# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:37:01 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(CNC(=O)c2csc3N=CNC(=O)c23)cc1
#
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
 21X  21X  N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide  ligand  36  22  .  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_21X
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
 21X  C1   C  CR16  0  -0.270  -4.2890   0.4201   0.6834
 21X  C5   C  CR16  0  -0.294  -5.1131  -0.4608  -1.3779
 21X  C2   C  CR16  0  -0.281  -3.0820  -0.2282   0.4781
 21X  C4   C  CR16  0  -0.297  -3.9005  -1.1070  -1.5872
 21X  C14  C  CR15  0  -0.513   1.1184   1.4675   0.3560
 21X  C17  C  CR56  0  -0.058   2.8964  -0.0022   0.3436
 21X  C13  C  CR5   0   0.044   1.4799   0.1609   0.2714
 21X  C6   C  CR6   0   0.075  -5.3241   0.3172  -0.2455
 21X  C3   C  CR6   0   0.101  -2.8708  -1.0024  -0.6613
 21X  C16  C  CR56  0  -0.020   3.5603   1.2022   0.4911
 21X  C21  C  CR16  0   0.162   5.5828   0.2885   0.4891
 21X  C18  C  CR6   0   0.542   3.6842  -1.2020   0.1909
 21X  C11  C  C     0   0.504   0.4783  -0.9460   0.2614
 21X  C7   C  CH2   0  -0.336  -6.6273   1.0503  -0.0491
 21X  C9   C  CH2   0  -0.368  -1.5665  -1.7294  -0.8742
 21X  N22  N  N     0  -0.429   4.8975   1.3792   0.5738
 21X  N20  N  NR16  0  -0.652   5.0444  -0.9357   0.3146
 21X  N8   N  NH2   0  -0.793  -7.0130   1.1110   1.3497
 21X  N10  N  NH1   0  -0.616  -0.4213  -0.8600  -0.7312
 21X  O19  O  O     0  -0.447   3.2797  -2.3252  -0.0368
 21X  O12  O  O     0  -0.471   0.4853  -1.8088   1.1228
 21X  S15  S  S2    0   0.266   2.4612   2.5275   0.5411
 21X  H1   H  HCR6  0   0.246  -4.4372   1.0084   1.5799
 21X  H2   H  HCR6  0   0.246  -5.9036  -0.5663  -2.1123
 21X  H3   H  HCR6  0   0.246  -2.2988  -0.1311   1.2213
 21X  H4   H  HCR6  0   0.249  -3.7620  -1.7050  -2.4807
 21X  H6   H  HCR6  0   0.311   6.6625   0.3218   0.5516
 21X  H7   H  HCH2  0   0.240  -6.5044   2.0780  -0.4043
 21X  H8   H  HCH2  0   0.213  -7.3848   0.5974  -0.7029
 21X  H9   H  HCH2  0   0.270  -1.4637  -2.5422  -0.1553
 21X  H10  H  HCH2  0   0.269  -1.5529  -2.1823  -1.8673
 21X  H11  H  HNR6  0   0.439   5.6760  -1.7225   0.2327
 21X  H12  H  HNH2  0   0.354  -7.8306   1.6988   1.4474
 21X  H13  H  HNH2  0   0.344  -7.2886   0.1900   1.6664
 21X  H15  H  HNH1  0   0.411  -0.3133  -0.1234  -1.4106
 21X  H5   H  HCR5  0   0.314   0.1169   1.8718   0.3546

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
 21X  S15  C14  aromatic  1.721  0.020  1.721
 21X  S15  C16  aromatic  1.722  0.020  1.722
 21X  C14  C13  aromatic  1.358  0.020  1.358
 21X  C16  N22  single    1.351  0.020  1.351
 21X  C16  C17  aromatic  1.383  0.020  1.383
 21X  N22  C21  double    1.291  0.020  1.291
 21X  C13  C17  aromatic  1.428  0.020  1.428
 21X  C13  C11  single    1.493  0.020  1.493
 21X  O12  C11  double    1.219  0.020  1.219
 21X  C17  C18  single    1.443  0.020  1.443
 21X  C21  N20  single    1.349  0.020  1.349
 21X  C11  N10  single    1.342  0.020  1.342
 21X  C18  N20  single    1.392  0.020  1.392
 21X  C18  O19  double    1.215  0.020  1.215
 21X  N10  C9   single    1.445  0.020  1.445
 21X  C9   C3   single    1.508  0.020  1.508
 21X  C4   C5   aromatic  1.390  0.020  1.390
 21X  C4   C3   aromatic  1.389  0.020  1.389
 21X  C5   C6   aromatic  1.390  0.020  1.390
 21X  C3   C2   aromatic  1.394  0.020  1.394
 21X  C6   C7   single    1.508  0.020  1.508
 21X  C6   C1   aromatic  1.395  0.020  1.395
 21X  C2   C1   aromatic  1.385  0.020  1.385
 21X  C7   N8   single    1.452  0.020  1.452
 21X  C1   H1   single    0.930  0.020  1.080
 21X  C5   H2   single    0.930  0.020  1.080
 21X  C2   H3   single    0.930  0.020  1.080
 21X  C4   H4   single    0.930  0.020  1.080
 21X  C14  H5   single    0.930  0.020  1.080
 21X  C21  H6   single    0.930  0.020  1.080
 21X  C7   H7   single    0.970  0.020  1.090
 21X  C7   H8   single    0.970  0.020  1.090
 21X  C9   H9   single    0.970  0.020  1.090
 21X  C9   H10  single    0.970  0.020  1.090
 21X  N20  H11  single    0.860  0.020  1.020
 21X  N8   H12  single    0.890  0.020  1.040
 21X  N8   H13  single    0.890  0.020  1.040
 21X  N10  H15  single    0.860  0.020  1.020

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
 21X  H1   C1   C6   119.35  3.000
 21X  H1   C1   C2   119.76  3.000
 21X  C6   C1   C2   120.89  3.000
 21X  H2   C5   C6   119.71  3.000
 21X  H2   C5   C4   119.27  3.000
 21X  C6   C5   C4   121.02  3.000
 21X  H3   C2   C3   120.05  3.000
 21X  H3   C2   C1   119.07  3.000
 21X  C3   C2   C1   120.87  3.000
 21X  H4   C4   C3   119.76  3.000
 21X  H4   C4   C5   119.48  3.000
 21X  C3   C4   C5   120.76  3.000
 21X  H5   C14  S15  119.55  3.000
 21X  H5   C14  C13  127.36  3.000
 21X  S15  C14  C13  113.05  3.000
 21X  C18  C17  C16  118.24  3.000
 21X  C18  C17  C13  129.13  3.000
 21X  C16  C17  C13  112.47  3.000
 21X  C11  C13  C17  125.55  3.000
 21X  C11  C13  C14  122.35  3.000
 21X  C17  C13  C14  111.77  3.000
 21X  C7   C6   C5   120.62  3.000
 21X  C7   C6   C1   121.25  3.000
 21X  C5   C6   C1   118.12  3.000
 21X  C9   C3   C4   120.71  3.000
 21X  C4   C3   C2   118.33  3.000
 21X  C9   C3   C2   120.94  3.000
 21X  S15  C16  N22  121.93  3.000
 21X  N22  C16  C17  126.55  3.000
 21X  S15  C16  C17  111.52  3.000
 21X  H6   C21  N20  115.71  3.000
 21X  H6   C21  N22  119.99  3.000
 21X  N20  C21  N22  124.30  3.000
 21X  O19  C18  N20  121.26  3.000
 21X  O19  C18  C17  127.33  3.000
 21X  N20  C18  C17  111.41  3.000
 21X  O12  C11  N10  124.86  3.000
 21X  N10  C11  C13  114.03  3.000
 21X  O12  C11  C13  121.07  3.000
 21X  H8   C7   H7   105.75  3.000
 21X  H8   C7   N8   114.04  3.000
 21X  H7   C7   N8   107.65  3.000
 21X  H8   C7   C6   108.55  3.000
 21X  H7   C7   C6   108.50  3.000
 21X  N8   C7   C6   112.04  3.000
 21X  H10  C9   H9   106.83  3.000
 21X  H10  C9   N10  109.25  3.000
 21X  H9   C9   N10  107.98  3.000
 21X  H10  C9   C3   109.83  3.000
 21X  H9   C9   C3   110.36  3.000
 21X  N10  C9   C3   112.42  3.000
 21X  C21  N22  C16  114.24  3.000
 21X  H11  N20  C18  116.99  3.000
 21X  H11  N20  C21  117.84  3.000
 21X  C18  N20  C21  125.13  3.000
 21X  H13  N8   H12  106.17  3.000
 21X  H13  N8   C7   109.61  3.000
 21X  H12  N8   C7   109.39  3.000
 21X  H15  N10  C9   117.26  3.000
 21X  H15  N10  C11  118.25  3.000
 21X  C9   N10  C11  124.46  3.000
 21X  C16  S15  C14   91.19  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
 21X  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 21X  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 21X  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 21X  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 21X  CONST_05  C17  C16  S15  C14     0.00   0.0  0
 21X  CONST_06  C16  C17  C13  C14     0.00   0.0  0
 21X  CONST_07  S15  C14  C13  C17     0.00   0.0  0
 21X  CONST_08  C16  S15  C14  C13     0.00   0.0  0
 21X  CONST_09  S15  C16  C17  C13     0.00   0.0  0
 21X  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 21X  CONST_11  C3   C2   C1   C6      0.00   0.0  0
 21X  CONST_12  C21  N20  C18  C17     0.00   0.0  0
 21X  CONST_13  N20  C21  N22  C16     0.00   0.0  0
 21X  CONST_14  N22  C21  N20  C18     0.00   0.0  0
 21X  CONST_15  C9   C3   C2   C1    180.00   0.0  0
 21X  CONST_16  C9   C3   C4   C5    180.00   0.0  0
 21X  CONST_17  C7   C6   C1   C2    180.00   0.0  0
 21X  CONST_18  C7   C6   C5   C4    180.00   0.0  0
 21X  CONST_19  C11  C13  C17  C16   180.00   0.0  0
 21X  CONST_20  C11  C13  C17  C18     0.00   0.0  0
 21X  CONST_21  S15  C14  C13  C11   180.00   0.0  0
 21X  CONST_22  O19  C18  N20  C21   180.00   0.0  0
 21X  CONST_23  H2   C5   C6   C1    180.00   0.0  0
 21X  CONST_24  H1   C1   C6   C5    180.00   0.0  0
 21X  CONST_25  H4   C4   C3   C2    180.00   0.0  0
 21X  CONST_26  H3   C2   C3   C4    180.00   0.0  0
 21X  CONST_27  H5   C14  C13  C17   180.00   0.0  0
 21X  CONST_28  H11  N20  C18  C17   180.00   0.0  0
 21X  CONST_29  H6   C21  N22  C16   180.00   0.0  0
 21X  CONST_30  C9   N10  C11  C13   180.00   0.0  0
 21X  CONST_31  H15  N10  C11  C13     0.00   0.0  0
 21X  CONST_32  O12  C11  N10  C9      0.00   0.0  0
 21X  Var_01    N8   C7   C6   C1    -35.86  30.0  2
 21X  Var_02    N10  C9   C3   C2    -51.72  30.0  2
 21X  Var_03    O12  C11  C13  C14  -120.03  30.0  2
 21X  Var_04    C11  N10  C9   C3    112.38  30.0  1
 21X  Var_05    H12  N8   C7   C6    173.53  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
 21X  plan-1  C1   0.020
 21X  plan-1  C5   0.020
 21X  plan-1  C2   0.020
 21X  plan-1  C4   0.020
 21X  plan-1  C6   0.020
 21X  plan-1  C3   0.020
 21X  plan-1  C7   0.020
 21X  plan-1  C9   0.020
 21X  plan-1  H1   0.020
 21X  plan-1  H2   0.020
 21X  plan-1  H3   0.020
 21X  plan-1  H4   0.020
 21X  plan-2  C14  0.020
 21X  plan-2  C17  0.020
 21X  plan-2  C13  0.020
 21X  plan-2  C16  0.020
 21X  plan-2  C21  0.020
 21X  plan-2  C18  0.020
 21X  plan-2  C11  0.020
 21X  plan-2  N22  0.020
 21X  plan-2  N20  0.020
 21X  plan-2  O19  0.020
 21X  plan-2  S15  0.020
 21X  plan-2  H6   0.020
 21X  plan-2  H11  0.020
 21X  plan-2  H5   0.020
 21X  plan-3  C13  0.020
 21X  plan-3  C11  0.020
 21X  plan-3  C9   0.020
 21X  plan-3  N10  0.020
 21X  plan-3  O12  0.020
 21X  plan-3  H15  0.020

