# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:20:50 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-carbamoyl-1-(3-{2-[(E)-(hydroxyimino)methyl]-1H-imidazol-1-yl}propyl)pyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc[n+](CCCn2ccnc2\C=N\O)cc1
#
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
 LND  LND  4-carbamoyl-1-(3-{2-[(E)-(hydroxyimino)methyl]-1H-imidazol-1-yl}propyl)pyridin-1-ium  ligand  36  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LND
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
 LND  CAI  C  CR16  0   0.101  -2.4284   1.4501  -0.6882
 LND  CAF  C  CR16  0  -0.359  -3.6671   1.1886  -0.1558
 LND  CAQ  C  CR6   0   0.106  -4.0895  -0.1284  -0.0256
 LND  CAP  C  C     0   0.514  -5.4605  -0.3894   0.5399
 LND  OAB  O  O     0  -0.452  -6.3481   0.4243   0.3568
 LND  NAA  N  NH2   0  -0.799  -5.5950  -1.5324   1.2135
 LND  CAG  C  CR16  0  -0.369  -3.2539  -1.1446  -0.4711
 LND  CAJ  C  CR16  0   0.105  -2.0306  -0.8240  -1.0125
 LND  NAT  N  NR6   1  -0.410  -1.6396   0.4518  -1.1077
 LND  CAM  C  CH2   0  -0.357  -0.2999   0.7627  -1.6334
 LND  CAK  C  CH2   0  -0.450   0.7318   0.7407  -0.5171
 LND  CAL  C  CH2   0  -0.343   2.0870   1.1900  -1.0491
 LND  NAS  N  NR5   0  -0.458   3.1083   1.1397  -0.0228
 LND  CAH  C  CR15  0  -0.103   3.4469   2.1745   0.7966
 LND  CAE  C  CR15  0  -0.215   4.3949   1.6774   1.6478
 LND  NAO  N  N     0  -0.446   4.6362   0.3706   1.3727
 LND  CAR  C  CR5   0   0.444   3.8463   0.0655   0.3670
 LND  CAD  C  C1    0  -0.132   3.7403  -1.2278  -0.2821
 LND  NAN  N  N     0  -0.102   4.4446  -2.2002   0.1328
 LND  OAC  O  OH1   0  -0.540   4.2296  -3.3347  -0.5825
 LND  H1   H  HCR6  0   0.359  -2.0470   2.4543  -0.7982
 LND  H2   H  HCR6  0   0.322  -4.2856   2.0161   0.1590
 LND  H3   H  HNH2  0   0.426  -4.8117  -2.1162   1.4539
 LND  H4   H  HNH2  0   0.421  -6.4780  -1.7558   1.6460
 LND  H5   H  HCR6  0   0.324  -3.5352  -2.1868  -0.4282
 LND  H6   H  HCR6  0   0.359  -1.3483  -1.5744  -1.3832
 LND  H7   H  HCH2  0   0.314  -0.0729   0.0313  -2.4066
 LND  H8   H  HCH2  0   0.311  -0.3559   1.7408  -2.1081
 LND  H9   H  HCH2  0   0.278   0.4217   1.4075   0.2909
 LND  H10  H  HCH2  0   0.270   0.8037  -0.2663  -0.0994
 LND  H11  H  HCH2  0   0.286   2.4008   0.5841  -1.8990
 LND  H12  H  HCH2  0   0.297   2.0303   2.2170  -1.4081
 LND  H13  H  HCR5  0   0.297   3.0008   3.1503   0.6999
 LND  H14  H  HCR5  0   0.256   4.9124   2.2015   2.4363
 LND  H15  H  H     0   0.261   3.0540  -1.3379  -1.1201
 LND  H16  H  HOH1  0   0.480   4.8151  -3.9861  -0.1816

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
 LND  OAB  CAP  double    1.218  0.020  1.218
 LND  CAP  NAA  single    1.333  0.020  1.333
 LND  CAP  CAQ  single    1.506  0.020  1.506
 LND  CAQ  CAF  aromatic  1.389  0.020  1.389
 LND  CAQ  CAG  aromatic  1.389  0.020  1.389
 LND  CAF  CAI  aromatic  1.373  0.020  1.373
 LND  CAG  CAJ  aromatic  1.376  0.020  1.376
 LND  CAI  NAT  aromatic  1.340  0.020  1.340
 LND  CAJ  NAT  aromatic  1.338  0.020  1.338
 LND  NAT  CAM  single    1.472  0.020  1.472
 LND  CAK  CAM  single    1.520  0.020  1.520
 LND  CAK  CAL  single    1.524  0.020  1.524
 LND  CAL  NAS  single    1.449  0.020  1.449
 LND  CAH  NAS  aromatic  1.363  0.020  1.363
 LND  CAH  CAE  aromatic  1.368  0.020  1.368
 LND  NAS  CAR  aromatic  1.360  0.020  1.360
 LND  CAE  NAO  aromatic  1.357  0.020  1.357
 LND  CAR  NAO  aromatic  1.315  0.020  1.315
 LND  CAR  CAD  single    1.451  0.020  1.451
 LND  CAD  NAN  double    1.270  0.020  1.270
 LND  NAN  OAC  single    1.358  0.020  1.358
 LND  CAI  H1   single    0.930  0.020  1.080
 LND  CAF  H2   single    0.930  0.020  1.080
 LND  NAA  H3   single    0.860  0.020  1.020
 LND  NAA  H4   single    0.860  0.020  1.020
 LND  CAG  H5   single    0.930  0.020  1.080
 LND  CAJ  H6   single    0.930  0.020  1.080
 LND  CAM  H7   single    0.970  0.020  1.090
 LND  CAM  H8   single    0.970  0.020  1.090
 LND  CAK  H9   single    0.970  0.020  1.090
 LND  CAK  H10  single    0.970  0.020  1.090
 LND  CAL  H11  single    0.970  0.020  1.090
 LND  CAL  H12  single    0.970  0.020  1.090
 LND  CAH  H13  single    0.930  0.020  1.080
 LND  CAE  H14  single    0.930  0.020  1.080
 LND  CAD  H15  single    0.930  0.020  1.080
 LND  OAC  H16  single    0.850  0.020  0.980

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
 LND  H1   CAI  NAT  116.94  3.000
 LND  H1   CAI  CAF  122.36  3.000
 LND  NAT  CAI  CAF  120.70  3.000
 LND  H2   CAF  CAQ  121.66  3.000
 LND  H2   CAF  CAI  118.92  3.000
 LND  CAQ  CAF  CAI  119.41  3.000
 LND  CAG  CAQ  CAP  122.78  3.000
 LND  CAG  CAQ  CAF  118.73  3.000
 LND  CAP  CAQ  CAF  118.44  3.000
 LND  NAA  CAP  OAB  125.10  3.000
 LND  NAA  CAP  CAQ  115.47  3.000
 LND  OAB  CAP  CAQ  119.42  3.000
 LND  H4   NAA  H3   116.79  3.000
 LND  H4   NAA  CAP  119.67  3.000
 LND  H3   NAA  CAP  122.65  3.000
 LND  H5   CAG  CAJ  118.16  3.000
 LND  H5   CAG  CAQ  122.44  3.000
 LND  CAJ  CAG  CAQ  119.39  3.000
 LND  H6   CAJ  NAT  116.97  3.000
 LND  H6   CAJ  CAG  122.35  3.000
 LND  NAT  CAJ  CAG  120.68  3.000
 LND  CAM  NAT  CAJ  119.52  3.000
 LND  CAM  NAT  CAI  119.35  3.000
 LND  CAJ  NAT  CAI  121.08  3.000
 LND  H8   CAM  H7   107.75  3.000
 LND  H8   CAM  CAK  111.60  3.000
 LND  H7   CAM  CAK  111.74  3.000
 LND  H8   CAM  NAT  107.38  3.000
 LND  H7   CAM  NAT  107.55  3.000
 LND  CAK  CAM  NAT  110.62  3.000
 LND  H10  CAK  H9   107.37  3.000
 LND  H10  CAK  CAL  110.29  3.000
 LND  H9   CAK  CAL  109.31  3.000
 LND  H10  CAK  CAM  109.80  3.000
 LND  H9   CAK  CAM  109.98  3.000
 LND  CAL  CAK  CAM  110.06  3.000
 LND  H12  CAL  H11  106.38  3.000
 LND  H12  CAL  NAS  107.63  3.000
 LND  H11  CAL  NAS  109.27  3.000
 LND  H12  CAL  CAK  110.29  3.000
 LND  H11  CAL  CAK  111.38  3.000
 LND  NAS  CAL  CAK  111.68  3.000
 LND  CAR  NAS  CAH  107.01  3.000
 LND  CAR  NAS  CAL  127.79  3.000
 LND  CAH  NAS  CAL  125.09  3.000
 LND  H13  CAH  CAE  132.23  3.000
 LND  H13  CAH  NAS  122.08  3.000
 LND  CAE  CAH  NAS  105.69  3.000
 LND  H14  CAE  NAO  122.05  3.000
 LND  H14  CAE  CAH  127.64  3.000
 LND  NAO  CAE  CAH  110.31  3.000
 LND  CAR  NAO  CAE  105.77  3.000
 LND  CAD  CAR  NAO  126.37  3.000
 LND  CAD  CAR  NAS  122.41  3.000
 LND  NAO  CAR  NAS  111.21  3.000
 LND  H15  CAD  NAN  121.56  3.000
 LND  H15  CAD  CAR  118.72  3.000
 LND  NAN  CAD  CAR  119.71  3.000
 LND  OAC  NAN  CAD  112.31  3.000
 LND  H16  OAC  NAN  104.44  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
 LND  CONST_01  CAG  CAQ  CAF  CAI     0.00   0.0  0
 LND  CONST_02  CAG  CAJ  NAT  CAI     0.00   0.0  0
 LND  CONST_03  CAJ  CAG  CAQ  CAF     0.00   0.0  0
 LND  CONST_04  CAJ  NAT  CAI  CAF     0.00   0.0  0
 LND  CONST_05  NAT  CAI  CAF  CAQ     0.00   0.0  0
 LND  CONST_06  NAT  CAJ  CAG  CAQ     0.00   0.0  0
 LND  CONST_07  NAO  CAE  CAH  NAS     0.00   0.0  0
 LND  CONST_08  CAE  NAO  CAR  NAS     0.00   0.0  0
 LND  CONST_09  NAO  CAR  NAS  CAH     0.00   0.0  0
 LND  CONST_10  CAR  NAO  CAE  CAH     0.00   0.0  0
 LND  CONST_11  CAR  NAS  CAH  CAE     0.00   0.0  0
 LND  CONST_12  CAP  CAQ  CAF  CAI   180.00   0.0  0
 LND  CONST_13  CAM  NAT  CAI  CAF   180.00   0.0  0
 LND  CONST_14  CAJ  CAG  CAQ  CAP   180.00   0.0  0
 LND  CONST_15  CAM  NAT  CAJ  CAG   180.00   0.0  0
 LND  CONST_16  CAE  CAH  NAS  CAL   180.00   0.0  0
 LND  CONST_17  NAO  CAR  NAS  CAL   180.00   0.0  0
 LND  CONST_18  CAD  CAR  NAS  CAH   180.00   0.0  0
 LND  CONST_19  CAD  CAR  NAO  CAE   180.00   0.0  0
 LND  CONST_20  H6   CAJ  NAT  CAI   180.00   0.0  0
 LND  CONST_21  H5   CAG  CAQ  CAF   180.00   0.0  0
 LND  CONST_22  H1   CAI  CAF  CAQ   180.00   0.0  0
 LND  CONST_23  H2   CAF  CAQ  CAG   180.00   0.0  0
 LND  CONST_24  H14  CAE  CAH  NAS   180.00   0.0  0
 LND  CONST_25  H13  CAH  CAE  NAO   180.00   0.0  0
 LND  CONST_26  H3   NAA  CAP  CAQ     0.00   0.0  0
 LND  CONST_27  H4   NAA  CAP  CAQ   180.00   0.0  0
 LND  Var_01    CAK  CAM  NAT  CAI    90.55  30.0  2
 LND  Var_02    OAB  CAP  CAQ  CAF    30.51  30.0  2
 LND  Var_03    CAH  NAS  CAL  CAK   -91.70  30.0  2
 LND  Var_04    NAN  CAD  CAR  NAS  -179.29  30.0  2
 LND  Var_05    CAL  CAK  CAM  NAT  -174.75  30.0  2
 LND  Var_06    NAS  CAL  CAK  CAM  -178.09  30.0  3

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
 LND  plan-1  CAL  0.020
 LND  plan-1  NAS  0.020
 LND  plan-1  CAH  0.020
 LND  plan-1  CAE  0.020
 LND  plan-1  NAO  0.020
 LND  plan-1  CAR  0.020
 LND  plan-1  CAD  0.020
 LND  plan-1  H13  0.020
 LND  plan-1  H14  0.020
 LND  plan-2  CAI  0.020
 LND  plan-2  CAF  0.020
 LND  plan-2  CAQ  0.020
 LND  plan-2  CAP  0.020
 LND  plan-2  CAG  0.020
 LND  plan-2  CAJ  0.020
 LND  plan-2  NAT  0.020
 LND  plan-2  CAM  0.020
 LND  plan-2  H1   0.020
 LND  plan-2  H2   0.020
 LND  plan-2  H5   0.020
 LND  plan-2  H6   0.020
 LND  plan-3  CAQ  0.020
 LND  plan-3  CAP  0.020
 LND  plan-3  OAB  0.020
 LND  plan-3  NAA  0.020
 LND  plan-3  H3   0.020
 LND  plan-3  H4   0.020
 LND  plan-4  CAR  0.020
 LND  plan-4  CAD  0.020
 LND  plan-4  NAN  0.020
 LND  plan-4  OAC  0.020
 LND  plan-4  H15  0.020

