# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 00:32:13 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CCNCc2cccc(NC(=N)c3sccc3)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
 5H3  5H3  N-[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide  ligand  45  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 GRAND
;

data_comp_5H3
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
 5H3  F23  F  F     0  -0.318  -8.1282   0.3969   1.1620
 5H3  C23  C  CR6   0   0.538  -7.0836   0.9457   0.5171
 5H3  C24  C  CR16  0  -0.426  -7.3269   1.8844  -0.4665
 5H3  C25  C  CR16  0  -0.225  -6.2338   2.4376  -1.1198
 5H3  C22  C  CR16  0  -0.464  -5.8080   0.5477   0.8667
 5H3  C21  C  CR6   0   0.138  -4.7150   1.1067   0.2084
 5H3  C26  C  CR16  0  -0.320  -4.9420   2.0534  -0.7881
 5H3  C20  C  CH2   0  -0.532  -3.3213   0.6528   0.5343
 5H3  C19  C  CH2   0  -0.244  -2.9383  -0.5876  -0.2698
 5H3  N18  N  NH1   0  -0.597  -1.5800  -0.9908   0.0292
 5H3  C17  C  CH2   0  -0.308  -1.1566  -2.1589  -0.7143
 5H3  C15  C  CR6   0   0.085   0.2897  -2.4929  -0.4551
 5H3  C14  C  CR16  0  -0.331   0.7045  -3.8169  -0.3585
 5H3  C13  C  CR16  0  -0.232   2.0474  -4.1136  -0.1674
 5H3  C12  C  CR16  0  -0.346   2.9820  -3.0991  -0.0435
 5H3  C16  C  CR16  0  -0.365   1.2308  -1.4740  -0.3484
 5H3  C11  C  CR6   0   0.377   2.5756  -1.7679  -0.1324
 5H3  N07  N  NH1   0  -0.763   3.5395  -0.7561  -0.0566
 5H3  C06  C  C     0   0.369   3.4066   0.4296   0.6396
 5H3  N08  N  N     0  -0.622   2.4633   0.7786   1.4201
 5H3  C05  C  CR5   0  -0.242   4.5084   1.3756   0.4060
 5H3  S01  S  S2    0   0.237   5.4320   1.3623  -1.0506
 5H3  C02  C  CR15  0  -0.460   6.3797   2.6855  -0.5297
 5H3  C03  C  CR15  0  -0.177   6.0004   3.1241   0.7042
 5H3  C04  C  CR15  0  -0.199   4.9238   2.3746   1.2395
 5H3  H1   H  HCR6  0   0.277  -8.3388   2.1768  -0.7133
 5H3  H2   H  HCR6  0   0.266  -6.3940   3.1766  -1.8937
 5H3  H3   H  HCR6  0   0.270  -5.6664  -0.1905   1.6473
 5H3  H4   H  HCR6  0   0.253  -4.1003   2.4961  -1.3065
 5H3  H5   H  HCH2  0   0.249  -2.6058   1.4499   0.3209
 5H3  H6   H  HCH2  0   0.247  -3.2413   0.4286   1.6019
 5H3  H7   H  HCH2  0   0.200  -3.6759  -1.3841  -0.0814
 5H3  H8   H  HCH2  0   0.227  -3.0022  -0.3571  -1.3377
 5H3  H9   H  HNH1  0   0.344  -1.4997  -1.1849   1.0208
 5H3  H11  H  HCH2  0   0.217  -1.7742  -3.0476  -0.5144
 5H3  H12  H  HCH2  0   0.243  -1.2853  -1.9417  -1.7805
 5H3  H13  H  HCR6  0   0.249  -0.0217  -4.6171  -0.4328
 5H3  H14  H  HCR6  0   0.258   2.3679  -5.1449  -0.0946
 5H3  H15  H  HCR6  0   0.265   4.0257  -3.3352   0.1262
 5H3  H16  H  HCR6  0   0.269   0.9015  -0.4483  -0.4534
 5H3  H17  H  HNH1  0   0.406   4.4864  -1.0572  -0.2326
 5H3  H18  H  H     0   0.341   1.7952   0.0291   1.5732
 5H3  H19  H  HCR5  0   0.303   7.1614   3.0763  -1.1628
 5H3  H20  H  HCR5  0   0.273   6.4737   3.9505   1.2139
 5H3  H21  H  HCR5  0   0.268   4.4788   2.5553   2.2071

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
 5H3  C03  C02  aromatic  1.363  0.020  1.363
 5H3  C03  C04  aromatic  1.417  0.020  1.417
 5H3  C02  S01  aromatic  1.709  0.020  1.709
 5H3  C04  C05  aromatic  1.366  0.020  1.366
 5H3  S01  C05  aromatic  1.725  0.020  1.725
 5H3  C05  C06  single    1.471  0.020  1.471
 5H3  C06  N08  double    1.273  0.020  1.273
 5H3  C06  N07  single    1.381  0.020  1.381
 5H3  C12  C13  aromatic  1.385  0.020  1.385
 5H3  C12  C11  aromatic  1.395  0.020  1.395
 5H3  C13  C14  aromatic  1.389  0.020  1.389
 5H3  N07  C11  single    1.399  0.020  1.399
 5H3  C11  C16  aromatic  1.393  0.020  1.393
 5H3  C14  C15  aromatic  1.391  0.020  1.391
 5H3  C16  C15  aromatic  1.391  0.020  1.391
 5H3  C15  C17  single    1.507  0.020  1.507
 5H3  C17  N18  single    1.448  0.020  1.448
 5H3  N18  C19  single    1.448  0.020  1.448
 5H3  C19  C20  single    1.527  0.020  1.527
 5H3  C26  C25  aromatic  1.388  0.020  1.388
 5H3  C26  C21  aromatic  1.393  0.020  1.393
 5H3  C25  C24  aromatic  1.388  0.020  1.388
 5H3  C20  C21  single    1.502  0.020  1.502
 5H3  C21  C22  aromatic  1.393  0.020  1.393
 5H3  C24  C23  aromatic  1.381  0.020  1.381
 5H3  C22  C23  aromatic  1.381  0.020  1.381
 5H3  C23  F23  single    1.345  0.020  1.345
 5H3  C24  H1   single    0.930  0.020  1.080
 5H3  C25  H2   single    0.930  0.020  1.080
 5H3  C22  H3   single    0.930  0.020  1.080
 5H3  C26  H4   single    0.930  0.020  1.080
 5H3  C20  H5   single    0.970  0.020  1.090
 5H3  C20  H6   single    0.970  0.020  1.090
 5H3  C19  H7   single    0.970  0.020  1.090
 5H3  C19  H8   single    0.970  0.020  1.090
 5H3  N18  H9   single    0.890  0.020  1.040
 5H3  C17  H11  single    0.970  0.020  1.090
 5H3  C17  H12  single    0.970  0.020  1.090
 5H3  C14  H13  single    0.930  0.020  1.080
 5H3  C13  H14  single    0.930  0.020  1.080
 5H3  C12  H15  single    0.930  0.020  1.080
 5H3  C16  H16  single    0.930  0.020  1.080
 5H3  N07  H17  single    0.890  0.020  1.040
 5H3  N08  H18  single    0.890  0.020  1.040
 5H3  C02  H19  single    0.930  0.020  1.080
 5H3  C03  H20  single    0.930  0.020  1.080
 5H3  C04  H21  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
 5H3  C22  C23  C24  122.60  3.000
 5H3  C22  C23  F23  118.58  3.000
 5H3  C24  C23  F23  118.81  3.000
 5H3  H1   C24  C25  121.43  3.000
 5H3  H1   C24  C23  120.73  3.000
 5H3  C25  C24  C23  117.85  3.000
 5H3  H2   C25  C26  119.85  3.000
 5H3  H2   C25  C24  119.48  3.000
 5H3  C26  C25  C24  120.67  3.000
 5H3  H3   C22  C21  120.74  3.000
 5H3  H3   C22  C23  119.95  3.000
 5H3  C21  C22  C23  119.30  3.000
 5H3  C20  C21  C26  120.79  3.000
 5H3  C20  C21  C22  120.30  3.000
 5H3  C26  C21  C22  118.87  3.000
 5H3  H4   C26  C21  119.57  3.000
 5H3  H4   C26  C25  119.72  3.000
 5H3  C21  C26  C25  120.71  3.000
 5H3  H6   C20  H5   107.00  3.000
 5H3  H6   C20  C19  109.21  3.000
 5H3  H5   C20  C19  109.00  3.000
 5H3  H6   C20  C21  109.98  3.000
 5H3  H5   C20  C21  110.19  3.000
 5H3  C19  C20  C21  111.35  3.000
 5H3  H8   C19  H7   106.26  3.000
 5H3  H8   C19  N18  108.35  3.000
 5H3  H7   C19  N18  113.04  3.000
 5H3  H8   C19  C20  109.15  3.000
 5H3  H7   C19  C20  109.22  3.000
 5H3  N18  C19  C20  110.65  3.000
 5H3  H9   N18  C17  108.94  3.000
 5H3  H9   N18  C19  109.24  3.000
 5H3  C17  N18  C19  113.13  3.000
 5H3  H12  C17  H11  105.71  3.000
 5H3  H12  C17  C15  108.91  3.000
 5H3  H11  C17  C15  109.18  3.000
 5H3  H12  C17  N18  107.78  3.000
 5H3  H11  C17  N18  113.21  3.000
 5H3  C15  C17  N18  111.79  3.000
 5H3  C16  C15  C14  119.35  3.000
 5H3  C16  C15  C17  120.01  3.000
 5H3  C14  C15  C17  120.61  3.000
 5H3  H13  C14  C13  120.00  3.000
 5H3  H13  C14  C15  119.91  3.000
 5H3  C13  C14  C15  120.09  3.000
 5H3  H14  C13  C12  119.48  3.000
 5H3  H14  C13  C14  119.95  3.000
 5H3  C12  C13  C14  120.56  3.000
 5H3  H15  C12  C11  119.91  3.000
 5H3  H15  C12  C13  120.30  3.000
 5H3  C11  C12  C13  119.79  3.000
 5H3  H16  C16  C11  120.56  3.000
 5H3  H16  C16  C15  118.74  3.000
 5H3  C11  C16  C15  120.69  3.000
 5H3  N07  C11  C16  121.38  3.000
 5H3  C16  C11  C12  119.50  3.000
 5H3  N07  C11  C12  119.07  3.000
 5H3  H17  N07  C06  115.74  3.000
 5H3  H17  N07  C11  114.90  3.000
 5H3  C06  N07  C11  125.57  3.000
 5H3  C05  C06  N08  118.43  3.000
 5H3  N08  C06  N07  127.99  3.000
 5H3  C05  C06  N07  113.58  3.000
 5H3  H18  N08  C06  112.18  3.000
 5H3  C04  C05  S01  110.99  3.000
 5H3  S01  C05  C06  122.02  3.000
 5H3  C04  C05  C06  126.97  3.000
 5H3  C02  S01  C05   91.92  3.000
 5H3  H19  C02  C03  128.02  3.000
 5H3  H19  C02  S01  120.22  3.000
 5H3  C03  C02  S01  111.76  3.000
 5H3  H20  C03  C04  124.01  3.000
 5H3  H20  C03  C02  123.46  3.000
 5H3  C04  C03  C02  112.53  3.000
 5H3  H21  C04  C03  124.27  3.000
 5H3  H21  C04  C05  122.93  3.000
 5H3  C03  C04  C05  112.80  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
 5H3  CONST_01  C26  C25  C24  C23     0.00   0.0  0
 5H3  CONST_02  C26  C21  C22  C23     0.00   0.0  0
 5H3  CONST_03  C21  C26  C25  C24     0.00   0.0  0
 5H3  CONST_04  C21  C22  C23  C24     0.00   0.0  0
 5H3  CONST_05  C22  C21  C26  C25     0.00   0.0  0
 5H3  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 5H3  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 5H3  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 5H3  CONST_09  C11  C12  C13  C14     0.00   0.0  0
 5H3  CONST_10  C11  C16  C15  C14     0.00   0.0  0
 5H3  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 5H3  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 5H3  CONST_13  C02  C03  C04  C05     0.00   0.0  0
 5H3  CONST_14  C03  C02  S01  C05     0.00   0.0  0
 5H3  CONST_15  C04  C03  C02  S01     0.00   0.0  0
 5H3  CONST_16  C03  C04  C05  S01     0.00   0.0  0
 5H3  CONST_17  C04  C05  S01  C02     0.00   0.0  0
 5H3  CONST_18  C25  C24  C23  F23   180.00   0.0  0
 5H3  CONST_19  C21  C22  C23  F23   180.00   0.0  0
 5H3  CONST_20  C20  C21  C22  C23   180.00   0.0  0
 5H3  CONST_21  C20  C21  C26  C25   180.00   0.0  0
 5H3  CONST_22  C13  C14  C15  C17   180.00   0.0  0
 5H3  CONST_23  C11  C16  C15  C17   180.00   0.0  0
 5H3  CONST_24  N07  C11  C16  C15   180.00   0.0  0
 5H3  CONST_25  N07  C11  C12  C13   180.00   0.0  0
 5H3  CONST_26  C03  C04  C05  C06   180.00   0.0  0
 5H3  CONST_27  C02  S01  C05  C06   180.00   0.0  0
 5H3  CONST_28  H2   C25  C24  C23   180.00   0.0  0
 5H3  CONST_29  H4   C26  C25  C24   180.00   0.0  0
 5H3  CONST_30  H3   C22  C23  C24   180.00   0.0  0
 5H3  CONST_31  H1   C24  C23  C22   180.00   0.0  0
 5H3  CONST_32  H14  C13  C14  C15   180.00   0.0  0
 5H3  CONST_33  H15  C12  C13  C14   180.00   0.0  0
 5H3  CONST_34  H16  C16  C15  C14   180.00   0.0  0
 5H3  CONST_35  H13  C14  C13  C12   180.00   0.0  0
 5H3  CONST_36  H20  C03  C04  C05   180.00   0.0  0
 5H3  CONST_37  H19  C02  S01  C05   180.00   0.0  0
 5H3  CONST_38  H21  C04  C05  S01   180.00   0.0  0
 5H3  CONST_41  C05  C06  N07  C11   180.00   0.0  0
 5H3  CONST_43  N08  C06  N07  C11     0.00   0.0  0
 5H3  CONST_44  H18  N08  C06  C05   180.00   0.0  0
 5H3  Var_01    C19  C20  C21  C22    85.44  30.0  2
 5H3  Var_02    C14  C15  C17  N18   142.09  30.0  2
 5H3  Var_03    C04  C05  C06  N07  -155.37  30.0  3
 5H3  Var_04    N18  C19  C20  C21   178.46  30.0  2
 5H3  Var_05    C15  C17  N18  C19   175.92  30.0  1
 5H3  Var_06    C17  N18  C19  C20  -179.53  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
 5H3  plan-1  C06  0.020
 5H3  plan-1  C05  0.020
 5H3  plan-1  S01  0.020
 5H3  plan-1  C02  0.020
 5H3  plan-1  C03  0.020
 5H3  plan-1  C04  0.020
 5H3  plan-1  H19  0.020
 5H3  plan-1  H20  0.020
 5H3  plan-1  H21  0.020
 5H3  plan-2  F23  0.020
 5H3  plan-2  C23  0.020
 5H3  plan-2  C24  0.020
 5H3  plan-2  C25  0.020
 5H3  plan-2  C22  0.020
 5H3  plan-2  C21  0.020
 5H3  plan-2  C26  0.020
 5H3  plan-2  C20  0.020
 5H3  plan-2  H1   0.020
 5H3  plan-2  H2   0.020
 5H3  plan-2  H3   0.020
 5H3  plan-2  H4   0.020
 5H3  plan-3  C17  0.020
 5H3  plan-3  C15  0.020
 5H3  plan-3  C14  0.020
 5H3  plan-3  C13  0.020
 5H3  plan-3  C12  0.020
 5H3  plan-3  C16  0.020
 5H3  plan-3  C11  0.020
 5H3  plan-3  N07  0.020
 5H3  plan-3  H13  0.020
 5H3  plan-3  H14  0.020
 5H3  plan-3  H15  0.020
 5H3  plan-3  H16  0.020
 5H3  plan-4  C11  0.020
 5H3  plan-4  N07  0.020
 5H3  plan-4  C06  0.020
 5H3  plan-4  N08  0.020
 5H3  plan-4  C05  0.020
 5H3  plan-4  H17  0.020
 5H3  plan-4  H18  0.020

