 ZX7  chir_02  CAW  OAE  CAV  CAU  negativ
 ZX7  chir_03  CAU  OAC  CAW  CAS  negativ
 ZX7  chir_04  CAS  NAM  CAU  CAA  positiv
 ZX7  chir_05  CAT  NAM  CAK  CAV  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
 ZX7  plan-1  CAO   0.020
 ZX7  plan-1  CAP   0.020
 ZX7  plan-1  CAJ   0.020
 ZX7  plan-1  CAQ   0.020
 ZX7  plan-1  CAH   0.020
 ZX7  plan-1  CAF   0.020
 ZX7  plan-1  CAG   0.020
 ZX7  plan-1  CAI   0.020
 ZX7  plan-1  CAR   0.020
 ZX7  plan-1  NAN   0.020
 ZX7  plan-1  HAJ   0.020
 ZX7  plan-1  HAH   0.020
 ZX7  plan-1  HAF   0.020
 ZX7  plan-1  HAG   0.020
 ZX7  plan-1  HAI   0.020
 ZX7  plan-1  HNAN  0.020
 ZX7  plan-2  CAK   0.020
 ZX7  plan-2  NAL   0.020
 ZX7  plan-2  CAO   0.020
 ZX7  plan-2  OAB   0.020
 ZX7  plan-2  CAP   0.020
 ZX7  plan-2  HNAL  0.020

