# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 04:20:27 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[3-({ethyl[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CCc1cccc(F)c1)Cc2cccc(NC(=N)c3sccc3)c2
#
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
 5H4  5H4  N-[3-({ethyl[2-(3-fluorophenyl)ethyl]amino}methyl)phenyl]thiophene-2-carboximidamide  ligand  51  27  .  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_5H4
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
 5H4  F33  F  F     0  -0.318   2.0542   4.3665  -2.1009
 5H4  C33  C  CR6   0   0.539   3.0366   3.7896  -1.3865
 5H4  C34  C  CR16  0  -0.426   3.9542   4.5974  -0.7429
 5H4  C35  C  CR16  0  -0.224   4.9598   3.9811  -0.0106
 5H4  C36  C  CR16  0  -0.324   5.0330   2.5969   0.0666
 5H4  C32  C  CR16  0  -0.463   3.0881   2.4113  -1.3255
 5H4  C31  C  CR6   0   0.146   4.1005   1.7975  -0.5905
 5H4  C22  C  CH2   0  -0.523   4.1384   0.3011  -0.4706
 5H4  C21  C  CH2   0  -0.271   3.2052  -0.1874   0.6388
 5H4  N18  N  NT    0  -0.416   3.2117  -1.6348   0.7577
 5H4  C19  C  CH2   0  -0.285   4.3308  -2.1270   1.5464
 5H4  C20  C  CH3   0  -0.665   4.6938  -3.5677   1.2287
 5H4  C17  C  CH2   0  -0.327   1.9379  -2.1485   1.2134
 5H4  C15  C  CR6   0   0.097   0.8602  -2.0289   0.1647
 5H4  C14  C  CR16  0  -0.294   1.1482  -2.2260  -1.1834
 5H4  C13  C  CR16  0  -0.234   0.1342  -2.1484  -2.1258
 5H4  C12  C  CR16  0  -0.339  -1.1741  -1.8803  -1.7486
 5H4  C11  C  CR6   0   0.371  -1.4678  -1.6629  -0.4036
 5H4  C16  C  CR16  0  -0.400  -0.4441  -1.7354   0.5398
 5H4  N07  N  NH1   0  -0.763  -2.7765  -1.4114   0.0298
 5H4  C06  C  C     0   0.368  -3.6373  -0.4939  -0.5406
 5H4  N08  N  N     0  -0.623  -3.3962   0.3192  -1.4901
 5H4  C05  C  CR5   0  -0.242  -4.9863  -0.5059   0.0454
 5H4  S01  S  S2    0   0.236  -5.6449  -1.9064   0.8073
 5H4  C02  C  CR15  0  -0.460  -7.1162  -1.1032   1.1410
 5H4  C03  C  CR15  0  -0.176  -7.1065   0.1806   0.6824
 5H4  C04  C  CR15  0  -0.199  -5.8856   0.5221   0.0499
 5H4  H1   H  HCR6  0   0.277   3.8867   5.6750  -0.8128
 5H4  H2   H  HCR6  0   0.266   5.6933   4.5900   0.5014
 5H4  H3   H  HCR6  0   0.252   5.8259   2.1314   0.6392
 5H4  H4   H  HCR6  0   0.267   2.3470   1.8178  -1.8480
 5H4  H5   H  HCH2  0   0.247   3.8280  -0.1647  -1.4087
 5H4  H6   H  HCH2  0   0.249   5.1626  -0.0253  -0.2760
 5H4  H7   H  HCH2  0   0.215   3.4666   0.3030   1.5899
 5H4  H8   H  HCH2  0   0.242   2.1919   0.1416   0.3957
 5H4  H10  H  HCH2  0   0.232   5.1985  -1.5020   1.3284
 5H4  H11  H  HCH2  0   0.198   4.1447  -2.0136   2.6269
 5H4  H12  H  HCH3  0   0.222   3.8920  -4.2656   1.4719
 5H4  H13  H  HCH3  0   0.223   4.9275  -3.6799   0.1698
 5H4  H14  H  HCH3  0   0.228   5.5680  -3.8719   1.8051
 5H4  H15  H  HCH2  0   0.256   2.0553  -3.2079   1.4561
 5H4  H16  H  HCH2  0   0.219   1.5982  -1.6642   2.1438
 5H4  H17  H  HCR6  0   0.245   2.1662  -2.4334  -1.4854
 5H4  H18  H  HCR6  0   0.256   0.3585  -2.3102  -3.1723
 5H4  H19  H  HCR6  0   0.276  -1.9562  -1.8590  -2.4961
 5H4  H20  H  HCR6  0   0.258  -0.6703  -1.5503   1.5845
 5H4  H21  H  HNH1  0   0.406  -2.9493  -1.6284   1.0003
 5H4  H22  H  H     0   0.341  -2.4214   0.2980  -1.7736
 5H4  H23  H  HCR5  0   0.303  -7.9128  -1.6214   1.6521
 5H4  H24  H  HCR5  0   0.273  -7.9393   0.8595   0.7940
 5H4  H25  H  HCR5  0   0.268  -5.6698   1.4910  -0.3763

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
 5H4  C03  C02  aromatic  1.363  0.020  1.363
 5H4  C03  C04  aromatic  1.417  0.020  1.417
 5H4  C02  S01  aromatic  1.709  0.020  1.709
 5H4  C04  C05  aromatic  1.366  0.020  1.366
 5H4  S01  C05  aromatic  1.725  0.020  1.725
 5H4  C05  C06  single    1.471  0.020  1.471
 5H4  C06  N08  double    1.273  0.020  1.273
 5H4  C06  N07  single    1.381  0.020  1.381
 5H4  C13  C12  aromatic  1.388  0.020  1.388
 5H4  C13  C14  aromatic  1.386  0.020  1.386
 5H4  C12  C11  aromatic  1.394  0.020  1.394
 5H4  C11  N07  single    1.401  0.020  1.401
 5H4  C11  C16  aromatic  1.394  0.020  1.394
 5H4  C14  C15  aromatic  1.392  0.020  1.392
 5H4  C16  C15  aromatic  1.389  0.020  1.389
 5H4  C15  C17  single    1.509  0.020  1.509
 5H4  C17  N18  single    1.447  0.020  1.447
 5H4  N18  C19  single    1.455  0.020  1.455
 5H4  N18  C21  single    1.452  0.020  1.452
 5H4  C19  C20  single    1.519  0.020  1.519
 5H4  C21  C22  single    1.530  0.020  1.530
 5H4  C35  C36  aromatic  1.388  0.020  1.388
 5H4  C35  C34  aromatic  1.388  0.020  1.388
 5H4  C36  C31  aromatic  1.393  0.020  1.393
 5H4  C34  C33  aromatic  1.382  0.020  1.382
 5H4  C31  C22  single    1.502  0.020  1.502
 5H4  C31  C32  aromatic  1.394  0.020  1.394
 5H4  C33  C32  aromatic  1.381  0.020  1.381
 5H4  C33  F33  single    1.345  0.020  1.345
 5H4  C34  H1   single    0.930  0.020  1.080
 5H4  C35  H2   single    0.930  0.020  1.080
 5H4  C36  H3   single    0.930  0.020  1.080
 5H4  C32  H4   single    0.930  0.020  1.080
 5H4  C22  H5   single    0.970  0.020  1.090
 5H4  C22  H6   single    0.970  0.020  1.090
 5H4  C21  H7   single    0.970  0.020  1.090
 5H4  C21  H8   single    0.970  0.020  1.090
 5H4  C19  H10  single    0.970  0.020  1.090
 5H4  C19  H11  single    0.970  0.020  1.090
 5H4  C20  H12  single    0.970  0.020  1.090
 5H4  C20  H13  single    0.970  0.020  1.090
 5H4  C20  H14  single    0.970  0.020  1.090
 5H4  C17  H15  single    0.970  0.020  1.090
 5H4  C17  H16  single    0.970  0.020  1.090
 5H4  C14  H17  single    0.930  0.020  1.080
 5H4  C13  H18  single    0.930  0.020  1.080
 5H4  C12  H19  single    0.930  0.020  1.080
 5H4  C16  H20  single    0.930  0.020  1.080
 5H4  N07  H21  single    0.890  0.020  1.040
 5H4  N08  H22  single    0.890  0.020  1.040
 5H4  C02  H23  single    0.930  0.020  1.080
 5H4  C03  H24  single    0.930  0.020  1.080
 5H4  C04  H25  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
 5H4  C32  C33  C34  122.57  3.000
 5H4  C32  C33  F33  118.62  3.000
 5H4  C34  C33  F33  118.81  3.000
 5H4  H1   C34  C35  121.42  3.000
 5H4  H1   C34  C33  120.72  3.000
 5H4  C35  C34  C33  117.86  3.000
 5H4  H2   C35  C36  119.93  3.000
 5H4  H2   C35  C34  119.40  3.000
 5H4  C36  C35  C34  120.67  3.000
 5H4  H3   C36  C31  119.53  3.000
 5H4  H3   C36  C35  119.76  3.000
 5H4  C31  C36  C35  120.71  3.000
 5H4  H4   C32  C31  120.65  3.000
 5H4  H4   C32  C33  119.99  3.000
 5H4  C31  C32  C33  119.35  3.000
 5H4  C22  C31  C32  119.96  3.000
 5H4  C32  C31  C36  118.84  3.000
 5H4  C22  C31  C36  121.15  3.000
 5H4  H6   C22  H5   106.97  3.000
 5H4  H6   C22  C21  110.33  3.000
 5H4  H5   C22  C21  108.26  3.000
 5H4  H6   C22  C31  109.61  3.000
 5H4  H5   C22  C31  110.43  3.000
 5H4  C21  C22  C31  111.14  3.000
 5H4  H8   C21  H7   106.15  3.000
 5H4  H8   C21  N18  108.81  3.000
 5H4  H7   C21  N18  111.84  3.000
 5H4  H8   C21  C22  107.95  3.000
 5H4  H7   C21  C22  109.83  3.000
 5H4  N18  C21  C22  112.01  3.000
 5H4  C17  N18  C19  112.72  3.000
 5H4  C19  N18  C21  112.64  3.000
 5H4  C17  N18  C21  112.06  3.000
 5H4  H11  C19  H10  105.73  3.000
 5H4  H11  C19  C20  110.05  3.000
 5H4  H10  C19  C20  108.14  3.000
 5H4  H11  C19  N18  111.52  3.000
 5H4  H10  C19  N18  108.03  3.000
 5H4  C20  C19  N18  113.03  3.000
 5H4  H14  C20  H13  108.23  3.000
 5H4  H14  C20  H12  107.04  3.000
 5H4  H13  C20  H12  107.96  3.000
 5H4  H14  C20  C19  110.22  3.000
 5H4  H13  C20  C19  110.60  3.000
 5H4  H12  C20  C19  112.62  3.000
 5H4  H16  C17  H15  105.75  3.000
 5H4  H16  C17  C15  109.37  3.000
 5H4  H15  C17  C15  107.93  3.000
 5H4  H16  C17  N18  112.40  3.000
 5H4  H15  C17  N18  108.63  3.000
 5H4  C15  C17  N18  112.45  3.000
 5H4  C16  C15  C14  119.06  3.000
 5H4  C16  C15  C17  120.00  3.000
 5H4  C14  C15  C17  120.93  3.000
 5H4  H17  C14  C13  120.61  3.000
 5H4  H17  C14  C15  119.47  3.000
 5H4  C13  C14  C15  119.92  3.000
 5H4  H18  C13  C12  119.14  3.000
 5H4  H18  C13  C14  119.82  3.000
 5H4  C12  C13  C14  121.04  3.000
 5H4  H19  C12  C11  120.74  3.000
 5H4  H19  C12  C13  119.83  3.000
 5H4  C11  C12  C13  119.41  3.000
 5H4  N07  C11  C16  119.07  3.000
 5H4  C16  C11  C12  119.35  3.000
 5H4  N07  C11  C12  121.55  3.000
 5H4  H20  C16  C11  119.33  3.000
 5H4  H20  C16  C15  119.47  3.000
 5H4  C11  C16  C15  121.20  3.000
 5H4  H21  N07  C06  115.67  3.000
 5H4  H21  N07  C11  114.75  3.000
 5H4  C06  N07  C11  124.99  3.000
 5H4  C05  C06  N08  118.42  3.000
 5H4  N08  C06  N07  127.90  3.000
 5H4  C05  C06  N07  113.68  3.000
 5H4  H22  N08  C06  112.12  3.000
 5H4  C04  C05  S01  110.99  3.000
 5H4  S01  C05  C06  122.19  3.000
 5H4  C04  C05  C06  126.81  3.000
 5H4  C02  S01  C05   91.91  3.000
 5H4  H23  C02  C03  128.09  3.000
 5H4  H23  C02  S01  120.15  3.000
 5H4  C03  C02  S01  111.76  3.000
 5H4  H24  C03  C04  123.98  3.000
 5H4  H24  C03  C02  123.48  3.000
 5H4  C04  C03  C02  112.54  3.000
 5H4  H25  C04  C03  124.37  3.000
 5H4  H25  C04  C05  122.83  3.000
 5H4  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
 5H4  CONST_01  C36  C35  C34  C33     0.00   0.0  0
 5H4  CONST_02  C36  C31  C32  C33     0.00   0.0  0
 5H4  CONST_03  C31  C36  C35  C34     0.00   0.0  0
 5H4  CONST_04  C31  C32  C33  C34     0.00   0.0  0
 5H4  CONST_05  C32  C31  C36  C35     0.00   0.0  0
 5H4  CONST_06  C32  C33  C34  C35     0.00   0.0  0
 5H4  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 5H4  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 5H4  CONST_09  C11  C12  C13  C14     0.00   0.0  0
 5H4  CONST_10  C11  C16  C15  C14     0.00   0.0  0
 5H4  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 5H4  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 5H4  CONST_13  C02  C03  C04  C05     0.00   0.0  0
 5H4  CONST_14  C03  C02  S01  C05     0.00   0.0  0
 5H4  CONST_15  C04  C03  C02  S01     0.00   0.0  0
 5H4  CONST_16  C03  C04  C05  S01     0.00   0.0  0
 5H4  CONST_17  C04  C05  S01  C02     0.00   0.0  0
 5H4  CONST_18  C35  C34  C33  F33   180.00   0.0  0
 5H4  CONST_19  C31  C32  C33  F33   180.00   0.0  0
 5H4  CONST_20  C22  C31  C32  C33   180.00   0.0  0
 5H4  CONST_21  C22  C31  C36  C35   180.00   0.0  0
 5H4  CONST_22  C13  C14  C15  C17   180.00   0.0  0
 5H4  CONST_23  C11  C16  C15  C17   180.00   0.0  0
 5H4  CONST_24  N07  C11  C16  C15   180.00   0.0  0
 5H4  CONST_25  N07  C11  C12  C13   180.00   0.0  0
 5H4  CONST_26  C03  C04  C05  C06   180.00   0.0  0
 5H4  CONST_27  C02  S01  C05  C06   180.00   0.0  0
 5H4  CONST_28  H2   C35  C34  C33   180.00   0.0  0
 5H4  CONST_29  H3   C36  C35  C34   180.00   0.0  0
 5H4  CONST_30  H4   C32  C33  C34   180.00   0.0  0
 5H4  CONST_31  H1   C34  C35  C36   180.00   0.0  0
 5H4  CONST_32  H18  C13  C14  C15   180.00   0.0  0
 5H4  CONST_33  H19  C12  C13  C14   180.00   0.0  0
 5H4  CONST_34  H20  C16  C15  C14   180.00   0.0  0
 5H4  CONST_35  H17  C14  C13  C12   180.00   0.0  0
 5H4  CONST_36  H24  C03  C04  C05   180.00   0.0  0
 5H4  CONST_37  H23  C02  S01  C05   180.00   0.0  0
 5H4  CONST_38  H25  C04  C05  S01   180.00   0.0  0
 5H4  CONST_40  C05  C06  N07  C11   180.00   0.0  0
 5H4  CONST_43  N08  C06  N07  C11     0.00   0.0  0
 5H4  CONST_44  H22  N08  C06  C05   180.00   0.0  0
 5H4  Var_01    C21  C22  C31  C36    94.52  30.0  2
 5H4  Var_02    C14  C15  C17  N18    37.03  30.0  2
 5H4  Var_03    C04  C05  C06  N07   155.69  30.0  3
 5H4  Var_04    N18  C21  C22  C31   179.12  30.0  1
 5H4  Var_05    C15  C17  N18  C21    70.74  30.0  2
 5H4  Var_06    C17  N18  C21  C22  -149.18  30.0  2
 5H4  Var_07    C20  C19  N18  C21  -156.42  30.0  3
 5H4  Var_08    H12  C20  C19  N18   -63.53  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
 5H4  plan-1  C06  0.020
 5H4  plan-1  C05  0.020
 5H4  plan-1  S01  0.020
 5H4  plan-1  C02  0.020
 5H4  plan-1  C03  0.020
 5H4  plan-1  C04  0.020
 5H4  plan-1  H23  0.020
 5H4  plan-1  H24  0.020
 5H4  plan-1  H25  0.020
 5H4  plan-2  F33  0.020
 5H4  plan-2  C33  0.020
 5H4  plan-2  C34  0.020
 5H4  plan-2  C35  0.020
 5H4  plan-2  C36  0.020
 5H4  plan-2  C32  0.020
 5H4  plan-2  C31  0.020
 5H4  plan-2  C22  0.020
 5H4  plan-2  H1   0.020
 5H4  plan-2  H2   0.020
 5H4  plan-2  H3   0.020
 5H4  plan-2  H4   0.020
 5H4  plan-3  C17  0.020
 5H4  plan-3  C15  0.020
 5H4  plan-3  C14  0.020
 5H4  plan-3  C13  0.020
 5H4  plan-3  C12  0.020
 5H4  plan-3  C11  0.020
 5H4  plan-3  C16  0.020
 5H4  plan-3  N07  0.020
 5H4  plan-3  H17  0.020
 5H4  plan-3  H18  0.020
 5H4  plan-3  H19  0.020
 5H4  plan-3  H20  0.020
 5H4  plan-4  C11  0.020
 5H4  plan-4  N07  0.020
 5H4  plan-4  C06  0.020
 5H4  plan-4  N08  0.020
 5H4  plan-4  C05  0.020
 5H4  plan-4  H21  0.020
 5H4  plan-4  H22  0.020

