# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:33:29 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5-methyl-4-(methylamino)-2-(2-phenylethyl)thieno[2,3-d]pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(CCc2ccccc2)nc3sc(C(O)=O)c(C)c13
#
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
 753  753  '5-methyl-4-(methylamino)-2-(2-phenylethyl)thieno[2,3-d]pyrimidine-6-carboxylic acid'  ligand  39  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_753
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
 753  C1   C  CR5    0   0.211   3.2454  -0.5742  -0.1083
 753  C2   C  CR5    0  -0.424   3.6941   0.7135  -0.0869
 753  C3   C  C      0   0.411   5.0580   1.3344  -0.2612
 753  C4   C  CR56   0  -0.040   1.2464   0.6197   0.2941
 753  C5   C  CR56   0   0.001   1.8219  -0.6373   0.1126
 753  C6   C  CR6    0   0.495   0.8975  -1.7195   0.1788
 753  C7   C  CH3    0  -0.512   0.3143  -4.0933   0.1017
 753  C8   C  CR6    0   0.330  -0.8052  -0.2174   0.5581
 753  O1   O  OC    -1  -0.595   5.0601   2.5785  -0.1671
 753  N1   N  N      0  -0.484  -0.3942  -1.4738   0.3985
 753  N2   N  N      0  -0.457  -0.0467   0.8630   0.5182
 753  N    N  NH1    0  -0.666   1.2544  -3.0004   0.0342
 753  C    C  CH3    0  -0.820   4.1069  -1.7784  -0.3293
 753  O    O  O      0  -0.571   6.0314   0.5917  -0.4767
 753  S    S  S2     0   0.190   2.4250   1.8717   0.1996
 753  C9   C  CH2    0  -0.487  -2.2791  -0.0118   0.7446
 753  C10  C  CH2    0  -0.512  -2.9829   0.1672  -0.6090
 753  C11  C  CR6    0   0.129  -4.4615   0.3753  -0.4406
 753  C16  C  CR16   0  -0.311  -5.3405  -0.7054  -0.4505
 753  C15  C  CR16   0  -0.240  -6.7024  -0.5179  -0.2536
 753  C14  C  CR16   0  -0.273  -7.2071   0.7586  -0.0426
 753  C13  C  CR16   0  -0.240  -6.3403   1.8440  -0.0295
 753  C12  C  CR16   0  -0.309  -4.9796   1.6510  -0.2263
 753  H1   H  HCH3   0   0.237  -0.4367  -4.0327  -0.6866
 753  H2   H  HCH3   0   0.249   0.8675  -5.0205  -0.0174
 753  H3   H  HCH3   0   0.237  -0.2041  -4.1199   1.0604
 753  H5   H  HNH1   0   0.424   2.2162  -3.2241  -0.1429
 753  H6   H  HCH3   0   0.245   4.0630  -2.4570   0.5257
 753  H7   H  HCH3   0   0.244   3.7890  -2.3344  -1.2145
 753  H8   H  HCH3   0   0.287   5.1416  -1.4875  -0.4721
 753  H9   H  HCH2   0   0.249  -2.7066  -0.8703   1.2651
 753  H10  H  HCH2   0   0.250  -2.4461   0.8734   1.3606
 753  H11  H  HCH2   0   0.252  -2.5419   1.0205  -1.1295
 753  H12  H  HCH2   0   0.252  -2.7995  -0.7134  -1.2289
 753  H13  H  HCR6   0   0.246  -4.9569  -1.7051  -0.6205
 753  H14  H  HCR6   0   0.253  -7.3711  -1.3690  -0.2684
 753  H15  H  HCR6   0   0.253  -8.2689   0.9068   0.1065
 753  H16  H  HCR6   0   0.253  -6.7243   2.8434   0.1316
 753  H17  H  HCR6   0   0.247  -4.3098   2.5035  -0.2186

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
 753  C15  C14  aromatic  1.389  0.020  1.389
 753  C15  C16  aromatic  1.389  0.020  1.389
 753  C14  C13  aromatic  1.389  0.020  1.389
 753  C16  C11  aromatic  1.393  0.020  1.393
 753  C13  C12  aromatic  1.388  0.020  1.388
 753  C11  C12  aromatic  1.393  0.020  1.393
 753  C11  C10  single    1.503  0.020  1.503
 753  C10  C9   single    1.536  0.020  1.536
 753  C9   C8   single    1.500  0.020  1.500
 753  C7   N    single    1.443  0.020  1.443
 753  N1   C8   aromatic  1.332  0.020  1.332
 753  N1   C6   aromatic  1.333  0.020  1.333
 753  C8   N2   aromatic  1.321  0.020  1.321
 753  N    C6   single    1.338  0.020  1.338
 753  C6   C5   aromatic  1.425  0.020  1.425
 753  N2   C4   aromatic  1.335  0.020  1.335
 753  C4   C5   aromatic  1.394  0.020  1.394
 753  C4   S    aromatic  1.722  0.020  1.722
 753  C5   C1   aromatic  1.442  0.020  1.442
 753  C1   C    single    1.497  0.020  1.497
 753  C1   C2   aromatic  1.364  0.020  1.364
 753  S    C2   aromatic  1.742  0.020  1.742
 753  C2   C3   single    1.509  0.020  1.509
 753  C3   O    deloc     1.243  0.020  1.243
 753  C3   O1   deloc     1.248  0.020  1.248
 753  C7   H1   single    0.970  0.020  1.090
 753  C7   H2   single    0.970  0.020  1.090
 753  C7   H3   single    0.970  0.020  1.090
 753  N    H5   single    0.860  0.020  1.020
 753  C    H6   single    0.970  0.020  1.090
 753  C    H7   single    0.970  0.020  1.090
 753  C    H8   single    0.970  0.020  1.090
 753  C9   H9   single    0.970  0.020  1.090
 753  C9   H10  single    0.970  0.020  1.090
 753  C10  H11  single    0.970  0.020  1.090
 753  C10  H12  single    0.970  0.020  1.090
 753  C16  H13  single    0.930  0.020  1.080
 753  C15  H14  single    0.930  0.020  1.080
 753  C14  H15  single    0.930  0.020  1.080
 753  C13  H16  single    0.930  0.020  1.080
 753  C12  H17  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
 753  C    C1   C5   123.75  3.000
 753  C    C1   C2   124.92  3.000
 753  C5   C1   C2   111.33  3.000
 753  S    C2   C3   113.83  3.000
 753  C3   C2   C1   133.17  3.000
 753  S    C2   C1   113.00  3.000
 753  O    C3   O1   127.41  3.000
 753  O1   C3   C2   113.78  3.000
 753  O    C3   C2   118.81  3.000
 753  S    C4   N2   122.67  3.000
 753  S    C4   C5   111.46  3.000
 753  N2   C4   C5   125.88  3.000
 753  C6   C5   C4   114.26  3.000
 753  C4   C5   C1   112.83  3.000
 753  C6   C5   C1   132.91  3.000
 753  N    C6   N1   116.93  3.000
 753  N    C6   C5   123.31  3.000
 753  N1   C6   C5   119.76  3.000
 753  H3   C7   H2   108.53  3.000
 753  H3   C7   H1   108.03  3.000
 753  H2   C7   H1   108.59  3.000
 753  H3   C7   N    111.68  3.000
 753  H2   C7   N    108.03  3.000
 753  H1   C7   N    111.88  3.000
 753  C9   C8   N2   117.14  3.000
 753  N2   C8   N1   126.23  3.000
 753  C9   C8   N1   116.59  3.000
 753  C8   N1   C6   119.52  3.000
 753  C8   N2   C4   114.36  3.000
 753  H5   N    C7   117.63  3.000
 753  H5   N    C6   119.24  3.000
 753  C7   N    C6   123.12  3.000
 753  H8   C    H7   107.91  3.000
 753  H8   C    H6   107.94  3.000
 753  H7   C    H6   107.83  3.000
 753  H8   C    C1   110.66  3.000
 753  H7   C    C1   111.19  3.000
 753  H6   C    C1   111.16  3.000
 753  C4   S    C2    91.39  3.000
 753  H10  C9   H9   108.00  3.000
 753  H10  C9   C10  109.44  3.000
 753  H9   C9   C10  109.42  3.000
 753  H10  C9   C8   109.38  3.000
 753  H9   C9   C8   109.67  3.000
 753  C10  C9   C8   110.90  3.000
 753  H12  C10  H11  106.95  3.000
 753  H12  C10  C11  109.90  3.000
 753  H11  C10  C11  110.02  3.000
 753  H12  C10  C9   109.22  3.000
 753  H11  C10  C9   109.02  3.000
 753  C11  C10  C9   111.61  3.000
 753  C12  C11  C16  118.47  3.000
 753  C12  C11  C10  120.66  3.000
 753  C16  C11  C10  120.84  3.000
 753  H13  C16  C15  119.59  3.000
 753  H13  C16  C11  119.55  3.000
 753  C15  C16  C11  120.87  3.000
 753  H14  C15  C14  120.02  3.000
 753  H14  C15  C16  119.85  3.000
 753  C14  C15  C16  120.14  3.000
 753  H15  C14  C13  120.25  3.000
 753  H15  C14  C15  120.22  3.000
 753  C13  C14  C15  119.53  3.000
 753  H16  C13  C12  119.80  3.000
 753  H16  C13  C14  120.09  3.000
 753  C12  C13  C14  120.11  3.000
 753  H17  C12  C13  119.68  3.000
 753  H17  C12  C11  119.42  3.000
 753  C13  C12  C11  120.90  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
 753  CONST_01  N1   C6   C5   C1    180.00   0.0  0
 753  CONST_02  N2   C4   C5   C1    180.00   0.0  0
 753  CONST_03  S    C4   C5   C1      0.00   0.0  0
 753  CONST_04  C4   S    C2   C1      0.00   0.0  0
 753  CONST_05  C6   C5   C1   C2    180.00   0.0  0
 753  CONST_06  C4   C5   C1   C2      0.00   0.0  0
 753  CONST_07  N2   C4   S    C2    180.00   0.0  0
 753  CONST_08  C5   C4   S    C2      0.00   0.0  0
 753  CONST_09  N1   C8   N2   C4      0.00   0.0  0
 753  CONST_10  N1   C6   C5   C4      0.00   0.0  0
 753  CONST_11  C8   N1   C6   C5      0.00   0.0  0
 753  CONST_12  C8   N2   C4   C5      0.00   0.0  0
 753  CONST_13  S    C2   C1   C5      0.00   0.0  0
 753  CONST_14  N2   C8   N1   C6      0.00   0.0  0
 753  CONST_15  N2   C4   C5   C6      0.00   0.0  0
 753  CONST_16  S    C4   C5   C6    180.00   0.0  0
 753  CONST_17  S    C4   N2   C8    180.00   0.0  0
 753  CONST_18  C14  C15  C16  C11     0.00   0.0  0
 753  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 753  CONST_20  C13  C14  C15  C16     0.00   0.0  0
 753  CONST_21  C13  C12  C11  C16     0.00   0.0  0
 753  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 753  CONST_23  C12  C11  C16  C15     0.00   0.0  0
 753  CONST_24  N    C6   C5   C1      0.00   0.0  0
 753  CONST_25  C5   C1   C2   C3    180.00   0.0  0
 753  CONST_26  C4   S    C2   C3    180.00   0.0  0
 753  CONST_27  C9   C8   N2   C4    180.00   0.0  0
 753  CONST_28  N    C6   C5   C4    180.00   0.0  0
 753  CONST_29  C    C1   C5   C4    180.00   0.0  0
 753  CONST_30  C9   C8   N1   C6    180.00   0.0  0
 753  CONST_31  C    C1   C5   C6      0.00   0.0  0
 753  CONST_32  N    C6   N1   C8    180.00   0.0  0
 753  CONST_33  S    C2   C1   C     180.00   0.0  0
 753  CONST_34  C15  C16  C11  C10   180.00   0.0  0
 753  CONST_35  C13  C12  C11  C10   180.00   0.0  0
 753  CONST_36  H14  C15  C16  C11   180.00   0.0  0
 753  CONST_37  H16  C13  C12  C11   180.00   0.0  0
 753  CONST_38  H15  C14  C15  C16   180.00   0.0  0
 753  CONST_39  H17  C12  C11  C16   180.00   0.0  0
 753  CONST_40  H13  C16  C15  C14   180.00   0.0  0
 753  CONST_41  C7   N    C6   C5    180.00   0.0  0
 753  CONST_42  N1   C6   N    C7      0.00   0.0  0
 753  CONST_43  H5   N    C6   C5      0.00   0.0  0
 753  Var_01    O    C3   C2   C1      0.26  30.0  2
 753  Var_02    C11  C10  C9   C8   -179.96  30.0  2
 753  Var_03    C10  C9   C8   N1    -89.05  30.0  1
 753  Var_04    C16  C11  C10  C9    -91.16  30.0  2
 753  Var_05    H6   C    C1   C2    119.87  30.0  2
 753  Var_06    H1   C7   N    C6     62.21  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
 753  plan-1  C10  0.020
 753  plan-1  C11  0.020
 753  plan-1  C16  0.020
 753  plan-1  C15  0.020
 753  plan-1  C14  0.020
 753  plan-1  C13  0.020
 753  plan-1  C12  0.020
 753  plan-1  H13  0.020
 753  plan-1  H14  0.020
 753  plan-1  H15  0.020
 753  plan-1  H16  0.020
 753  plan-1  H17  0.020
 753  plan-2  C1   0.020
 753  plan-2  C2   0.020
 753  plan-2  C3   0.020
 753  plan-2  C4   0.020
 753  plan-2  C5   0.020
 753  plan-2  C6   0.020
 753  plan-2  C8   0.020
 753  plan-2  N1   0.020
 753  plan-2  N2   0.020
 753  plan-2  N    0.020
 753  plan-2  C    0.020
 753  plan-2  S    0.020
 753  plan-2  C9   0.020
 753  plan-3  C6   0.020
 753  plan-3  C7   0.020
 753  plan-3  N    0.020
 753  plan-3  H5   0.020
 753  plan-4  C2   0.020
 753  plan-4  C3   0.020
 753  plan-4  O1   0.020
 753  plan-4  O    0.020

