# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:21:53 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-(methyl{2-[methyl(1-methylpiperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl}amino)propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)N(C)c2nc3ccsc3c(n2)N(C)CCC#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
 6KV  6KV  3-(methyl{2-[methyl(1-methylpiperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl}amino)propanenitrile  ligand  48  24  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6KV
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
 6KV  N1    N  NS    0  -0.274  -3.2353  -4.9442  -0.1055
 6KV  C3    C  CSP   0   0.119  -3.1739  -3.8126  -0.3050
 6KV  C2    C  CH2   0  -0.548  -3.0947  -2.3801  -0.5312
 6KV  C1    C  CH2   0  -0.314  -3.2830  -1.5968   0.7769
 6KV  N     N  NT    0  -0.489  -3.2239  -0.1679   0.5624
 6KV  C     C  CH3   0  -0.559  -4.4657   0.5360   0.3125
 6KV  C4    C  CR6   0   0.588  -2.0158   0.4328   0.4591
 6KV  C9    C  CR56  0  -0.371  -1.8139   1.8290   0.3328
 6KV  S     S  S2    0   0.199  -2.9112   3.1783   0.3058
 6KV  C8    C  CR15  0  -0.440  -1.6031   4.2835   0.1731
 6KV  C7    C  CR15  0  -0.213  -0.3896   3.6872   0.1517
 6KV  C6    C  CR56  0   0.313  -0.4835   2.2603   0.2500
 6KV  N3    N  N     0  -0.537   0.5718   1.4412   0.2747
 6KV  C5    C  CR6   0   0.615   0.2801   0.1513   0.3990
 6KV  N2    N  N     0  -0.545  -0.9553  -0.3601   0.4873
 6KV  N4    N  NT    0  -0.500   1.2923  -0.7531   0.4448
 6KV  C10   C  CH3   0  -0.529   0.9705  -2.1646   0.4834
 6KV  C11   C  CH1   0  -0.106   2.6675  -0.3592   0.1766
 6KV  C16   C  CH2   0  -0.430   3.1638  -0.8742  -1.1719
 6KV  C15   C  CH2   0  -0.279   4.6037  -0.4443  -1.4089
 6KV  N5    N  NT    0  -0.409   5.4734  -0.8856  -0.3352
 6KV  C14   C  CH3   0  -0.517   6.8529  -0.5569  -0.6132
 6KV  C13   C  CH2   0  -0.280   5.0464  -0.3423   0.9401
 6KV  C12   C  CH2   0  -0.430   3.6297  -0.7807   1.2833
 6KV  H21C  H  HCH2  0   0.316  -2.1177  -2.1540  -0.9600
 6KV  H22C  H  HCH2  0   0.312  -3.8567  -2.1065  -1.2635
 6KV  H11C  H  HCH2  0   0.280  -4.2536  -1.8334   1.2106
 6KV  H12C  H  HCH2  0   0.279  -2.5211  -1.8974   1.4931
 6KV  HC1   H  HCH3  0   0.279  -5.2744  -0.1877   0.2568
 6KV  HC2   H  HCH3  0   0.255  -4.7146   1.2343   1.1137
 6KV  HC3   H  HCH3  0   0.255  -4.4492   1.0676  -0.6394
 6KV  H8    H  HCR5  0   0.305  -1.8125   5.3412   0.1164
 6KV  H7    H  HCR5  0   0.269   0.5480   4.2180   0.0731
 6KV  H101  H  HCH3  0   0.231   0.4804  -2.5067  -0.4319
 6KV  H102  H  HCH3  0   0.242   1.8867  -2.7365   0.6040
 6KV  H103  H  HCH3  0   0.246   0.3147  -2.4026   1.3194
 6KV  H11   H  HCH1  0   0.256   2.6736   0.7302   0.1400
 6KV  H161  H  HCH2  0   0.223   3.1028  -1.9660  -1.2112
 6KV  H162  H  HCH2  0   0.236   2.5340  -0.4844  -1.9754
 6KV  H121  H  HCH2  0   0.237   3.3268  -0.3304   2.2312
 6KV  H122  H  HCH2  0   0.219   3.6191  -1.8653   1.4219
 6KV  H151  H  HCH2  0   0.236   4.9635  -0.8702  -2.3490
 6KV  H152  H  HCH2  0   0.185   4.6409   0.6546  -1.5281
 6KV  H141  H  HCH3  0   0.189   7.0290   0.5261  -0.7120
 6KV  H142  H  HCH3  0   0.231   7.4969  -0.9263   0.1865
 6KV  H143  H  HCH3  0   0.231   7.1709  -1.0303  -1.5434
 6KV  H131  H  HCH2  0   0.236   5.7339  -0.6874   1.7161
 6KV  H132  H  HCH2  0   0.185   5.0973   0.7626   0.9433

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
 6KV  N1   C3    triple    1.151  0.020  1.151
 6KV  C3   C2    single    1.452  0.020  1.452
 6KV  C2   C1    single    1.536  0.020  1.536
 6KV  C1   N     single    1.446  0.020  1.446
 6KV  N    C     single    1.449  0.020  1.449
 6KV  N    C4    single    1.353  0.020  1.353
 6KV  C4   C9    aromatic  1.416  0.020  1.416
 6KV  C4   N2    aromatic  1.324  0.020  1.324
 6KV  C9   S     aromatic  1.739  0.020  1.739
 6KV  C9   C6    aromatic  1.401  0.020  1.401
 6KV  S    C8    aromatic  1.718  0.020  1.718
 6KV  C8   C7    aromatic  1.352  0.020  1.352
 6KV  C7   C6    aromatic  1.433  0.020  1.433
 6KV  C6   N3    aromatic  1.336  0.020  1.336
 6KV  N3   C5    aromatic  1.328  0.020  1.328
 6KV  C5   N2    aromatic  1.340  0.020  1.340
 6KV  C5   N4    single    1.358  0.020  1.358
 6KV  N4   C10   single    1.448  0.020  1.448
 6KV  N4   C11   single    1.455  0.020  1.455
 6KV  C11  C16   single    1.526  0.020  1.526
 6KV  C11  C12   single    1.526  0.020  1.526
 6KV  C16  C15   single    1.521  0.020  1.521
 6KV  C15  N5    single    1.451  0.020  1.451
 6KV  N5   C14   single    1.445  0.020  1.445
 6KV  N5   C13   single    1.450  0.020  1.450
 6KV  C13  C12   single    1.522  0.020  1.522
 6KV  C2   H21C  single    0.970  0.020  1.090
 6KV  C2   H22C  single    0.970  0.020  1.090
 6KV  C1   H11C  single    0.970  0.020  1.090
 6KV  C1   H12C  single    0.970  0.020  1.090
 6KV  C    HC1   single    0.970  0.020  1.090
 6KV  C    HC2   single    0.970  0.020  1.090
 6KV  C    HC3   single    0.970  0.020  1.090
 6KV  C8   H8    single    0.930  0.020  1.080
 6KV  C7   H7    single    0.930  0.020  1.080
 6KV  C10  H101  single    0.970  0.020  1.090
 6KV  C10  H102  single    0.970  0.020  1.090
 6KV  C10  H103  single    0.970  0.020  1.090
 6KV  C11  H11   single    0.970  0.020  1.090
 6KV  C16  H161  single    0.970  0.020  1.090
 6KV  C16  H162  single    0.970  0.020  1.090
 6KV  C12  H121  single    0.970  0.020  1.090
 6KV  C12  H122  single    0.970  0.020  1.090
 6KV  C15  H151  single    0.970  0.020  1.090
 6KV  C15  H152  single    0.970  0.020  1.090
 6KV  C14  H141  single    0.970  0.020  1.090
 6KV  C14  H142  single    0.970  0.020  1.090
 6KV  C14  H143  single    0.970  0.020  1.090
 6KV  C13  H131  single    0.970  0.020  1.090
 6KV  C13  H132  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
 6KV  C2    C3   N1    180.00  3.000
 6KV  H22C  C2   H21C  108.04  3.000
 6KV  H22C  C2   C1    110.96  3.000
 6KV  H21C  C2   C1    109.80  3.000
 6KV  H22C  C2   C3    108.28  3.000
 6KV  H21C  C2   C3    108.34  3.000
 6KV  C1    C2   C3    111.32  3.000
 6KV  H12C  C1   H11C  107.57  3.000
 6KV  H12C  C1   N     110.00  3.000
 6KV  H11C  C1   N     108.07  3.000
 6KV  H12C  C1   C2    109.50  3.000
 6KV  H11C  C1   C2    109.73  3.000
 6KV  N     C1   C2    111.87  3.000
 6KV  C4    N    C     122.43  3.000
 6KV  C4    N    C1    119.11  3.000
 6KV  C     N    C1    118.07  3.000
 6KV  HC3   C    HC2   109.41  3.000
 6KV  HC3   C    HC1   106.93  3.000
 6KV  HC2   C    HC1   107.10  3.000
 6KV  HC3   C    N     111.99  3.000
 6KV  HC2   C    N     112.30  3.000
 6KV  HC1   C    N     108.85  3.000
 6KV  N2    C4   C9    118.55  3.000
 6KV  N2    C4   N     116.58  3.000
 6KV  C9    C4   N     124.87  3.000
 6KV  C6    C9   S     111.06  3.000
 6KV  C6    C9   C4    116.37  3.000
 6KV  S     C9   C4    132.54  3.000
 6KV  C8    S    C9     91.14  3.000
 6KV  H8    C8   C7    127.25  3.000
 6KV  H8    C8   S     119.12  3.000
 6KV  C7    C8   S     113.63  3.000
 6KV  H7    C7   C6    123.44  3.000
 6KV  H7    C7   C8    124.28  3.000
 6KV  C6    C7   C8    112.28  3.000
 6KV  N3    C6   C7    124.05  3.000
 6KV  N3    C6   C9    124.07  3.000
 6KV  C7    C6   C9    111.88  3.000
 6KV  C5    N3   C6    115.06  3.000
 6KV  N4    C5   N2    115.51  3.000
 6KV  N4    C5   N3    119.09  3.000
 6KV  N2    C5   N3    125.40  3.000
 6KV  C5    N2   C4    120.55  3.000
 6KV  C11   N4   C10   118.60  3.000
 6KV  C11   N4   C5    121.18  3.000
 6KV  C10   N4   C5    118.97  3.000
 6KV  H103  C10  H102  107.91  3.000
 6KV  H103  C10  H101  107.72  3.000
 6KV  H102  C10  H101  107.84  3.000
 6KV  H103  C10  N4    111.55  3.000
 6KV  H102  C10  N4    109.18  3.000
 6KV  H101  C10  N4    112.48  3.000
 6KV  H11   C11  C12   107.27  3.000
 6KV  H11   C11  C16   107.80  3.000
 6KV  C12   C11  C16   110.03  3.000
 6KV  H11   C11  N4    106.38  3.000
 6KV  C12   C11  N4    112.79  3.000
 6KV  C16   C11  N4    112.25  3.000
 6KV  H162  C16  H161  107.30  3.000
 6KV  H162  C16  C15   109.27  3.000
 6KV  H161  C16  C15   109.21  3.000
 6KV  H162  C16  C11   109.99  3.000
 6KV  H161  C16  C11   110.50  3.000
 6KV  C15   C16  C11   110.49  3.000
 6KV  H152  C15  H151  106.46  3.000
 6KV  H152  C15  N5    111.22  3.000
 6KV  H151  C15  N5    108.71  3.000
 6KV  H152  C15  C16   109.23  3.000
 6KV  H151  C15  C16   109.60  3.000
 6KV  N5    C15  C16   111.48  3.000
 6KV  C13   N5   C14   111.41  3.000
 6KV  C13   N5   C15   111.12  3.000
 6KV  C14   N5   C15   111.15  3.000
 6KV  H143  C14  H142  107.81  3.000
 6KV  H143  C14  H141  107.67  3.000
 6KV  H142  C14  H141  107.70  3.000
 6KV  H143  C14  N5    110.10  3.000
 6KV  H142  C14  N5    110.21  3.000
 6KV  H141  C14  N5    113.17  3.000
 6KV  H132  C13  H131  106.52  3.000
 6KV  H132  C13  C12   109.26  3.000
 6KV  H131  C13  C12   109.54  3.000
 6KV  H132  C13  N5    111.30  3.000
 6KV  H131  C13  N5    108.72  3.000
 6KV  C12   C13  N5    111.37  3.000
 6KV  H122  C12  H121  107.23  3.000
 6KV  H122  C12  C13   108.87  3.000
 6KV  H121  C12  C13   109.58  3.000
 6KV  H122  C12  C11   111.09  3.000
 6KV  H121  C12  C11   109.92  3.000
 6KV  C13   C12  C11   110.11  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
 6KV  CONST_01  C8    S    C9   C4    180.00   0.0  0
 6KV  CONST_02  C7    C6   C9   C4    180.00   0.0  0
 6KV  CONST_03  N3    C6   C9   C4      0.00   0.0  0
 6KV  CONST_04  N3    C5   N2   C4      0.00   0.0  0
 6KV  CONST_05  C5    N2   C4   C9      0.00   0.0  0
 6KV  CONST_06  C7    C8   S    C9      0.00   0.0  0
 6KV  CONST_07  C8    C7   C6   C9      0.00   0.0  0
 6KV  CONST_08  C5    N3   C6   C9      0.00   0.0  0
 6KV  CONST_09  N2    C4   C9   S     180.00   0.0  0
 6KV  CONST_10  C7    C6   C9   S       0.00   0.0  0
 6KV  CONST_11  N3    C6   C9   S     180.00   0.0  0
 6KV  CONST_12  C6    C7   C8   S       0.00   0.0  0
 6KV  CONST_13  C6    C9   S    C8      0.00   0.0  0
 6KV  CONST_14  N3    C6   C7   C8    180.00   0.0  0
 6KV  CONST_15  C5    N3   C6   C7    180.00   0.0  0
 6KV  CONST_16  N2    C4   C9   C6      0.00   0.0  0
 6KV  CONST_17  N2    C5   N3   C6      0.00   0.0  0
 6KV  CONST_18  S     C9   C4   N       0.00   0.0  0
 6KV  CONST_19  C6    C9   C4   N     180.00   0.0  0
 6KV  CONST_20  C5    N2   C4   N     180.00   0.0  0
 6KV  CONST_21  N4    C5   N2   C4    180.00   0.0  0
 6KV  CONST_22  N4    C5   N3   C6    180.00   0.0  0
 6KV  CONST_23  C11   N4   C5   N3      0.00   0.0  0
 6KV  CONST_24  C11   N4   C5   N2    180.00   0.0  0
 6KV  CONST_25  H8    C8   S    C9    180.00   0.0  0
 6KV  CONST_26  H7    C7   C6   C9    180.00   0.0  0
 6KV  CONST_27  C9    C4   N    C1    180.00   0.0  0
 6KV  CONST_28  N2    C4   N    C1      0.00   0.0  0
 6KV  CONST_29  C9    C4   N    C       0.00   0.0  0
 6KV  CONST_30  N2    C4   N    C     180.00   0.0  0
 6KV  CONST_31  C10   N4   C5   N3    180.00   0.0  0
 6KV  CONST_32  C10   N4   C5   N2      0.00   0.0  0
 6KV  Var_01    N5    C15  C16  C11    56.23  30.0  1
 6KV  Var_02    N5    C13  C12  C11   -57.20  30.0  1
 6KV  Var_03    C13   N5   C15  C16   -59.41  30.0  1
 6KV  Var_04    C12   C13  N5   C15    59.97  30.0  1
 6KV  Var_05    H141  C14  N5   C15    61.32  30.0  3
 6KV  Var_06    C4    N    C1   C2    -80.82  30.0  3
 6KV  Var_07    HC1   C    N    C4    168.56  30.0  3
 6KV  Var_08    H101  C10  N4   C5     65.19  30.0  3
 6KV  Var_09    C1    C2   C3   N1    -12.49  30.0  3
 6KV  Var_10    N     C1   C2   C3   -179.24  30.0  3

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
 6KV  chir_01  C11  N4  C16  C12  positiv

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
 6KV  plan-1  N    0.020
 6KV  plan-1  C4   0.020
 6KV  plan-1  C9   0.020
 6KV  plan-1  S    0.020
 6KV  plan-1  C8   0.020
 6KV  plan-1  C7   0.020
 6KV  plan-1  C6   0.020
 6KV  plan-1  N3   0.020
 6KV  plan-1  C5   0.020
 6KV  plan-1  N2   0.020
 6KV  plan-1  N4   0.020
 6KV  plan-1  H8   0.020
 6KV  plan-1  H7   0.020
 6KV  plan-2  C1   0.020
 6KV  plan-2  N    0.020
 6KV  plan-2  C    0.020
 6KV  plan-2  C4   0.020
 6KV  plan-3  C5   0.020
 6KV  plan-3  N4   0.020
 6KV  plan-3  C10  0.020
 6KV  plan-3  C11  0.020

