# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 06:35:21 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(2-hydroxyphenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1NC(=O)NCCCNCc2cc(Cl)cc(Cl)c2
#
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
 392  392  1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(2-hydroxyphenyl)urea  ligand  43  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_392
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
 392  CAJ  C   CR16  0  -0.244    4.3744  -0.9436   0.2468
 392  CAT  C   CR6   0  -0.024    5.5510  -1.3436   0.8554
 392  CLC  CL  CL    0  -0.119    5.5405  -2.7384   1.8827
 392  CAI  C   CR16  0  -0.192    6.7447  -0.6626   0.6696
 392  CAU  C   CR6   0  -0.026    6.7242   0.4484  -0.1566
 392  CLD  CL  CL    0  -0.117    8.1925   1.3320  -0.4068
 392  CAK  C   CR16  0  -0.263    5.5625   0.8758  -0.7799
 392  CAW  C   CR6   0   0.070    4.3791   0.1737  -0.5833
 392  CAO  C   CH2   0  -0.305    3.1200   0.5977  -1.2945
 392  NAP  N   NH1   0  -0.600    1.9485   0.4239  -0.4648
 392  CAM  C   CH2   0  -0.250    0.7077   0.6599  -1.1786
 392  CAL  C   CH2   0  -0.494   -0.4883   0.4530  -0.2643
 392  CAN  C   CH2   0  -0.231   -1.8025   0.6635  -0.9992
 392  NAQ  N   NH1   0  -0.685   -2.9146   0.4481  -0.1004
 392  CAS  C   C     0   0.716   -4.1904   0.3660  -0.5422
 392  OAA  O   O     0  -0.526   -4.4899   0.4108  -1.7266
 392  NAR  N   NH1   0  -0.767   -5.1194   0.2257   0.4628
 392  CAX  C   CR6   0   0.264   -6.4874   0.0339   0.2226
 392  CAH  C   CR16  0  -0.285   -7.2220   0.9085  -0.5696
 392  CAF  C   CR16  0  -0.285   -8.5784   0.7072  -0.7846
 392  CAE  C   CR16  0  -0.257   -9.2185  -0.3660  -0.1825
 392  CAG  C   CR16  0  -0.382   -8.5030  -1.2378   0.6258
 392  CAV  C   CR6   0   0.301   -7.1392  -1.0528   0.8212
 392  OAB  O   OH1   0  -0.629   -6.3888  -1.8770   1.5813
 392  H1   H   HCR6  0   0.274    3.4534  -1.4853   0.4135
 392  H2   H   HCR6  0   0.300    7.6554  -0.9843   1.1550
 392  H3   H   HCR6  0   0.279    5.5782   1.7524  -1.4147
 392  H4   H   HCH2  0   0.224    3.2450   1.6239  -1.6697
 392  H5   H   HCH2  0   0.252    3.0021  -0.0332  -2.1818
 392  H6   H   HNH1  0   0.346    2.0045   1.0618   0.3212
 392  H8   H   HCH2  0   0.196    0.6608   1.6655  -1.6250
 392  H9   H   HCH2  0   0.224    0.6562  -0.0483  -2.0114
 392  H10  H   HCH2  0   0.237   -0.4566  -0.5568   0.1533
 392  H11  H   HCH2  0   0.232   -0.4270   1.1505   0.5783
 392  H12  H   HCH2  0   0.224   -1.8306   1.6711  -1.4290
 392  H13  H   HCH2  0   0.233   -1.8706  -0.0384  -1.8327
 392  H14  H   HNH1  0   0.394   -2.7427   0.5694   0.8847
 392  H15  H   HNH1  0   0.398   -4.7812  -0.0439   1.3743
 392  H16  H   HCR6  0   0.260   -6.7271   1.7609  -1.0134
 392  H17  H   HCR6  0   0.253   -9.1317   1.3959  -1.4088
 392  H18  H   HCR6  0   0.258  -10.2773  -0.5288  -0.3344
 392  H19  H   HCR6  0   0.271   -9.0039  -2.0771   1.0955
 392  H20  H   HOH1  0   0.478   -6.9371  -2.5669   1.9710

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
 392  CAE  CAG  aromatic  1.388  0.020  1.388
 392  CAE  CAF  aromatic  1.387  0.020  1.387
 392  CAG  CAV  aromatic  1.390  0.020  1.390
 392  CAF  CAH  aromatic  1.388  0.020  1.388
 392  CAV  OAB  single    1.349  0.020  1.349
 392  CAV  CAX  aromatic  1.401  0.020  1.401
 392  CAH  CAX  aromatic  1.390  0.020  1.390
 392  CAX  NAR  single    1.402  0.020  1.402
 392  NAR  CAS  single    1.376  0.020  1.376
 392  CAS  OAA  double    1.223  0.020  1.223
 392  CAS  NAQ  single    1.353  0.020  1.353
 392  NAQ  CAN  single    1.446  0.020  1.446
 392  CAN  CAL  single    1.520  0.020  1.520
 392  CAL  CAM  single    1.520  0.020  1.520
 392  CAM  NAP  single    1.451  0.020  1.451
 392  NAP  CAO  single    1.446  0.020  1.446
 392  CAI  CAU  aromatic  1.385  0.020  1.385
 392  CAI  CAT  aromatic  1.387  0.020  1.387
 392  CAU  CLD  single    1.732  0.020  1.732
 392  CAU  CAK  aromatic  1.386  0.020  1.386
 392  CLC  CAT  single    1.732  0.020  1.732
 392  CAW  CAJ  aromatic  1.392  0.020  1.392
 392  CAW  CAK  aromatic  1.390  0.020  1.390
 392  CAW  CAO  single    1.507  0.020  1.507
 392  CAT  CAJ  aromatic  1.384  0.020  1.384
 392  CAJ  H1   single    0.930  0.020  1.080
 392  CAI  H2   single    0.930  0.020  1.080
 392  CAK  H3   single    0.930  0.020  1.080
 392  CAO  H4   single    0.970  0.020  1.090
 392  CAO  H5   single    0.970  0.020  1.090
 392  NAP  H6   single    0.890  0.020  1.040
 392  CAM  H8   single    0.970  0.020  1.090
 392  CAM  H9   single    0.970  0.020  1.090
 392  CAL  H10  single    0.970  0.020  1.090
 392  CAL  H11  single    0.970  0.020  1.090
 392  CAN  H12  single    0.970  0.020  1.090
 392  CAN  H13  single    0.970  0.020  1.090
 392  NAQ  H14  single    0.860  0.020  1.020
 392  NAR  H15  single    0.890  0.020  1.040
 392  CAH  H16  single    0.930  0.020  1.080
 392  CAF  H17  single    0.930  0.020  1.080
 392  CAE  H18  single    0.930  0.020  1.080
 392  CAG  H19  single    0.930  0.020  1.080
 392  OAB  H20  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
 392  H1   CAJ  CAW  119.79  3.000
 392  H1   CAJ  CAT  120.77  3.000
 392  CAW  CAJ  CAT  119.44  3.000
 392  CAI  CAT  CLC  118.69  3.000
 392  CLC  CAT  CAJ  119.24  3.000
 392  CAI  CAT  CAJ  122.07  3.000
 392  H2   CAI  CAU  121.28  3.000
 392  H2   CAI  CAT  121.26  3.000
 392  CAU  CAI  CAT  117.47  3.000
 392  CAK  CAU  CLD  119.23  3.000
 392  CAK  CAU  CAI  121.88  3.000
 392  CLD  CAU  CAI  118.88  3.000
 392  H3   CAK  CAW  120.29  3.000
 392  H3   CAK  CAU  120.09  3.000
 392  CAW  CAK  CAU  119.62  3.000
 392  CAO  CAW  CAK  120.17  3.000
 392  CAO  CAW  CAJ  120.30  3.000
 392  CAK  CAW  CAJ  119.51  3.000
 392  H5   CAO  H4   105.87  3.000
 392  H5   CAO  NAP  107.96  3.000
 392  H4   CAO  NAP  113.57  3.000
 392  H5   CAO  CAW  108.08  3.000
 392  H4   CAO  CAW  109.19  3.000
 392  NAP  CAO  CAW  111.86  3.000
 392  H6   NAP  CAM  109.05  3.000
 392  H6   NAP  CAO  108.93  3.000
 392  CAM  NAP  CAO  113.02  3.000
 392  H9   CAM  H8   106.28  3.000
 392  H9   CAM  CAL  109.43  3.000
 392  H8   CAM  CAL  109.56  3.000
 392  H9   CAM  NAP  108.02  3.000
 392  H8   CAM  NAP  112.61  3.000
 392  CAL  CAM  NAP  110.79  3.000
 392  H11  CAL  H10  107.02  3.000
 392  H11  CAL  CAN  109.38  3.000
 392  H10  CAL  CAN  109.73  3.000
 392  H11  CAL  CAM  109.39  3.000
 392  H10  CAL  CAM  109.44  3.000
 392  CAN  CAL  CAM  111.75  3.000
 392  H13  CAN  H12  106.87  3.000
 392  H13  CAN  NAQ  109.31  3.000
 392  H12  CAN  NAQ  111.16  3.000
 392  H13  CAN  CAL  109.50  3.000
 392  H12  CAN  CAL  109.82  3.000
 392  NAQ  CAN  CAL  110.10  3.000
 392  H14  NAQ  CAS  119.19  3.000
 392  H14  NAQ  CAN  117.30  3.000
 392  CAS  NAQ  CAN  122.10  3.000
 392  NAR  CAS  OAA  123.09  3.000
 392  OAA  CAS  NAQ  123.05  3.000
 392  NAR  CAS  NAQ  113.86  3.000
 392  H15  NAR  CAX  116.44  3.000
 392  H15  NAR  CAS  117.44  3.000
 392  CAX  NAR  CAS  123.21  3.000
 392  CAV  CAX  CAH  119.04  3.000
 392  CAH  CAX  NAR  121.82  3.000
 392  CAV  CAX  NAR  119.13  3.000
 392  H16  CAH  CAF  119.88  3.000
 392  H16  CAH  CAX  119.22  3.000
 392  CAF  CAH  CAX  120.90  3.000
 392  H17  CAF  CAE  120.47  3.000
 392  H17  CAF  CAH  119.80  3.000
 392  CAE  CAF  CAH  119.73  3.000
 392  H18  CAE  CAG  119.46  3.000
 392  H18  CAE  CAF  120.47  3.000
 392  CAG  CAE  CAF  120.07  3.000
 392  H19  CAG  CAV  119.69  3.000
 392  H19  CAG  CAE  120.03  3.000
 392  CAV  CAG  CAE  120.28  3.000
 392  OAB  CAV  CAG  122.92  3.000
 392  OAB  CAV  CAX  117.11  3.000
 392  CAG  CAV  CAX  119.97  3.000
 392  H20  OAB  CAV  110.41  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
 392  CONST_01  CAU  CAK  CAW  CAJ     0.00   0.0  0
 392  CONST_02  CAU  CAI  CAT  CAJ     0.00   0.0  0
 392  CONST_03  CAK  CAU  CAI  CAT     0.00   0.0  0
 392  CONST_04  CAK  CAW  CAJ  CAT     0.00   0.0  0
 392  CONST_05  CAW  CAK  CAU  CAI     0.00   0.0  0
 392  CONST_06  CAW  CAJ  CAT  CAI     0.00   0.0  0
 392  CONST_07  CAE  CAG  CAV  CAX     0.00   0.0  0
 392  CONST_08  CAE  CAF  CAH  CAX     0.00   0.0  0
 392  CONST_09  CAG  CAE  CAF  CAH     0.00   0.0  0
 392  CONST_10  CAG  CAV  CAX  CAH     0.00   0.0  0
 392  CONST_11  CAV  CAG  CAE  CAF     0.00   0.0  0
 392  CONST_12  CAV  CAX  CAH  CAF     0.00   0.0  0
 392  CONST_13  CLD  CAU  CAI  CAT   180.00   0.0  0
 392  CONST_14  CAO  CAW  CAJ  CAT   180.00   0.0  0
 392  CONST_15  CAU  CAI  CAT  CLC   180.00   0.0  0
 392  CONST_16  CAW  CAJ  CAT  CLC   180.00   0.0  0
 392  CONST_17  CAO  CAW  CAK  CAU   180.00   0.0  0
 392  CONST_18  CAW  CAK  CAU  CLD   180.00   0.0  0
 392  CONST_19  CAG  CAV  CAX  NAR   180.00   0.0  0
 392  CONST_20  CAF  CAH  CAX  NAR   180.00   0.0  0
 392  CONST_21  OAB  CAV  CAX  CAH   180.00   0.0  0
 392  CONST_22  OAB  CAV  CAG  CAE   180.00   0.0  0
 392  CONST_23  H3   CAK  CAW  CAJ   180.00   0.0  0
 392  CONST_24  H2   CAI  CAT  CAJ   180.00   0.0  0
 392  CONST_25  H1   CAJ  CAT  CAI   180.00   0.0  0
 392  CONST_26  H19  CAG  CAV  CAX   180.00   0.0  0
 392  CONST_27  H17  CAF  CAH  CAX   180.00   0.0  0
 392  CONST_28  H18  CAE  CAF  CAH   180.00   0.0  0
 392  CONST_29  H16  CAH  CAF  CAE   180.00   0.0  0
 392  CONST_33  CAX  NAR  CAS  OAA     0.00   0.0  0
 392  CONST_34  CAX  NAR  CAS  NAQ   180.00   0.0  0
 392  CONST_35  OAA  CAS  NAQ  CAN     0.00   0.0  0
 392  CONST_36  NAR  CAS  NAQ  CAN   180.00   0.0  0
 392  CONST_37  H14  NAQ  CAS  OAA   180.00   0.0  0
 392  Var_01    NAP  CAO  CAW  CAJ    38.26  30.0  2
 392  Var_02    CAM  NAP  CAO  CAW  -172.54  30.0  1
 392  Var_03    CAL  CAM  NAP  CAO   179.54  30.0  2
 392  Var_04    CAN  CAL  CAM  NAP  -178.68  30.0  1
 392  Var_05    NAQ  CAN  CAL  CAM   179.56  30.0  1
 392  Var_06    CAS  NAQ  CAN  CAL  -169.48  30.0  2

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
 392  plan-1  CAJ  0.020
 392  plan-1  CAT  0.020
 392  plan-1  CLC  0.020
 392  plan-1  CAI  0.020
 392  plan-1  CAU  0.020
 392  plan-1  CLD  0.020
 392  plan-1  CAK  0.020
 392  plan-1  CAW  0.020
 392  plan-1  CAO  0.020
 392  plan-1  H1   0.020
 392  plan-1  H2   0.020
 392  plan-1  H3   0.020
 392  plan-2  NAR  0.020
 392  plan-2  CAX  0.020
 392  plan-2  CAH  0.020
 392  plan-2  CAF  0.020
 392  plan-2  CAE  0.020
 392  plan-2  CAG  0.020
 392  plan-2  CAV  0.020
 392  plan-2  OAB  0.020
 392  plan-2  H16  0.020
 392  plan-2  H17  0.020
 392  plan-2  H18  0.020
 392  plan-2  H19  0.020
 392  plan-3  CAN  0.020
 392  plan-3  NAQ  0.020
 392  plan-3  CAS  0.020
 392  plan-3  OAA  0.020
 392  plan-3  NAR  0.020
 392  plan-3  CAX  0.020
 392  plan-3  H14  0.020
 392  plan-3  H15  0.020

