# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:06:56 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: 3-(5-thiophen-2-ylthiophen-2-yl)-1~{H}-pyrazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1ccc(n1)c2sc(cc2)c3sccc3
#
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
 MKN  MKN  3-(5-thiophen-2-ylthiophen-2-yl)-1~{H}-pyrazole  ligand  23  15  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MKN
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
 MKN  N1   N  NR15  0  -0.414   -6.3032  -11.6433  92.3590
 MKN  C4   C  CR15  0  -0.469  -15.8847  -12.2663  90.1583
 MKN  C5   C  CR5   0  -0.166  -12.1305  -11.7290  91.0234
 MKN  C6   C  CR15  0  -0.227  -11.6391  -10.4516  91.0888
 MKN  C7   C  CR15  0  -0.194  -10.2613  -10.3980  91.3979
 MKN  C8   C  CR5   0  -0.226   -9.7011  -11.6338  91.5676
 MKN  C10  C  CR15  0  -0.521   -7.7444  -13.2410  92.0512
 MKN  C1   C  CR15  0  -0.165  -15.3624  -13.4948  90.4222
 MKN  C2   C  CR15  0  -0.255  -13.9852  -13.4434  90.7563
 MKN  C3   C  CR5   0  -0.175  -13.4762  -12.1710  90.7407
 MKN  S1   S  S2    0   0.218  -14.7047  -11.0330  90.3089
 MKN  S2   S  S2    0   0.232  -10.8767  -12.8754  91.3420
 MKN  C9   C  CR5   0   0.271   -8.3275  -11.9658  91.8934
 MKN  C11  C  CR15  0   0.024   -6.4300  -12.9794  92.3533
 MKN  N2   N  N     0  -0.297   -7.4309  -11.0073  92.0859
 MKN  H1   H  HNR5  0   0.426   -5.4667  -11.1147  92.5492
 MKN  H4   H  HCR5  0   0.267  -12.2441   -9.5699  90.9258
 MKN  H5   H  HCR5  0   0.264   -9.7026   -9.4784  91.4958
 MKN  H6   H  HCR5  0   0.270   -8.2103  -14.2083  91.9570
 MKN  H7   H  HCR5  0   0.272  -15.9374  -14.4083  90.3811
 MKN  H9   H  HCR5  0   0.267  -13.3996  -14.3195  91.0008
 MKN  H12  H  HCR5  0   0.296   -5.5990  -13.6330  92.5593
 MKN  H2   H  HCR5  0   0.300  -16.8973  -12.0152  89.8837

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
 MKN  S1   C4   aromatic  1.714  0.020  1.714
 MKN  S1   C3   aromatic  1.729  0.020  1.729
 MKN  C4   C1   aromatic  1.361  0.020  1.361
 MKN  C1   C2   aromatic  1.418  0.020  1.418
 MKN  C2   C3   aromatic  1.370  0.020  1.370
 MKN  C3   C5   single    1.444  0.020  1.444
 MKN  C5   C6   aromatic  1.370  0.020  1.370
 MKN  C5   S2   aromatic  1.729  0.020  1.729
 MKN  C6   C7   aromatic  1.413  0.020  1.413
 MKN  S2   C8   aromatic  1.725  0.020  1.725
 MKN  C7   C8   aromatic  1.367  0.020  1.367
 MKN  C8   C9   single    1.450  0.020  1.450
 MKN  N2   C9   aromatic  1.327  0.020  1.327
 MKN  N2   N1   aromatic  1.323  0.020  1.323
 MKN  C9   C10  aromatic  1.411  0.020  1.411
 MKN  N1   C11  aromatic  1.342  0.020  1.342
 MKN  C10  C11  aromatic  1.374  0.020  1.374
 MKN  N1   H1   single    0.860  0.020  1.020
 MKN  C4   H2   single    0.930  0.020  1.080
 MKN  C6   H4   single    0.930  0.020  1.080
 MKN  C7   H5   single    0.930  0.020  1.080
 MKN  C10  H6   single    0.930  0.020  1.080
 MKN  C1   H7   single    0.930  0.020  1.080
 MKN  C2   H9   single    0.930  0.020  1.080
 MKN  C11  H12  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
 MKN  H1   N1   N2   119.62  3.000
 MKN  H1   N1   C11  126.98  3.000
 MKN  N2   N1   C11  113.40  3.000
 MKN  H2   C4   S1   120.08  3.000
 MKN  H2   C4   C1   128.30  3.000
 MKN  S1   C4   C1   111.62  3.000
 MKN  S2   C5   C3   120.59  3.000
 MKN  S2   C5   C6   110.45  3.000
 MKN  C3   C5   C6   128.96  3.000
 MKN  H4   C6   C7   123.20  3.000
 MKN  H4   C6   C5   123.51  3.000
 MKN  C7   C6   C5   113.29  3.000
 MKN  H5   C7   C8   123.10  3.000
 MKN  H5   C7   C6   123.79  3.000
 MKN  C8   C7   C6   113.10  3.000
 MKN  C9   C8   S2   120.67  3.000
 MKN  C9   C8   C7   128.52  3.000
 MKN  S2   C8   C7   110.80  3.000
 MKN  H6   C10  C11  127.13  3.000
 MKN  H6   C10  C9   128.51  3.000
 MKN  C11  C10  C9   104.35  3.000
 MKN  H7   C1   C2   123.82  3.000
 MKN  H7   C1   C4   123.49  3.000
 MKN  C2   C1   C4   112.69  3.000
 MKN  H9   C2   C3   123.60  3.000
 MKN  H9   C2   C1   123.34  3.000
 MKN  C3   C2   C1   113.06  3.000
 MKN  S1   C3   C2   110.49  3.000
 MKN  C2   C3   C5   128.90  3.000
 MKN  S1   C3   C5   120.62  3.000
 MKN  C3   S1   C4    92.15  3.000
 MKN  C8   S2   C5    92.35  3.000
 MKN  N2   C9   C10  110.94  3.000
 MKN  C10  C9   C8   128.57  3.000
 MKN  N2   C9   C8   120.49  3.000
 MKN  H12  C11  C10  131.66  3.000
 MKN  H12  C11  N1   122.03  3.000
 MKN  C10  C11  N1   106.31  3.000
 MKN  C9   N2   N1   105.00  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
 MKN  CONST_01  C8   C9   N2   N1   180.00  0.0  0
 MKN  CONST_02  C10  C9   N2   N1     0.00  0.0  0
 MKN  CONST_03  C9   C10  C11  N1     0.00  0.0  0
 MKN  CONST_04  C2   C3   S1   C4     0.00  0.0  0
 MKN  CONST_05  C5   C3   S1   C4   180.00  0.0  0
 MKN  CONST_06  C3   C2   C1   C4     0.00  0.0  0
 MKN  CONST_07  C1   C2   C3   C5   180.00  0.0  0
 MKN  CONST_08  C8   C7   C6   C5     0.00  0.0  0
 MKN  CONST_09  C7   C8   S2   C5     0.00  0.0  0
 MKN  CONST_10  C9   C8   S2   C5   180.00  0.0  0
 MKN  CONST_11  S1   C3   C5   C6     0.00  0.0  0
 MKN  CONST_12  C2   C3   C5   C6   180.00  0.0  0
 MKN  CONST_13  C8   S2   C5   C6     0.00  0.0  0
 MKN  CONST_14  S2   C8   C7   C6     0.00  0.0  0
 MKN  CONST_15  C9   C8   C7   C6   180.00  0.0  0
 MKN  CONST_16  C3   C5   C6   C7   180.00  0.0  0
 MKN  CONST_17  S2   C5   C6   C7     0.00  0.0  0
 MKN  CONST_18  N2   C9   C8   C7     0.00  0.0  0
 MKN  CONST_19  C10  C9   C8   C7   180.00  0.0  0
 MKN  CONST_20  C3   C5   S2   C8   180.00  0.0  0
 MKN  CONST_21  C11  C10  C9   C8   180.00  0.0  0
 MKN  CONST_22  S2   C8   C9   C10    0.00  0.0  0
 MKN  CONST_23  N2   N1   C11  C10    0.00  0.0  0
 MKN  CONST_24  C3   S1   C4   C1     0.00  0.0  0
 MKN  CONST_25  S1   C3   C2   C1     0.00  0.0  0
 MKN  CONST_26  S1   C4   C1   C2     0.00  0.0  0
 MKN  CONST_27  S2   C5   C3   C2     0.00  0.0  0
 MKN  CONST_28  S2   C5   C3   S1   180.00  0.0  0
 MKN  CONST_29  N2   C9   C8   S2   180.00  0.0  0
 MKN  CONST_30  C11  N1   N2   C9     0.00  0.0  0
 MKN  CONST_31  N2   C9   C10  C11    0.00  0.0  0
 MKN  CONST_32  H6   C10  C11  N1   180.00  0.0  0
 MKN  CONST_33  H9   C2   C1   C4   180.00  0.0  0
 MKN  CONST_34  H5   C7   C6   C5   180.00  0.0  0
 MKN  CONST_35  H4   C6   C7   C8   180.00  0.0  0
 MKN  CONST_36  H1   N1   C11  C10  180.00  0.0  0
 MKN  CONST_37  H2   C4   C1   C2   180.00  0.0  0
 MKN  CONST_38  H7   C1   C2   C3   180.00  0.0  0
 MKN  CONST_39  H12  C11  C10  C9   180.00  0.0  0

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
 MKN  plan-1  C5   0.020
 MKN  plan-1  C6   0.020
 MKN  plan-1  C7   0.020
 MKN  plan-1  C8   0.020
 MKN  plan-1  C3   0.020
 MKN  plan-1  S2   0.020
 MKN  plan-1  C9   0.020
 MKN  plan-1  H4   0.020
 MKN  plan-1  H5   0.020
 MKN  plan-2  C4   0.020
 MKN  plan-2  C5   0.020
 MKN  plan-2  C1   0.020
 MKN  plan-2  C2   0.020
 MKN  plan-2  C3   0.020
 MKN  plan-2  S1   0.020
 MKN  plan-2  H7   0.020
 MKN  plan-2  H9   0.020
 MKN  plan-2  H2   0.020
 MKN  plan-3  N1   0.020
 MKN  plan-3  C8   0.020
 MKN  plan-3  C10  0.020
 MKN  plan-3  C9   0.020
 MKN  plan-3  C11  0.020
 MKN  plan-3  N2   0.020
 MKN  plan-3  H1   0.020
 MKN  plan-3  H6   0.020
 MKN  plan-3  H12  0.020

