# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 21:20:13 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2csc(C=O)c2C)c(N)n1
#
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
 2VY  2VY  4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophene-2-carbaldehyde  ligand  30  17  .  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_2VY
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
 2VY  CM2  C  CH3   0  -0.729   4.8503  -1.1424  -1.3325
 2VY  O1   O  O     0  -0.402  -4.7454  -0.6533  -1.1764
 2VY  C6   C  C1    0   0.139  -3.7187  -1.0625  -0.6747
 2VY  C2   C  CR15  0  -0.546  -1.6258   1.7494   0.9094
 2VY  S1   S  S2    0   0.263  -3.0868   1.4855   0.0766
 2VY  C5   C  CR5   0  -0.341  -2.7563  -0.2047  -0.0192
 2VY  C4   C  CR5   0   0.168  -1.5586  -0.5404   0.5721
 2VY  C3   C  CR5   0   0.196  -0.8984   0.6076   1.1047
 2VY  C7A  C  CH2   0  -0.631   0.4287   0.5782   1.8126
 2VY  C4A  C  CR6   0   0.457   2.0420   0.8615  -0.1699
 2VY  N3A  N  N     0  -0.466   3.0771   0.4245  -0.8895
 2VY  C2A  C  CR6   0   0.351   3.6711  -0.7026  -0.5223
 2VY  N1A  N  N     0  -0.446   3.3248  -1.4526   0.5143
 2VY  C6A  C  CR16  0  -0.096   2.2868  -1.0113   1.2272
 2VY  C5A  C  CR6   0  -0.019   1.5795   0.1347   0.9519
 2VY  H1   H  HCH3  0   0.256   5.7497  -0.6215  -0.9962
 2VY  H2   H  HCH3  0   0.245   5.0252  -2.2100  -1.2199
 2VY  H3   H  HCH3  0   0.247   4.7147  -0.9079  -2.3867
 2VY  H4   H  HNH2  0   0.410   0.5969   2.3190  -0.1993
 2VY  H5   H  HNH2  0   0.397   1.7839   2.4336  -1.4201
 2VY  H6   H  HCH3  0   0.265  -0.1896  -2.0695  -0.0381
 2VY  H7   H  HCH3  0   0.257  -0.6068  -2.1111   1.6672
 2VY  H8   H  HCH3  0   0.261  -1.7550  -2.6872   0.4712
 2VY  H10  H  H     0   0.198  -3.4615  -2.1325  -0.6962
 2VY  H12  H  HCR5  0   0.314  -1.3643   2.7461   1.2373
 2VY  H13  H  HCH2  0   0.284   0.6305   1.5707   2.2264
 2VY  H14  H  HCH2  0   0.285   0.3665  -0.0968   2.6712
 2VY  H15  H  HCR6  0   0.259   1.9982  -1.6178   2.0816
 2VY  N4A  N  NH2   0  -0.826   1.4951   2.0316  -0.5439
 2VY  CM4  C  CH3   0  -0.749  -1.0062  -1.9244   0.6699

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
 2VY  CM2  C2A  single    1.497  0.020  1.497
 2VY  C2A  N3A  aromatic  1.326  0.020  1.326
 2VY  C2A  N1A  aromatic  1.326  0.020  1.326
 2VY  N3A  C4A  aromatic  1.334  0.020  1.334
 2VY  N1A  C6A  aromatic  1.334  0.020  1.334
 2VY  C4A  N4A  single    1.345  0.020  1.345
 2VY  C4A  C5A  aromatic  1.414  0.020  1.414
 2VY  C2   S1   aromatic  1.702  0.020  1.702
 2VY  C2   C3   aromatic  1.368  0.020  1.368
 2VY  S1   C5   aromatic  1.725  0.020  1.725
 2VY  C6A  C5A  aromatic  1.374  0.020  1.374
 2VY  C5A  C7A  single    1.504  0.020  1.504
 2VY  C3   C7A  single    1.504  0.020  1.504
 2VY  C3   C4   aromatic  1.427  0.020  1.427
 2VY  C5   C4   aromatic  1.377  0.020  1.377
 2VY  C5   C6   single    1.446  0.020  1.446
 2VY  C4   CM4  single    1.493  0.020  1.493
 2VY  C6   O1   double    1.214  0.020  1.214
 2VY  CM2  H1   single    0.970  0.020  1.090
 2VY  CM2  H2   single    0.970  0.020  1.090
 2VY  CM2  H3   single    0.970  0.020  1.090
 2VY  N4A  H4   single    0.890  0.020  1.040
 2VY  N4A  H5   single    0.890  0.020  1.040
 2VY  CM4  H6   single    0.970  0.020  1.090
 2VY  CM4  H7   single    0.970  0.020  1.090
 2VY  CM4  H8   single    0.970  0.020  1.090
 2VY  C6   H10  single    0.930  0.020  1.080
 2VY  C2   H12  single    0.930  0.020  1.080
 2VY  C7A  H13  single    0.970  0.020  1.090
 2VY  C7A  H14  single    0.970  0.020  1.090
 2VY  C6A  H15  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
 2VY  H3   CM2  H2   109.37  3.000
 2VY  H3   CM2  H1   107.34  3.000
 2VY  H2   CM2  H1   107.68  3.000
 2VY  H3   CM2  C2A  111.28  3.000
 2VY  H2   CM2  C2A  111.04  3.000
 2VY  H1   CM2  C2A  110.00  3.000
 2VY  H10  C6   C5   115.47  3.000
 2VY  H10  C6   O1   121.15  3.000
 2VY  C5   C6   O1   123.38  3.000
 2VY  H12  C2   C3   126.69  3.000
 2VY  H12  C2   S1   119.92  3.000
 2VY  C3   C2   S1   113.38  3.000
 2VY  C5   S1   C2    90.84  3.000
 2VY  C4   C5   S1   112.44  3.000
 2VY  C4   C5   C6   128.95  3.000
 2VY  S1   C5   C6   118.61  3.000
 2VY  C3   C4   C5   111.49  3.000
 2VY  C5   C4   CM4  125.15  3.000
 2VY  C3   C4   CM4  123.36  3.000
 2VY  C7A  C3   C4   124.60  3.000
 2VY  C4   C3   C2   111.85  3.000
 2VY  C7A  C3   C2   123.54  3.000
 2VY  H14  C7A  H13  105.86  3.000
 2VY  H14  C7A  C5A  108.10  3.000
 2VY  H13  C7A  C5A  110.05  3.000
 2VY  H14  C7A  C3   109.35  3.000
 2VY  H13  C7A  C3   108.85  3.000
 2VY  C5A  C7A  C3   114.30  3.000
 2VY  C5A  C4A  N3A  120.87  3.000
 2VY  C5A  C4A  N4A  122.33  3.000
 2VY  N3A  C4A  N4A  116.78  3.000
 2VY  C2A  N3A  C4A  118.46  3.000
 2VY  N1A  C2A  N3A  125.49  3.000
 2VY  N1A  C2A  CM2  117.57  3.000
 2VY  N3A  C2A  CM2  116.92  3.000
 2VY  C6A  N1A  C2A  115.71  3.000
 2VY  H15  C6A  C5A  119.09  3.000
 2VY  H15  C6A  N1A  116.23  3.000
 2VY  C5A  C6A  N1A  124.68  3.000
 2VY  C6A  C5A  C4A  114.77  3.000
 2VY  C6A  C5A  C7A  121.67  3.000
 2VY  C4A  C5A  C7A  123.54  3.000
 2VY  H5   N4A  H4   116.18  3.000
 2VY  H5   N4A  C4A  118.23  3.000
 2VY  H4   N4A  C4A  121.17  3.000
 2VY  H8   CM4  H7   107.41  3.000
 2VY  H8   CM4  H6   107.67  3.000
 2VY  H7   CM4  H6   107.26  3.000
 2VY  H8   CM4  C4   112.55  3.000
 2VY  H7   CM4  C4   110.74  3.000
 2VY  H6   CM4  C4   110.97  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
 2VY  CONST_01  C4   C5   S1   C2      0.00   0.0  0
 2VY  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 2VY  CONST_03  C4   C3   C2   S1      0.00   0.0  0
 2VY  CONST_04  C3   C4   C5   S1      0.00   0.0  0
 2VY  CONST_05  C3   C2   S1   C5      0.00   0.0  0
 2VY  CONST_06  N1A  C2A  N3A  C4A     0.00   0.0  0
 2VY  CONST_07  N1A  C6A  C5A  C4A     0.00   0.0  0
 2VY  CONST_08  C6A  N1A  C2A  N3A     0.00   0.0  0
 2VY  CONST_09  C6A  C5A  C4A  N3A     0.00   0.0  0
 2VY  CONST_10  C5A  C4A  N3A  C2A     0.00   0.0  0
 2VY  CONST_11  C5A  C6A  N1A  C2A     0.00   0.0  0
 2VY  CONST_12  C4A  N3A  C2A  CM2   180.00   0.0  0
 2VY  CONST_13  C6A  N1A  C2A  CM2   180.00   0.0  0
 2VY  CONST_14  C2A  N3A  C4A  N4A   180.00   0.0  0
 2VY  CONST_15  C6A  C5A  C4A  N4A   180.00   0.0  0
 2VY  CONST_16  C2   C3   C4   CM4   180.00   0.0  0
 2VY  CONST_17  S1   C5   C4   CM4   180.00   0.0  0
 2VY  CONST_18  C2   S1   C5   C6    180.00   0.0  0
 2VY  CONST_19  C3   C4   C5   C6    180.00   0.0  0
 2VY  CONST_20  C7A  C3   C2   S1    180.00   0.0  0
 2VY  CONST_21  C7A  C3   C4   C5    180.00   0.0  0
 2VY  CONST_22  N3A  C4A  C5A  C7A   180.00   0.0  0
 2VY  CONST_23  N1A  C6A  C5A  C7A   180.00   0.0  0
 2VY  CONST_24  H12  C2   S1   C5    180.00   0.0  0
 2VY  CONST_25  H15  C6A  C5A  C4A   180.00   0.0  0
 2VY  CONST_26  H4   N4A  C4A  N3A   180.00   0.0  0
 2VY  CONST_27  H5   N4A  C4A  N3A     0.00   0.0  0
 2VY  Var_01    C5A  C7A  C3   C2   -116.93  30.0  2
 2VY  Var_02    C4A  C5A  C7A  C3     64.91  30.0  3
 2VY  Var_03    S1   C5   C6   O1      0.82  30.0  2
 2VY  Var_04    H6   CM4  C4   C5    105.10  30.0  2
 2VY  Var_05    H1   CM2  C2A  N3A    82.73  30.0  2

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
 2VY  plan-1  C6   0.020
 2VY  plan-1  C2   0.020
 2VY  plan-1  S1   0.020
 2VY  plan-1  C5   0.020
 2VY  plan-1  C4   0.020
 2VY  plan-1  C3   0.020
 2VY  plan-1  C7A  0.020
 2VY  plan-1  H12  0.020
 2VY  plan-1  CM4  0.020
 2VY  plan-2  CM2  0.020
 2VY  plan-2  C7A  0.020
 2VY  plan-2  C4A  0.020
 2VY  plan-2  N3A  0.020
 2VY  plan-2  C2A  0.020
 2VY  plan-2  N1A  0.020
 2VY  plan-2  C6A  0.020
 2VY  plan-2  C5A  0.020
 2VY  plan-2  H15  0.020
 2VY  plan-2  N4A  0.020
 2VY  plan-3  C4A  0.020
 2VY  plan-3  H4   0.020
 2VY  plan-3  H5   0.020
 2VY  plan-3  N4A  0.020
 2VY  plan-4  O1   0.020
 2VY  plan-4  C6   0.020
 2VY  plan-4  C5   0.020
 2VY  plan-4  H10  0.020

