# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:10:50 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-(1-ethyl-1H-benzimidazol-2-yl)-3-(2-methoxyphenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c(NC(=O)Nc2ccccc2OC)nc3ccccc13
#
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
 36K  36K  1-(1-ethyl-1H-benzimidazol-2-yl)-3-(2-methoxyphenyl)urea  ligand  41  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_36K
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
 36K  CAF   C  CH3   0  -0.658  -2.6142  -3.2548   0.3506
 36K  CAE   C  CH2   0  -0.364  -2.6064  -2.0065   1.2178
 36K  NAD   N  NR5   0  -0.563  -2.6573  -0.7847   0.4377
 36K  CAC   C  CR56  0   0.351  -3.7980  -0.1667  -0.0188
 36K  CAB   C  CR16  0  -0.313  -5.1437  -0.4711   0.1265
 36K  CAA   C  CR16  0  -0.280  -6.0475   0.4010  -0.4627
 36K  CAI   C  CR16  0  -0.274  -5.6165   1.5289  -1.1719
 36K  CAJ   C  CR16  0  -0.338  -4.2689   1.8202  -1.3150
 36K  CAK   C  CR56  0   0.147  -3.3470   0.9557  -0.7307
 36K  NAL   N  N     0  -0.485  -1.9731   0.9950  -0.7345
 36K  CAM   C  CR5   0   0.702  -1.6127  -0.0460  -0.0403
 36K  NAN   N  NH1   0  -0.806  -0.3251  -0.4525   0.2144
 36K  CAO   C  C     0   0.713   0.7711   0.3892   0.2709
 36K  OAT   O  O     0  -0.472   0.6889   1.5963   0.2142
 36K  NAP   N  NH1   0  -0.771   1.9390  -0.2979   0.4215
 36K  CAQ   C  CR6   0   0.258   3.2007   0.3160   0.4700
 36K  CAU   C  CR16  0  -0.283   3.4606   1.4062   1.2873
 36K  CAV   C  CR16  0  -0.283   4.7224   1.9868   1.3128
 36K  CAW   C  CR16  0  -0.252   5.7377   1.4572   0.5349
 36K  CAS   C  CR16  0  -0.386   5.5004   0.3513  -0.2732
 36K  CAR   C  CR6   0   0.345   4.2335  -0.2189  -0.3189
 36K  OAG   O  O2    0  -0.471   3.9022  -1.2828  -1.0744
 36K  CAH   C  CH3   0  -0.436   4.9107  -1.9077  -1.8443
 36K  HAF1  H  HCH3  0   0.234  -1.7462  -3.2918  -0.3084
 36K  HAF2  H  HCH3  0   0.247  -2.5946  -4.1436   0.9801
 36K  HAF3  H  HCH3  0   0.241  -3.5112  -3.2977  -0.2671
 36K  HAE1  H  HCH2  0   0.279  -3.4626  -2.0009   1.8917
 36K  HAE2  H  HCH2  0   0.273  -1.7208  -1.9737   1.8528
 36K  HAB   H  HCR6  0   0.266  -5.4839  -1.3445   0.6679
 36K  HAA   H  HCR6  0   0.253  -7.1074   0.2026  -0.3732
 36K  HAI   H  HCR6  0   0.251  -6.3529   2.1851  -1.6174
 36K  HAJ   H  HCR6  0   0.252  -3.9397   2.6931  -1.8642
 36K  HAN   H  HNH1  0   0.426  -0.1777  -1.4354   0.3855
 36K  HAP   H  HNH1  0   0.409   1.9323  -1.2968   0.2780
 36K  HAU   H  HCR6  0   0.266   2.6754   1.8025   1.9152
 36K  HAV   H  HCR6  0   0.255   4.9052   2.8429   1.9481
 36K  HAW   H  HCR6  0   0.259   6.7266   1.8958   0.5531
 36K  HAS   H  HCR6  0   0.283   6.3080  -0.0473  -0.8717
 36K  HAH1  H  HCH3  0   0.232   5.7254  -2.2836  -1.2202
 36K  HAH2  H  HCH3  0   0.262   4.4376  -2.7464  -2.3485
 36K  HAH3  H  HCH3  0   0.231   5.3244  -1.2319  -2.5971

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
 36K  CAF  CAE   single    1.520  0.020  1.520
 36K  CAE  NAD   single    1.451  0.020  1.451
 36K  NAD  CAC   aromatic  1.375  0.020  1.375
 36K  NAD  CAM   aromatic  1.366  0.020  1.366
 36K  CAC  CAB   aromatic  1.387  0.020  1.387
 36K  CAC  CAK   aromatic  1.404  0.020  1.404
 36K  CAB  CAA   aromatic  1.387  0.020  1.387
 36K  CAA  CAI   aromatic  1.400  0.020  1.400
 36K  CAI  CAJ   aromatic  1.386  0.020  1.386
 36K  CAJ  CAK   aromatic  1.392  0.020  1.392
 36K  CAK  NAL   aromatic  1.374  0.020  1.374
 36K  NAL  CAM   aromatic  1.302  0.020  1.302
 36K  CAM  NAN   single    1.374  0.020  1.374
 36K  NAN  CAO   single    1.383  0.020  1.383
 36K  CAO  OAT   double    1.211  0.020  1.211
 36K  CAO  NAP   single    1.363  0.020  1.363
 36K  NAP  CAQ   single    1.404  0.020  1.404
 36K  CAQ  CAU   aromatic  1.387  0.020  1.387
 36K  CAQ  CAR   aromatic  1.405  0.020  1.405
 36K  CAU  CAV   aromatic  1.389  0.020  1.389
 36K  CAV  CAW   aromatic  1.384  0.020  1.384
 36K  CAW  CAS   aromatic  1.390  0.020  1.390
 36K  CAS  CAR   aromatic  1.390  0.020  1.390
 36K  CAR  OAG   single    1.346  0.020  1.346
 36K  OAG  CAH   single    1.414  0.020  1.414
 36K  CAF  HAF1  single    0.970  0.020  1.090
 36K  CAF  HAF2  single    0.970  0.020  1.090
 36K  CAF  HAF3  single    0.970  0.020  1.090
 36K  CAE  HAE1  single    0.970  0.020  1.090
 36K  CAE  HAE2  single    0.970  0.020  1.090
 36K  CAB  HAB   single    0.930  0.020  1.080
 36K  CAA  HAA   single    0.930  0.020  1.080
 36K  CAI  HAI   single    0.930  0.020  1.080
 36K  CAJ  HAJ   single    0.930  0.020  1.080
 36K  NAN  HAN   single    0.860  0.020  1.020
 36K  NAP  HAP   single    0.860  0.020  1.020
 36K  CAU  HAU   single    0.930  0.020  1.080
 36K  CAV  HAV   single    0.930  0.020  1.080
 36K  CAW  HAW   single    0.930  0.020  1.080
 36K  CAS  HAS   single    0.930  0.020  1.080
 36K  CAH  HAH1  single    0.970  0.020  1.090
 36K  CAH  HAH2  single    0.970  0.020  1.090
 36K  CAH  HAH3  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
 36K  HAF3  CAF  HAF2  108.07  3.000
 36K  HAF3  CAF  HAF1  108.13  3.000
 36K  HAF2  CAF  HAF1  107.89  3.000
 36K  HAF3  CAF  CAE   111.10  3.000
 36K  HAF2  CAF  CAE   109.90  3.000
 36K  HAF1  CAF  CAE   111.63  3.000
 36K  HAE2  CAE  HAE1  106.13  3.000
 36K  HAE2  CAE  NAD   108.44  3.000
 36K  HAE1  CAE  NAD   107.50  3.000
 36K  HAE2  CAE  CAF   111.18  3.000
 36K  HAE1  CAE  CAF   110.68  3.000
 36K  NAD   CAE  CAF   112.63  3.000
 36K  CAM   NAD  CAC   105.98  3.000
 36K  CAM   NAD  CAE   128.09  3.000
 36K  CAC   NAD  CAE   125.88  3.000
 36K  CAK   CAC  CAB   122.70  3.000
 36K  CAK   CAC  NAD   105.14  3.000
 36K  CAB   CAC  NAD   132.16  3.000
 36K  HAB   CAB  CAA   120.99  3.000
 36K  HAB   CAB  CAC   122.29  3.000
 36K  CAA   CAB  CAC   116.71  3.000
 36K  HAA   CAA  CAI   119.41  3.000
 36K  HAA   CAA  CAB   119.19  3.000
 36K  CAI   CAA  CAB   121.40  3.000
 36K  HAI   CAI  CAJ   119.44  3.000
 36K  HAI   CAI  CAA   119.17  3.000
 36K  CAJ   CAI  CAA   121.39  3.000
 36K  HAJ   CAJ  CAK   120.81  3.000
 36K  HAJ   CAJ  CAI   121.16  3.000
 36K  CAK   CAJ  CAI   118.03  3.000
 36K  NAL   CAK  CAJ   130.01  3.000
 36K  NAL   CAK  CAC   110.21  3.000
 36K  CAJ   CAK  CAC   119.78  3.000
 36K  CAM   NAL  CAK   104.62  3.000
 36K  NAN   CAM  NAL   126.50  3.000
 36K  NAN   CAM  NAD   119.46  3.000
 36K  NAL   CAM  NAD   114.03  3.000
 36K  HAN   NAN  CAO   118.05  3.000
 36K  HAN   NAN  CAM   117.18  3.000
 36K  CAO   NAN  CAM   124.76  3.000
 36K  NAP   CAO  OAT   124.44  3.000
 36K  NAP   CAO  NAN   112.14  3.000
 36K  OAT   CAO  NAN   123.41  3.000
 36K  HAP   NAP  CAQ   116.34  3.000
 36K  HAP   NAP  CAO   118.51  3.000
 36K  CAQ   NAP  CAO   123.60  3.000
 36K  CAR   CAQ  CAU   119.48  3.000
 36K  CAR   CAQ  NAP   118.33  3.000
 36K  CAU   CAQ  NAP   122.17  3.000
 36K  HAU   CAU  CAV   119.74  3.000
 36K  HAU   CAU  CAQ   119.63  3.000
 36K  CAV   CAU  CAQ   120.63  3.000
 36K  HAV   CAV  CAW   120.59  3.000
 36K  HAV   CAV  CAU   119.68  3.000
 36K  CAW   CAV  CAU   119.73  3.000
 36K  HAW   CAW  CAS   119.23  3.000
 36K  HAW   CAW  CAV   120.38  3.000
 36K  CAS   CAW  CAV   120.39  3.000
 36K  HAS   CAS  CAR   120.75  3.000
 36K  HAS   CAS  CAW   119.18  3.000
 36K  CAR   CAS  CAW   120.07  3.000
 36K  OAG   CAR  CAS   124.53  3.000
 36K  OAG   CAR  CAQ   115.78  3.000
 36K  CAS   CAR  CAQ   119.68  3.000
 36K  CAH   OAG  CAR   118.63  3.000
 36K  HAH3  CAH  HAH2  108.81  3.000
 36K  HAH3  CAH  HAH1  108.90  3.000
 36K  HAH2  CAH  HAH1  108.90  3.000
 36K  HAH3  CAH  OAG   111.81  3.000
 36K  HAH2  CAH  OAG   106.44  3.000
 36K  HAH1  CAH  OAG   111.88  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
 36K  CONST_01  CAA   CAB  CAC  NAD  180.00   0.0  0
 36K  CONST_02  CAJ   CAK  CAC  NAD  180.00   0.0  0
 36K  CONST_03  NAL   CAK  CAC  NAD    0.00   0.0  0
 36K  CONST_04  CAK   NAL  CAM  NAD    0.00   0.0  0
 36K  CONST_05  NAL   CAM  NAD  CAC    0.00   0.0  0
 36K  CONST_06  CAI   CAA  CAB  CAC    0.00   0.0  0
 36K  CONST_07  CAI   CAJ  CAK  CAC    0.00   0.0  0
 36K  CONST_08  CAM   NAL  CAK  CAC    0.00   0.0  0
 36K  CONST_09  CAM   NAD  CAC  CAB  180.00   0.0  0
 36K  CONST_10  CAJ   CAK  CAC  CAB    0.00   0.0  0
 36K  CONST_11  NAL   CAK  CAC  CAB  180.00   0.0  0
 36K  CONST_12  CAJ   CAI  CAA  CAB    0.00   0.0  0
 36K  CONST_13  CAK   CAC  CAB  CAA    0.00   0.0  0
 36K  CONST_14  CAK   CAJ  CAI  CAA    0.00   0.0  0
 36K  CONST_15  NAL   CAK  CAJ  CAI  180.00   0.0  0
 36K  CONST_16  CAM   NAL  CAK  CAJ  180.00   0.0  0
 36K  CONST_17  CAM   NAD  CAC  CAK    0.00   0.0  0
 36K  CONST_18  CAW   CAV  CAU  CAQ    0.00   0.0  0
 36K  CONST_19  CAW   CAS  CAR  CAQ    0.00   0.0  0
 36K  CONST_20  CAS   CAR  CAQ  CAU    0.00   0.0  0
 36K  CONST_21  CAS   CAW  CAV  CAU    0.00   0.0  0
 36K  CONST_22  CAR   CAQ  CAU  CAV    0.00   0.0  0
 36K  CONST_23  CAR   CAS  CAW  CAV    0.00   0.0  0
 36K  CONST_24  CAB   CAC  NAD  CAE    0.00   0.0  0
 36K  CONST_25  CAK   CAC  NAD  CAE  180.00   0.0  0
 36K  CONST_26  NAL   CAM  NAD  CAE  180.00   0.0  0
 36K  CONST_27  NAN   CAM  NAD  CAC  180.00   0.0  0
 36K  CONST_28  NAN   CAM  NAL  CAK  180.00   0.0  0
 36K  CONST_29  CAV   CAU  CAQ  NAP  180.00   0.0  0
 36K  CONST_30  CAS   CAR  CAQ  NAP  180.00   0.0  0
 36K  CONST_31  OAG   CAR  CAQ  CAU  180.00   0.0  0
 36K  CONST_32  OAG   CAR  CAS  CAW  180.00   0.0  0
 36K  CONST_33  HAB   CAB  CAC  NAD    0.00   0.0  0
 36K  CONST_34  HAA   CAA  CAB  CAC  180.00   0.0  0
 36K  CONST_35  HAJ   CAJ  CAK  CAC  180.00   0.0  0
 36K  CONST_36  HAI   CAI  CAA  CAB  180.00   0.0  0
 36K  CONST_37  HAV   CAV  CAU  CAQ  180.00   0.0  0
 36K  CONST_38  HAS   CAS  CAR  CAQ  180.00   0.0  0
 36K  CONST_39  HAW   CAW  CAV  CAU  180.00   0.0  0
 36K  CONST_40  HAU   CAU  CAV  CAW  180.00   0.0  0
 36K  CONST_47  OAT   CAO  NAN  CAM    0.00   0.0  0
 36K  CONST_48  CAQ   NAP  CAO  OAT    0.00   0.0  0
 36K  CONST_49  NAP   CAO  NAN  CAM  180.00   0.0  0
 36K  CONST_50  CAQ   NAP  CAO  NAN  180.00   0.0  0
 36K  Var_01    CAC   NAD  CAE  CAF   86.15  30.0  2
 36K  Var_02    HAF1  CAF  CAE  NAD   61.44  30.0  3
 36K  Var_03    HAH1  CAH  OAG  CAR   59.72  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
 36K  plan-1  NAP  0.020
 36K  plan-1  CAQ  0.020
 36K  plan-1  CAU  0.020
 36K  plan-1  CAV  0.020
 36K  plan-1  CAW  0.020
 36K  plan-1  CAS  0.020
 36K  plan-1  CAR  0.020
 36K  plan-1  OAG  0.020
 36K  plan-1  HAU  0.020
 36K  plan-1  HAV  0.020
 36K  plan-1  HAW  0.020
 36K  plan-1  HAS  0.020
 36K  plan-2  CAE  0.020
 36K  plan-2  NAD  0.020
 36K  plan-2  CAC  0.020
 36K  plan-2  CAB  0.020
 36K  plan-2  CAA  0.020
 36K  plan-2  CAI  0.020
 36K  plan-2  CAJ  0.020
 36K  plan-2  CAK  0.020
 36K  plan-2  NAL  0.020
 36K  plan-2  CAM  0.020
 36K  plan-2  NAN  0.020
 36K  plan-2  HAB  0.020
 36K  plan-2  HAA  0.020
 36K  plan-2  HAI  0.020
 36K  plan-2  HAJ  0.020
 36K  plan-3  CAM  0.020
 36K  plan-3  NAN  0.020
 36K  plan-3  CAO  0.020
 36K  plan-3  OAT  0.020
 36K  plan-3  NAP  0.020
 36K  plan-3  CAQ  0.020
 36K  plan-3  HAN  0.020
 36K  plan-3  HAP  0.020

