# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:37:32 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: ~{N}-(4-morpholin-4-ylthieno[2,3-d]pyrimidin-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1nc2sccc2c(n1)N3CCOCC3
#
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
 7NT  7NT  ~{N}-(4-morpholin-4-ylthieno[2,3-d]pyrimidin-2-yl)propanamide  ligand  36  20  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7NT
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
 7NT  C01   C  CH3   0  -0.658   5.9820   2.0126  -0.1430
 7NT  C02   C  CH2   0  -0.590   4.4868   2.2019   0.0275
 7NT  C03   C  C     0   0.548   3.7010   0.9102  -0.0496
 7NT  O04   O  O     0  -0.439   4.2176  -0.1793  -0.1545
 7NT  N05   N  NH1   0  -0.720   2.3455   1.1175   0.0180
 7NT  C06   C  CR6   0   0.583   1.3063   0.2058   0.0048
 7NT  N07   N  N     0  -0.521   0.1071   0.7901  -0.0060
 7NT  C08   C  CR6   0   0.532  -0.9868   0.0429  -0.0219
 7NT  N09   N  NT    0  -0.503  -2.1844   0.6824  -0.0657
 7NT  C10   C  CH2   0  -0.319  -2.2213   2.1302   0.0798
 7NT  C11   C  CH2   0  -0.190  -3.5939   2.5444   0.5799
 7NT  O12   O  O2    0  -0.481  -4.6303   2.0862  -0.2583
 7NT  C13   C  CH2   0  -0.183  -4.6021   0.6820  -0.3665
 7NT  C14   C  CH2   0  -0.335  -3.2724   0.1985  -0.9088
 7NT  C15   C  CR56  0   0.023  -0.8591  -1.3732   0.0488
 7NT  C16   C  CR15  0  -0.204  -1.7951  -2.4467   0.2127
 7NT  C17   C  CR15  0  -0.468  -1.1924  -3.6550   0.2642
 7NT  S18   S  S2    0   0.214   0.5303  -3.5585   0.1371
 7NT  C19   C  CR56  0  -0.010   0.4583  -1.8332   0.0304
 7NT  N20   N  N     0  -0.456   1.5569  -1.0841  -0.0086
 7NT  H1    H  HCH3  0   0.237   6.4873   2.9737  -0.0558
 7NT  H2    H  HCH3  0   0.230   6.3943   1.3515   0.6181
 7NT  H3    H  HCH3  0   0.230   6.2265   1.5966  -1.1196
 7NT  H021  H  HCH2  0   0.276   4.2672   2.6711   0.9915
 7NT  H022  H  HCH2  0   0.271   4.0991   2.8925  -0.7270
 7NT  H051  H  HNH1  0   0.417   2.0333   2.0767   0.0646
 7NT  H101  H  HCH2  0   0.267  -1.4738   2.4493   0.8028
 7NT  H102  H  HCH2  0   0.236  -1.9916   2.6245  -0.8722
 7NT  H111  H  HCH2  0   0.209  -3.7334   2.1685   1.6032
 7NT  H112  H  HCH2  0   0.246  -3.6540   3.6330   0.6118
 7NT  H131  H  HCH2  0   0.211  -4.7932   0.2131   0.6089
 7NT  H132  H  HCH2  0   0.247  -5.4015   0.3869  -1.0473
 7NT  H141  H  HCH2  0   0.251  -3.1301   0.5725  -1.9305
 7NT  H142  H  HCH2  0   0.267  -3.2827  -0.8844  -0.9691
 7NT  H161  H  HCR5  0   0.276  -2.8630  -2.3372   0.3224
 7NT  H171  H  HCR5  0   0.304  -1.6664  -4.6162   0.3870

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
 7NT  C01  C02   single    1.517  0.020  1.517
 7NT  C02  C03   single    1.514  0.020  1.514
 7NT  C03  O04   double    1.210  0.020  1.210
 7NT  C03  N05   single    1.373  0.020  1.373
 7NT  N05  C06   single    1.382  0.020  1.382
 7NT  C06  N07   aromatic  1.334  0.020  1.334
 7NT  C06  N20   aromatic  1.314  0.020  1.314
 7NT  N07  C08   aromatic  1.325  0.020  1.325
 7NT  C08  N09   single    1.358  0.020  1.358
 7NT  C08  C15   aromatic  1.424  0.020  1.424
 7NT  N09  C10   single    1.455  0.020  1.455
 7NT  N09  C14   single    1.459  0.020  1.459
 7NT  C10  C11   single    1.519  0.020  1.519
 7NT  C11  O12   single    1.410  0.020  1.410
 7NT  O12  C13   single    1.409  0.020  1.409
 7NT  C13  C14   single    1.515  0.020  1.515
 7NT  C15  C16   aromatic  1.434  0.020  1.434
 7NT  C15  C19   aromatic  1.396  0.020  1.396
 7NT  C16  C17   aromatic  1.351  0.020  1.351
 7NT  C17  S18   aromatic  1.730  0.020  1.730
 7NT  S18  C19   aromatic  1.730  0.020  1.730
 7NT  C19  N20   aromatic  1.330  0.020  1.330
 7NT  C01  H1    single    0.970  0.020  1.090
 7NT  C01  H2    single    0.970  0.020  1.090
 7NT  C01  H3    single    0.970  0.020  1.090
 7NT  C02  H021  single    0.970  0.020  1.090
 7NT  C02  H022  single    0.970  0.020  1.090
 7NT  N05  H051  single    0.860  0.020  1.020
 7NT  C10  H101  single    0.970  0.020  1.090
 7NT  C10  H102  single    0.970  0.020  1.090
 7NT  C11  H111  single    0.970  0.020  1.090
 7NT  C11  H112  single    0.970  0.020  1.090
 7NT  C13  H131  single    0.970  0.020  1.090
 7NT  C13  H132  single    0.970  0.020  1.090
 7NT  C14  H141  single    0.970  0.020  1.090
 7NT  C14  H142  single    0.970  0.020  1.090
 7NT  C16  H161  single    0.930  0.020  1.080
 7NT  C17  H171  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
 7NT  H3    C01  H2    108.04  3.000
 7NT  H3    C01  H1    107.73  3.000
 7NT  H2    C01  H1    107.70  3.000
 7NT  H3    C01  C02   111.70  3.000
 7NT  H2    C01  C02   111.74  3.000
 7NT  H1    C01  C02   109.76  3.000
 7NT  H022  C02  H021  105.42  3.000
 7NT  H022  C02  C03   108.63  3.000
 7NT  H021  C02  C03   107.85  3.000
 7NT  H022  C02  C01   110.53  3.000
 7NT  H021  C02  C01   110.51  3.000
 7NT  C03   C02  C01   113.55  3.000
 7NT  N05   C03  O04   124.16  3.000
 7NT  N05   C03  C02   112.41  3.000
 7NT  O04   C03  C02   123.43  3.000
 7NT  H051  N05  C06   113.23  3.000
 7NT  H051  N05  C03   116.80  3.000
 7NT  C06   N05  C03   129.95  3.000
 7NT  N20   C06  N07   126.96  3.000
 7NT  N20   C06  N05   120.27  3.000
 7NT  N07   C06  N05   112.76  3.000
 7NT  C08   N07  C06   119.69  3.000
 7NT  C15   C08  N09   123.30  3.000
 7NT  C15   C08  N07   119.10  3.000
 7NT  N09   C08  N07   117.57  3.000
 7NT  C14   N09  C10   111.64  3.000
 7NT  C14   N09  C08   121.33  3.000
 7NT  C10   N09  C08   119.17  3.000
 7NT  H102  C10  H101  107.50  3.000
 7NT  H102  C10  C11   110.62  3.000
 7NT  H101  C10  C11   108.80  3.000
 7NT  H102  C10  N09   110.87  3.000
 7NT  H101  C10  N09   109.93  3.000
 7NT  C11   C10  N09   109.10  3.000
 7NT  H112  C11  H111  107.89  3.000
 7NT  H112  C11  O12   107.54  3.000
 7NT  H111  C11  O12   110.44  3.000
 7NT  H112  C11  C10   109.37  3.000
 7NT  H111  C11  C10   109.15  3.000
 7NT  O12   C11  C10   112.34  3.000
 7NT  C13   O12  C11   110.79  3.000
 7NT  H132  C13  H131  108.13  3.000
 7NT  H132  C13  C14   109.48  3.000
 7NT  H131  C13  C14   109.52  3.000
 7NT  H132  C13  O12   107.64  3.000
 7NT  H131  C13  O12   110.71  3.000
 7NT  C14   C13  O12   111.29  3.000
 7NT  H142  C14  H141  106.84  3.000
 7NT  H142  C14  C13   109.28  3.000
 7NT  H141  C14  C13   109.77  3.000
 7NT  H142  C14  N09   111.74  3.000
 7NT  H141  C14  N09   109.17  3.000
 7NT  C13   C14  N09   109.99  3.000
 7NT  C19   C15  C16   111.78  3.000
 7NT  C19   C15  C08   114.33  3.000
 7NT  C16   C15  C08   133.78  3.000
 7NT  H161  C16  C17   121.88  3.000
 7NT  H161  C16  C15   125.58  3.000
 7NT  C17   C16  C15   112.50  3.000
 7NT  H171  C17  S18   119.70  3.000
 7NT  H171  C17  C16   127.24  3.000
 7NT  S18   C17  C16   113.05  3.000
 7NT  C19   S18  C17    91.07  3.000
 7NT  N20   C19  S18   121.94  3.000
 7NT  N20   C19  C15   126.46  3.000
 7NT  S18   C19  C15   111.54  3.000
 7NT  C19   N20  C06   113.27  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
 7NT  CONST_01  C15   C08  N07  C06     0.00   0.0  0
 7NT  CONST_02  C15   C19  N20  C06     0.00   0.0  0
 7NT  CONST_03  S18   C19  N20  C06   180.00   0.0  0
 7NT  CONST_04  C19   N20  C06  N07     0.00   0.0  0
 7NT  CONST_05  C16   C15  C08  N07   180.00   0.0  0
 7NT  CONST_06  C19   C15  C08  N07     0.00   0.0  0
 7NT  CONST_07  N20   C06  N07  C08     0.00   0.0  0
 7NT  CONST_08  C17   C16  C15  C08   180.00   0.0  0
 7NT  CONST_09  S18   C19  C15  C08   180.00   0.0  0
 7NT  CONST_10  N20   C19  C15  C08     0.00   0.0  0
 7NT  CONST_11  S18   C17  C16  C15     0.00   0.0  0
 7NT  CONST_12  C17   S18  C19  C15     0.00   0.0  0
 7NT  CONST_13  S18   C19  C15  C16     0.00   0.0  0
 7NT  CONST_14  N20   C19  C15  C16   180.00   0.0  0
 7NT  CONST_15  C19   S18  C17  C16     0.00   0.0  0
 7NT  CONST_16  C19   C15  C16  C17     0.00   0.0  0
 7NT  CONST_17  N20   C19  S18  C17   180.00   0.0  0
 7NT  CONST_18  N09   C08  N07  C06   180.00   0.0  0
 7NT  CONST_19  C16   C15  C08  N09     0.00   0.0  0
 7NT  CONST_20  C19   C15  C08  N09   180.00   0.0  0
 7NT  CONST_21  C08   N07  C06  N05   180.00   0.0  0
 7NT  CONST_22  C19   N20  C06  N05   180.00   0.0  0
 7NT  CONST_23  H161  C16  C15  C08     0.00   0.0  0
 7NT  CONST_24  H171  C17  C16  C15   180.00   0.0  0
 7NT  CONST_25  N07   C06  N05  C03   180.00   0.0  0
 7NT  CONST_26  N20   C06  N05  C03     0.00   0.0  0
 7NT  CONST_27  H051  N05  C06  N07     0.00   0.0  0
 7NT  CONST_28  C06   N05  C03  C02   180.00   0.0  0
 7NT  CONST_29  C06   N05  C03  O04     0.00   0.0  0
 7NT  Var_01    C10   N09  C08  N07    -7.81  30.0  2
 7NT  Var_02    C11   C10  N09  C08  -156.26  30.0  1
 7NT  Var_03    C13   C14  N09  C08   156.23  30.0  1
 7NT  Var_04    O12   C11  C10  N09   -56.02  30.0  1
 7NT  Var_05    O12   C13  C14  N09    56.43  30.0  1
 7NT  Var_06    C14   C13  O12  C11   -58.31  30.0  1
 7NT  Var_07    O04   C03  C02  C01     4.30  30.0  3
 7NT  Var_08    H1    C01  C02  C03  -178.79  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
 7NT  plan-1  N05   0.020
 7NT  plan-1  C06   0.020
 7NT  plan-1  N07   0.020
 7NT  plan-1  C08   0.020
 7NT  plan-1  N09   0.020
 7NT  plan-1  C15   0.020
 7NT  plan-1  C16   0.020
 7NT  plan-1  C17   0.020
 7NT  plan-1  S18   0.020
 7NT  plan-1  C19   0.020
 7NT  plan-1  N20   0.020
 7NT  plan-1  H161  0.020
 7NT  plan-1  H171  0.020
 7NT  plan-2  C02   0.020
 7NT  plan-2  C03   0.020
 7NT  plan-2  O04   0.020
 7NT  plan-2  N05   0.020
 7NT  plan-2  C06   0.020
 7NT  plan-2  H051  0.020

