# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:37:57 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 4-amino-3-fluoro-N-(1-{[(2Z)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1F)C(=O)NC2(CCCCC2)C(=O)NCC=N
#
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
 3XT  3XT  4-amino-3-fluoro-N-(1-{[(2Z)-2-iminoethyl]carbamoyl}cyclohexyl)benzamide  ligand  44  23  .  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_3XT
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
 3XT  C11  C  CH2   0  -0.462   2.3903  -1.7011   1.3178
 3XT  C10  C  CH2   0  -0.431   1.6954  -3.0283   1.6104
 3XT  C9   C  CH2   0  -0.412   1.7866  -3.9866   0.4297
 3XT  C8   C  CH2   0  -0.430   1.2780  -3.3318  -0.8494
 3XT  C1   C  C1    0  -0.048   2.3619   3.4692  -0.3732
 3XT  C2   C  CH2   0  -0.320   3.1566   2.5295   0.4886
 3XT  N1   N  N     0  -0.571   2.1232   4.6526  -0.0040
 3XT  C7   C  CH2   0  -0.433   2.0163  -2.0302  -1.1383
 3XT  C4   C  C     0   0.542   2.7551   0.2145  -0.2236
 3XT  C6   C  CT    0  -0.027   1.8882  -1.0345   0.0224
 3XT  C15  C  CR6   0  -0.050  -1.6322   0.3032  -0.3765
 3XT  C16  C  CR16  0  -0.492  -2.3917  -0.6234   0.3409
 3XT  C17  C  CR6   0   0.431  -3.7305  -0.3999   0.5380
 3XT  C18  C  CR6   0   0.270  -4.3986   0.7297   0.0527
 3XT  C19  C  CR16  0  -0.310  -3.6215   1.6438  -0.6702
 3XT  C20  C  CR16  0  -0.340  -2.2739   1.4299  -0.8858
 3XT  O14  O  O     0  -0.425   0.3534   0.6246  -1.6242
 3XT  N3   N  NH1   0  -0.732   2.5105   1.2451   0.6060
 3XT  N12  N  NH1   0  -0.663   0.5021  -0.6445   0.2291
 3XT  N21  N  NH2   0  -0.870  -5.7208   0.9436   0.3154
 3XT  F22  F  F     0  -0.226  -4.4561  -1.3088   1.2199
 3XT  H1   H  HCH2  0   0.255   2.2699  -1.0164   2.1617
 3XT  H2   H  HCH2  0   0.208   3.4642  -1.8749   1.2083
 3XT  H3   H  HCH2  0   0.228   2.1487  -3.4707   2.4998
 3XT  H4   H  HCH2  0   0.184   0.6433  -2.8649   1.8671
 3XT  H5   H  HCH2  0   0.245   2.8295  -4.2905   0.2896
 3XT  H6   H  HCH2  0   0.234   1.2245  -4.8982   0.6445
 3XT  H7   H  HCH2  0   0.194   1.4053  -4.0102  -1.6958
 3XT  H8   H  HCH2  0   0.200   0.2020  -3.1464  -0.7689
 3XT  H9   H  H     0   0.269   2.0181   3.0475  -1.3215
 3XT  H10  H  HCH2  0   0.249   4.1477   2.3896   0.0537
 3XT  H11  H  HCH2  0   0.265   3.2909   2.9645   1.4788
 3XT  H12  H  H     0   0.349   1.5894   5.1469  -0.7139
 3XT  H13  H  HCH2  0   0.245   3.0752  -2.2486  -1.2917
 3XT  H14  H  HCH2  0   0.289   1.6560  -1.5806  -2.0642
 3XT  H15  H  HCR6  0   0.213  -1.9663  -1.5420   0.7266
 3XT  H16  H  HCR6  0   0.248  -4.0956   2.5321  -1.0689
 3XT  H17  H  HCR6  0   0.246  -1.7109   2.1571  -1.4553
 3XT  H18  H  HNH1  0   0.358   1.7133   1.1915   1.2200
 3XT  H19  H  HNH1  0   0.335   0.0472  -0.9384   1.0784
 3XT  H20  H  HNH2  0   0.407  -6.2945   0.1442   0.5280
 3XT  H21  H  HNH2  0   0.389  -6.1872   1.6179  -0.2689
 3XT  O5   O  O     0  -0.218   3.6560   0.2244  -1.0465
 3XT  C13  C  C     0   0.609  -0.1869   0.1117  -0.6530

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
 3XT  C10  C11  single    1.526  0.020  1.526
 3XT  C10  C9   single    1.523  0.020  1.523
 3XT  C11  C6   single    1.541  0.020  1.541
 3XT  O14  C13  double    1.224  0.020  1.224
 3XT  C9   C8   single    1.524  0.020  1.524
 3XT  C16  C15  aromatic  1.396  0.020  1.396
 3XT  C16  C17  aromatic  1.372  0.020  1.372
 3XT  C13  C15  single    1.484  0.020  1.484
 3XT  C13  N12  single    1.351  0.020  1.351
 3XT  F22  C17  single    1.348  0.020  1.348
 3XT  C15  C20  aromatic  1.393  0.020  1.393
 3XT  C17  C18  aromatic  1.399  0.020  1.399
 3XT  N12  C6   single    1.455  0.020  1.455
 3XT  C6   C4   single    1.540  0.020  1.540
 3XT  C6   C7   single    1.535  0.020  1.535
 3XT  N3   C4   single    1.345  0.020  1.345
 3XT  N3   C2   single    1.443  0.020  1.443
 3XT  C20  C19  aromatic  1.381  0.020  1.381
 3XT  C18  C19  aromatic  1.401  0.020  1.401
 3XT  C18  N21  single    1.365  0.020  1.365
 3XT  C8   C7   single    1.524  0.020  1.524
 3XT  C4   O5   double    1.220  0.020  1.220
 3XT  C2   C1   single    1.502  0.020  1.502
 3XT  C1   N1   double    1.262  0.020  1.262
 3XT  C11  H1   single    0.970  0.020  1.090
 3XT  C11  H2   single    0.970  0.020  1.090
 3XT  C10  H3   single    0.970  0.020  1.090
 3XT  C10  H4   single    0.970  0.020  1.090
 3XT  C9   H5   single    0.970  0.020  1.090
 3XT  C9   H6   single    0.970  0.020  1.090
 3XT  C8   H7   single    0.970  0.020  1.090
 3XT  C8   H8   single    0.970  0.020  1.090
 3XT  C1   H9   single    0.930  0.020  1.080
 3XT  C2   H10  single    0.970  0.020  1.090
 3XT  C2   H11  single    0.970  0.020  1.090
 3XT  N1   H12  single    0.890  0.020  1.040
 3XT  C7   H13  single    0.970  0.020  1.090
 3XT  C7   H14  single    0.970  0.020  1.090
 3XT  C16  H15  single    0.930  0.020  1.080
 3XT  C19  H16  single    0.930  0.020  1.080
 3XT  C20  H17  single    0.930  0.020  1.080
 3XT  N3   H18  single    0.860  0.020  1.020
 3XT  N12  H19  single    0.860  0.020  1.020
 3XT  N21  H20  single    0.890  0.020  1.040
 3XT  N21  H21  single    0.890  0.020  1.040

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
 3XT  H2   C11  H1   106.56  3.000
 3XT  H2   C11  C6   107.74  3.000
 3XT  H1   C11  C6   110.00  3.000
 3XT  H2   C11  C10  109.15  3.000
 3XT  H1   C11  C10  110.26  3.000
 3XT  C6   C11  C10  112.89  3.000
 3XT  H4   C10  H3   105.56  3.000
 3XT  H4   C10  C9   109.45  3.000
 3XT  H3   C10  C9   110.58  3.000
 3XT  H4   C10  C11  110.64  3.000
 3XT  H3   C10  C11  108.63  3.000
 3XT  C9   C10  C11  111.79  3.000
 3XT  H6   C9   H5   106.47  3.000
 3XT  H6   C9   C8   110.60  3.000
 3XT  H5   C9   C8   109.24  3.000
 3XT  H6   C9   C10  109.99  3.000
 3XT  H5   C9   C10  109.31  3.000
 3XT  C8   C9   C10  111.11  3.000
 3XT  H8   C8   H7   106.07  3.000
 3XT  H8   C8   C7   110.21  3.000
 3XT  H7   C8   C7   109.10  3.000
 3XT  H8   C8   C9   109.81  3.000
 3XT  H7   C8   C9   110.15  3.000
 3XT  C7   C8   C9   111.36  3.000
 3XT  H9   C1   N1   123.76  3.000
 3XT  H9   C1   C2   115.00  3.000
 3XT  N1   C1   C2   121.24  3.000
 3XT  H11  C2   H10  107.54  3.000
 3XT  H11  C2   N3   109.67  3.000
 3XT  H10  C2   N3   108.97  3.000
 3XT  H11  C2   C1   109.67  3.000
 3XT  H10  C2   C1   109.39  3.000
 3XT  N3   C2   C1   111.51  3.000
 3XT  H12  N1   C1   110.55  3.000
 3XT  H14  C7   H13  106.47  3.000
 3XT  H14  C7   C6   110.31  3.000
 3XT  H13  C7   C6   108.48  3.000
 3XT  H14  C7   C8   110.67  3.000
 3XT  H13  C7   C8   109.00  3.000
 3XT  C6   C7   C8   111.73  3.000
 3XT  N3   C4   C6   114.86  3.000
 3XT  N3   C4   O5   122.95  3.000
 3XT  C6   C4   O5   122.00  3.000
 3XT  N12  C6   C4   109.97  3.000
 3XT  C4   C6   C7   111.00  3.000
 3XT  N12  C6   C7   111.16  3.000
 3XT  C7   C6   C11  109.14  3.000
 3XT  C4   C6   C11  107.56  3.000
 3XT  N12  C6   C11  107.88  3.000
 3XT  C20  C15  C16  118.29  3.000
 3XT  C20  C15  C13  119.00  3.000
 3XT  C16  C15  C13  122.67  3.000
 3XT  H15  C16  C17  118.05  3.000
 3XT  H15  C16  C15  122.14  3.000
 3XT  C17  C16  C15  119.77  3.000
 3XT  F22  C17  C18  117.56  3.000
 3XT  C18  C17  C16  123.22  3.000
 3XT  F22  C17  C16  119.22  3.000
 3XT  N21  C18  C19  122.31  3.000
 3XT  N21  C18  C17  121.49  3.000
 3XT  C19  C18  C17  116.16  3.000
 3XT  H16  C19  C20  119.78  3.000
 3XT  H16  C19  C18  118.85  3.000
 3XT  C20  C19  C18  121.38  3.000
 3XT  H17  C20  C19  119.06  3.000
 3XT  H17  C20  C15  119.77  3.000
 3XT  C19  C20  C15  121.17  3.000
 3XT  H18  N3   C4   118.61  3.000
 3XT  H18  N3   C2   116.83  3.000
 3XT  C4   N3   C2   123.39  3.000
 3XT  H19  N12  C13  118.92  3.000
 3XT  H19  N12  C6   118.16  3.000
 3XT  C13  N12  C6   122.91  3.000
 3XT  H21  N21  H20  112.98  3.000
 3XT  H21  N21  C18  116.23  3.000
 3XT  H20  N21  C18  117.92  3.000
 3XT  N12  C13  O14  121.84  3.000
 3XT  N12  C13  C15  116.57  3.000
 3XT  O14  C13  C15  121.58  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
 3XT  CONST_01  C18  C17  C16  C15    0.00   0.0  0
 3XT  CONST_02  C18  C19  C20  C15    0.00   0.0  0
 3XT  CONST_03  C19  C20  C15  C16    0.00   0.0  0
 3XT  CONST_04  C19  C18  C17  C16    0.00   0.0  0
 3XT  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 3XT  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 3XT  CONST_07  C17  C16  C15  C13  180.00   0.0  0
 3XT  CONST_08  C19  C20  C15  C13  180.00   0.0  0
 3XT  CONST_09  F22  C17  C16  C15  180.00   0.0  0
 3XT  CONST_10  N21  C18  C17  C16  180.00   0.0  0
 3XT  CONST_11  F22  C17  C18  C19  180.00   0.0  0
 3XT  CONST_12  N21  C18  C19  C20  180.00   0.0  0
 3XT  CONST_13  H16  C19  C20  C15  180.00   0.0  0
 3XT  CONST_14  H17  C20  C15  C16  180.00   0.0  0
 3XT  CONST_15  H15  C16  C17  C18  180.00   0.0  0
 3XT  CONST_16  C15  C13  N12  C6   180.00   0.0  0
 3XT  CONST_19  C6   C4   N3   C2   180.00   0.0  0
 3XT  CONST_20  O14  C13  N12  C6     0.00   0.0  0
 3XT  CONST_21  H18  N3   C4   C6     0.00   0.0  0
 3XT  CONST_22  H19  N12  C13  C15    0.00   0.0  0
 3XT  CONST_23  O5   C4   N3   C2     0.00   0.0  0
 3XT  Var_01    C8   C9   C10  C11  -53.43  30.0  1
 3XT  Var_02    C7   C8   C9   C10   55.46  30.0  1
 3XT  Var_03    C6   C11  C10  C9    53.88  30.0  1
 3XT  Var_04    C6   C7   C8   C9   -57.64  30.0  1
 3XT  Var_05    O14  C13  C15  C16  153.72  30.0  2
 3XT  Var_06    C4   N3   C2   C1    91.46  30.0  1
 3XT  Var_07    N3   C2   C1   N1   132.36  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3XT  chir_01  C6  C11  C4  C7  negativ

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
 3XT  plan-1  C15  0.020
 3XT  plan-1  C16  0.020
 3XT  plan-1  C17  0.020
 3XT  plan-1  C18  0.020
 3XT  plan-1  C19  0.020
 3XT  plan-1  C20  0.020
 3XT  plan-1  N21  0.020
 3XT  plan-1  F22  0.020
 3XT  plan-1  H15  0.020
 3XT  plan-1  H16  0.020
 3XT  plan-1  H17  0.020
 3XT  plan-1  C13  0.020
 3XT  plan-2  C6   0.020
 3XT  plan-2  C15  0.020
 3XT  plan-2  O14  0.020
 3XT  plan-2  N12  0.020
 3XT  plan-2  H19  0.020
 3XT  plan-2  C13  0.020
 3XT  plan-3  C18  0.020
 3XT  plan-3  N21  0.020
 3XT  plan-3  H20  0.020
 3XT  plan-3  H21  0.020
 3XT  plan-4  C2   0.020
 3XT  plan-4  C4   0.020
 3XT  plan-4  C6   0.020
 3XT  plan-4  N3   0.020
 3XT  plan-4  H18  0.020
 3XT  plan-4  O5   0.020
 3XT  plan-5  C1   0.020
 3XT  plan-5  C2   0.020
 3XT  plan-5  N1   0.020
 3XT  plan-5  H9   0.020
 3XT  plan-5  H12  0.020

