# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 23:34:42 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cl)cc(CNCCCNC(=O)Nc2ccccc2)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
 415  415  1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea  ligand  46  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 PERFECT
;

data_comp_415
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
 415  CAA  C   CH3   0  -0.441    8.4768   1.9778   0.1679
 415  OAS  O   O2    0  -0.469    7.2411   1.9788  -0.5206
 415  CAX  C   CR6   0   0.407    6.2918   1.1064  -0.1442
 415  CAK  C   CR16  0  -0.405    5.0850   1.1668  -0.8469
 415  CAJ  C   CR16  0  -0.360    6.4510   0.1819   0.8831
 415  CAU  C   CR6   0  -0.003    5.3851  -0.6590   1.1791
 415  CLC  CL  CL    0  -0.132    5.5829  -1.8102   2.4644
 415  CAI  C   CR16  0  -0.285    4.1863  -0.6132   0.4980
 415  CAV  C   CR6   0   0.096    4.0410   0.3137  -0.5363
 415  CAO  C   CH2   0  -0.313    2.7598   0.3620  -1.3270
 415  NAP  N   NH1   0  -0.597    1.5975   0.2872  -0.4675
 415  CAM  C   CH2   0  -0.251    0.3519   0.2289  -1.2081
 415  CAL  C   CH2   0  -0.498   -0.8363   0.1844  -0.2613
 415  CAN  C   CH2   0  -0.231   -2.1537   0.1048  -1.0153
 415  NAQ  N   NH1   0  -0.692   -3.2589   0.0883  -0.0818
 415  CAT  C   C     0   0.741   -4.5288  -0.1463  -0.4833
 415  OAB  O   O     0  -0.523   -4.8109  -0.4514  -1.6339
 415  NAR  N   NH1   0  -0.790   -5.4552  -0.0261   0.5255
 415  CAW  C   CR6   0   0.374   -6.8388  -0.1675   0.4556
 415  CAG  C   CR16  0  -0.321   -7.5323  -0.7013  -0.6341
 415  CAE  C   CR16  0  -0.245   -8.9168  -0.8055  -0.5863
 415  CAD  C   CR16  0  -0.280   -9.6374  -0.3980   0.5263
 415  CAF  C   CR16  0  -0.244   -8.9468   0.1238   1.6128
 415  CAH  C   CR16  0  -0.354   -7.5682   0.2399   1.5786
 415  H1   H   HCH3  0   0.232    8.3518   2.2049   1.2297
 415  H2   H   HCH3  0   0.232    8.9977   1.0220   0.0697
 415  H3   H   HCH3  0   0.263    9.0843   2.7556  -0.2875
 415  H4   H   HCR6  0   0.263    4.9748   1.8953  -1.6414
 415  H5   H   HCR6  0   0.297    7.3689   0.1063   1.4489
 415  H6   H   HCR6  0   0.265    3.3722  -1.2759   0.7570
 415  H7   H   HCH2  0   0.220    2.7656   1.2528  -1.9725
 415  H8   H   HCH2  0   0.246    2.7345  -0.4992  -2.0032
 415  H9   H   HNH1  0   0.344    1.5858   1.0996   0.1389
 415  H11  H   HCH2  0   0.195    0.2332   1.0736  -1.9054
 415  H12  H   HCH2  0   0.224    0.3618  -0.6768  -1.8227
 415  H13  H   HCH2  0   0.238   -0.7386  -0.6767   0.4050
 415  H14  H   HCH2  0   0.232   -0.8289   1.0806   0.3687
 415  H15  H   HCH2  0   0.226   -2.2378   0.9502  -1.7071
 415  H16  H   HCH2  0   0.235   -2.1743  -0.8040  -1.6206
 415  H17  H   HNH1  0   0.397   -3.0868   0.4521   0.8416
 415  H18  H   HNH1  0   0.406   -5.1120   0.2799   1.4234
 415  H19  H   HCR6  0   0.275   -7.0068  -1.0383  -1.5117
 415  H20  H   HCR6  0   0.254   -9.4337  -1.2202  -1.4425
 415  H21  H   HCR6  0   0.251  -10.7153  -0.4869   0.5490
 415  H22  H   HCR6  0   0.256   -9.4816   0.4492   2.4958
 415  H23  H   HCR6  0   0.265   -7.0468   0.6546   2.4337

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
 415  CAD  CAE  aromatic  1.387  0.020  1.387
 415  CAD  CAF  aromatic  1.389  0.020  1.389
 415  CAE  CAG  aromatic  1.389  0.020  1.389
 415  CAF  CAH  aromatic  1.384  0.020  1.384
 415  CAG  CAW  aromatic  1.398  0.020  1.398
 415  CAH  CAW  aromatic  1.400  0.020  1.400
 415  CAW  NAR  single    1.393  0.020  1.393
 415  NAR  CAT  single    1.375  0.020  1.375
 415  OAB  CAT  double    1.223  0.020  1.223
 415  CAT  NAQ  single    1.352  0.020  1.352
 415  NAQ  CAN  single    1.447  0.020  1.447
 415  CAN  CAL  single    1.520  0.020  1.520
 415  CAL  CAM  single    1.520  0.020  1.520
 415  CAM  NAP  single    1.450  0.020  1.450
 415  NAP  CAO  single    1.447  0.020  1.447
 415  CAA  OAS  single    1.415  0.020  1.415
 415  CLC  CAU  single    1.737  0.020  1.737
 415  CAU  CAI  aromatic  1.379  0.020  1.379
 415  CAU  CAJ  aromatic  1.390  0.020  1.390
 415  CAI  CAV  aromatic  1.397  0.020  1.397
 415  CAJ  CAX  aromatic  1.391  0.020  1.391
 415  CAV  CAO  single    1.506  0.020  1.506
 415  CAV  CAK  aromatic  1.384  0.020  1.384
 415  CAX  CAK  aromatic  1.398  0.020  1.398
 415  CAX  OAS  single    1.343  0.020  1.343
 415  CAA  H1   single    0.970  0.020  1.090
 415  CAA  H2   single    0.970  0.020  1.090
 415  CAA  H3   single    0.970  0.020  1.090
 415  CAK  H4   single    0.930  0.020  1.080
 415  CAJ  H5   single    0.930  0.020  1.080
 415  CAI  H6   single    0.930  0.020  1.080
 415  CAO  H7   single    0.970  0.020  1.090
 415  CAO  H8   single    0.970  0.020  1.090
 415  NAP  H9   single    0.890  0.020  1.040
 415  CAM  H11  single    0.970  0.020  1.090
 415  CAM  H12  single    0.970  0.020  1.090
 415  CAL  H13  single    0.970  0.020  1.090
 415  CAL  H14  single    0.970  0.020  1.090
 415  CAN  H15  single    0.970  0.020  1.090
 415  CAN  H16  single    0.970  0.020  1.090
 415  NAQ  H17  single    0.860  0.020  1.020
 415  NAR  H18  single    0.860  0.020  1.020
 415  CAG  H19  single    0.930  0.020  1.080
 415  CAE  H20  single    0.930  0.020  1.080
 415  CAD  H21  single    0.930  0.020  1.080
 415  CAF  H22  single    0.930  0.020  1.080
 415  CAH  H23  single    0.930  0.020  1.080

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
 415  H3   CAA  H2   108.77  3.000
 415  H3   CAA  H1   108.80  3.000
 415  H2   CAA  H1   108.87  3.000
 415  H3   CAA  OAS  106.49  3.000
 415  H2   CAA  OAS  111.92  3.000
 415  H1   CAA  OAS  111.88  3.000
 415  CAX  OAS  CAA  118.72  3.000
 415  CAJ  CAX  CAK  119.92  3.000
 415  CAK  CAX  OAS  116.18  3.000
 415  CAJ  CAX  OAS  123.90  3.000
 415  H4   CAK  CAV  120.16  3.000
 415  H4   CAK  CAX  119.04  3.000
 415  CAV  CAK  CAX  120.80  3.000
 415  H5   CAJ  CAU  119.84  3.000
 415  H5   CAJ  CAX  122.02  3.000
 415  CAU  CAJ  CAX  118.14  3.000
 415  CAI  CAU  CLC  119.10  3.000
 415  CAI  CAU  CAJ  122.78  3.000
 415  CLC  CAU  CAJ  118.13  3.000
 415  H6   CAI  CAV  120.39  3.000
 415  H6   CAI  CAU  121.05  3.000
 415  CAV  CAI  CAU  118.56  3.000
 415  CAO  CAV  CAI  119.91  3.000
 415  CAO  CAV  CAK  120.28  3.000
 415  CAI  CAV  CAK  119.80  3.000
 415  H8   CAO  H7   105.93  3.000
 415  H8   CAO  NAP  107.90  3.000
 415  H7   CAO  NAP  113.23  3.000
 415  H8   CAO  CAV  108.58  3.000
 415  H7   CAO  CAV  109.24  3.000
 415  NAP  CAO  CAV  111.69  3.000
 415  H9   NAP  CAM  109.12  3.000
 415  H9   NAP  CAO  108.85  3.000
 415  CAM  NAP  CAO  112.86  3.000
 415  H12  CAM  H11  106.26  3.000
 415  H12  CAM  CAL  109.43  3.000
 415  H11  CAM  CAL  109.42  3.000
 415  H12  CAM  NAP  108.19  3.000
 415  H11  CAM  NAP  112.64  3.000
 415  CAL  CAM  NAP  110.76  3.000
 415  H14  CAL  H13  107.06  3.000
 415  H14  CAL  CAN  109.51  3.000
 415  H13  CAL  CAN  109.79  3.000
 415  H14  CAL  CAM  109.21  3.000
 415  H13  CAL  CAM  109.44  3.000
 415  CAN  CAL  CAM  111.72  3.000
 415  H16  CAN  H15  106.90  3.000
 415  H16  CAN  NAQ  109.50  3.000
 415  H15  CAN  NAQ  110.95  3.000
 415  H16  CAN  CAL  109.56  3.000
 415  H15  CAN  CAL  109.83  3.000
 415  NAQ  CAN  CAL  110.03  3.000
 415  H17  NAQ  CAT  119.69  3.000
 415  H17  NAQ  CAN  117.18  3.000
 415  CAT  NAQ  CAN  121.85  3.000
 415  NAR  CAT  OAB  123.81  3.000
 415  OAB  CAT  NAQ  122.62  3.000
 415  NAR  CAT  NAQ  113.56  3.000
 415  H18  NAR  CAW  114.43  3.000
 415  H18  NAR  CAT  116.76  3.000
 415  CAW  NAR  CAT  128.59  3.000
 415  CAH  CAW  CAG  118.56  3.000
 415  CAH  CAW  NAR  116.61  3.000
 415  CAG  CAW  NAR  124.82  3.000
 415  H19  CAG  CAE  119.40  3.000
 415  H19  CAG  CAW  120.84  3.000
 415  CAE  CAG  CAW  119.76  3.000
 415  H20  CAE  CAD  119.92  3.000
 415  H20  CAE  CAG  118.51  3.000
 415  CAD  CAE  CAG  121.56  3.000
 415  H21  CAD  CAF  120.65  3.000
 415  H21  CAD  CAE  120.70  3.000
 415  CAF  CAD  CAE  118.66  3.000
 415  H22  CAF  CAH  119.15  3.000
 415  H22  CAF  CAD  120.36  3.000
 415  CAH  CAF  CAD  120.49  3.000
 415  H23  CAH  CAF  119.46  3.000
 415  H23  CAH  CAW  119.57  3.000
 415  CAF  CAH  CAW  120.97  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
 415  CONST_01  CAI  CAU  CAJ  CAX     0.00   0.0  0
 415  CONST_02  CAI  CAV  CAK  CAX     0.00   0.0  0
 415  CONST_03  CAU  CAI  CAV  CAK     0.00   0.0  0
 415  CONST_04  CAU  CAJ  CAX  CAK     0.00   0.0  0
 415  CONST_05  CAV  CAI  CAU  CAJ     0.00   0.0  0
 415  CONST_06  CAV  CAK  CAX  CAJ     0.00   0.0  0
 415  CONST_07  CAD  CAE  CAG  CAW     0.00   0.0  0
 415  CONST_08  CAD  CAF  CAH  CAW     0.00   0.0  0
 415  CONST_09  CAF  CAD  CAE  CAG     0.00   0.0  0
 415  CONST_10  CAF  CAH  CAW  CAG     0.00   0.0  0
 415  CONST_11  CAH  CAF  CAD  CAE     0.00   0.0  0
 415  CONST_12  CAH  CAW  CAG  CAE     0.00   0.0  0
 415  CONST_13  CAU  CAJ  CAX  OAS   180.00   0.0  0
 415  CONST_14  CAV  CAK  CAX  OAS   180.00   0.0  0
 415  CONST_15  CLC  CAU  CAJ  CAX   180.00   0.0  0
 415  CONST_16  CAO  CAV  CAK  CAX   180.00   0.0  0
 415  CONST_17  CAO  CAV  CAI  CAU   180.00   0.0  0
 415  CONST_18  CAV  CAI  CAU  CLC   180.00   0.0  0
 415  CONST_19  CAE  CAG  CAW  NAR   180.00   0.0  0
 415  CONST_20  CAF  CAH  CAW  NAR   180.00   0.0  0
 415  CONST_21  H6   CAI  CAV  CAK   180.00   0.0  0
 415  CONST_22  H5   CAJ  CAX  CAK   180.00   0.0  0
 415  CONST_23  H4   CAK  CAX  CAJ   180.00   0.0  0
 415  CONST_24  H20  CAE  CAG  CAW   180.00   0.0  0
 415  CONST_25  H22  CAF  CAH  CAW   180.00   0.0  0
 415  CONST_26  H21  CAD  CAE  CAG   180.00   0.0  0
 415  CONST_27  H23  CAH  CAW  CAG   180.00   0.0  0
 415  CONST_28  H19  CAG  CAE  CAD   180.00   0.0  0
 415  CONST_29  CAG  CAW  NAR  CAT     0.00   0.0  0
 415  CONST_30  CAH  CAW  NAR  CAT   180.00   0.0  0
 415  CONST_31  H18  NAR  CAW  CAG   180.00   0.0  0
 415  CONST_32  CAW  NAR  CAT  OAB     0.00   0.0  0
 415  CONST_33  CAW  NAR  CAT  NAQ   180.00   0.0  0
 415  CONST_34  OAB  CAT  NAQ  CAN     0.00   0.0  0
 415  CONST_35  NAR  CAT  NAQ  CAN   180.00   0.0  0
 415  CONST_36  H17  NAQ  CAT  OAB   180.00   0.0  0
 415  Var_01    CAJ  CAX  OAS  CAA    -0.64  30.0  2
 415  Var_02    NAP  CAO  CAV  CAK  -136.78  30.0  2
 415  Var_03    CAM  NAP  CAO  CAV  -175.59  30.0  1
 415  Var_04    H1   CAA  OAS  CAX   -60.78  30.0  3
 415  Var_05    CAL  CAM  NAP  CAO  -178.68  30.0  1
 415  Var_06    CAN  CAL  CAM  NAP  -179.26  30.0  1
 415  Var_07    NAQ  CAN  CAL  CAM  -178.99  30.0  1
 415  Var_08    CAT  NAQ  CAN  CAL  -171.59  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
 415  plan-1  OAS  0.020
 415  plan-1  CAX  0.020
 415  plan-1  CAK  0.020
 415  plan-1  CAJ  0.020
 415  plan-1  CAU  0.020
 415  plan-1  CLC  0.020
 415  plan-1  CAI  0.020
 415  plan-1  CAV  0.020
 415  plan-1  CAO  0.020
 415  plan-1  H4   0.020
 415  plan-1  H5   0.020
 415  plan-1  H6   0.020
 415  plan-2  NAR  0.020
 415  plan-2  CAW  0.020
 415  plan-2  CAG  0.020
 415  plan-2  CAE  0.020
 415  plan-2  CAD  0.020
 415  plan-2  CAF  0.020
 415  plan-2  CAH  0.020
 415  plan-2  H19  0.020
 415  plan-2  H20  0.020
 415  plan-2  H21  0.020
 415  plan-2  H22  0.020
 415  plan-2  H23  0.020
 415  plan-3  CAN  0.020
 415  plan-3  NAQ  0.020
 415  plan-3  CAT  0.020
 415  plan-3  OAB  0.020
 415  plan-3  NAR  0.020
 415  plan-3  CAW  0.020
 415  plan-3  H17  0.020
 415  plan-3  H18  0.020

