# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:05:01 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-(5-cyanopyridin-2-yl)-3-[2-(4-ethoxy-3-fluoropyridin-2-yl)ethyl]thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccnc(CCNC(=S)Nc2ccc(cn2)C#N)c1F
#
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
 FPT  FPT  1-(5-cyanopyridin-2-yl)-3-[2-(4-ethoxy-3-fluoropyridin-2-yl)ethyl]thiourea  ligand  40  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FPT
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
 FPT  C1    C  CR6   0   0.556  -0.4829  -0.2264  -4.1061
 FPT  N2    N  N     0  -0.410   0.8184  -0.1189  -4.3297
 FPT  C3    C  CR16  0  -0.030   1.2480  -0.1413  -5.5767
 FPT  C4    C  CR6   0  -0.102   0.4018  -0.2945  -6.6720
 FPT  C5    C  CR16  0  -0.113  -0.9684  -0.4329  -6.4330
 FPT  C6    C  CR16  0  -0.382  -1.4187  -0.3946  -5.1364
 FPT  C7    C  CSP   0   0.047   0.9302  -0.3186  -7.9912
 FPT  N7    N  NS    0  -0.250   1.3625  -0.3397  -9.0596
 FPT  N8    N  NH1   0  -0.730  -0.9451  -0.2357  -2.8073
 FPT  C9    C  C     0   0.409  -0.4007   0.3521  -1.6906
 FPT  S9    S  S1    0  -0.365   0.7168   1.5864  -1.7226
 FPT  N10   N  NH1   0  -0.615  -0.9134  -0.1215  -0.5553
 FPT  C11   C  CH2   0  -0.224  -0.5719   0.3787   0.7582
 FPT  C12   C  CH2   0  -0.553  -1.4475  -0.2944   1.8113
 FPT  C13   C  CR6   0   0.060  -1.1168   0.2321   3.1769
 FPT  N14   N  N     0  -0.419  -1.7122   1.3637   3.5610
 FPT  C15   C  CR16  0  -0.085  -1.4134   1.8594   4.7497
 FPT  C16   C  CR16  0  -0.438  -0.5189   1.2792   5.6377
 FPT  C17   C  CR6   0   0.350   0.1144   0.1009   5.2586
 FPT  C18   C  CR6   0   0.390  -0.2083  -0.4029   3.9965
 FPT  O17   O  O2    0  -0.453   0.9935  -0.5875   5.9776
 FPT  CA    C  CH2   0  -0.197   1.3628  -0.0875   7.2647
 FPT  CB    C  CH3   0  -0.683   2.3675  -1.0385   7.8655
 FPT  F18   F  F     0  -0.302   0.3935  -1.5309   3.5929
 FPT  H3    H  HCR6  0   0.290   2.3180  -0.0504  -5.7242
 FPT  H5    H  HCR6  0   0.298  -1.6632  -0.5566  -7.2521
 FPT  H6    H  HCR6  0   0.298  -2.4743  -0.4829  -4.9178
 FPT  HN8   H  HNH1  0   0.425  -1.8543  -0.6597  -2.6863
 FPT  H10   H  HNH1  0   0.413  -1.5072  -0.9380  -0.5967
 FPT  H111  H  HCH2  0   0.254  -0.7168   1.4600   0.7858
 FPT  H112  H  HCH2  0   0.251   0.4858   0.1926   0.9619
 FPT  H121  H  HCH2  0   0.270  -1.3209  -1.3775   1.7659
 FPT  H122  H  HCH2  0   0.275  -2.4976  -0.0783   1.6069
 FPT  H15   H  HCR6  0   0.269  -1.9131   2.7791   5.0312
 FPT  H16   H  HCR6  0   0.300  -0.3348   1.7478   6.5939
 FPT  HA1   H  HCH2  0   0.237   0.4757  -0.0116   7.9004
 FPT  HA2   H  HCH2  0   0.237   1.7897   0.9143   7.1613
 FPT  HB1   H  HCH3  0   0.243   2.6700  -0.6635   8.8425
 FPT  HB2   H  HCH3  0   0.239   1.9433  -2.0326   8.0046
 FPT  HB3   H  HCH3  0   0.239   3.2606  -1.1214   7.2466

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
 FPT  C1   N2    aromatic  1.325  0.020  1.325
 FPT  C1   C6    aromatic  1.402  0.020  1.402
 FPT  C1   N8    single    1.379  0.020  1.379
 FPT  N2   C3    aromatic  1.319  0.020  1.319
 FPT  C3   C4    aromatic  1.393  0.020  1.393
 FPT  C3   H3    single    0.930  0.020  1.080
 FPT  C4   C5    aromatic  1.398  0.020  1.398
 FPT  C4   C7    single    1.421  0.020  1.421
 FPT  C5   C6    aromatic  1.373  0.020  1.373
 FPT  C5   H5    single    0.930  0.020  1.080
 FPT  C6   H6    single    0.930  0.020  1.080
 FPT  C7   N7    triple    1.153  0.020  1.153
 FPT  N8   C9    single    1.374  0.020  1.374
 FPT  N8   HN8   single    0.860  0.020  1.020
 FPT  C9   S9    double    1.665  0.020  1.665
 FPT  C9   N10   single    1.333  0.020  1.333
 FPT  N10  C11   single    1.446  0.020  1.446
 FPT  N10  H10   single    0.860  0.020  1.020
 FPT  C11  C12   single    1.526  0.020  1.526
 FPT  C11  H111  single    0.970  0.020  1.090
 FPT  C11  H112  single    0.970  0.020  1.090
 FPT  C12  C13   single    1.501  0.020  1.501
 FPT  C12  H121  single    0.970  0.020  1.090
 FPT  C12  H122  single    0.970  0.020  1.090
 FPT  C13  N14   aromatic  1.335  0.020  1.335
 FPT  C13  C18   aromatic  1.379  0.020  1.379
 FPT  N14  C15   aromatic  1.322  0.020  1.322
 FPT  C15  C16   aromatic  1.388  0.020  1.388
 FPT  C15  H15   single    0.930  0.020  1.080
 FPT  C16  C17   aromatic  1.390  0.020  1.390
 FPT  C16  H16   single    0.930  0.020  1.080
 FPT  C17  C18   aromatic  1.397  0.020  1.397
 FPT  C17  O17   single    1.328  0.020  1.328
 FPT  C18  F18   single    1.341  0.020  1.341
 FPT  O17  CA    single    1.429  0.020  1.429
 FPT  CA   CB    single    1.508  0.020  1.508
 FPT  CA   HA1   single    0.970  0.020  1.090
 FPT  CA   HA2   single    0.970  0.020  1.090
 FPT  CB   HB1   single    0.970  0.020  1.090
 FPT  CB   HB2   single    0.970  0.020  1.090
 FPT  CB   HB3   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
 FPT  N8    C1   C6    117.89  3.000
 FPT  N8    C1   N2    119.27  3.000
 FPT  C6    C1   N2    122.78  3.000
 FPT  C3    N2   C1    118.56  3.000
 FPT  H3    C3   C4    120.14  3.000
 FPT  H3    C3   N2    116.66  3.000
 FPT  C4    C3   N2    123.19  3.000
 FPT  C7    C4   C5    121.43  3.000
 FPT  C7    C4   C3    120.40  3.000
 FPT  C5    C4   C3    118.17  3.000
 FPT  H5    C5   C6    120.52  3.000
 FPT  H5    C5   C4    120.78  3.000
 FPT  C6    C5   C4    118.69  3.000
 FPT  H6    C6   C5    120.57  3.000
 FPT  H6    C6   C1    120.85  3.000
 FPT  C5    C6   C1    118.58  3.000
 FPT  N7    C7   C4    180.00  3.000
 FPT  HN8   N8   C9    116.01  3.000
 FPT  HN8   N8   C1    114.67  3.000
 FPT  C9    N8   C1    129.03  3.000
 FPT  N10   C9   S9    122.54  3.000
 FPT  N10   C9   N8    112.82  3.000
 FPT  S9    C9   N8    124.55  3.000
 FPT  H10   N10  C11   117.09  3.000
 FPT  H10   N10  C9    118.58  3.000
 FPT  C11   N10  C9    124.05  3.000
 FPT  H112  C11  H111  107.01  3.000
 FPT  H112  C11  C12   110.58  3.000
 FPT  H111  C11  C12   110.09  3.000
 FPT  H112  C11  N10   109.80  3.000
 FPT  H111  C11  N10   109.52  3.000
 FPT  C12   C11  N10   109.80  3.000
 FPT  H122  C12  H121  107.48  3.000
 FPT  H122  C12  C13   108.24  3.000
 FPT  H121  C12  C13   111.13  3.000
 FPT  H122  C12  C11   109.60  3.000
 FPT  H121  C12  C11   110.03  3.000
 FPT  C13   C12  C11   110.29  3.000
 FPT  C18   C13  N14   120.89  3.000
 FPT  C18   C13  C12   121.65  3.000
 FPT  N14   C13  C12   117.45  3.000
 FPT  C15   N14  C13   118.40  3.000
 FPT  H15   C15  C16   119.06  3.000
 FPT  H15   C15  N14   116.58  3.000
 FPT  C16   C15  N14   124.36  3.000
 FPT  H16   C16  C17   122.09  3.000
 FPT  H16   C16  C15   119.65  3.000
 FPT  C17   C16  C15   118.26  3.000
 FPT  O17   C17  C18   117.08  3.000
 FPT  O17   C17  C16   126.38  3.000
 FPT  C18   C17  C16   116.54  3.000
 FPT  F18   C18  C17   118.15  3.000
 FPT  F18   C18  C13   120.29  3.000
 FPT  C17   C18  C13   121.56  3.000
 FPT  CA    O17  C17   118.50  3.000
 FPT  HA2   CA   HA1   107.93  3.000
 FPT  HA2   CA   CB    110.80  3.000
 FPT  HA1   CA   CB    110.64  3.000
 FPT  HA2   CA   O17   109.64  3.000
 FPT  HA1   CA   O17   109.76  3.000
 FPT  CB    CA   O17   108.07  3.000
 FPT  HB3   CB   HB2   108.80  3.000
 FPT  HB3   CB   HB1   107.94  3.000
 FPT  HB2   CB   HB1   107.91  3.000
 FPT  HB3   CB   CA    111.57  3.000
 FPT  HB2   CB   CA    111.51  3.000
 FPT  HB1   CB   CA    108.98  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
 FPT  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 FPT  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 FPT  CONST_03  C5   C6   C1   N2      0.00   0.0  0
 FPT  CONST_04  C5   C4   C3   N2      0.00   0.0  0
 FPT  CONST_05  C6   C1   N2   C3      0.00   0.0  0
 FPT  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 FPT  CONST_07  C16  C15  N14  C13     0.00   0.0  0
 FPT  CONST_08  C16  C17  C18  C13     0.00   0.0  0
 FPT  CONST_09  C17  C18  C13  N14     0.00   0.0  0
 FPT  CONST_10  C17  C16  C15  N14     0.00   0.0  0
 FPT  CONST_11  C18  C13  N14  C15     0.00   0.0  0
 FPT  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 FPT  CONST_13  C7   C4   C3   N2    180.00   0.0  0
 FPT  CONST_14  N8   C1   N2   C3    180.00   0.0  0
 FPT  CONST_15  N8   C1   C6   C5    180.00   0.0  0
 FPT  CONST_16  C7   C4   C5   C6    180.00   0.0  0
 FPT  CONST_17  C15  N14  C13  C12   180.00   0.0  0
 FPT  CONST_18  C17  C18  C13  C12   180.00   0.0  0
 FPT  CONST_19  O17  C17  C18  C13   180.00   0.0  0
 FPT  CONST_20  F18  C18  C13  N14   180.00   0.0  0
 FPT  CONST_21  O17  C17  C16  C15   180.00   0.0  0
 FPT  CONST_22  F18  C18  C17  C16   180.00   0.0  0
 FPT  CONST_23  H3   C3   N2   C1    180.00   0.0  0
 FPT  CONST_24  H5   C5   C6   C1    180.00   0.0  0
 FPT  CONST_25  H6   C6   C1   N2    180.00   0.0  0
 FPT  CONST_26  H15  C15  N14  C13   180.00   0.0  0
 FPT  CONST_27  H16  C16  C15  N14   180.00   0.0  0
 FPT  CONST_33  C11  N10  C9   N8    180.00   0.0  0
 FPT  CONST_34  C11  N10  C9   S9      0.00   0.0  0
 FPT  CONST_35  H10  N10  C9   N8      0.00   0.0  0
 FPT  Var_01    N14  C13  C12  C11    84.53  30.0  2
 FPT  Var_02    C13  C12  C11  N10  -179.13  30.0  3
 FPT  Var_03    CB   CA   O17  C17  -179.73  30.0  3
 FPT  Var_04    C12  C11  N10  C9    174.30  30.0  3
 FPT  Var_05    HB1  CB   CA   O17   179.22  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
 FPT  plan-1  C1   0.020
 FPT  plan-1  N2   0.020
 FPT  plan-1  C3   0.020
 FPT  plan-1  C4   0.020
 FPT  plan-1  C5   0.020
 FPT  plan-1  C6   0.020
 FPT  plan-1  C7   0.020
 FPT  plan-1  N7   0.020
 FPT  plan-1  N8   0.020
 FPT  plan-1  H3   0.020
 FPT  plan-1  H5   0.020
 FPT  plan-1  H6   0.020
 FPT  plan-2  C12  0.020
 FPT  plan-2  C13  0.020
 FPT  plan-2  N14  0.020
 FPT  plan-2  C15  0.020
 FPT  plan-2  C16  0.020
 FPT  plan-2  C17  0.020
 FPT  plan-2  C18  0.020
 FPT  plan-2  O17  0.020
 FPT  plan-2  F18  0.020
 FPT  plan-2  H15  0.020
 FPT  plan-2  H16  0.020
 FPT  plan-3  C1   0.020
 FPT  plan-3  N8   0.020
 FPT  plan-3  C9   0.020
 FPT  plan-3  S9   0.020
 FPT  plan-3  N10  0.020
 FPT  plan-3  C11  0.020
 FPT  plan-3  HN8  0.020
 FPT  plan-3  H10  0.020

