# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:42:24 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(NC(=O)NCCCNCc2cc(Cl)cc(Cl)c2)c1
#
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
 387  387  1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-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_387
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
 387  CAI  C   CR16  0  -0.259    5.6561  -0.5346   1.0858
 387  CAU  C   CR6   0  -0.027    6.8404  -0.3091   0.4036
 387  CLC  CL  CL    0  -0.117    8.3090  -1.0000   1.0069
 387  CAH  C   CR16  0  -0.193    6.8844   0.4482  -0.7554
 387  CAV  C   CR6   0  -0.023    5.6912   0.9836  -1.2142
 387  CLD  CL  CL    0  -0.119    5.7090   1.9328  -2.6632
 387  CAJ  C   CR16  0  -0.249    4.4917   0.7820  -0.5529
 387  CAW  C   CR6   0   0.063    4.4719   0.0183   0.6101
 387  CAO  C   CH2   0  -0.299    3.1885  -0.1838   1.3740
 387  NAP  N   NH1   0  -0.601    2.0359  -0.2065   0.5024
 387  CAM  C   CH2   0  -0.250    0.7790  -0.2491   1.2245
 387  CAL  C   CH2   0  -0.487   -0.3959  -0.2735   0.2603
 387  CAN  C   CH2   0  -0.239   -1.7265  -0.2703   0.9965
 387  NAQ  N   NH1   0  -0.690   -2.8202  -0.3622   0.0540
 387  CAS  C   C     0   0.742   -4.0915  -0.0401   0.3940
 387  OAA  O   O     0  -0.520   -4.3822   0.4770   1.4629
 387  NAR  N   NH1   0  -0.792   -5.0079  -0.3318  -0.5884
 387  CAX  C   CR6   0   0.392   -6.3853  -0.1382  -0.5904
 387  CAK  C   CR16  0  -0.427   -7.0943   0.4864   0.4338
 387  CAG  C   CR16  0  -0.383   -7.0769  -0.6069  -1.7158
 387  CAE  C   CR16  0  -0.232   -8.4470  -0.4494  -1.7999
 387  CAF  C   CR16  0  -0.411   -9.1662   0.1686  -0.7864
 387  CAT  C   CR6   0   0.380   -8.4763   0.6337   0.3277
 387  OAB  O   OH1   0  -0.635   -9.0975   1.2489   1.3552
 387  H1   H   HCR6  0   0.278    5.6530  -1.1416   1.9821
 387  H2   H   HCR6  0   0.299    7.8130   0.6109  -1.2840
 387  H3   H   HCR6  0   0.276    3.5734   1.2062  -0.9349
 387  H4   H   HCH2  0   0.223    3.2796  -1.0828   2.0015
 387  H5   H   HCH2  0   0.196    0.7114  -1.1109   1.9070
 387  H6   H   HCH2  0   0.224    0.7162   0.6450   1.8528
 387  H7   H   HCH2  0   0.237   -0.3399   0.5917  -0.4048
 387  H8   H   HCH2  0   0.230   -0.3259  -1.1671  -0.3699
 387  H9   H   HCH2  0   0.226   -1.7571  -1.0967   1.7161
 387  H10  H   HCH2  0   0.240   -1.8254   0.6528   1.5686
 387  H11  H   HNH1  0   0.395   -2.6610  -0.9341  -0.7606
 387  H12  H   HNH1  0   0.408   -4.6499  -0.7583  -1.4292
 387  H13  H   HCR6  0   0.282   -6.5941   0.8662   1.3097
 387  H14  H   HCR6  0   0.263   -6.5380  -1.0933  -2.5198
 387  H15  H   HCR6  0   0.260   -8.9686  -0.8177  -2.6738
 387  H16  H   HCR6  0   0.266  -10.2407   0.2857  -0.8652
 387  H17  H   HOH1  0   0.473  -10.0435   1.3107   1.1831
 387  H18  H   HCH2  0   0.253    3.0693   0.6534   2.0701
 387  H19  H   HNH1  0   0.346    2.0982  -1.0143  -0.1072

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
 387  OAB  CAT  single    1.349  0.020  1.349
 387  CAF  CAT  aromatic  1.391  0.020  1.391
 387  CAF  CAE  aromatic  1.388  0.020  1.388
 387  CAT  CAK  aromatic  1.394  0.020  1.394
 387  CAE  CAG  aromatic  1.382  0.020  1.382
 387  CAK  CAX  aromatic  1.394  0.020  1.394
 387  CAG  CAX  aromatic  1.402  0.020  1.402
 387  CAX  NAR  single    1.391  0.020  1.391
 387  NAR  CAS  single    1.375  0.020  1.375
 387  OAA  CAS  double    1.222  0.020  1.222
 387  CAS  NAQ  single    1.355  0.020  1.355
 387  NAQ  CAN  single    1.447  0.020  1.447
 387  CAN  CAL  single    1.521  0.020  1.521
 387  CAL  CAM  single    1.520  0.020  1.520
 387  CAM  NAP  single    1.450  0.020  1.450
 387  NAP  CAO  single    1.445  0.020  1.445
 387  CLD  CAV  single    1.732  0.020  1.732
 387  CAW  CAJ  aromatic  1.392  0.020  1.392
 387  CAW  CAI  aromatic  1.391  0.020  1.391
 387  CAW  CAO  single    1.507  0.020  1.507
 387  CAV  CAH  aromatic  1.386  0.020  1.386
 387  CAV  CAJ  aromatic  1.384  0.020  1.384
 387  CAH  CAU  aromatic  1.385  0.020  1.385
 387  CAU  CAI  aromatic  1.385  0.020  1.385
 387  CAU  CLC  single    1.732  0.020  1.732
 387  CAI  H1   single    0.930  0.020  1.080
 387  CAH  H2   single    0.930  0.020  1.080
 387  CAJ  H3   single    0.930  0.020  1.080
 387  CAO  H4   single    0.970  0.020  1.090
 387  CAM  H5   single    0.970  0.020  1.090
 387  CAM  H6   single    0.970  0.020  1.090
 387  CAL  H7   single    0.970  0.020  1.090
 387  CAL  H8   single    0.970  0.020  1.090
 387  CAN  H9   single    0.970  0.020  1.090
 387  CAN  H10  single    0.970  0.020  1.090
 387  NAQ  H11  single    0.860  0.020  1.020
 387  NAR  H12  single    0.860  0.020  1.020
 387  CAK  H13  single    0.930  0.020  1.080
 387  CAG  H14  single    0.930  0.020  1.080
 387  CAE  H15  single    0.930  0.020  1.080
 387  CAF  H16  single    0.930  0.020  1.080
 387  OAB  H17  single    0.850  0.020  0.980
 387  CAO  H18  single    0.970  0.020  1.090
 387  NAP  H19  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
 387  H1   CAI  CAW  120.24  3.000
 387  H1   CAI  CAU  120.10  3.000
 387  CAW  CAI  CAU  119.66  3.000
 387  CAH  CAU  CLC  118.86  3.000
 387  CLC  CAU  CAI  119.25  3.000
 387  CAH  CAU  CAI  121.89  3.000
 387  H2   CAH  CAV  121.31  3.000
 387  H2   CAH  CAU  121.25  3.000
 387  CAV  CAH  CAU  117.44  3.000
 387  CAJ  CAV  CLD  119.22  3.000
 387  CAJ  CAV  CAH  122.11  3.000
 387  CLD  CAV  CAH  118.67  3.000
 387  H3   CAJ  CAW  119.90  3.000
 387  H3   CAJ  CAV  120.66  3.000
 387  CAW  CAJ  CAV  119.44  3.000
 387  CAO  CAW  CAJ  120.62  3.000
 387  CAO  CAW  CAI  119.90  3.000
 387  CAJ  CAW  CAI  119.47  3.000
 387  H18  CAO  H4   105.73  3.000
 387  H18  CAO  NAP  107.97  3.000
 387  H4   CAO  NAP  113.40  3.000
 387  H18  CAO  CAW  108.20  3.000
 387  H4   CAO  CAW  109.15  3.000
 387  NAP  CAO  CAW  112.06  3.000
 387  H19  NAP  CAM  109.22  3.000
 387  H19  NAP  CAO  109.04  3.000
 387  CAM  NAP  CAO  113.04  3.000
 387  H6   CAM  H5   106.25  3.000
 387  H6   CAM  CAL  109.44  3.000
 387  H5   CAM  CAL  109.45  3.000
 387  H6   CAM  NAP  108.15  3.000
 387  H5   CAM  NAP  112.63  3.000
 387  CAL  CAM  NAP  110.77  3.000
 387  H8   CAL  H7   107.00  3.000
 387  H8   CAL  CAN  109.64  3.000
 387  H7   CAL  CAN  109.75  3.000
 387  H8   CAL  CAM  109.18  3.000
 387  H7   CAL  CAM  109.50  3.000
 387  CAN  CAL  CAM  111.67  3.000
 387  H10  CAN  H9   106.93  3.000
 387  H10  CAN  NAQ  109.08  3.000
 387  H9   CAN  NAQ  111.02  3.000
 387  H10  CAN  CAL  109.58  3.000
 387  H9   CAN  CAL  109.92  3.000
 387  NAQ  CAN  CAL  110.24  3.000
 387  H11  NAQ  CAS  119.08  3.000
 387  H11  NAQ  CAN  116.30  3.000
 387  CAS  NAQ  CAN  122.06  3.000
 387  NAR  CAS  OAA  123.78  3.000
 387  OAA  CAS  NAQ  122.90  3.000
 387  NAR  CAS  NAQ  113.31  3.000
 387  H12  NAR  CAX  114.15  3.000
 387  H12  NAR  CAS  116.67  3.000
 387  CAX  NAR  CAS  129.17  3.000
 387  CAG  CAX  CAK  119.27  3.000
 387  CAG  CAX  NAR  116.31  3.000
 387  CAK  CAX  NAR  124.41  3.000
 387  H13  CAK  CAT  119.00  3.000
 387  H13  CAK  CAX  121.27  3.000
 387  CAT  CAK  CAX  119.73  3.000
 387  H14  CAG  CAE  119.95  3.000
 387  H14  CAG  CAX  120.04  3.000
 387  CAE  CAG  CAX  120.00  3.000
 387  H15  CAE  CAF  119.43  3.000
 387  H15  CAE  CAG  119.23  3.000
 387  CAF  CAE  CAG  121.34  3.000
 387  H16  CAF  CAT  120.93  3.000
 387  H16  CAF  CAE  120.58  3.000
 387  CAT  CAF  CAE  118.49  3.000
 387  OAB  CAT  CAF  122.29  3.000
 387  CAF  CAT  CAK  121.17  3.000
 387  OAB  CAT  CAK  116.54  3.000
 387  H17  OAB  CAT  110.20  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
 387  CONST_01  CAV  CAJ  CAW  CAI     0.00   0.0  0
 387  CONST_02  CAV  CAH  CAU  CAI     0.00   0.0  0
 387  CONST_03  CAJ  CAV  CAH  CAU     0.00   0.0  0
 387  CONST_04  CAJ  CAW  CAI  CAU     0.00   0.0  0
 387  CONST_05  CAW  CAJ  CAV  CAH     0.00   0.0  0
 387  CONST_06  CAW  CAI  CAU  CAH     0.00   0.0  0
 387  CONST_07  CAF  CAT  CAK  CAX     0.00   0.0  0
 387  CONST_08  CAF  CAE  CAG  CAX     0.00   0.0  0
 387  CONST_09  CAE  CAF  CAT  CAK     0.00   0.0  0
 387  CONST_10  CAE  CAG  CAX  CAK     0.00   0.0  0
 387  CONST_11  CAT  CAF  CAE  CAG     0.00   0.0  0
 387  CONST_12  CAT  CAK  CAX  CAG     0.00   0.0  0
 387  CONST_13  CLD  CAV  CAH  CAU   180.00   0.0  0
 387  CONST_14  CAO  CAW  CAI  CAU   180.00   0.0  0
 387  CONST_15  CAV  CAH  CAU  CLC   180.00   0.0  0
 387  CONST_16  CAW  CAI  CAU  CLC   180.00   0.0  0
 387  CONST_17  CAO  CAW  CAJ  CAV   180.00   0.0  0
 387  CONST_18  CAW  CAJ  CAV  CLD   180.00   0.0  0
 387  CONST_19  CAT  CAK  CAX  NAR   180.00   0.0  0
 387  CONST_20  CAE  CAG  CAX  NAR   180.00   0.0  0
 387  CONST_21  OAB  CAT  CAK  CAX   180.00   0.0  0
 387  CONST_22  OAB  CAT  CAF  CAE   180.00   0.0  0
 387  CONST_23  H3   CAJ  CAW  CAI   180.00   0.0  0
 387  CONST_24  H2   CAH  CAU  CAI   180.00   0.0  0
 387  CONST_25  H1   CAI  CAU  CAH   180.00   0.0  0
 387  CONST_26  H15  CAE  CAG  CAX   180.00   0.0  0
 387  CONST_27  H16  CAF  CAT  CAK   180.00   0.0  0
 387  CONST_28  H14  CAG  CAX  CAK   180.00   0.0  0
 387  CONST_29  H13  CAK  CAX  CAG   180.00   0.0  0
 387  CONST_30  CAK  CAX  NAR  CAS     0.00   0.0  0
 387  CONST_31  CAG  CAX  NAR  CAS   180.00   0.0  0
 387  CONST_32  H12  NAR  CAX  CAK   180.00   0.0  0
 387  CONST_33  CAX  NAR  CAS  OAA     0.00   0.0  0
 387  CONST_34  CAX  NAR  CAS  NAQ   180.00   0.0  0
 387  CONST_35  OAA  CAS  NAQ  CAN     0.00   0.0  0
 387  CONST_36  NAR  CAS  NAQ  CAN   180.00   0.0  0
 387  CONST_37  H11  NAQ  CAS  OAA   180.00   0.0  0
 387  Var_01    NAP  CAO  CAW  CAI  -149.44  30.0  2
 387  Var_02    CAM  NAP  CAO  CAW  -173.50  30.0  1
 387  Var_03    CAL  CAM  NAP  CAO  -179.92  30.0  1
 387  Var_04    CAN  CAL  CAM  NAP  -178.06  30.0  1
 387  Var_05    NAQ  CAN  CAL  CAM  -177.11  30.0  1
 387  Var_06    CAS  NAQ  CAN  CAL  -162.75  30.0  1

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
 387  plan-1  CAI  0.020
 387  plan-1  CAU  0.020
 387  plan-1  CLC  0.020
 387  plan-1  CAH  0.020
 387  plan-1  CAV  0.020
 387  plan-1  CLD  0.020
 387  plan-1  CAJ  0.020
 387  plan-1  CAW  0.020
 387  plan-1  CAO  0.020
 387  plan-1  H1   0.020
 387  plan-1  H2   0.020
 387  plan-1  H3   0.020
 387  plan-2  NAR  0.020
 387  plan-2  CAX  0.020
 387  plan-2  CAK  0.020
 387  plan-2  CAG  0.020
 387  plan-2  CAE  0.020
 387  plan-2  CAF  0.020
 387  plan-2  CAT  0.020
 387  plan-2  OAB  0.020
 387  plan-2  H13  0.020
 387  plan-2  H14  0.020
 387  plan-2  H15  0.020
 387  plan-2  H16  0.020
 387  plan-3  CAN  0.020
 387  plan-3  NAQ  0.020
 387  plan-3  CAS  0.020
 387  plan-3  OAA  0.020
 387  plan-3  NAR  0.020
 387  plan-3  CAX  0.020
 387  plan-3  H11  0.020
 387  plan-3  H12  0.020

