# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 04:10:27 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(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
 C13  C13  1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea  ligand  42  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C13
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
 C13  OAA   O   O     0  -0.522   -4.7682  -0.5103  -1.6164
 C13  CLC   CL  CL    0  -0.117    7.8586   1.2781  -0.8814
 C13  CAD   C   CR16  0  -0.280   -9.5964  -0.4003   0.5575
 C13  CAE   C   CR16  0  -0.244   -8.8798  -0.8067  -0.5578
 C13  CAF   C   CR16  0  -0.244   -8.9052   0.1539   1.6276
 C13  CAG   C   CR16  0  -0.322   -7.4988  -0.6701  -0.6247
 C13  CAH   C   CR16  0  -0.355   -7.5303   0.3008   1.5751
 C13  CAI   C   CR16  0  -0.193    6.4811  -0.3406   0.7664
 C13  CAJ   C   CR16  0  -0.248    4.1106  -0.7750   0.5035
 C13  CAK   C   CR16  0  -0.261    5.2335   0.6900  -1.0352
 C13  CAL   C   CH2   0  -0.490   -0.8050   0.2110  -0.3000
 C13  CAM   C   CH2   0  -0.251    0.3786   0.2345  -1.2537
 C13  CAN   C   CH2   0  -0.236   -2.1281   0.1947  -1.0490
 C13  CAO   C   CH2   0  -0.302    2.7896   0.2378  -1.3846
 C13  NAP   N   NH1   0  -0.602    1.6302   0.2120  -0.5214
 C13  NAQ   N   NH1   0  -0.690   -3.2321   0.2025  -0.1141
 C13  NAR   N   NH1   0  -0.789   -5.4252   0.0776   0.4991
 C13  CAS   C   C     0   0.740   -4.4956  -0.1006  -0.4968
 C13  CAT   C   CR6   0  -0.023    5.3086  -0.9587   1.1723
 C13  CAU   C   CR6   0  -0.026    6.4173   0.4817  -0.3463
 C13  CAV   C   CR6   0   0.066    4.0711   0.0542  -0.6134
 C13  CAW   C   CR6   0   0.375   -6.8046  -0.1059   0.4491
 C13  HAD   H   HCR6  0   0.251  -10.6716  -0.5140   0.5949
 C13  HAE   H   HCR6  0   0.254   -9.3971  -1.2447  -1.4021
 C13  HAF   H   HCR6  0   0.257   -9.4369   0.4798   2.5124
 C13  HAG   H   HCR6  0   0.276   -6.9764  -1.0063  -1.5044
 C13  HAH   H   HCR6  0   0.265   -7.0087   0.7385   2.4185
 C13  HAI   H   HCR6  0   0.299    7.4088  -0.4905   1.3007
 C13  HAJ   H   HCR6  0   0.275    3.2085  -1.2640   0.8446
 C13  HAK   H   HCR6  0   0.278    5.2135   1.3480  -1.8945
 C13  HAL   H   HCH2  0   0.237   -0.7355  -0.6682   0.3456
 C13  HALA  H   HCH2  0   0.231   -0.7612   1.0912   0.3511
 C13  HAM   H   HCH2  0   0.225    0.3439  -0.6503  -1.8973
 C13  HAMA  H   HCH2  0   0.196    0.2944   1.1058  -1.9223
 C13  HAN   H   HCH2  0   0.225   -2.1815   1.0521  -1.7298
 C13  HANA  H   HCH2  0   0.238   -2.1884  -0.7038  -1.6648
 C13  HAO   H   HCH2  0   0.253    2.6978  -0.5879  -2.0982
 C13  HAOA  H   HCH2  0   0.224    2.8610   1.1519  -1.9924
 C13  HNAP  H   HNH1  0   0.346    1.6660   1.0103   0.1025
 C13  HNAQ  H   HNH1  0   0.395   -3.0854   0.6919   0.7547
 C13  HNAR  H   HNH1  0   0.407   -5.0834   0.4296   1.3806
 C13  CLB   CL  CL    0  -0.118    5.3517  -1.9919   2.5618

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
 C13  OAA  CAS   double    1.223  0.020  1.223
 C13  CLB  CAT   single    1.732  0.020  1.732
 C13  CLC  CAU   single    1.731  0.020  1.731
 C13  CAD  CAE   aromatic  1.387  0.020  1.387
 C13  CAD  CAF   aromatic  1.389  0.020  1.389
 C13  CAE  CAG   aromatic  1.389  0.020  1.389
 C13  CAF  CAH   aromatic  1.384  0.020  1.384
 C13  CAG  CAW   aromatic  1.398  0.020  1.398
 C13  CAH  CAW   aromatic  1.400  0.020  1.400
 C13  CAI  CAT   aromatic  1.386  0.020  1.386
 C13  CAI  CAU   aromatic  1.385  0.020  1.385
 C13  CAJ  CAT   aromatic  1.384  0.020  1.384
 C13  CAJ  CAV   aromatic  1.392  0.020  1.392
 C13  CAK  CAU   aromatic  1.385  0.020  1.385
 C13  CAK  CAV   aromatic  1.390  0.020  1.390
 C13  CAL  CAM   single    1.520  0.020  1.520
 C13  CAL  CAN   single    1.520  0.020  1.520
 C13  CAM  NAP   single    1.450  0.020  1.450
 C13  CAN  NAQ   single    1.447  0.020  1.447
 C13  CAO  NAP   single    1.446  0.020  1.446
 C13  CAO  CAV   single    1.507  0.020  1.507
 C13  NAQ  CAS   single    1.355  0.020  1.355
 C13  NAR  CAS   single    1.374  0.020  1.374
 C13  NAR  CAW   single    1.392  0.020  1.392
 C13  CAD  HAD   single    0.930  0.020  1.080
 C13  CAE  HAE   single    0.930  0.020  1.080
 C13  CAF  HAF   single    0.930  0.020  1.080
 C13  CAG  HAG   single    0.930  0.020  1.080
 C13  CAH  HAH   single    0.930  0.020  1.080
 C13  CAI  HAI   single    0.930  0.020  1.080
 C13  CAJ  HAJ   single    0.930  0.020  1.080
 C13  CAK  HAK   single    0.930  0.020  1.080
 C13  CAL  HAL   single    0.970  0.020  1.090
 C13  CAL  HALA  single    0.970  0.020  1.090
 C13  CAM  HAM   single    0.970  0.020  1.090
 C13  CAM  HAMA  single    0.970  0.020  1.090
 C13  CAN  HAN   single    0.970  0.020  1.090
 C13  CAN  HANA  single    0.970  0.020  1.090
 C13  CAO  HAO   single    0.970  0.020  1.090
 C13  CAO  HAOA  single    0.970  0.020  1.090
 C13  NAP  HNAP  single    0.890  0.020  1.040
 C13  NAQ  HNAQ  single    0.860  0.020  1.020
 C13  NAR  HNAR  single    0.860  0.020  1.020

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
 C13  HAD   CAD  CAF  120.65  3.000
 C13  HAD   CAD  CAE  120.71  3.000
 C13  CAF   CAD  CAE  118.64  3.000
 C13  HAE   CAE  CAG  118.50  3.000
 C13  HAE   CAE  CAD  119.92  3.000
 C13  CAG   CAE  CAD  121.58  3.000
 C13  HAF   CAF  CAH  119.15  3.000
 C13  HAF   CAF  CAD  120.35  3.000
 C13  CAH   CAF  CAD  120.49  3.000
 C13  HAG   CAG  CAW  120.84  3.000
 C13  HAG   CAG  CAE  119.39  3.000
 C13  CAW   CAG  CAE  119.76  3.000
 C13  HAH   CAH  CAW  119.58  3.000
 C13  HAH   CAH  CAF  119.44  3.000
 C13  CAW   CAH  CAF  120.98  3.000
 C13  HAI   CAI  CAU  121.26  3.000
 C13  HAI   CAI  CAT  121.29  3.000
 C13  CAU   CAI  CAT  117.45  3.000
 C13  HAJ   CAJ  CAV  119.93  3.000
 C13  HAJ   CAJ  CAT  120.64  3.000
 C13  CAV   CAJ  CAT  119.44  3.000
 C13  HAK   CAK  CAV  120.22  3.000
 C13  HAK   CAK  CAU  120.12  3.000
 C13  CAV   CAK  CAU  119.65  3.000
 C13  HALA  CAL  HAL  107.02  3.000
 C13  HALA  CAL  CAN  109.64  3.000
 C13  HAL   CAL  CAN  109.73  3.000
 C13  HALA  CAL  CAM  109.23  3.000
 C13  HAL   CAL  CAM  109.48  3.000
 C13  CAN   CAL  CAM  111.63  3.000
 C13  HAMA  CAM  HAM  106.26  3.000
 C13  HAMA  CAM  NAP  112.62  3.000
 C13  HAM   CAM  NAP  108.16  3.000
 C13  HAMA  CAM  CAL  109.48  3.000
 C13  HAM   CAM  CAL  109.38  3.000
 C13  NAP   CAM  CAL  110.79  3.000
 C13  HANA  CAN  HAN  106.92  3.000
 C13  HANA  CAN  NAQ  109.08  3.000
 C13  HAN   CAN  NAQ  111.10  3.000
 C13  HANA  CAN  CAL  109.57  3.000
 C13  HAN   CAN  CAL  109.88  3.000
 C13  NAQ   CAN  CAL  110.22  3.000
 C13  HAOA  CAO  HAO  105.78  3.000
 C13  HAOA  CAO  CAV  109.20  3.000
 C13  HAO   CAO  CAV  108.23  3.000
 C13  HAOA  CAO  NAP  113.37  3.000
 C13  HAO   CAO  NAP  107.97  3.000
 C13  CAV   CAO  NAP  111.98  3.000
 C13  HNAP  NAP  CAO  108.97  3.000
 C13  HNAP  NAP  CAM  109.21  3.000
 C13  CAO   NAP  CAM  112.98  3.000
 C13  HNAQ  NAQ  CAS  119.20  3.000
 C13  HNAQ  NAQ  CAN  116.66  3.000
 C13  CAS   NAQ  CAN  121.87  3.000
 C13  HNAR  NAR  CAW  114.39  3.000
 C13  HNAR  NAR  CAS  116.70  3.000
 C13  CAW   NAR  CAS  128.84  3.000
 C13  NAR   CAS  NAQ  113.41  3.000
 C13  NAR   CAS  OAA  123.79  3.000
 C13  NAQ   CAS  OAA  122.79  3.000
 C13  CAJ   CAT  CAI  122.10  3.000
 C13  CAJ   CAT  CLB  119.23  3.000
 C13  CAI   CAT  CLB  118.68  3.000
 C13  CAK   CAU  CAI  121.88  3.000
 C13  CAK   CAU  CLC  119.24  3.000
 C13  CAI   CAU  CLC  118.88  3.000
 C13  CAO   CAV  CAK  120.00  3.000
 C13  CAO   CAV  CAJ  120.50  3.000
 C13  CAK   CAV  CAJ  119.48  3.000
 C13  NAR   CAW  CAH  116.51  3.000
 C13  NAR   CAW  CAG  124.95  3.000
 C13  CAH   CAW  CAG  118.54  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
 C13  CONST_01  CAW   CAG  CAE  CAD     0.00   0.0  0
 C13  CONST_02  CAW   CAH  CAF  CAD     0.00   0.0  0
 C13  CONST_03  CAH   CAF  CAD  CAE     0.00   0.0  0
 C13  CONST_04  CAH   CAW  CAG  CAE     0.00   0.0  0
 C13  CONST_05  CAG   CAE  CAD  CAF     0.00   0.0  0
 C13  CONST_06  CAG   CAW  CAH  CAF     0.00   0.0  0
 C13  CONST_07  CAV   CAJ  CAT  CAI     0.00   0.0  0
 C13  CONST_08  CAV   CAK  CAU  CAI     0.00   0.0  0
 C13  CONST_09  CAU   CAI  CAT  CAJ     0.00   0.0  0
 C13  CONST_10  CAU   CAK  CAV  CAJ     0.00   0.0  0
 C13  CONST_11  CAT   CAI  CAU  CAK     0.00   0.0  0
 C13  CONST_12  CAT   CAJ  CAV  CAK     0.00   0.0  0
 C13  CONST_13  CAU   CAI  CAT  CLB   180.00   0.0  0
 C13  CONST_14  CAV   CAJ  CAT  CLB   180.00   0.0  0
 C13  CONST_15  CAT   CAI  CAU  CLC   180.00   0.0  0
 C13  CONST_16  CAV   CAK  CAU  CLC   180.00   0.0  0
 C13  CONST_17  NAR   CAW  CAG  CAE   180.00   0.0  0
 C13  CONST_18  NAR   CAW  CAH  CAF   180.00   0.0  0
 C13  CONST_19  CAT   CAJ  CAV  CAO   180.00   0.0  0
 C13  CONST_20  CAU   CAK  CAV  CAO   180.00   0.0  0
 C13  CONST_21  HAG   CAG  CAE  CAD   180.00   0.0  0
 C13  CONST_22  HAH   CAH  CAF  CAD   180.00   0.0  0
 C13  CONST_23  HAF   CAF  CAD  CAE   180.00   0.0  0
 C13  CONST_24  HAE   CAE  CAD  CAF   180.00   0.0  0
 C13  CONST_25  HAD   CAD  CAE  CAG   180.00   0.0  0
 C13  CONST_26  HAJ   CAJ  CAT  CAI   180.00   0.0  0
 C13  CONST_27  HAK   CAK  CAU  CAI   180.00   0.0  0
 C13  CONST_28  HAI   CAI  CAT  CAJ   180.00   0.0  0
 C13  CONST_29  CAS   NAR  CAW  CAG     0.00   0.0  0
 C13  CONST_30  CAS   NAR  CAW  CAH   180.00   0.0  0
 C13  CONST_31  HNAR  NAR  CAW  CAG   180.00   0.0  0
 C13  CONST_32  CAW   NAR  CAS  OAA     0.00   0.0  0
 C13  CONST_33  CAW   NAR  CAS  NAQ   180.00   0.0  0
 C13  CONST_34  CAN   NAQ  CAS  OAA     0.00   0.0  0
 C13  CONST_35  NAR   CAS  NAQ  CAN   180.00   0.0  0
 C13  CONST_36  HNAQ  NAQ  CAS  OAA   180.00   0.0  0
 C13  Var_01    NAP   CAO  CAV  CAJ    34.69  30.0  3
 C13  Var_02    CAV   CAO  NAP  CAM  -173.43  30.0  1
 C13  Var_03    CAO   NAP  CAM  CAL  -179.80  30.0  3
 C13  Var_04    CAS   NAQ  CAN  CAL  -165.29  30.0  3
 C13  Var_05    NAQ   CAN  CAL  CAM  -178.74  30.0  3
 C13  Var_06    NAP   CAM  CAL  CAN  -178.41  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
 C13  plan-1  CAD   0.020
 C13  plan-1  CAE   0.020
 C13  plan-1  CAF   0.020
 C13  plan-1  CAG   0.020
 C13  plan-1  CAH   0.020
 C13  plan-1  NAR   0.020
 C13  plan-1  CAW   0.020
 C13  plan-1  HAD   0.020
 C13  plan-1  HAE   0.020
 C13  plan-1  HAF   0.020
 C13  plan-1  HAG   0.020
 C13  plan-1  HAH   0.020
 C13  plan-2  CLC   0.020
 C13  plan-2  CAI   0.020
 C13  plan-2  CAJ   0.020
 C13  plan-2  CAK   0.020
 C13  plan-2  CAO   0.020
 C13  plan-2  CAT   0.020
 C13  plan-2  CAU   0.020
 C13  plan-2  CAV   0.020
 C13  plan-2  HAI   0.020
 C13  plan-2  HAJ   0.020
 C13  plan-2  HAK   0.020
 C13  plan-2  CLB   0.020
 C13  plan-3  OAA   0.020
 C13  plan-3  CAN   0.020
 C13  plan-3  NAQ   0.020
 C13  plan-3  NAR   0.020
 C13  plan-3  CAS   0.020
 C13  plan-3  CAW   0.020
 C13  plan-3  HNAQ  0.020
 C13  plan-3  HNAR  0.020

