# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:32:12 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-[2-amino-5-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)pyridin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(cc1)c2cc(cnc2N)c3scc4OCCOc34
#
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
 WTI  WTI  4-[2-amino-5-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)pyridin-3-yl]benzamide  ligand  40  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WTI
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
 WTI  N01   N  NH2   0  -0.813   6.6052   2.2682   0.1964
 WTI  C02   C  C     0   0.487   6.3454   0.9974   0.5392
 WTI  O03   O  O     0  -0.480   7.1835   0.2632   1.0445
 WTI  C04   C  CR6   0  -0.047   4.9597   0.5053   0.2651
 WTI  C05   C  CR16  0  -0.249   4.4966  -0.5937   0.9846
 WTI  C06   C  CR16  0  -0.292   3.2296  -1.1020   0.7608
 WTI  C07   C  CR6   0   0.049   2.3939  -0.5371  -0.2054
 WTI  C08   C  CR6   0  -0.037   1.0283  -1.0475  -0.4367
 WTI  C09   C  CR16  0  -0.245  -0.0472  -0.1805  -0.4357
 WTI  C10   C  CR6   0   0.058  -1.3523  -0.6368  -0.6383
 WTI  C11   C  CR5   0  -0.373  -2.4933   0.2692  -0.6474
 WTI  S12   S  S2    0   0.204  -2.3852   1.8352  -1.3767
 WTI  C13   C  CR15  0  -0.573  -4.0034   2.2340  -0.9647
 WTI  C14   C  CR5   0   0.389  -4.6052   1.2073  -0.3078
 WTI  O15   O  O2    0  -0.475  -5.8718   1.2271   0.1528
 WTI  C16   C  CH2   0  -0.232  -6.3531  -0.0646   0.5151
 WTI  C17   C  CH2   0  -0.233  -5.3129  -0.8279   1.3015
 WTI  O18   O  O2    0  -0.468  -4.1375  -1.0326   0.5216
 WTI  C19   C  CR5   0   0.335  -3.7417   0.0821  -0.1245
 WTI  C20   C  CR16  0  -0.100  -1.4960  -2.0059  -0.8369
 WTI  N21   N  N     0  -0.444  -0.4859  -2.8599  -0.8528
 WTI  C22   C  CR6   0   0.408   0.7556  -2.4173  -0.6684
 WTI  N23   N  NH2   0  -0.827   1.7420  -3.3544  -0.6969
 WTI  C24   C  CR16  0  -0.284   2.8675   0.5537  -0.9338
 WTI  C25   C  CR16  0  -0.267   4.1310   1.0716  -0.7003
 WTI  H011  H  HNH2  0   0.406   7.5181   2.6544   0.3750
 WTI  H012  H  HNH2  0   0.413   5.8871   2.9141  -0.0808
 WTI  H05   H  HCR6  0   0.264   5.1266  -1.0481   1.7371
 WTI  H25   H  HCR6  0   0.262   4.4667   1.9026  -1.3073
 WTI  H06   H  HCR6  0   0.268   2.8828  -1.9389   1.3530
 WTI  H24   H  HCR6  0   0.261   2.2501   0.9930  -1.7070
 WTI  H09   H  HCR6  0   0.264   0.1294   0.8715  -0.2405
 WTI  H20   H  HCR6  0   0.260  -2.4774  -2.4333  -1.0088
 WTI  H13   H  HCR5  0   0.303  -4.4267   3.1897  -1.2308
 WTI  H161  H  HCH2  0   0.265  -7.2432   0.0865   1.1236
 WTI  H162  H  HCH2  0   0.247  -6.6392  -0.6226  -0.3826
 WTI  H171  H  HCH2  0   0.247  -5.0607  -0.2934   2.2233
 WTI  H172  H  HCH2  0   0.265  -5.6948  -1.8121   1.5669
 WTI  H231  H  HNH2  0   0.396   2.6809  -3.0599  -0.9077
 WTI  H232  H  HNH2  0   0.389   1.4862  -4.2434  -1.0950

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
 WTI  N01  C02   single    1.342  0.020  1.342
 WTI  C02  O03   double    1.223  0.020  1.223
 WTI  C02  C04   single    1.496  0.020  1.496
 WTI  C04  C05   aromatic  1.393  0.020  1.393
 WTI  C04  C25   aromatic  1.393  0.020  1.393
 WTI  C05  C06   aromatic  1.383  0.020  1.383
 WTI  C06  C07   aromatic  1.397  0.020  1.397
 WTI  C07  C08   single    1.476  0.020  1.476
 WTI  C07  C24   aromatic  1.395  0.020  1.395
 WTI  C08  C09   aromatic  1.382  0.020  1.382
 WTI  C08  C22   aromatic  1.416  0.020  1.416
 WTI  C09  C10   aromatic  1.397  0.020  1.397
 WTI  C10  C11   single    1.457  0.020  1.457
 WTI  C10  C20   aromatic  1.391  0.020  1.391
 WTI  C11  S12   aromatic  1.731  0.020  1.731
 WTI  C11  C19   aromatic  1.366  0.020  1.366
 WTI  S12  C13   aromatic  1.717  0.020  1.717
 WTI  C13  C14   aromatic  1.359  0.020  1.359
 WTI  C14  O15   single    1.348  0.020  1.348
 WTI  C14  C19   aromatic  1.430  0.020  1.430
 WTI  O15  C16   single    1.425  0.020  1.425
 WTI  C16  C17   single    1.511  0.020  1.511
 WTI  C17  O18   single    1.425  0.020  1.425
 WTI  O18  C19   single    1.348  0.020  1.348
 WTI  C20  N21   aromatic  1.323  0.020  1.323
 WTI  N21  C22   aromatic  1.331  0.020  1.331
 WTI  C22  N23   single    1.361  0.020  1.361
 WTI  C24  C25   aromatic  1.385  0.020  1.385
 WTI  N01  H011  single    0.860  0.020  1.020
 WTI  N01  H012  single    0.860  0.020  1.020
 WTI  C05  H05   single    0.930  0.020  1.080
 WTI  C25  H25   single    0.930  0.020  1.080
 WTI  C06  H06   single    0.930  0.020  1.080
 WTI  C24  H24   single    0.930  0.020  1.080
 WTI  C09  H09   single    0.930  0.020  1.080
 WTI  C20  H20   single    0.930  0.020  1.080
 WTI  C13  H13   single    0.930  0.020  1.080
 WTI  C16  H161  single    0.970  0.020  1.090
 WTI  C16  H162  single    0.970  0.020  1.090
 WTI  C17  H171  single    0.970  0.020  1.090
 WTI  C17  H172  single    0.970  0.020  1.090
 WTI  N23  H231  single    0.890  0.020  1.040
 WTI  N23  H232  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
 WTI  H012  N01  H011  116.76  3.000
 WTI  H012  N01  C02   122.75  3.000
 WTI  H011  N01  C02   119.56  3.000
 WTI  C04   C02  O03   120.86  3.000
 WTI  C04   C02  N01   116.37  3.000
 WTI  O03   C02  N01   122.77  3.000
 WTI  C25   C04  C05   118.75  3.000
 WTI  C25   C04  C02   122.99  3.000
 WTI  C05   C04  C02   118.23  3.000
 WTI  H05   C05  C06   119.45  3.000
 WTI  H05   C05  C04   119.82  3.000
 WTI  C06   C05  C04   120.72  3.000
 WTI  H06   C06  C07   119.97  3.000
 WTI  H06   C06  C05   119.28  3.000
 WTI  C07   C06  C05   120.75  3.000
 WTI  C24   C07  C08   120.18  3.000
 WTI  C24   C07  C06   118.33  3.000
 WTI  C08   C07  C06   121.47  3.000
 WTI  C22   C08  C09   117.22  3.000
 WTI  C22   C08  C07   122.58  3.000
 WTI  C09   C08  C07   120.21  3.000
 WTI  H09   C09  C10   119.67  3.000
 WTI  H09   C09  C08   118.83  3.000
 WTI  C10   C09  C08   121.47  3.000
 WTI  C20   C10  C11   122.02  3.000
 WTI  C20   C10  C09   116.02  3.000
 WTI  C11   C10  C09   121.95  3.000
 WTI  C19   C11  S12   110.01  3.000
 WTI  C19   C11  C10   128.90  3.000
 WTI  S12   C11  C10   121.08  3.000
 WTI  C13   S12  C11    92.87  3.000
 WTI  H13   C13  C14   127.93  3.000
 WTI  H13   C13  S12   121.10  3.000
 WTI  C14   C13  S12   110.97  3.000
 WTI  C19   C14  O15   122.35  3.000
 WTI  C19   C14  C13   112.88  3.000
 WTI  O15   C14  C13   124.76  3.000
 WTI  C16   O15  C14   113.01  3.000
 WTI  H162  C16  H161  108.38  3.000
 WTI  H162  C16  C17   110.43  3.000
 WTI  H161  C16  C17   110.00  3.000
 WTI  H162  C16  O15   109.98  3.000
 WTI  H161  C16  O15   107.00  3.000
 WTI  C17   C16  O15   110.95  3.000
 WTI  H172  C17  H171  108.47  3.000
 WTI  H172  C17  O18   107.03  3.000
 WTI  H171  C17  O18   109.93  3.000
 WTI  H172  C17  C16   110.00  3.000
 WTI  H171  C17  C16   110.50  3.000
 WTI  O18   C17  C16   110.82  3.000
 WTI  C19   O18  C17   112.69  3.000
 WTI  O18   C19  C14   122.33  3.000
 WTI  O18   C19  C11   124.40  3.000
 WTI  C14   C19  C11   113.26  3.000
 WTI  H20   C20  N21   115.77  3.000
 WTI  H20   C20  C10   120.28  3.000
 WTI  N21   C20  C10   123.94  3.000
 WTI  C22   N21  C20   119.73  3.000
 WTI  N23   C22  N21   116.37  3.000
 WTI  N23   C22  C08   122.01  3.000
 WTI  N21   C22  C08   121.61  3.000
 WTI  H232  N23  H231  114.36  3.000
 WTI  H232  N23  C22   115.60  3.000
 WTI  H231  N23  C22   118.63  3.000
 WTI  H24   C24  C25   119.26  3.000
 WTI  H24   C24  C07   119.80  3.000
 WTI  C25   C24  C07   120.93  3.000
 WTI  H25   C25  C24   118.38  3.000
 WTI  H25   C25  C04   121.09  3.000
 WTI  C24   C25  C04   120.50  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
 WTI  CONST_01  C07   C06  C05  C04     0.00   0.0  0
 WTI  CONST_02  C07   C24  C25  C04     0.00   0.0  0
 WTI  CONST_03  C24   C25  C04  C05     0.00   0.0  0
 WTI  CONST_04  C08   C07  C06  C05   180.00   0.0  0
 WTI  CONST_05  C24   C07  C06  C05     0.00   0.0  0
 WTI  CONST_06  C25   C04  C05  C06     0.00   0.0  0
 WTI  CONST_09  C25   C24  C07  C06     0.00   0.0  0
 WTI  CONST_10  C10   C09  C08  C07   180.00   0.0  0
 WTI  CONST_11  N21   C22  C08  C07   180.00   0.0  0
 WTI  CONST_12  C25   C24  C07  C08   180.00   0.0  0
 WTI  CONST_13  C11   C10  C09  C08   180.00   0.0  0
 WTI  CONST_14  C20   C10  C09  C08     0.00   0.0  0
 WTI  CONST_15  C20   N21  C22  C08     0.00   0.0  0
 WTI  CONST_17  N21   C22  C08  C09     0.00   0.0  0
 WTI  CONST_20  N21   C20  C10  C09     0.00   0.0  0
 WTI  CONST_21  C22   C08  C09  C10     0.00   0.0  0
 WTI  CONST_22  C13   S12  C11  C10   180.00   0.0  0
 WTI  CONST_23  C14   C19  C11  C10   180.00   0.0  0
 WTI  CONST_24  C22   N21  C20  C10     0.00   0.0  0
 WTI  CONST_25  N21   C20  C10  C11   180.00   0.0  0
 WTI  CONST_26  C14   C13  S12  C11     0.00   0.0  0
 WTI  CONST_27  C13   C14  C19  C11     0.00   0.0  0
 WTI  CONST_29  C14   C19  C11  S12     0.00   0.0  0
 WTI  CONST_30  C19   C14  C13  S12     0.00   0.0  0
 WTI  CONST_31  C19   C11  S12  C13     0.00   0.0  0
 WTI  CONST_34  O18   C19  C11  C10     0.00   0.0  0
 WTI  CONST_35  C06   C05  C04  C02   180.00   0.0  0
 WTI  CONST_36  C24   C25  C04  C02   180.00   0.0  0
 WTI  CONST_37  N23   C22  C08  C07     0.00   0.0  0
 WTI  CONST_38  N23   C22  C08  C09   180.00   0.0  0
 WTI  CONST_39  N23   C22  N21  C20   180.00   0.0  0
 WTI  CONST_40  H06   C06  C05  C04   180.00   0.0  0
 WTI  CONST_41  H24   C24  C25  C04   180.00   0.0  0
 WTI  CONST_42  H25   C25  C04  C05   180.00   0.0  0
 WTI  CONST_43  H05   C05  C06  C07   180.00   0.0  0
 WTI  CONST_44  H09   C09  C08  C07     0.00   0.0  0
 WTI  CONST_45  H20   C20  C10  C09   180.00   0.0  0
 WTI  CONST_46  H13   C13  S12  C11   180.00   0.0  0
 WTI  CONST_49  H011  N01  C02  C04   180.00   0.0  0
 WTI  CONST_50  H012  N01  C02  C04     0.00   0.0  0
 WTI  Var_01    C17   C16  O15  C14    44.20  30.0  1
 WTI  Var_02    O18   C17  C16  O15   -61.65  30.0  1
 WTI  Var_03    C19   C14  O15  C16   -15.05  30.0  1
 WTI  Var_04    C05   C04  C02  N01  -158.35  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
 WTI  plan-1  C02   0.020
 WTI  plan-1  C04   0.020
 WTI  plan-1  C05   0.020
 WTI  plan-1  C06   0.020
 WTI  plan-1  C07   0.020
 WTI  plan-1  C08   0.020
 WTI  plan-1  C24   0.020
 WTI  plan-1  C25   0.020
 WTI  plan-1  H05   0.020
 WTI  plan-1  H25   0.020
 WTI  plan-1  H06   0.020
 WTI  plan-1  H24   0.020
 WTI  plan-2  C07   0.020
 WTI  plan-2  C08   0.020
 WTI  plan-2  C09   0.020
 WTI  plan-2  C10   0.020
 WTI  plan-2  C11   0.020
 WTI  plan-2  C20   0.020
 WTI  plan-2  N21   0.020
 WTI  plan-2  C22   0.020
 WTI  plan-2  N23   0.020
 WTI  plan-2  H09   0.020
 WTI  plan-2  H20   0.020
 WTI  plan-3  C10   0.020
 WTI  plan-3  C11   0.020
 WTI  plan-3  S12   0.020
 WTI  plan-3  C13   0.020
 WTI  plan-3  C14   0.020
 WTI  plan-3  O15   0.020
 WTI  plan-3  O18   0.020
 WTI  plan-3  C19   0.020
 WTI  plan-3  H13   0.020
 WTI  plan-4  N01   0.020
 WTI  plan-4  C02   0.020
 WTI  plan-4  O03   0.020
 WTI  plan-4  C04   0.020
 WTI  plan-4  H011  0.020
 WTI  plan-4  H012  0.020
 WTI  plan-5  C22   0.020
 WTI  plan-5  N23   0.020
 WTI  plan-5  H231  0.020
 WTI  plan-5  H232  0.020

