# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:59:42 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(=O)NC(=N)NCc2ccc(C)cc2)cc1OC
#
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
 2S4  2S4  2-(3,4-dimethoxyphenyl)-N-[N-(4-methylbenzyl)carbamimidoyl]acetamide  ligand  48  25  .  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_2S4
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
 2S4  C1   C  CR16  0  -0.419  -3.3010   0.3969  -0.5966
 2S4  C2   C  CR6   0   0.155  -2.9200  -0.9491  -0.5763
 2S4  C3   C  CR6   0   0.321  -4.6306   0.7651  -0.4990
 2S4  C8   C  CH3   0  -0.437  -4.1396   3.0798  -0.5998
 2S4  C10  C  CH3   0  -0.436  -7.9292  -0.7364  -0.2092
 2S4  C11  C  CH2   0  -0.709  -1.4688  -1.3074  -0.6764
 2S4  C12  C  C     0   0.559  -0.7169  -1.0874   0.6282
 2S4  C14  C  C     0   0.624   1.6322  -0.8663   1.4158
 2S4  C19  C  CR6   0   0.064   5.1375   0.1553   0.7675
 2S4  C20  C  CR16  0  -0.280   6.7124  -0.5679  -0.9141
 2S4  C21  C  CR6   0   0.087   7.3159   0.6915  -0.9368
 2S4  C22  C  CR16  0  -0.268   5.6417  -0.8323  -0.0780
 2S4  C24  C  CR16  0  -0.289   5.7312   1.4092   0.7469
 2S4  O15  O  O     0  -0.431  -1.2725  -1.0123   1.6998
 2S4  C4   C  CR16  0  -0.331  -3.8964  -1.9164  -0.4571
 2S4  C6   C  CR16  0  -0.373  -5.2433  -1.5621  -0.3614
 2S4  C5   C  CR6   0   0.297  -5.6230  -0.2324  -0.3814
 2S4  O9   O  O2    0  -0.464  -6.8903   0.2161  -0.3001
 2S4  O7   O  O2    0  -0.465  -5.0837   2.0330  -0.5103
 2S4  N13  N  NH1   0  -0.722   0.6344  -1.0042   0.4436
 2S4  N17  N  N     0  -0.670   1.4396  -1.2393   2.6157
 2S4  N16  N  NH1   0  -0.663   2.7793  -0.3659   0.8617
 2S4  C18  C  CH2   0  -0.357   3.9631  -0.1333   1.6609
 2S4  C23  C  CR16  0  -0.291   6.8069   1.6733  -0.0945
 2S4  C25  C  CH3   0  -0.723   8.4878   0.9604  -1.8350
 2S4  H1   H  HCR6  0   0.276  -2.5313   1.1524  -0.6910
 2S4  H2   H  HCH3  0   0.228  -3.4418   3.0754   0.2419
 2S4  H3   H  HCH3  0   0.227  -3.5686   3.0397  -1.5313
 2S4  H4   H  HCH3  0   0.260  -4.7052   4.0082  -0.5791
 2S4  H5   H  HCH3  0   0.227  -7.9568  -1.3967  -1.0803
 2S4  H6   H  HCH3  0   0.227  -7.8490  -1.3479   0.6937
 2S4  H7   H  HCH3  0   0.259  -8.8598  -0.1755  -0.1680
 2S4  H8   H  HCH2  0   0.306  -1.3550  -2.3649  -0.9345
 2S4  H9   H  HCH2  0   0.285  -0.9861  -0.7482  -1.4825
 2S4  H10  H  HCR6  0   0.247   7.0886  -1.3523  -1.5607
 2S4  H11  H  HCR6  0   0.249   5.1925  -1.8186  -0.0803
 2S4  H12  H  HCR6  0   0.251   5.3521   2.1933   1.3919
 2S4  H13  H  HCR6  0   0.248  -3.6272  -2.9652  -0.4413
 2S4  H14  H  HCR6  0   0.280  -5.9821  -2.3470  -0.2761
 2S4  H15  H  HNH1  0   0.415   0.9546  -1.0252  -0.5131
 2S4  H16  H  H     0   0.346   2.2311  -1.0089   3.2043
 2S4  H17  H  HNH1  0   0.395   2.6653   0.2550   0.0745
 2S4  H18  H  HCH2  0   0.258   4.1634  -1.0314   2.2512
 2S4  H19  H  HCH2  0   0.252   3.8237   0.6897   2.3714
 2S4  H20  H  HCR6  0   0.248   7.2505   2.6620  -0.0945
 2S4  H21  H  HCH3  0   0.245   8.2903   0.6335  -2.8565
 2S4  H22  H  HCH3  0   0.244   8.7363   2.0205  -1.8635
 2S4  H23  H  HCH3  0   0.248   9.3748   0.4232  -1.4933

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
 2S4  C4   C6   aromatic  1.396  0.020  1.396
 2S4  C4   C2   aromatic  1.380  0.020  1.380
 2S4  C11  C2   single    1.498  0.020  1.498
 2S4  C11  C12  single    1.522  0.020  1.522
 2S4  C6   C5   aromatic  1.383  0.020  1.383
 2S4  C2   C1   aromatic  1.399  0.020  1.399
 2S4  C5   O9   single    1.347  0.020  1.347
 2S4  C5   C3   aromatic  1.412  0.020  1.412
 2S4  C1   C3   aromatic  1.383  0.020  1.383
 2S4  O9   C10  single    1.412  0.020  1.412
 2S4  C3   O7   single    1.346  0.020  1.346
 2S4  N13  C12  single    1.366  0.020  1.366
 2S4  N13  C14  single    1.400  0.020  1.400
 2S4  C12  O15  double    1.209  0.020  1.209
 2S4  O7   C8   single    1.412  0.020  1.412
 2S4  N17  C14  double    1.271  0.020  1.271
 2S4  C14  N16  single    1.369  0.020  1.369
 2S4  N16  C18  single    1.447  0.020  1.447
 2S4  C22  C20  aromatic  1.384  0.020  1.384
 2S4  C22  C19  aromatic  1.394  0.020  1.394
 2S4  C20  C21  aromatic  1.397  0.020  1.397
 2S4  C18  C19  single    1.503  0.020  1.503
 2S4  C19  C24  aromatic  1.388  0.020  1.388
 2S4  C21  C25  single    1.501  0.020  1.501
 2S4  C21  C23  aromatic  1.390  0.020  1.390
 2S4  C24  C23  aromatic  1.391  0.020  1.391
 2S4  C1   H1   single    0.930  0.020  1.080
 2S4  C8   H2   single    0.970  0.020  1.090
 2S4  C8   H3   single    0.970  0.020  1.090
 2S4  C8   H4   single    0.970  0.020  1.090
 2S4  C10  H5   single    0.970  0.020  1.090
 2S4  C10  H6   single    0.970  0.020  1.090
 2S4  C10  H7   single    0.970  0.020  1.090
 2S4  C11  H8   single    0.970  0.020  1.090
 2S4  C11  H9   single    0.970  0.020  1.090
 2S4  C20  H10  single    0.930  0.020  1.080
 2S4  C22  H11  single    0.930  0.020  1.080
 2S4  C24  H12  single    0.930  0.020  1.080
 2S4  C4   H13  single    0.930  0.020  1.080
 2S4  C6   H14  single    0.930  0.020  1.080
 2S4  N13  H15  single    0.860  0.020  1.020
 2S4  N17  H16  single    0.890  0.020  1.040
 2S4  N16  H17  single    0.890  0.020  1.040
 2S4  C18  H18  single    0.970  0.020  1.090
 2S4  C18  H19  single    0.970  0.020  1.090
 2S4  C23  H20  single    0.930  0.020  1.080
 2S4  C25  H21  single    0.970  0.020  1.090
 2S4  C25  H22  single    0.970  0.020  1.090
 2S4  C25  H23  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
 2S4  H1   C1   C3   120.26  3.000
 2S4  H1   C1   C2   118.62  3.000
 2S4  C3   C1   C2   121.13  3.000
 2S4  C4   C2   C11  121.58  3.000
 2S4  C11  C2   C1   119.53  3.000
 2S4  C4   C2   C1   118.89  3.000
 2S4  O7   C3   C5   115.43  3.000
 2S4  O7   C3   C1   125.00  3.000
 2S4  C5   C3   C1   119.57  3.000
 2S4  H4   C8   H3   108.61  3.000
 2S4  H4   C8   H2   108.71  3.000
 2S4  H3   C8   H2   108.81  3.000
 2S4  H4   C8   O7   106.49  3.000
 2S4  H3   C8   O7   112.08  3.000
 2S4  H2   C8   O7   112.02  3.000
 2S4  H7   C10  H6   108.66  3.000
 2S4  H7   C10  H5   108.67  3.000
 2S4  H6   C10  H5   108.79  3.000
 2S4  H7   C10  O9   106.50  3.000
 2S4  H6   C10  O9   112.10  3.000
 2S4  H5   C10  O9   112.00  3.000
 2S4  H9   C11  H8   105.92  3.000
 2S4  H9   C11  C12  109.88  3.000
 2S4  H8   C11  C12  106.89  3.000
 2S4  H9   C11  C2   110.77  3.000
 2S4  H8   C11  C2   110.34  3.000
 2S4  C12  C11  C2   112.75  3.000
 2S4  N13  C12  O15  124.77  3.000
 2S4  O15  C12  C11  122.79  3.000
 2S4  N13  C12  C11  112.43  3.000
 2S4  N16  C14  N17  128.05  3.000
 2S4  N16  C14  N13  110.62  3.000
 2S4  N17  C14  N13  121.24  3.000
 2S4  C18  C19  C24  121.10  3.000
 2S4  C24  C19  C22  118.44  3.000
 2S4  C18  C19  C22  120.45  3.000
 2S4  H10  C20  C22  119.38  3.000
 2S4  H10  C20  C21  119.53  3.000
 2S4  C22  C20  C21  121.09  3.000
 2S4  C25  C21  C23  121.46  3.000
 2S4  C23  C21  C20  117.96  3.000
 2S4  C25  C21  C20  120.57  3.000
 2S4  H11  C22  C20  119.56  3.000
 2S4  H11  C22  C19  119.73  3.000
 2S4  C20  C22  C19  120.71  3.000
 2S4  H12  C24  C23  119.55  3.000
 2S4  H12  C24  C19  119.69  3.000
 2S4  C23  C24  C19  120.77  3.000
 2S4  H13  C4   C6   118.99  3.000
 2S4  H13  C4   C2   120.29  3.000
 2S4  C6   C4   C2   120.72  3.000
 2S4  H14  C6   C5   120.76  3.000
 2S4  H14  C6   C4   118.72  3.000
 2S4  C5   C6   C4   120.52  3.000
 2S4  O9   C5   C6   125.29  3.000
 2S4  O9   C5   C3   115.54  3.000
 2S4  C6   C5   C3   119.17  3.000
 2S4  C5   O9   C10  118.13  3.000
 2S4  C8   O7   C3   118.26  3.000
 2S4  H15  N13  C14  115.74  3.000
 2S4  H15  N13  C12  116.15  3.000
 2S4  C14  N13  C12  128.10  3.000
 2S4  H16  N17  C14  111.31  3.000
 2S4  H17  N16  C18  115.11  3.000
 2S4  H17  N16  C14  116.49  3.000
 2S4  C18  N16  C14  121.38  3.000
 2S4  H19  C18  H18  106.87  3.000
 2S4  H19  C18  N16  112.00  3.000
 2S4  H18  C18  N16  108.42  3.000
 2S4  H19  C18  C19  109.90  3.000
 2S4  H18  C18  C19  109.60  3.000
 2S4  N16  C18  C19  109.97  3.000
 2S4  H20  C23  C24  119.33  3.000
 2S4  H20  C23  C21  119.64  3.000
 2S4  C24  C23  C21  121.03  3.000
 2S4  H23  C25  H22  107.56  3.000
 2S4  H23  C25  H21  107.03  3.000
 2S4  H22  C25  H21  107.97  3.000
 2S4  H23  C25  C21  111.03  3.000
 2S4  H22  C25  C21  111.60  3.000
 2S4  H21  C25  C21  111.43  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
 2S4  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 2S4  CONST_02  C6   C5   C3   C1      0.00   0.0  0
 2S4  CONST_03  C5   C6   C4   C2      0.00   0.0  0
 2S4  CONST_04  C5   C3   C1   C2      0.00   0.0  0
 2S4  CONST_05  C4   C6   C5   C3      0.00   0.0  0
 2S4  CONST_06  C4   C2   C1   C3      0.00   0.0  0
 2S4  CONST_07  C21  C20  C22  C19     0.00   0.0  0
 2S4  CONST_08  C21  C23  C24  C19     0.00   0.0  0
 2S4  CONST_09  C24  C19  C22  C20     0.00   0.0  0
 2S4  CONST_10  C24  C23  C21  C20     0.00   0.0  0
 2S4  CONST_11  C23  C21  C20  C22     0.00   0.0  0
 2S4  CONST_12  C23  C24  C19  C22     0.00   0.0  0
 2S4  CONST_13  O9   C5   C3   C1    180.00   0.0  0
 2S4  CONST_14  O7   C3   C1   C2    180.00   0.0  0
 2S4  CONST_15  C11  C2   C1   C3    180.00   0.0  0
 2S4  CONST_16  C6   C4   C2   C11   180.00   0.0  0
 2S4  CONST_17  C18  C19  C22  C20   180.00   0.0  0
 2S4  CONST_18  C25  C21  C20  C22   180.00   0.0  0
 2S4  CONST_19  C25  C21  C23  C24   180.00   0.0  0
 2S4  CONST_20  O9   C5   C6   C4    180.00   0.0  0
 2S4  CONST_21  O7   C3   C5   C6    180.00   0.0  0
 2S4  CONST_22  C23  C24  C19  C18   180.00   0.0  0
 2S4  CONST_23  H13  C4   C2   C1    180.00   0.0  0
 2S4  CONST_24  H14  C6   C4   C2    180.00   0.0  0
 2S4  CONST_25  H10  C20  C22  C19   180.00   0.0  0
 2S4  CONST_26  H20  C23  C24  C19   180.00   0.0  0
 2S4  CONST_27  H11  C22  C20  C21   180.00   0.0  0
 2S4  CONST_28  H12  C24  C23  C21   180.00   0.0  0
 2S4  CONST_29  H1   C1   C2   C4    180.00   0.0  0
 2S4  CONST_30  C14  N13  C12  C11   180.00   0.0  0
 2S4  CONST_31  O15  C12  N13  C14     0.00   0.0  0
 2S4  CONST_34  C18  N16  C14  N13   180.00   0.0  0
 2S4  CONST_35  C18  N16  C14  N17     0.00   0.0  0
 2S4  CONST_36  H15  N13  C12  C11     0.00   0.0  0
 2S4  CONST_37  H16  N17  C14  N13   180.00   0.0  0
 2S4  Var_01    C12  C11  C2   C1     76.83  30.0  2
 2S4  Var_02    C5   C3   O7   C8    178.80  30.0  1
 2S4  Var_03    C6   C5   O9   C10    -1.13  30.0  2
 2S4  Var_04    N16  C18  C19  C22   -66.27  30.0  2
 2S4  Var_05    H21  C25  C21  C20    49.62  30.0  2
 2S4  Var_06    N13  C12  C11  C2   -160.78  30.0  3
 2S4  Var_07    C19  C18  N16  C14   168.95  30.0  3
 2S4  Var_08    H2   C8   O7   C3    -60.47  30.0  3
 2S4  Var_09    H5   C10  O9   C5    -60.55  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
 2S4  plan-1  C19  0.020
 2S4  plan-1  C20  0.020
 2S4  plan-1  C21  0.020
 2S4  plan-1  C22  0.020
 2S4  plan-1  C24  0.020
 2S4  plan-1  C18  0.020
 2S4  plan-1  C23  0.020
 2S4  plan-1  C25  0.020
 2S4  plan-1  H10  0.020
 2S4  plan-1  H11  0.020
 2S4  plan-1  H12  0.020
 2S4  plan-1  H20  0.020
 2S4  plan-2  C1   0.020
 2S4  plan-2  C2   0.020
 2S4  plan-2  C3   0.020
 2S4  plan-2  C11  0.020
 2S4  plan-2  C4   0.020
 2S4  plan-2  C6   0.020
 2S4  plan-2  C5   0.020
 2S4  plan-2  O9   0.020
 2S4  plan-2  O7   0.020
 2S4  plan-2  H1   0.020
 2S4  plan-2  H13  0.020
 2S4  plan-2  H14  0.020
 2S4  plan-3  C11  0.020
 2S4  plan-3  C12  0.020
 2S4  plan-3  C14  0.020
 2S4  plan-3  O15  0.020
 2S4  plan-3  N13  0.020
 2S4  plan-3  N17  0.020
 2S4  plan-3  N16  0.020
 2S4  plan-3  C18  0.020
 2S4  plan-3  H15  0.020
 2S4  plan-3  H16  0.020
 2S4  plan-3  H17  0.020

