# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 09:40:13 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccc(CNCc2[nH]ccn2)cc1)c3csc4N=CNC(=O)c34
#
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
 21W  21W  N-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide  ligand  46  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_21W
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
 21W  C2   C  CR16  0  -0.164   0.8396   0.2842  -1.0283
 21W  C4   C  CR16  0  -0.300   1.8698   1.1010   0.9680
 21W  C1   C  CR16  0  -0.290   1.9865  -0.4379  -1.3204
 21W  C5   C  CR16  0  -0.279   3.0180   0.3768   0.6760
 21W  C13  C  CR15  0  -0.110   9.0656   0.6112   1.3352
 21W  C12  C  CR15  0  -0.155   9.8800   0.0990   0.3669
 21W  C20  C  CR15  0  -0.512  -3.2523  -1.4945   0.1628
 21W  C23  C  CR56  0  -0.077  -5.0270  -0.0327  -0.0273
 21W  C19  C  CR5   0   0.045  -3.6087  -0.1964  -0.0206
 21W  C3   C  CR6   0   0.040   0.7666   1.0645   0.1229
 21W  C6   C  CR6   0   0.080   3.0896  -0.4086  -0.4702
 21W  C22  C  CR56  0  -0.009  -5.6975  -1.2306   0.1432
 21W  C10  C  CR5   0   0.427   7.9137  -0.5932  -0.0932
 21W  C27  C  CR16  0   0.158  -7.7168  -0.3121   0.0819
 21W  C24  C  CR6   0   0.522  -5.8051   1.1819  -0.0878
 21W  C17  C  C     0   0.519  -2.6075   0.8671  -0.3285
 21W  C15  C  CH2   0  -0.320  -0.4818   1.8466   0.4460
 21W  C7   C  CH2   0  -0.386   4.3140  -1.2303  -0.7758
 21W  C9   C  CH2   0  -0.359   6.7330  -1.2884  -0.6826
 21W  N14  N  NR15  0  -0.599   7.8171   0.1553   1.0240
 21W  N28  N  N     0  -0.457  -7.0369  -1.4036   0.1949
 21W  N11  N  N     0  -0.527   9.1511  -0.6457  -0.5208
 21W  N26  N  NR16  0  -0.561  -7.1700   0.9127  -0.0550
 21W  N16  N  NH1   0  -0.640  -1.6411   0.9937   0.5945
 21W  N8   N  NH1   0  -0.591   5.5322  -0.5057  -0.4730
 21W  O25  O  O     0  -0.460  -5.3897   2.3227  -0.1401
 21W  O18  O  O     0  -0.382  -2.6732   1.5145  -1.3595
 21W  S21  S  S2    0   0.276  -4.6031  -2.5505   0.3073
 21W  H1   H  HCR6  0   0.248   0.0011   0.2484  -1.7137
 21W  H2   H  HCR6  0   0.247   1.8354   1.7019   1.8695
 21W  H3   H  HCR6  0   0.228   2.0240  -1.0315  -2.2266
 21W  H4   H  HCR6  0   0.261   3.8672   0.4221   1.3459
 21W  H6   H  HCR5  0   0.257  10.9451   0.2332   0.2578
 21W  H7   H  HCR5  0   0.301  -2.2524  -1.9018   0.1841
 21W  H8   H  HCR6  0   0.312  -8.7982  -0.3444   0.0997
 21W  H9   H  HCH2  0   0.191  -0.3416   2.4071   1.3712
 21W  H10  H  HCH2  0   0.233  -0.6935   2.5733  -0.3376
 21W  H11  H  HCH2  0   0.230   4.3030  -2.1324  -0.1548
 21W  H12  H  HCH2  0   0.219   4.2644  -1.5796  -1.8174
 21W  H13  H  HCH2  0   0.259   6.9488  -1.5195  -1.7339
 21W  H14  H  HCH2  0   0.262   6.5965  -2.2527  -0.1807
 21W  H15  H  HNR5  0   0.419   6.9582   0.3506   1.5143
 21W  H17  H  HNR6  0   0.447  -7.7961   1.7056  -0.1152
 21W  H18  H  HNH1  0   0.383  -1.6832   0.4133   1.4176
 21W  H19  H  HNH1  0   0.357   5.5725   0.3326  -1.0409
 21W  H5   H  HCR5  0   0.259   9.2568   1.2431   2.1853

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
 21W  S21  C20  aromatic  1.721  0.020  1.721
 21W  S21  C22  aromatic  1.722  0.020  1.722
 21W  C20  C19  aromatic  1.359  0.020  1.359
 21W  C22  N28  single    1.351  0.020  1.351
 21W  C22  C23  aromatic  1.383  0.020  1.383
 21W  N28  C27  double    1.291  0.020  1.291
 21W  O18  C17  double    1.219  0.020  1.219
 21W  C19  C23  aromatic  1.428  0.020  1.428
 21W  C19  C17  single    1.493  0.020  1.493
 21W  C23  C24  single    1.444  0.020  1.444
 21W  C17  N16  single    1.342  0.020  1.342
 21W  C27  N26  single    1.348  0.020  1.348
 21W  C24  N26  single    1.392  0.020  1.392
 21W  C24  O25  double    1.215  0.020  1.215
 21W  N16  C15  single    1.447  0.020  1.447
 21W  C15  C3   single    1.508  0.020  1.508
 21W  C2   C3   aromatic  1.393  0.020  1.393
 21W  C2   C1   aromatic  1.386  0.020  1.386
 21W  C3   C4   aromatic  1.390  0.020  1.390
 21W  C1   C6   aromatic  1.393  0.020  1.393
 21W  C4   C5   aromatic  1.389  0.020  1.389
 21W  C6   C5   aromatic  1.391  0.020  1.391
 21W  C6   C7   single    1.506  0.020  1.506
 21W  C7   N8   single    1.449  0.020  1.449
 21W  N8   C9   single    1.449  0.020  1.449
 21W  C9   C10  single    1.492  0.020  1.492
 21W  N11  C10  aromatic  1.310  0.020  1.310
 21W  N11  C12  aromatic  1.369  0.020  1.369
 21W  C10  N14  aromatic  1.348  0.020  1.348
 21W  C12  C13  aromatic  1.365  0.020  1.365
 21W  N14  C13  aromatic  1.365  0.020  1.365
 21W  C2   H1   single    0.930  0.020  1.080
 21W  C4   H2   single    0.930  0.020  1.080
 21W  C1   H3   single    0.930  0.020  1.080
 21W  C5   H4   single    0.930  0.020  1.080
 21W  C13  H5   single    0.930  0.020  1.080
 21W  C12  H6   single    0.930  0.020  1.080
 21W  C20  H7   single    0.930  0.020  1.080
 21W  C27  H8   single    0.930  0.020  1.080
 21W  C15  H9   single    0.970  0.020  1.090
 21W  C15  H10  single    0.970  0.020  1.090
 21W  C7   H11  single    0.970  0.020  1.090
 21W  C7   H12  single    0.970  0.020  1.090
 21W  C9   H13  single    0.970  0.020  1.090
 21W  C9   H14  single    0.970  0.020  1.090
 21W  N14  H15  single    0.860  0.020  1.020
 21W  N26  H17  single    0.860  0.020  1.020
 21W  N16  H18  single    0.860  0.020  1.020
 21W  N8   H19  single    0.890  0.020  1.040

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
 21W  H1   C2   C3   120.06  3.000
 21W  H1   C2   C1   119.31  3.000
 21W  C3   C2   C1   120.62  3.000
 21W  H2   C4   C3   119.67  3.000
 21W  H2   C4   C5   119.36  3.000
 21W  C3   C4   C5   120.98  3.000
 21W  H3   C1   C6   119.63  3.000
 21W  H3   C1   C2   119.34  3.000
 21W  C6   C1   C2   121.03  3.000
 21W  H4   C5   C6   119.55  3.000
 21W  H4   C5   C4   119.78  3.000
 21W  C6   C5   C4   120.67  3.000
 21W  H5   C13  N14  122.58  3.000
 21W  H5   C13  C12  132.42  3.000
 21W  N14  C13  C12  104.99  3.000
 21W  H6   C12  N11  121.85  3.000
 21W  H6   C12  C13  127.88  3.000
 21W  N11  C12  C13  110.27  3.000
 21W  H7   C20  S21  119.59  3.000
 21W  H7   C20  C19  127.30  3.000
 21W  S21  C20  C19  113.07  3.000
 21W  C24  C23  C22  118.19  3.000
 21W  C24  C23  C19  129.20  3.000
 21W  C22  C23  C19  112.43  3.000
 21W  C17  C19  C23  125.70  3.000
 21W  C17  C19  C20  122.18  3.000
 21W  C23  C19  C20  111.76  3.000
 21W  C15  C3   C4   120.86  3.000
 21W  C4   C3   C2   118.40  3.000
 21W  C15  C3   C2   120.74  3.000
 21W  C7   C6   C5   121.13  3.000
 21W  C7   C6   C1   120.56  3.000
 21W  C5   C6   C1   118.29  3.000
 21W  S21  C22  N28  121.87  3.000
 21W  N28  C22  C23  126.58  3.000
 21W  S21  C22  C23  111.55  3.000
 21W  N11  C10  N14  111.13  3.000
 21W  N14  C10  C9   121.97  3.000
 21W  N11  C10  C9   126.86  3.000
 21W  H8   C27  N26  115.73  3.000
 21W  H8   C27  N28  119.98  3.000
 21W  N26  C27  N28  124.29  3.000
 21W  O25  C24  N26  121.20  3.000
 21W  O25  C24  C23  127.39  3.000
 21W  N26  C24  C23  111.40  3.000
 21W  O18  C17  N16  124.76  3.000
 21W  N16  C17  C19  114.09  3.000
 21W  O18  C17  C19  121.11  3.000
 21W  H10  C15  H9   107.00  3.000
 21W  H10  C15  N16  108.14  3.000
 21W  H9   C15  N16  108.59  3.000
 21W  H10  C15  C3   110.65  3.000
 21W  H9   C15  C3   109.99  3.000
 21W  N16  C15  C3   112.30  3.000
 21W  H12  C7   H11  105.96  3.000
 21W  H12  C7   N8   113.24  3.000
 21W  H11  C7   N8   107.56  3.000
 21W  H12  C7   C6   109.19  3.000
 21W  H11  C7   C6   109.04  3.000
 21W  N8   C7   C6   111.60  3.000
 21W  H14  C9   H13  106.13  3.000
 21W  H14  C9   N8   107.82  3.000
 21W  H13  C9   N8   114.54  3.000
 21W  H14  C9   C10  109.13  3.000
 21W  H13  C9   C10  108.72  3.000
 21W  N8   C9   C10  110.31  3.000
 21W  H15  N14  C10  124.86  3.000
 21W  H15  N14  C13  127.14  3.000
 21W  C10  N14  C13  107.98  3.000
 21W  C27  N28  C22  114.23  3.000
 21W  C10  N11  C12  105.63  3.000
 21W  H17  N26  C24  116.98  3.000
 21W  H17  N26  C27  117.83  3.000
 21W  C24  N26  C27  125.17  3.000
 21W  H18  N16  C15  117.17  3.000
 21W  H18  N16  C17  118.50  3.000
 21W  C15  N16  C17  124.18  3.000
 21W  H19  N8   C9   109.44  3.000
 21W  H19  N8   C7   109.26  3.000
 21W  C9   N8   C7   113.35  3.000
 21W  C22  S21  C20   91.18  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
 21W  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 21W  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 21W  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 21W  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 21W  CONST_05  C10  N11  C12  C13     0.00   0.0  0
 21W  CONST_06  N11  C10  N14  C13     0.00   0.0  0
 21W  CONST_07  N14  C10  N11  C12     0.00   0.0  0
 21W  CONST_08  C10  N14  C13  C12     0.00   0.0  0
 21W  CONST_09  C23  C22  S21  C20     0.00   0.0  0
 21W  CONST_10  C22  C23  C19  C20     0.00   0.0  0
 21W  CONST_11  S21  C20  C19  C23     0.00   0.0  0
 21W  CONST_12  C22  S21  C20  C19     0.00   0.0  0
 21W  CONST_13  S21  C22  C23  C19     0.00   0.0  0
 21W  CONST_14  C6   C1   C2   C3      0.00   0.0  0
 21W  CONST_15  C6   C5   C4   C3      0.00   0.0  0
 21W  CONST_16  N11  C12  C13  N14     0.00   0.0  0
 21W  CONST_17  C27  N26  C24  C23     0.00   0.0  0
 21W  CONST_18  N26  C27  N28  C22     0.00   0.0  0
 21W  CONST_19  N28  C27  N26  C24     0.00   0.0  0
 21W  CONST_20  C7   C6   C1   C2    180.00   0.0  0
 21W  CONST_21  C7   C6   C5   C4    180.00   0.0  0
 21W  CONST_22  C15  C3   C2   C1    180.00   0.0  0
 21W  CONST_23  C15  C3   C4   C5    180.00   0.0  0
 21W  CONST_24  C9   C10  N14  C13   180.00   0.0  0
 21W  CONST_25  C9   C10  N11  C12   180.00   0.0  0
 21W  CONST_26  C17  C19  C23  C22   180.00   0.0  0
 21W  CONST_27  C17  C19  C23  C24     0.00   0.0  0
 21W  CONST_28  S21  C20  C19  C17   180.00   0.0  0
 21W  CONST_29  O25  C24  N26  C27   180.00   0.0  0
 21W  CONST_30  H2   C4   C3   C2    180.00   0.0  0
 21W  CONST_31  H1   C2   C3   C4    180.00   0.0  0
 21W  CONST_32  H4   C5   C6   C1    180.00   0.0  0
 21W  CONST_33  H3   C1   C6   C5    180.00   0.0  0
 21W  CONST_34  H15  N14  C13  C12   180.00   0.0  0
 21W  CONST_35  H7   C20  C19  C23   180.00   0.0  0
 21W  CONST_36  H6   C12  N11  C10   180.00   0.0  0
 21W  CONST_37  H5   C13  N14  C10   180.00   0.0  0
 21W  CONST_38  H17  N26  C24  C23   180.00   0.0  0
 21W  CONST_39  H8   C27  N28  C22   180.00   0.0  0
 21W  CONST_40  C15  N16  C17  C19   180.00   0.0  0
 21W  CONST_41  H18  N16  C17  C19     0.00   0.0  0
 21W  CONST_42  O18  C17  N16  C15     0.00   0.0  0
 21W  Var_01    N16  C15  C3   C2     60.02  30.0  2
 21W  Var_02    N8   C7   C6   C1    140.34  30.0  2
 21W  Var_03    O18  C17  C19  C20   119.83  30.0  2
 21W  Var_04    N8   C9   C10  N14    33.53  30.0  1
 21W  Var_05    C17  N16  C15  C3   -104.10  30.0  1
 21W  Var_06    C9   N8   C7   C6    176.76  30.0  3
 21W  Var_07    C7   N8   C9   C10  -168.36  30.0  1

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
 21W  plan-1  C13  0.020
 21W  plan-1  C12  0.020
 21W  plan-1  C10  0.020
 21W  plan-1  C9   0.020
 21W  plan-1  N14  0.020
 21W  plan-1  N11  0.020
 21W  plan-1  H6   0.020
 21W  plan-1  H15  0.020
 21W  plan-1  H5   0.020
 21W  plan-2  C2   0.020
 21W  plan-2  C4   0.020
 21W  plan-2  C1   0.020
 21W  plan-2  C5   0.020
 21W  plan-2  C3   0.020
 21W  plan-2  C6   0.020
 21W  plan-2  C15  0.020
 21W  plan-2  C7   0.020
 21W  plan-2  H1   0.020
 21W  plan-2  H2   0.020
 21W  plan-2  H3   0.020
 21W  plan-2  H4   0.020
 21W  plan-3  C20  0.020
 21W  plan-3  C23  0.020
 21W  plan-3  C19  0.020
 21W  plan-3  C22  0.020
 21W  plan-3  C27  0.020
 21W  plan-3  C24  0.020
 21W  plan-3  C17  0.020
 21W  plan-3  N28  0.020
 21W  plan-3  N26  0.020
 21W  plan-3  O25  0.020
 21W  plan-3  S21  0.020
 21W  plan-3  H7   0.020
 21W  plan-3  H8   0.020
 21W  plan-3  H17  0.020
 21W  plan-4  C19  0.020
 21W  plan-4  C17  0.020
 21W  plan-4  C15  0.020
 21W  plan-4  N16  0.020
 21W  plan-4  O18  0.020
 21W  plan-4  H18  0.020

