# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:13:17 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[trans-4-(aminomethyl)cyclohexyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CC[C@@H](CC1)NC(N)=N
#
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
 05T  05T  1-[trans-4-(aminomethyl)cyclohexyl]guanidine  ligand  30  12  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_05T
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
 05T  CAA   C  CH2   0  -0.434  -0.2431   1.4027  -0.0927
 05T  CAB   C  CH1   0  -0.042   0.7179   0.2236  -0.1971
 05T  NAC   N  NH1   0  -0.650   2.0444   0.6415   0.2092
 05T  CAD   C  C     0   0.551   3.1570  -0.0800  -0.1329
 05T  NAE   N  NH2   0  -0.843   4.2801   0.2676   0.5912
 05T  NAF   N  N     0  -0.716   3.1034  -0.9933  -1.0320
 05T  CAG   C  CH2   0  -0.428   0.1963  -0.9625   0.6143
 05T  CAH   C  CH2   0  -0.427  -1.2182  -1.3473   0.1963
 05T  CAI   C  CH1   0  -0.225  -2.1873  -0.1721   0.3069
 05T  CAJ   C  CH2   0  -0.435  -1.6579   1.0104  -0.5043
 05T  CAK   C  CH2   0  -0.269  -3.5916  -0.5844  -0.1196
 05T  NAL   N  NH2   0  -0.806  -4.5629   0.4821   0.0838
 05T  HAA   H  HCH2  0   0.211  -0.2559   1.7676   0.9421
 05T  HAAA  H  HCH2  0   0.234   0.1165   2.2287  -0.7115
 05T  HAB   H  HCH1  0   0.226   0.7849  -0.0773  -1.2460
 05T  HNAC  H  HNH1  0   0.371   2.0814   1.0990   1.1081
 05T  HNAE  H  HNH2  0   0.381   4.3169   1.2153   0.9348
 05T  HNAA  H  HNH2  0   0.383   5.1559  -0.0093   0.1771
 05T  HNAF  H  H     0   0.313   4.0258  -1.3763  -1.2039
 05T  HAG   H  HCH2  0   0.233   0.8754  -1.8098   0.4965
 05T  HAGA  H  HCH2  0   0.204   0.2043  -0.6918   1.6766
 05T  HAH   H  HCH2  0   0.207  -1.2059  -1.7069  -0.8402
 05T  HAHA  H  HCH2  0   0.226  -1.5723  -2.1840   0.8056
 05T  HAI   H  HCH1  0   0.205  -2.2373   0.1325   1.3607
 05T  HAJ   H  HCH2  0   0.230  -2.3158   1.8765  -0.3961
 05T  HAJA  H  HCH2  0   0.208  -1.6676   0.7438  -1.5685
 05T  HAK   H  HCH2  0   0.182  -3.5503  -0.9474  -1.1586
 05T  HAKA  H  HCH2  0   0.218  -3.9012  -1.4401   0.4877
 05T  HNAL  H  HNH2  0   0.342  -4.4232   1.2064  -0.6091
 05T  H2    H  HNH2  0   0.346  -5.4931   0.1234  -0.0890

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
 05T  CAB  CAA   single  1.525  0.020  1.525
 05T  CAA  CAJ   single  1.525  0.020  1.525
 05T  CAA  HAA   single  0.970  0.020  1.090
 05T  CAA  HAAA  single  0.970  0.020  1.090
 05T  NAC  CAB   single  1.449  0.020  1.449
 05T  CAB  CAG   single  1.529  0.020  1.529
 05T  CAB  HAB   single  0.970  0.020  1.090
 05T  CAD  NAC   single  1.369  0.020  1.369
 05T  NAC  HNAC  single  0.890  0.020  1.040
 05T  NAF  CAD   double  1.283  0.020  1.283
 05T  CAD  NAE   single  1.381  0.020  1.381
 05T  NAE  HNAE  single  0.890  0.020  1.040
 05T  NAE  HNAA  single  0.890  0.020  1.040
 05T  NAF  HNAF  single  0.890  0.020  1.040
 05T  CAG  CAH   single  1.524  0.020  1.524
 05T  CAG  HAG   single  0.970  0.020  1.090
 05T  CAG  HAGA  single  0.970  0.020  1.090
 05T  CAH  CAI   single  1.527  0.020  1.527
 05T  CAH  HAH   single  0.970  0.020  1.090
 05T  CAH  HAHA  single  0.970  0.020  1.090
 05T  CAJ  CAI   single  1.529  0.020  1.529
 05T  CAI  CAK   single  1.524  0.020  1.524
 05T  CAI  HAI   single  0.970  0.020  1.090
 05T  CAJ  HAJ   single  0.970  0.020  1.090
 05T  CAJ  HAJA  single  0.970  0.020  1.090
 05T  CAK  NAL   single  1.457  0.020  1.457
 05T  CAK  HAK   single  0.970  0.020  1.090
 05T  CAK  HAKA  single  0.970  0.020  1.090
 05T  NAL  HNAL  single  0.890  0.020  1.040
 05T  NAL  H2    single  0.890  0.020  1.040

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
 05T  HAAA  CAA  HAA   106.64  3.000
 05T  HAAA  CAA  CAJ   110.29  3.000
 05T  HAA   CAA  CAJ   109.22  3.000
 05T  HAAA  CAA  CAB   109.78  3.000
 05T  HAA   CAA  CAB   109.22  3.000
 05T  CAJ   CAA  CAB   111.55  3.000
 05T  HAB   CAB  CAG   108.46  3.000
 05T  HAB   CAB  NAC   107.00  3.000
 05T  CAG   CAB  NAC   112.78  3.000
 05T  HAB   CAB  CAA   108.50  3.000
 05T  CAG   CAB  CAA   110.40  3.000
 05T  NAC   CAB  CAA   109.56  3.000
 05T  HNAC  NAC  CAD   115.57  3.000
 05T  HNAC  NAC  CAB   114.46  3.000
 05T  CAD   NAC  CAB   121.45  3.000
 05T  NAF   CAD  NAE   125.51  3.000
 05T  NAE   CAD  NAC   113.40  3.000
 05T  NAF   CAD  NAC   121.09  3.000
 05T  HNAA  NAE  HNAE  111.50  3.000
 05T  HNAA  NAE  CAD   114.98  3.000
 05T  HNAE  NAE  CAD   116.41  3.000
 05T  HNAF  NAF  CAD   110.48  3.000
 05T  HAGA  CAG  HAG   106.95  3.000
 05T  HAGA  CAG  CAH   109.56  3.000
 05T  HAG   CAG  CAH   110.58  3.000
 05T  HAGA  CAG  CAB   108.68  3.000
 05T  HAG   CAG  CAB   109.42  3.000
 05T  CAH   CAG  CAB   111.52  3.000
 05T  HAHA  CAH  HAH   106.21  3.000
 05T  HAHA  CAH  CAI   110.05  3.000
 05T  HAH   CAH  CAI   109.13  3.000
 05T  HAHA  CAH  CAG   109.92  3.000
 05T  HAH   CAH  CAG   109.36  3.000
 05T  CAI   CAH  CAG   112.01  3.000
 05T  HAI   CAI  CAK   107.55  3.000
 05T  HAI   CAI  CAJ   108.09  3.000
 05T  CAK   CAI  CAJ   112.32  3.000
 05T  HAI   CAI  CAH   108.17  3.000
 05T  CAK   CAI  CAH   110.86  3.000
 05T  CAJ   CAI  CAH   109.70  3.000
 05T  HAJA  CAJ  HAJ   106.45  3.000
 05T  HAJA  CAJ  CAI   108.89  3.000
 05T  HAJ   CAJ  CAI   110.61  3.000
 05T  HAJA  CAJ  CAA   109.43  3.000
 05T  HAJ   CAJ  CAA   109.15  3.000
 05T  CAI   CAJ  CAA   112.15  3.000
 05T  HAKA  CAK  HAK   106.05  3.000
 05T  HAKA  CAK  NAL   107.84  3.000
 05T  HAK   CAK  NAL   113.45  3.000
 05T  HAKA  CAK  CAI   108.48  3.000
 05T  HAK   CAK  CAI   108.58  3.000
 05T  NAL   CAK  CAI   112.15  3.000
 05T  H2    NAL  HNAL  105.29  3.000
 05T  H2    NAL  CAK   109.24  3.000
 05T  HNAL  NAL  CAK   109.66  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
 05T  CONST_01  NAF   CAD  NAC  CAB    0.00   0.0  0
 05T  CONST_02  NAE   CAD  NAC  CAB  180.00   0.0  0
 05T  CONST_03  HNAF  NAF  CAD  NAC  180.00   0.0  0
 05T  Var_01    CAI   CAJ  CAA  CAB   55.96  30.0  1
 05T  Var_02    CAI   CAH  CAG  CAB  -56.22  30.0  1
 05T  Var_03    HNAL  NAL  CAK  CAI   72.93  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
 05T  chir_01  CAB  CAA  NAC  CAG  negativ
 05T  chir_02  CAI  CAH  CAJ  CAK  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
 05T  plan-1  CAB   0.020
 05T  plan-1  NAC   0.020
 05T  plan-1  CAD   0.020
 05T  plan-1  NAE   0.020
 05T  plan-1  NAF   0.020
 05T  plan-1  HNAC  0.020
 05T  plan-1  HNAE  0.020
 05T  plan-1  HNAA  0.020
 05T  plan-1  HNAF  0.020

