# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 13:50:10 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-(cyclopentylamino)-3-ethyl-7-ethynylthieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)c2scc(C#C)c2N=C1NC3CCCC3
#
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
 32V  32V  2-(cyclopentylamino)-3-ethyl-7-ethynylthieno[3,2-d]pyrimidin-4(3H)-one  ligand  37  20  .  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_32V
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
 32V  C1   C  CR56  0  -0.442  -2.0811   0.5412  -0.0674
 32V  C2   C  CR6   0   0.768   0.5794   0.3971   0.3167
 32V  N1   N  NR6   0  -0.586  -0.0275   1.6376   0.2673
 32V  N2   N  N     0  -0.515  -0.0724  -0.7338   0.2148
 32V  C3   C  CR56  0   0.315  -1.4005  -0.6513   0.0374
 32V  C4   C  CR6   0   0.596  -1.3995   1.7859   0.0282
 32V  S1   S  S2    0   0.273  -3.7698   0.3314  -0.3217
 32V  C5   C  CR5   0   0.021  -2.2909  -1.7740  -0.0880
 32V  C6   C  CR15  0  -0.516  -3.5824  -1.3671  -0.2823
 32V  N3   N  NH1   0  -0.698   1.9063   0.3496   0.5052
 32V  C7   C  CSP   0   0.328  -1.8702  -3.1250  -0.0180
 32V  C8   C  CSP1  0  -0.574  -1.5109  -4.2722   0.0427
 32V  O1   O  O     0  -0.475  -1.9172   2.8870  -0.0692
 32V  C9   C  CH2   0  -0.375   0.7469   2.8707   0.4312
 32V  C10  C  CH1   0  -0.091   2.6399  -0.9067   0.5925
 32V  C11  C  CH2   0  -0.435   2.9367  -1.4930  -0.7903
 32V  C12  C  CH2   0  -0.477   4.0342  -0.6461   1.1909
 32V  C13  C  CH3   0  -0.655   1.3342   3.3766  -0.8756
 32V  C14  C  CH2   0  -0.449   5.0205  -0.5944   0.0024
 32V  C15  C  CH2   0  -0.454   4.1539  -0.7014  -1.2583
 32V  H1   H  HCR5  0   0.313  -4.4433  -2.0067  -0.4064
 32V  H2   H  HNH1  0   0.414   2.4509   1.1931   0.4748
 32V  H3   H  H     0   0.283  -1.1959  -5.2894   0.0916
 32V  H4   H  HCH2  0   0.288   0.0813   3.6177   0.8544
 32V  H5   H  HCH2  0   0.265   1.5151   2.7025   1.1849
 32V  H6   H  HCH1  0   0.263   2.0535  -1.5893   1.2054
 32V  H7   H  HCH2  0   0.228   3.2000  -2.5485  -0.6755
 32V  H8   H  HCH2  0   0.244   2.0793  -1.4395  -1.4608
 32V  H9   H  HCH2  0   0.243   4.0451   0.2679   1.7881
 32V  H10  H  HCH2  0   0.255   4.2903  -1.4551   1.8748
 32V  H11  H  HCH3  0   0.226   2.0233   2.6625  -1.3276
 32V  H12  H  HCH3  0   0.245   0.5471   3.5888  -1.5981
 32V  H13  H  HCH3  0   0.248   1.8834   4.3001  -0.6953
 32V  H14  H  HCH2  0   0.236   5.6332   0.3072   0.0097
 32V  H15  H  HCH2  0   0.231   5.7058  -1.4418   0.0525
 32V  H16  H  HCH2  0   0.237   4.6764  -1.1791  -2.0882
 32V  H17  H  HCH2  0   0.219   3.8486   0.2903  -1.6043

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
 32V  O1   C4   double    1.221  0.020  1.221
 32V  S1   C1   aromatic  1.721  0.020  1.721
 32V  S1   C6   aromatic  1.709  0.020  1.709
 32V  C4   C1   single    1.422  0.020  1.422
 32V  C4   N1   single    1.400  0.020  1.400
 32V  C9   N1   single    1.465  0.020  1.465
 32V  C9   C13  single    1.519  0.020  1.519
 32V  C1   C3   aromatic  1.377  0.020  1.377
 32V  N1   C2   single    1.382  0.020  1.382
 32V  C6   C5   aromatic  1.368  0.020  1.368
 32V  C3   C5   aromatic  1.438  0.020  1.438
 32V  C3   N2   single    1.342  0.020  1.342
 32V  C2   N2   double    1.309  0.020  1.309
 32V  C2   N3   single    1.341  0.020  1.341
 32V  C11  C15  single    1.526  0.020  1.526
 32V  C11  C10  single    1.531  0.020  1.531
 32V  C5   C7   single    1.417  0.020  1.417
 32V  N3   C10  single    1.457  0.020  1.457
 32V  C7   C8   triple    1.204  0.020  1.204
 32V  C15  C14  single    1.534  0.020  1.534
 32V  C10  C12  single    1.539  0.020  1.539
 32V  C14  C12  single    1.545  0.020  1.545
 32V  C6   H1   single    0.929  0.020  1.085
 32V  N3   H2   single    0.868  0.020  1.013
 32V  C8   H3   single    0.913  0.020  1.066
 32V  C9   H4   single    0.939  0.020  1.096
 32V  C9   H5   single    0.939  0.020  1.096
 32V  C10  H6   single    0.939  0.020  1.096
 32V  C11  H7   single    0.939  0.020  1.096
 32V  C11  H8   single    0.939  0.020  1.096
 32V  C12  H9   single    0.939  0.020  1.096
 32V  C12  H10  single    0.939  0.020  1.096
 32V  C13  H11  single    0.939  0.020  1.096
 32V  C13  H12  single    0.939  0.020  1.096
 32V  C13  H13  single    0.939  0.020  1.096
 32V  C14  H14  single    0.939  0.020  1.096
 32V  C14  H15  single    0.939  0.020  1.096
 32V  C15  H16  single    0.939  0.020  1.096
 32V  C15  H17  single    0.939  0.020  1.096

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
 32V  S1   C1   C4   125.94  3.000
 32V  C4   C1   C3   121.06  3.000
 32V  S1   C1   C3   113.00  3.000
 32V  N3   C2   N2   118.22  3.000
 32V  N3   C2   N1   118.13  3.000
 32V  N2   C2   N1   123.64  3.000
 32V  C9   N1   C4   116.60  3.000
 32V  C9   N1   C2   121.28  3.000
 32V  C4   N1   C2   122.10  3.000
 32V  C3   N2   C2   116.72  3.000
 32V  C5   C3   N2   125.16  3.000
 32V  N2   C3   C1   123.53  3.000
 32V  C5   C3   C1   111.30  3.000
 32V  O1   C4   N1   121.64  3.000
 32V  N1   C4   C1   112.85  3.000
 32V  O1   C4   C1   125.51  3.000
 32V  C6   S1   C1    90.58  3.000
 32V  C7   C5   C6   124.82  3.000
 32V  C7   C5   C3   123.80  3.000
 32V  C6   C5   C3   111.39  3.000
 32V  H1   C6   C5   126.37  3.000
 32V  H1   C6   S1   119.91  3.000
 32V  C5   C6   S1   113.72  3.000
 32V  H2   N3   C10  116.92  3.000
 32V  H2   N3   C2   120.16  3.000
 32V  C10  N3   C2   122.48  3.000
 32V  C8   C7   C5   180.00  3.000
 32V  H3   C8   C7   180.00  3.000
 32V  H5   C9   H4   105.59  3.000
 32V  H5   C9   C13  111.96  3.000
 32V  H4   C9   C13  110.06  3.000
 32V  H5   C9   N1   108.67  3.000
 32V  H4   C9   N1   107.36  3.000
 32V  C13  C9   N1   112.85  3.000
 32V  H6   C10  C12  112.03  3.000
 32V  H6   C10  C11  111.88  3.000
 32V  C12  C10  C11  103.90  3.000
 32V  H6   C10  N3   107.64  3.000
 32V  C12  C10  N3   109.47  3.000
 32V  C11  C10  N3   111.93  3.000
 32V  H8   C11  H7   107.54  3.000
 32V  H8   C11  C15  114.43  3.000
 32V  H7   C11  C15  109.93  3.000
 32V  H8   C11  C10  112.60  3.000
 32V  H7   C11  C10  108.75  3.000
 32V  C15  C11  C10  103.47  3.000
 32V  H10  C12  H9   106.01  3.000
 32V  H10  C12  C14  110.94  3.000
 32V  H9   C12  C14  112.72  3.000
 32V  H10  C12  C10  109.33  3.000
 32V  H9   C12  C10  111.31  3.000
 32V  C14  C12  C10  106.55  3.000
 32V  H13  C13  H12  108.00  3.000
 32V  H13  C13  H11  107.77  3.000
 32V  H12  C13  H11  108.01  3.000
 32V  H13  C13  C9   109.56  3.000
 32V  H12  C13  C9   110.86  3.000
 32V  H11  C13  C9   112.50  3.000
 32V  H15  C14  H14  106.80  3.000
 32V  H15  C14  C15  109.79  3.000
 32V  H14  C14  C15  112.38  3.000
 32V  H15  C14  C12  109.85  3.000
 32V  H14  C14  C12  112.41  3.000
 32V  C15  C14  C12  105.62  3.000
 32V  H17  C15  H16  106.86  3.000
 32V  H17  C15  C14  110.77  3.000
 32V  H16  C15  C14  112.66  3.000
 32V  H17  C15  C11  110.17  3.000
 32V  H16  C15  C11  112.85  3.000
 32V  C14  C15  C11  103.59  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
 32V  CONST_01  C5   C6   S1   C1     0.00   0.0  0
 32V  CONST_02  C6   C5   C3   C1     0.00   0.0  0
 32V  CONST_03  C6   S1   C1   C3     0.00   0.0  0
 32V  CONST_04  S1   C6   C5   C3     0.00   0.0  0
 32V  CONST_05  C5   C3   C1   S1     0.00   0.0  0
 32V  CONST_06  C2   N1   C4   C1     0.00   0.0  0
 32V  CONST_07  C3   N2   C2   N1     0.00   0.0  0
 32V  CONST_08  C4   N1   C2   N2     0.00   0.0  0
 32V  CONST_09  C7   C5   C3   C1   180.00   0.0  0
 32V  CONST_10  C7   C5   C3   N2     0.00   0.0  0
 32V  CONST_11  C7   C5   C6   S1   180.00   0.0  0
 32V  CONST_12  C9   N1   C4   C1   180.00   0.0  0
 32V  CONST_13  O1   C4   N1   C2   180.00   0.0  0
 32V  CONST_14  C10  N3   C2   N1   180.00   0.0  0
 32V  CONST_15  C9   N1   C2   N2   180.00   0.0  0
 32V  CONST_16  C10  N3   C2   N2     0.00   0.0  0
 32V  CONST_17  N3   C2   N2   C3   180.00   0.0  0
 32V  CONST_18  N3   C2   N1   C4   180.00   0.0  0
 32V  CONST_19  H1   C6   S1   C1   180.00   0.0  0
 32V  CONST_20  C9   N1   C2   N3     0.00   0.0  0
 32V  CONST_21  C9   N1   C4   O1     0.00   0.0  0
 32V  CONST_22  H2   N3   C2   N1     0.00   0.0  0
 32V  Var_01    C14  C15  C11  C10   40.91  30.0  1
 32V  Var_02    C15  C14  C12  C10    4.90  30.0  1
 32V  Var_03    C12  C14  C15  C11  -28.10  30.0  1
 32V  Var_04    C13  C9   N1   C2    86.96  30.0  2
 32V  Var_05    H11  C13  C9   N1   -61.05  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
 32V  chir_01  C10  C11  N3  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
 32V  plan-1  C1   0.020
 32V  plan-1  C2   0.020
 32V  plan-1  N1   0.020
 32V  plan-1  N2   0.020
 32V  plan-1  C3   0.020
 32V  plan-1  C4   0.020
 32V  plan-1  S1   0.020
 32V  plan-1  C5   0.020
 32V  plan-1  C6   0.020
 32V  plan-1  N3   0.020
 32V  plan-1  C7   0.020
 32V  plan-1  C8   0.020
 32V  plan-1  O1   0.020
 32V  plan-1  C9   0.020
 32V  plan-1  C10  0.020
 32V  plan-1  H1   0.020
 32V  plan-1  H2   0.020

