# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:06:57 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: ~{N}-[2-[5-chloranyl-2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]oxyphenyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(Nc2ncc(Cl)c(Oc3ccccc3NC(=O)C=C)n2)cn1
#
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
 6L4  6L4  ~{N}-[2-[5-chloranyl-2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]oxyphenyl]prop-2-enamide  ligand  41  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6L4
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
 6L4  C10   C   CH3   0  -0.506   5.9159  -2.8193   0.5889
 6L4  C17   C   CR16  0  -0.326  -3.1349   0.7035  -2.7962
 6L4  C20   C   CR16  0  -0.293  -3.4064  -1.8094  -1.6433
 6L4  C21   C   CR6   0   0.294  -2.8977  -0.7630  -0.8849
 6L4  C24   C   C1    0  -0.330  -1.0199  -1.5393   2.2129
 6L4  C02   C   CR6   0  -0.253  -0.6551   2.6604   0.5009
 6L4  C03   C   CR16  0   0.031   0.6409   2.6184   0.9679
 6L4  N04   N   N     0  -0.471   1.4716   1.6180   0.7070
 6L4  C05   C   CR6   0   0.618   0.9927   0.6397  -0.0553
 6L4  C07   C   CR5   0   0.081   3.0294  -0.7230   0.1495
 6L4  C08   C   CR15  0  -0.024   3.6983  -1.9049  -0.0995
 6L4  N09   N   NR5   0  -0.252   4.8907  -1.8062   0.5181
 6L4  N11   N   N     0  -0.282   5.0387  -0.6557   1.1501
 6L4  C12   C   CR15  0  -0.077   3.9223   0.0251   0.9404
 6L4  N13   N   N     0  -0.496  -0.2327   0.6112  -0.5955
 6L4  C14   C   CR6   0   0.614  -1.0478   1.5823  -0.3001
 6L4  O15   O   O2    0  -0.491  -2.3021   1.5712  -0.7582
 6L4  C16   C   CR6   0   0.338  -2.7554   0.4884  -1.4840
 6L4  C18   C   CR16  0  -0.257  -3.6447  -0.3509  -3.5405
 6L4  C19   C   CR16  0  -0.261  -3.7729  -1.6073  -2.9658
 6L4  C23   C   C     0   0.526  -1.4580  -1.7306   0.8087
 6L4  C25   C   C2    0  -0.462   0.1118  -2.0721   2.6592
 6L4  O26   O   O     0  -0.464  -0.9156  -2.5004   0.0370
 6L4  H1    H   HCH3  0   0.258   5.9155  -3.3060   1.5633
 6L4  H2    H   HCH3  0   0.259   5.7305  -3.5656  -0.1780
 6L4  H3    H   HCH3  0   0.262   6.8898  -2.3690   0.4145
 6L4  H4    H   HCR6  0   0.278  -3.0243   1.6888  -3.2302
 6L4  H5    H   HCR6  0   0.272  -3.5294  -2.7822  -1.1872
 6L4  H6    H   H     0   0.276  -1.6298  -0.9204   2.8616
 6L4  H8    H   HCR6  0   0.294   1.0199   3.4244   1.5863
 6L4  H9    H   HNH1  0   0.411   1.2927  -1.1608  -0.8502
 6L4  H10   H   HCR5  0   0.297   3.4097  -2.7772  -0.6637
 6L4  H11   H   HCR5  0   0.270   3.7936   1.0118   1.3487
 6L4  H12   H   HCR6  0   0.269  -3.9383  -0.1862  -4.5683
 6L4  H13   H   HCR6  0   0.266  -4.1697  -2.4321  -3.5423
 6L4  H14   H   HNH1  0   0.410  -2.8659  -0.2904   1.1349
 6L4  H15   H   H     0   0.265   0.4443  -1.9097   3.6749
 6L4  H16   H   H     0   0.259   0.7445  -2.6782   2.0239
 6L4  N06   N   NH1   0  -0.752   1.7605  -0.4318  -0.3336
 6L4  N22   N   NH1   0  -0.751  -2.5152  -0.9479   0.4545
 6L4  CL01  CL  CL    0  -0.102  -1.7303   3.9462   0.8785

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
 6L4  O26  C23   double    1.217  0.020  1.217
 6L4  C10  N09   single    1.443  0.020  1.443
 6L4  C24  C23   single    1.483  0.020  1.483
 6L4  C24  C25   double    1.328  0.020  1.328
 6L4  C23  N22   single    1.362  0.020  1.362
 6L4  C20  C19   aromatic  1.387  0.020  1.387
 6L4  C20  C21   aromatic  1.389  0.020  1.389
 6L4  C19  C18   aromatic  1.388  0.020  1.388
 6L4  N09  N11   aromatic  1.321  0.020  1.321
 6L4  N09  C08   aromatic  1.346  0.020  1.346
 6L4  N11  C12   aromatic  1.324  0.020  1.324
 6L4  C08  C07   aromatic  1.381  0.020  1.381
 6L4  N22  C21   single    1.405  0.020  1.405
 6L4  C21  C16   aromatic  1.395  0.020  1.395
 6L4  C18  C17   aromatic  1.388  0.020  1.388
 6L4  C12  C07   aromatic  1.408  0.020  1.408
 6L4  C07  N06   single    1.389  0.020  1.389
 6L4  N06  C05   single    1.347  0.020  1.347
 6L4  C16  C17   aromatic  1.383  0.020  1.383
 6L4  C16  O15   single    1.380  0.020  1.380
 6L4  N13  C05   aromatic  1.340  0.020  1.340
 6L4  N13  C14   aromatic  1.302  0.020  1.302
 6L4  C05  N04   aromatic  1.329  0.020  1.329
 6L4  O15  C14   single    1.335  0.020  1.335
 6L4  C14  C02   aromatic  1.399  0.020  1.399
 6L4  N04  C03   aromatic  1.326  0.020  1.326
 6L4  C02  C03   aromatic  1.378  0.020  1.378
 6L4  C02  CL01  single    1.718  0.020  1.718
 6L4  C10  H1    single    0.970  0.020  1.090
 6L4  C10  H2    single    0.970  0.020  1.090
 6L4  C10  H3    single    0.970  0.020  1.090
 6L4  C17  H4    single    0.930  0.020  1.080
 6L4  C20  H5    single    0.930  0.020  1.080
 6L4  C24  H6    single    0.930  0.020  1.080
 6L4  C03  H8    single    0.930  0.020  1.080
 6L4  N06  H9    single    0.860  0.020  1.020
 6L4  C08  H10   single    0.930  0.020  1.080
 6L4  C12  H11   single    0.930  0.020  1.080
 6L4  C18  H12   single    0.930  0.020  1.080
 6L4  C19  H13   single    0.930  0.020  1.080
 6L4  N22  H14   single    0.860  0.020  1.020
 6L4  C25  H15   single    0.930  0.020  1.080
 6L4  C25  H16   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
 6L4  H3   C10  H2    108.93  3.000
 6L4  H3   C10  H1    109.20  3.000
 6L4  H2   C10  H1    108.95  3.000
 6L4  H3   C10  N09   109.74  3.000
 6L4  H2   C10  N09   109.06  3.000
 6L4  H1   C10  N09   110.93  3.000
 6L4  H4   C17  C18   120.94  3.000
 6L4  H4   C17  C16   119.61  3.000
 6L4  C18  C17  C16   119.45  3.000
 6L4  H5   C20  C19   120.20  3.000
 6L4  H5   C20  C21   119.28  3.000
 6L4  C19  C20  C21   120.51  3.000
 6L4  N22  C21  C16   119.98  3.000
 6L4  C16  C21  C20   118.61  3.000
 6L4  N22  C21  C20   121.41  3.000
 6L4  H6   C24  C25   120.48  3.000
 6L4  H6   C24  C23   118.28  3.000
 6L4  C25  C24  C23   121.20  3.000
 6L4  C14  C02  C03   115.74  3.000
 6L4  C03  C02  CL01  122.47  3.000
 6L4  C14  C02  CL01  121.79  3.000
 6L4  H8   C03  N04   117.00  3.000
 6L4  H8   C03  C02   119.95  3.000
 6L4  N04  C03  C02   123.05  3.000
 6L4  C05  N04  C03   116.25  3.000
 6L4  N13  C05  N06   114.90  3.000
 6L4  N13  C05  N04   125.20  3.000
 6L4  N06  C05  N04   119.90  3.000
 6L4  C12  C07  C08   104.41  3.000
 6L4  C12  C07  N06   131.56  3.000
 6L4  C08  C07  N06   124.03  3.000
 6L4  H10  C08  N09   122.44  3.000
 6L4  H10  C08  C07   131.08  3.000
 6L4  N09  C08  C07   106.48  3.000
 6L4  N11  N09  C08   112.49  3.000
 6L4  C08  N09  C10   126.88  3.000
 6L4  N11  N09  C10   120.56  3.000
 6L4  C12  N11  N09   106.11  3.000
 6L4  H11  C12  N11   120.82  3.000
 6L4  H11  C12  C07   128.67  3.000
 6L4  N11  C12  C07   110.52  3.000
 6L4  C14  N13  C05   117.73  3.000
 6L4  O15  C14  N13   120.27  3.000
 6L4  O15  C14  C02   117.80  3.000
 6L4  N13  C14  C02   121.94  3.000
 6L4  C16  O15  C14   119.70  3.000
 6L4  O15  C16  C21   120.77  3.000
 6L4  O15  C16  C17   117.85  3.000
 6L4  C21  C16  C17   121.28  3.000
 6L4  H12  C18  C19   120.42  3.000
 6L4  H12  C18  C17   119.59  3.000
 6L4  C19  C18  C17   119.99  3.000
 6L4  H13  C19  C18   120.24  3.000
 6L4  H13  C19  C20   119.60  3.000
 6L4  C18  C19  C20   120.15  3.000
 6L4  O26  C23  N22   122.97  3.000
 6L4  N22  C23  C24   113.65  3.000
 6L4  O26  C23  C24   123.37  3.000
 6L4  H16  C25  H15   117.12  3.000
 6L4  H16  C25  C24   121.71  3.000
 6L4  H15  C25  C24   121.17  3.000
 6L4  H9   N06  C07   116.77  3.000
 6L4  H9   N06  C05   114.60  3.000
 6L4  C07  N06  C05   128.00  3.000
 6L4  H14  N22  C23   117.96  3.000
 6L4  H14  N22  C21   117.54  3.000
 6L4  C23  N22  C21   122.32  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
 6L4  CONST_01  C20  C19  C18  C17      0.00   0.0  0
 6L4  CONST_02  C20  C21  C16  C17      0.00   0.0  0
 6L4  CONST_03  C18  C19  C20  C21      0.00   0.0  0
 6L4  CONST_04  C18  C17  C16  C21      0.00   0.0  0
 6L4  CONST_05  C05  N13  C14  C02      0.00   0.0  0
 6L4  CONST_06  C05  N04  C03  C02      0.00   0.0  0
 6L4  CONST_07  N13  C05  N04  C03      0.00   0.0  0
 6L4  CONST_08  N13  C14  C02  C03      0.00   0.0  0
 6L4  CONST_09  C14  N13  C05  N04      0.00   0.0  0
 6L4  CONST_10  C14  C02  C03  N04      0.00   0.0  0
 6L4  CONST_11  N11  N09  C08  C07      0.00   0.0  0
 6L4  CONST_12  N09  N11  C12  C07      0.00   0.0  0
 6L4  CONST_13  C12  N11  N09  C08      0.00   0.0  0
 6L4  CONST_14  N11  C12  C07  C08      0.00   0.0  0
 6L4  CONST_15  C12  C07  C08  N09      0.00   0.0  0
 6L4  CONST_16  C19  C20  C21  C16      0.00   0.0  0
 6L4  CONST_17  C19  C18  C17  C16      0.00   0.0  0
 6L4  CONST_18  C12  N11  N09  C10    180.00   0.0  0
 6L4  CONST_19  C07  C08  N09  C10    180.00   0.0  0
 6L4  CONST_20  N22  C21  C16  C17    180.00   0.0  0
 6L4  CONST_21  O15  C16  C21  C20    180.00   0.0  0
 6L4  CONST_22  N13  C14  C02  CL01   180.00   0.0  0
 6L4  CONST_23  N04  C03  C02  CL01   180.00   0.0  0
 6L4  CONST_24  N06  C05  N04  C03    180.00   0.0  0
 6L4  CONST_25  O15  C14  C02  C03    180.00   0.0  0
 6L4  CONST_26  O15  C14  N13  C05    180.00   0.0  0
 6L4  CONST_27  N09  C08  C07  N06    180.00   0.0  0
 6L4  CONST_28  N11  C12  C07  N06    180.00   0.0  0
 6L4  CONST_29  C14  N13  C05  N06    180.00   0.0  0
 6L4  CONST_30  C18  C17  C16  O15    180.00   0.0  0
 6L4  CONST_31  N22  C21  C20  C19    180.00   0.0  0
 6L4  CONST_32  H13  C19  C18  C17    180.00   0.0  0
 6L4  CONST_33  H12  C18  C19  C20    180.00   0.0  0
 6L4  CONST_34  H4   C17  C16  C21    180.00   0.0  0
 6L4  CONST_35  H8   C03  N04  C05    180.00   0.0  0
 6L4  CONST_36  H11  C12  C07  C08    180.00   0.0  0
 6L4  CONST_37  H10  C08  N09  N11    180.00   0.0  0
 6L4  CONST_38  H5   C20  C21  C16    180.00   0.0  0
 6L4  CONST_42  O26  C23  N22  C21      0.00   0.0  0
 6L4  CONST_43  C24  C23  N22  C21    180.00   0.0  0
 6L4  Var_01    C07  N06  C05  N04      4.35  30.0  2
 6L4  Var_02    C08  C07  N06  C05    174.13  30.0  2
 6L4  Var_03    H1   C10  N09  C08   -102.59  30.0  2
 6L4  Var_04    C25  C24  C23  N22   -169.89  30.0  2
 6L4  Var_05    H15  C25  C24  C23    178.29   0.0  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
 6L4  plan-1  C10   0.020
 6L4  plan-1  C07   0.020
 6L4  plan-1  C08   0.020
 6L4  plan-1  N09   0.020
 6L4  plan-1  N11   0.020
 6L4  plan-1  C12   0.020
 6L4  plan-1  H10   0.020
 6L4  plan-1  H11   0.020
 6L4  plan-1  N06   0.020
 6L4  plan-2  C17   0.020
 6L4  plan-2  C20   0.020
 6L4  plan-2  C21   0.020
 6L4  plan-2  O15   0.020
 6L4  plan-2  C16   0.020
 6L4  plan-2  C18   0.020
 6L4  plan-2  C19   0.020
 6L4  plan-2  H4    0.020
 6L4  plan-2  H5    0.020
 6L4  plan-2  H12   0.020
 6L4  plan-2  H13   0.020
 6L4  plan-2  N22   0.020
 6L4  plan-3  C02   0.020
 6L4  plan-3  C03   0.020
 6L4  plan-3  N04   0.020
 6L4  plan-3  C05   0.020
 6L4  plan-3  N13   0.020
 6L4  plan-3  C14   0.020
 6L4  plan-3  O15   0.020
 6L4  plan-3  H8    0.020
 6L4  plan-3  N06   0.020
 6L4  plan-3  CL01  0.020
 6L4  plan-4  C21   0.020
 6L4  plan-4  C24   0.020
 6L4  plan-4  C23   0.020
 6L4  plan-4  O26   0.020
 6L4  plan-4  H14   0.020
 6L4  plan-4  N22   0.020
 6L4  plan-5  C24   0.020
 6L4  plan-5  C23   0.020
 6L4  plan-5  C25   0.020
 6L4  plan-5  H6    0.020
 6L4  plan-5  H15   0.020
 6L4  plan-5  H16   0.020

