# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:39:03 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-[2-methyl-4-(thiophen-3-ylmethoxy)-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2[nH]cc(c3ccnc(N)c3)c2c(OCc4cscc4)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
 QZW  QZW  4-[2-methyl-4-(thiophen-3-ylmethoxy)-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]pyridin-2-amine  ligand  39  24  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QZW
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
 QZW  C1   C  CH3   0  -0.725  44.8075  3.7344  18.4288
 QZW  N1   N  N     0  -0.490  44.1000  3.6691  16.1264
 QZW  O1   O  O2    0  -0.452  43.4261  3.4817  13.9492
 QZW  S1   S  S2    0   0.215  43.0988  0.2380  10.5184
 QZW  C2   C  CR6   0   0.344  44.3559  4.4459  17.1941
 QZW  N2   N  NR15  0  -0.664  43.5967  7.6164  15.8687
 QZW  C3   C  CR6   0   0.466  43.7094  4.2269  15.0036
 QZW  N3   N  NH2   0  -0.838  40.4372  7.7432  10.0418
 QZW  C4   C  CH2   0  -0.238  43.4881  2.0575  14.0610
 QZW  N4   N  N     0  -0.461  42.1062  6.1771   9.8132
 QZW  C5   C  CR5   0   0.140  43.0860  1.5109  12.7328
 QZW  N5   N  N     0  -0.450  44.2317  5.7563  17.2358
 QZW  C6   C  CR15  0  -0.522  43.8688  0.6893  11.9791
 QZW  C7   C  CR15  0  -0.458  41.7072  1.1649  10.9001
 QZW  C8   C  CR15  0  -0.203  41.8348  1.7847  12.1027
 QZW  C9   C  CR56  0  -0.108  43.5741  5.6181  14.8922
 QZW  C10  C  CR56  0   0.497  43.8359  6.3024  16.0864
 QZW  C11  C  CR15  0  -0.041  43.1859  7.7926  14.5778
 QZW  C12  C  CR5   0  -0.013  43.1557  6.5896  13.9226
 QZW  C13  C  CR6   0   0.134  42.7916  6.4196  12.5151
 QZW  C14  C  CR16  0  -0.458  41.7393  7.1407  11.9754
 QZW  C15  C  CR6   0   0.459  41.4315  7.0013  10.6118
 QZW  C16  C  CR16  0  -0.063  43.1136  5.4891  10.3437
 QZW  C17  C  CR16  0  -0.414  43.5064  5.5670  11.6630
 QZW  H1   H  HCH3  0   0.253  44.0370  3.0437  18.7749
 QZW  H2   H  HCH3  0   0.252  45.6994  3.1408  18.2250
 QZW  H3   H  HCH3  0   0.246  45.0284  4.4376  19.2277
 QZW  H4   H  HNR5  0   0.417  43.7139  8.3512  16.5489
 QZW  H5   H  HNH2  0   0.379  40.0775  7.4042   9.1645
 QZW  H6   H  HNH2  0   0.388  39.7368  8.1330  10.6506
 QZW  H7   H  HCH2  0   0.248  42.8079  1.7216  14.8480
 QZW  H8   H  HCH2  0   0.252  44.4952  1.7320  14.3286
 QZW  H9   H  HCR5  0   0.296  44.8602  0.3299  12.2117
 QZW  H10  H  HCR5  0   0.295  40.8700  1.2010  10.2201
 QZW  H11  H  HCR5  0   0.265  41.0684  2.4164  12.5301
 QZW  H12  H  HCR5  0   0.298  42.9668  8.7789  14.2010
 QZW  H13  H  HCR6  0   0.257  41.1419  7.7955  12.5980
 QZW  H14  H  HCR6  0   0.251  43.6460  4.8316   9.6640
 QZW  H15  H  HCR6  0   0.244  44.3497  4.9917  12.0139

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
 QZW  N4   C16  aromatic  1.330  0.020  1.330
 QZW  N4   C15  aromatic  1.331  0.020  1.331
 QZW  N3   C15  single    1.365  0.020  1.365
 QZW  C16  C17  aromatic  1.379  0.020  1.379
 QZW  C7   S1   aromatic  1.715  0.020  1.715
 QZW  C7   C8   aromatic  1.359  0.020  1.359
 QZW  C15  C14  aromatic  1.405  0.020  1.405
 QZW  S1   C6   aromatic  1.712  0.020  1.712
 QZW  C8   C5   aromatic  1.427  0.020  1.427
 QZW  C17  C13  aromatic  1.401  0.020  1.401
 QZW  C14  C13  aromatic  1.385  0.020  1.385
 QZW  C6   C5   aromatic  1.362  0.020  1.362
 QZW  C13  C12  single    1.464  0.020  1.464
 QZW  C5   C4   single    1.491  0.020  1.491
 QZW  C12  C11  aromatic  1.370  0.020  1.370
 QZW  C12  C9   aromatic  1.435  0.020  1.435
 QZW  O1   C4   single    1.430  0.020  1.430
 QZW  O1   C3   single    1.322  0.020  1.322
 QZW  C11  N2   aromatic  1.366  0.020  1.366
 QZW  C9   C3   aromatic  1.402  0.020  1.402
 QZW  C9   C10  aromatic  1.401  0.020  1.401
 QZW  C3   N1   aromatic  1.313  0.020  1.313
 QZW  N2   C10  aromatic  1.353  0.020  1.353
 QZW  C10  N5   aromatic  1.333  0.020  1.333
 QZW  N1   C2   aromatic  1.345  0.020  1.345
 QZW  C2   N5   aromatic  1.317  0.020  1.317
 QZW  C2   C1   single    1.495  0.020  1.495
 QZW  C1   H1   single    0.970  0.020  1.090
 QZW  C1   H2   single    0.970  0.020  1.090
 QZW  C1   H3   single    0.970  0.020  1.090
 QZW  N2   H4   single    0.860  0.020  1.020
 QZW  N3   H5   single    0.890  0.020  1.040
 QZW  N3   H6   single    0.890  0.020  1.040
 QZW  C4   H7   single    0.970  0.020  1.090
 QZW  C4   H8   single    0.970  0.020  1.090
 QZW  C6   H9   single    0.930  0.020  1.080
 QZW  C7   H10  single    0.930  0.020  1.080
 QZW  C8   H11  single    0.930  0.020  1.080
 QZW  C11  H12  single    0.930  0.020  1.080
 QZW  C14  H13  single    0.930  0.020  1.080
 QZW  C16  H14  single    0.930  0.020  1.080
 QZW  C17  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
 QZW  H3   C1   H2   108.86  3.000
 QZW  H3   C1   H1   108.65  3.000
 QZW  H2   C1   H1   107.00  3.000
 QZW  H3   C1   C2   111.13  3.000
 QZW  H2   C1   C2   110.59  3.000
 QZW  H1   C1   C2   110.49  3.000
 QZW  C3   N1   C2   119.34  3.000
 QZW  C4   O1   C3   119.33  3.000
 QZW  C7   S1   C6    91.87  3.000
 QZW  N5   C2   N1   125.59  3.000
 QZW  N5   C2   C1   118.42  3.000
 QZW  N1   C2   C1   115.99  3.000
 QZW  H4   N2   C11  125.35  3.000
 QZW  H4   N2   C10  125.36  3.000
 QZW  C11  N2   C10  109.29  3.000
 QZW  C9   C3   O1   118.38  3.000
 QZW  C9   C3   N1   121.20  3.000
 QZW  O1   C3   N1   120.41  3.000
 QZW  H6   N3   H5   114.13  3.000
 QZW  H6   N3   C15  117.69  3.000
 QZW  H5   N3   C15  116.16  3.000
 QZW  H8   C4   H7   107.82  3.000
 QZW  H8   C4   C5   110.96  3.000
 QZW  H7   C4   C5   111.15  3.000
 QZW  H8   C4   O1   110.86  3.000
 QZW  H7   C4   O1   109.60  3.000
 QZW  C5   C4   O1   106.48  3.000
 QZW  C16  N4   C15  117.69  3.000
 QZW  C8   C5   C6   112.03  3.000
 QZW  C6   C5   C4   123.97  3.000
 QZW  C8   C5   C4   123.99  3.000
 QZW  C10  N5   C2   114.10  3.000
 QZW  H9   C6   C5   127.53  3.000
 QZW  H9   C6   S1   120.59  3.000
 QZW  C5   C6   S1   111.88  3.000
 QZW  H10  C7   C8   127.97  3.000
 QZW  H10  C7   S1   120.48  3.000
 QZW  C8   C7   S1   111.55  3.000
 QZW  H11  C8   C7   123.35  3.000
 QZW  H11  C8   C5   123.98  3.000
 QZW  C7   C8   C5   112.67  3.000
 QZW  C12  C9   C10  107.44  3.000
 QZW  C10  C9   C3   113.51  3.000
 QZW  C12  C9   C3   138.90  3.000
 QZW  C9   C10  N5   126.19  3.000
 QZW  N5   C10  N2   126.10  3.000
 QZW  C9   C10  N2   107.71  3.000
 QZW  H12  C11  C12  129.16  3.000
 QZW  H12  C11  N2   120.61  3.000
 QZW  C12  C11  N2   110.20  3.000
 QZW  C13  C12  C11  124.56  3.000
 QZW  C11  C12  C9   105.36  3.000
 QZW  C13  C12  C9   130.07  3.000
 QZW  C17  C13  C14  117.86  3.000
 QZW  C14  C13  C12  120.22  3.000
 QZW  C17  C13  C12  121.90  3.000
 QZW  H13  C14  C15  119.81  3.000
 QZW  H13  C14  C13  120.64  3.000
 QZW  C15  C14  C13  119.54  3.000
 QZW  C14  C15  N4   122.19  3.000
 QZW  C14  C15  N3   120.72  3.000
 QZW  N4   C15  N3   117.07  3.000
 QZW  H14  C16  C17  119.59  3.000
 QZW  H14  C16  N4   115.79  3.000
 QZW  C17  C16  N4   124.62  3.000
 QZW  H15  C17  C16  120.23  3.000
 QZW  H15  C17  C13  121.67  3.000
 QZW  C16  C17  C13  118.09  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
 QZW  CONST_01  C12  C9   C3   N1    180.00   0.0  0
 QZW  CONST_02  C10  C9   C3   N1      0.00   0.0  0
 QZW  CONST_03  C10  N5   C2   N1      0.00   0.0  0
 QZW  CONST_04  C5   C8   C7   S1      0.00   0.0  0
 QZW  CONST_05  C8   C5   C6   S1      0.00   0.0  0
 QZW  CONST_06  C9   C3   N1   C2      0.00   0.0  0
 QZW  CONST_07  C9   C10  N5   C2      0.00   0.0  0
 QZW  CONST_08  N2   C10  N5   C2    180.00   0.0  0
 QZW  CONST_09  C13  C12  C11  N2    180.00   0.0  0
 QZW  CONST_10  C9   C12  C11  N2      0.00   0.0  0
 QZW  CONST_11  C12  C9   C10  N2      0.00   0.0  0
 QZW  CONST_12  C3   C9   C10  N2    180.00   0.0  0
 QZW  CONST_13  C13  C12  C9   C3      0.00   0.0  0
 QZW  CONST_14  C11  C12  C9   C3    180.00   0.0  0
 QZW  CONST_15  N5   C10  C9   C3      0.00   0.0  0
 QZW  CONST_16  N5   C2   N1   C3      0.00   0.0  0
 QZW  CONST_17  C13  C17  C16  N4      0.00   0.0  0
 QZW  CONST_18  C13  C14  C15  N4      0.00   0.0  0
 QZW  CONST_19  C7   S1   C6   C5      0.00   0.0  0
 QZW  CONST_20  C12  C9   C10  N5    180.00   0.0  0
 QZW  CONST_21  C11  N2   C10  N5    180.00   0.0  0
 QZW  CONST_22  C8   C7   S1   C6      0.00   0.0  0
 QZW  CONST_23  C7   C8   C5   C6      0.00   0.0  0
 QZW  CONST_26  C11  N2   C10  C9      0.00   0.0  0
 QZW  CONST_27  C13  C12  C9   C10   180.00   0.0  0
 QZW  CONST_28  C11  C12  C9   C10     0.00   0.0  0
 QZW  CONST_29  C12  C11  N2   C10     0.00   0.0  0
 QZW  CONST_32  C16  C17  C13  C12   180.00   0.0  0
 QZW  CONST_33  C15  C14  C13  C12   180.00   0.0  0
 QZW  CONST_34  C16  N4   C15  C14     0.00   0.0  0
 QZW  CONST_35  C16  C17  C13  C14     0.00   0.0  0
 QZW  CONST_36  C17  C16  N4   C15     0.00   0.0  0
 QZW  CONST_37  C17  C13  C14  C15     0.00   0.0  0
 QZW  CONST_38  C3   N1   C2   C1    180.00   0.0  0
 QZW  CONST_39  C10  N5   C2   C1    180.00   0.0  0
 QZW  CONST_40  C12  C9   C3   O1      0.00   0.0  0
 QZW  CONST_41  C10  C9   C3   O1    180.00   0.0  0
 QZW  CONST_42  C2   N1   C3   O1    180.00   0.0  0
 QZW  CONST_43  C4   C5   C6   S1    180.00   0.0  0
 QZW  CONST_44  C16  N4   C15  N3    180.00   0.0  0
 QZW  CONST_45  C13  C14  C15  N3    180.00   0.0  0
 QZW  CONST_46  C7   C8   C5   C4    180.00   0.0  0
 QZW  CONST_47  H11  C8   C7   S1    180.00   0.0  0
 QZW  CONST_48  H15  C17  C16  N4    180.00   0.0  0
 QZW  CONST_49  H13  C14  C15  N4    180.00   0.0  0
 QZW  CONST_50  H10  C7   C8   C5    180.00   0.0  0
 QZW  CONST_51  H4   N2   C10  N5      0.00   0.0  0
 QZW  CONST_52  H9   C6   S1   C7    180.00   0.0  0
 QZW  CONST_53  H12  C11  C12  C9    180.00   0.0  0
 QZW  CONST_54  H14  C16  C17  C13   180.00   0.0  0
 QZW  Var_01    C8   C5   C4   O1    -57.93  30.0  2
 QZW  Var_02    C5   C4   O1   C3    178.58  30.0  3
 QZW  Var_03    C9   C3   O1   C4   -176.69  30.0  2
 QZW  Var_04    H1   C1   C2   N1    -61.52  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
 QZW  plan-1  S1   0.020
 QZW  plan-1  C4   0.020
 QZW  plan-1  C5   0.020
 QZW  plan-1  C6   0.020
 QZW  plan-1  C7   0.020
 QZW  plan-1  C8   0.020
 QZW  plan-1  H9   0.020
 QZW  plan-1  H10  0.020
 QZW  plan-1  H11  0.020
 QZW  plan-2  N3   0.020
 QZW  plan-2  N4   0.020
 QZW  plan-2  C12  0.020
 QZW  plan-2  C13  0.020
 QZW  plan-2  C14  0.020
 QZW  plan-2  C15  0.020
 QZW  plan-2  C16  0.020
 QZW  plan-2  C17  0.020
 QZW  plan-2  H13  0.020
 QZW  plan-2  H14  0.020
 QZW  plan-2  H15  0.020
 QZW  plan-3  C1   0.020
 QZW  plan-3  N1   0.020
 QZW  plan-3  O1   0.020
 QZW  plan-3  C2   0.020
 QZW  plan-3  N2   0.020
 QZW  plan-3  C3   0.020
 QZW  plan-3  N5   0.020
 QZW  plan-3  C9   0.020
 QZW  plan-3  C10  0.020
 QZW  plan-3  C11  0.020
 QZW  plan-3  C12  0.020
 QZW  plan-3  C13  0.020
 QZW  plan-3  H4   0.020
 QZW  plan-3  H12  0.020
 QZW  plan-4  N3   0.020
 QZW  plan-4  C15  0.020
 QZW  plan-4  H5   0.020
 QZW  plan-4  H6   0.020

