# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:03:49 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[3-chloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-5-fluorophenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cc(F)cc(Cl)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2
#
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
 XL7  XL7  N-[3-chloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-5-fluorophenyl]propanamide  ligand  54  34  .  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_XL7
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
 XL7  C1   C   CR6   0   0.533  -6.0465  -0.6432  -0.3195
 XL7  C2   C   CR6   0  -0.293  -4.8311  -0.8947   0.3231
 XL7  C3   C   CR6   0   0.267  -3.9441   0.1348   0.6170
 XL7  C4   C   CR6   0  -0.275  -4.2798   1.4276   0.2273
 XL7  C5   C   CR6   0   0.531  -5.4893   1.7045  -0.4113
 XL7  C6   C   CR16  0  -0.569  -6.3683   0.6603  -0.6795
 XL7  O1   O   O2    0  -0.453  -6.8311  -1.6973  -0.5540
 XL7  O2   O   O2    0  -0.453  -5.7254   2.9789  -0.7295
 XL7  C7   C   CH3   0  -0.445  -8.0634  -1.4988  -1.2255
 XL7  C8   C   CH3   0  -0.444  -6.9402   3.3090  -1.3811
 XL7  C9   C   CH2   0  -0.263  -2.6353  -0.1220   1.3022
 XL7  O3   O   O2    0  -0.459  -1.6444  -0.1633   0.2885
 XL7  C10  C   CR6   0   0.265  -0.3623  -0.3055   0.6749
 XL7  C11  C   CR16  0  -0.129   0.0959  -0.4267   1.9794
 XL7  N1   N   N     0  -0.432   1.3863  -0.5661   2.2583
 XL7  C12  C   CR6   0   0.550   2.2293  -0.5871   1.2388
 XL7  N2   N   N     0  -0.412   1.8970  -0.4811  -0.0437
 XL7  C13  C   CR16  0  -0.089   0.6145  -0.3432  -0.3172
 XL7  CL1  CL  CL    0  -0.102  -4.4662  -2.5356   0.7296
 XL7  CL2  CL  CL    0  -0.099  -3.2021   2.7453   0.5259
 XL7  N3   N   NH1   0  -0.751   3.5685  -0.6932   1.5416
 XL7  C14  C   CR6   0   0.262   4.5005  -1.0931   0.5651
 XL7  C15  C   CR6   0   0.374   5.2712  -0.1164  -0.0918
 XL7  C16  C   CR16  0  -0.509   6.2004  -0.5037  -1.0568
 XL7  C17  C   CR6   0   0.569   6.3323  -1.8475  -1.3386
 XL7  C18  C   CR16  0  -0.421   5.5974  -2.8385  -0.7229
 XL7  C19  C   CR6   0  -0.043   4.6779  -2.4286   0.2280
 XL7  CL3  CL  CL    0  -0.093   3.7142  -3.6178   1.0218
 XL7  F1   F   F     0  -0.310   7.2298  -2.2091  -2.2636
 XL7  N4   N   NH1   0  -0.744   5.0493   1.1958   0.2871
 XL7  C20  C   C     0   0.559   5.5692   2.3495  -0.2278
 XL7  C21  C   CH2   0  -0.590   5.0407   3.5921   0.4537
 XL7  O4   O   O     0  -0.456   6.3680   2.3784  -1.1426
 XL7  C22  C   CH3   0  -0.658   5.6481   4.8778  -0.0752
 XL7  H1   H   HCR6  0   0.321  -7.3072   0.8658  -1.1729
 XL7  H2   H   HCH3  0   0.237  -8.7318  -0.8447  -0.6612
 XL7  H3   H   HCH3  0   0.238  -7.9169  -1.0850  -2.2258
 XL7  H4   H   HCH3  0   0.270  -8.5222  -2.4796  -1.3137
 XL7  H5   H   HCH3  0   0.237  -7.0239   2.8187  -2.3539
 XL7  H6   H   HCH3  0   0.237  -7.8090   3.0502  -0.7716
 XL7  H7   H   HCH3  0   0.270  -6.9221   4.3850  -1.5296
 XL7  H8   H   HCH2  0   0.255  -2.4282   0.6773   2.0198
 XL7  H9   H   HCH2  0   0.260  -2.6591  -1.0615   1.8586
 XL7  H10  H   HCR6  0   0.294  -0.5756  -0.4183   2.8303
 XL7  H11  H   HCR6  0   0.283   0.3341  -0.2569  -1.3623
 XL7  H12  H   HNH1  0   0.402   3.7673  -0.9475   2.4987
 XL7  H13  H   HCR6  0   0.307   6.8123   0.2137  -1.5780
 XL7  H14  H   HCR6  0   0.302   5.7312  -3.8807  -0.9759
 XL7  H15  H   HNH1  0   0.420   4.4020   1.2928   1.0583
 XL7  H16  H   HCH2  0   0.274   3.9530   3.6100   0.3350
 XL7  H17  H   HCH2  0   0.275   5.2159   3.4991   1.5293
 XL7  H18  H   HCH3  0   0.231   6.7266   4.9069   0.0757
 XL7  H19  H   HCH3  0   0.231   5.4530   5.0079  -1.1388
 XL7  H20  H   HCH3  0   0.238   5.2172   5.7304   0.4479

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
 XL7  CL3  C19  single    1.724  0.020  1.724
 XL7  C18  C19  aromatic  1.385  0.020  1.385
 XL7  C18  C17  aromatic  1.379  0.020  1.379
 XL7  F1   C17  single    1.339  0.020  1.339
 XL7  C19  C14  aromatic  1.389  0.020  1.389
 XL7  CL1  C2   single    1.729  0.020  1.729
 XL7  O1   C7   single    1.417  0.020  1.417
 XL7  O1   C1   single    1.335  0.020  1.335
 XL7  C17  C16  aromatic  1.379  0.020  1.379
 XL7  C2   C1   aromatic  1.398  0.020  1.398
 XL7  C2   C3   aromatic  1.390  0.020  1.390
 XL7  C1   C6   aromatic  1.390  0.020  1.390
 XL7  C14  N3   single    1.408  0.020  1.408
 XL7  C14  C15  aromatic  1.407  0.020  1.407
 XL7  C16  C15  aromatic  1.394  0.020  1.394
 XL7  N1   C11  aromatic  1.328  0.020  1.328
 XL7  N1   C12  aromatic  1.323  0.020  1.323
 XL7  N3   C12  single    1.377  0.020  1.377
 XL7  C6   C5   aromatic  1.391  0.020  1.391
 XL7  C3   C9   single    1.499  0.020  1.499
 XL7  C3   C4   aromatic  1.391  0.020  1.391
 XL7  C9   O3   single    1.418  0.020  1.418
 XL7  C11  C10  aromatic  1.388  0.020  1.388
 XL7  C12  N2   aromatic  1.329  0.020  1.329
 XL7  C15  N4   single    1.384  0.020  1.384
 XL7  C10  O3   single    1.347  0.020  1.347
 XL7  C10  C13  aromatic  1.393  0.020  1.393
 XL7  N2   C13  aromatic  1.319  0.020  1.319
 XL7  C4   C5   aromatic  1.395  0.020  1.395
 XL7  C4   CL2  single    1.728  0.020  1.728
 XL7  C5   O2   single    1.335  0.020  1.335
 XL7  C8   O2   single    1.418  0.020  1.418
 XL7  N4   C20  single    1.366  0.020  1.366
 XL7  O4   C20  double    1.215  0.020  1.215
 XL7  C20  C21  single    1.513  0.020  1.513
 XL7  C21  C22  single    1.517  0.020  1.517
 XL7  C6   H1   single    0.930  0.020  1.080
 XL7  C7   H2   single    0.970  0.020  1.090
 XL7  C7   H3   single    0.970  0.020  1.090
 XL7  C7   H4   single    0.970  0.020  1.090
 XL7  C8   H5   single    0.970  0.020  1.090
 XL7  C8   H6   single    0.970  0.020  1.090
 XL7  C8   H7   single    0.970  0.020  1.090
 XL7  C9   H8   single    0.970  0.020  1.090
 XL7  C9   H9   single    0.970  0.020  1.090
 XL7  C11  H10  single    0.930  0.020  1.080
 XL7  C13  H11  single    0.930  0.020  1.080
 XL7  N3   H12  single    0.890  0.020  1.040
 XL7  C16  H13  single    0.930  0.020  1.080
 XL7  C18  H14  single    0.930  0.020  1.080
 XL7  N4   H15  single    0.860  0.020  1.020
 XL7  C21  H16  single    0.970  0.020  1.090
 XL7  C21  H17  single    0.970  0.020  1.090
 XL7  C22  H18  single    0.970  0.020  1.090
 XL7  C22  H19  single    0.970  0.020  1.090
 XL7  C22  H20  single    0.970  0.020  1.090

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
 XL7  O1   C1   C6   123.99  3.000
 XL7  C6   C1   C2   119.28  3.000
 XL7  O1   C1   C2   116.73  3.000
 XL7  CL1  C2   C3   121.22  3.000
 XL7  C3   C2   C1   121.25  3.000
 XL7  CL1  C2   C1   117.53  3.000
 XL7  C9   C3   C4   119.85  3.000
 XL7  C4   C3   C2   118.35  3.000
 XL7  C9   C3   C2   121.78  3.000
 XL7  CL2  C4   C5   117.92  3.000
 XL7  CL2  C4   C3   120.63  3.000
 XL7  C5   C4   C3   121.44  3.000
 XL7  O2   C5   C6   123.99  3.000
 XL7  O2   C5   C4   116.87  3.000
 XL7  C6   C5   C4   119.14  3.000
 XL7  H1   C6   C5   119.63  3.000
 XL7  H1   C6   C1   119.85  3.000
 XL7  C5   C6   C1   120.52  3.000
 XL7  C7   O1   C1   118.93  3.000
 XL7  C8   O2   C5   118.92  3.000
 XL7  H4   C7   H3   108.93  3.000
 XL7  H4   C7   H2   108.91  3.000
 XL7  H3   C7   H2   109.17  3.000
 XL7  H4   C7   O1   106.21  3.000
 XL7  H3   C7   O1   111.73  3.000
 XL7  H2   C7   O1   111.79  3.000
 XL7  H7   C8   H6   108.91  3.000
 XL7  H7   C8   H5   108.91  3.000
 XL7  H6   C8   H5   109.24  3.000
 XL7  H7   C8   O2   106.21  3.000
 XL7  H6   C8   O2   111.71  3.000
 XL7  H5   C8   O2   111.75  3.000
 XL7  H9   C9   H8   107.36  3.000
 XL7  H9   C9   O3   110.75  3.000
 XL7  H8   C9   O3   110.97  3.000
 XL7  H9   C9   C3   111.17  3.000
 XL7  H8   C9   C3   109.87  3.000
 XL7  O3   C9   C3   106.75  3.000
 XL7  C10  O3   C9   117.59  3.000
 XL7  C13  C10  C11  115.82  3.000
 XL7  C13  C10  O3   117.79  3.000
 XL7  C11  C10  O3   126.39  3.000
 XL7  H10  C11  N1   115.98  3.000
 XL7  H10  C11  C10  122.18  3.000
 XL7  N1   C11  C10  121.84  3.000
 XL7  C12  N1   C11  117.33  3.000
 XL7  N3   C12  N2   117.48  3.000
 XL7  N2   C12  N1   125.67  3.000
 XL7  N3   C12  N1   116.83  3.000
 XL7  C13  N2   C12  116.84  3.000
 XL7  H11  C13  N2   117.34  3.000
 XL7  H11  C13  C10  120.16  3.000
 XL7  N2   C13  C10  122.50  3.000
 XL7  H12  N3   C14  117.09  3.000
 XL7  H12  N3   C12  114.78  3.000
 XL7  C14  N3   C12  120.87  3.000
 XL7  C19  C14  C15  118.97  3.000
 XL7  C15  C14  N3   119.29  3.000
 XL7  C19  C14  N3   121.74  3.000
 XL7  N4   C15  C16  124.03  3.000
 XL7  N4   C15  C14  116.27  3.000
 XL7  C16  C15  C14  119.69  3.000
 XL7  H13  C16  C17  119.70  3.000
 XL7  H13  C16  C15  121.90  3.000
 XL7  C17  C16  C15  118.40  3.000
 XL7  F1   C17  C18  118.15  3.000
 XL7  F1   C17  C16  117.93  3.000
 XL7  C18  C17  C16  123.92  3.000
 XL7  H14  C18  C19  121.90  3.000
 XL7  H14  C18  C17  121.50  3.000
 XL7  C19  C18  C17  116.60  3.000
 XL7  CL3  C19  C18  118.89  3.000
 XL7  C18  C19  C14  122.42  3.000
 XL7  CL3  C19  C14  118.69  3.000
 XL7  H15  N4   C20  116.74  3.000
 XL7  H15  N4   C15  113.72  3.000
 XL7  C20  N4   C15  129.54  3.000
 XL7  O4   C20  C21  123.33  3.000
 XL7  C21  C20  N4   113.02  3.000
 XL7  O4   C20  N4   123.65  3.000
 XL7  H17  C21  H16  105.50  3.000
 XL7  H17  C21  C22  110.53  3.000
 XL7  H16  C21  C22  110.26  3.000
 XL7  H17  C21  C20  108.49  3.000
 XL7  H16  C21  C20  108.17  3.000
 XL7  C22  C21  C20  113.53  3.000
 XL7  H20  C22  H19  107.73  3.000
 XL7  H20  C22  H18  107.71  3.000
 XL7  H19  C22  H18  108.02  3.000
 XL7  H20  C22  C21  109.73  3.000
 XL7  H19  C22  C21  111.71  3.000
 XL7  H18  C22  C21  111.76  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
 XL7  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 XL7  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 XL7  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 XL7  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 XL7  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 XL7  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 XL7  CONST_07  C12  N1   C11  C10    0.00   0.0  0
 XL7  CONST_08  C12  N2   C13  C10    0.00   0.0  0
 XL7  CONST_09  N2   C12  N1   C11    0.00   0.0  0
 XL7  CONST_10  N2   C13  C10  C11    0.00   0.0  0
 XL7  CONST_11  C13  C10  C11  N1     0.00   0.0  0
 XL7  CONST_12  C13  N2   C12  N1     0.00   0.0  0
 XL7  CONST_13  C17  C18  C19  C14    0.00   0.0  0
 XL7  CONST_14  C17  C16  C15  C14    0.00   0.0  0
 XL7  CONST_15  C18  C19  C14  C15    0.00   0.0  0
 XL7  CONST_16  C18  C17  C16  C15    0.00   0.0  0
 XL7  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 XL7  CONST_18  C19  C14  C15  C16    0.00   0.0  0
 XL7  CONST_19  C9   C3   C2   C1   180.00   0.0  0
 XL7  CONST_20  O2   C5   C6   C1   180.00   0.0  0
 XL7  CONST_21  CL2  C4   C3   C2   180.00   0.0  0
 XL7  CONST_22  O1   C1   C2   C3   180.00   0.0  0
 XL7  CONST_23  O2   C5   C4   C3   180.00   0.0  0
 XL7  CONST_24  CL1  C2   C3   C4   180.00   0.0  0
 XL7  CONST_25  O1   C1   C6   C5   180.00   0.0  0
 XL7  CONST_26  C9   C3   C4   C5   180.00   0.0  0
 XL7  CONST_27  CL1  C2   C1   C6   180.00   0.0  0
 XL7  CONST_28  CL2  C4   C5   C6   180.00   0.0  0
 XL7  CONST_29  N1   C11  C10  O3   180.00   0.0  0
 XL7  CONST_30  N2   C13  C10  O3   180.00   0.0  0
 XL7  CONST_31  N3   C12  N1   C11  180.00   0.0  0
 XL7  CONST_32  N3   C12  N2   C13  180.00   0.0  0
 XL7  CONST_33  C18  C19  C14  N3   180.00   0.0  0
 XL7  CONST_34  C16  C15  C14  N3   180.00   0.0  0
 XL7  CONST_35  CL3  C19  C14  C15  180.00   0.0  0
 XL7  CONST_36  F1   C17  C16  C15  180.00   0.0  0
 XL7  CONST_37  CL3  C19  C18  C17  180.00   0.0  0
 XL7  CONST_38  N4   C15  C16  C17  180.00   0.0  0
 XL7  CONST_39  F1   C17  C18  C19  180.00   0.0  0
 XL7  CONST_40  N4   C15  C14  C19  180.00   0.0  0
 XL7  CONST_41  H1   C6   C1   C2   180.00   0.0  0
 XL7  CONST_42  H11  C13  C10  C11  180.00   0.0  0
 XL7  CONST_43  H10  C11  N1   C12  180.00   0.0  0
 XL7  CONST_44  H14  C18  C19  C14  180.00   0.0  0
 XL7  CONST_45  H13  C16  C15  C14  180.00   0.0  0
 XL7  CONST_46  C20  N4   C15  C14  180.00   0.0  0
 XL7  CONST_47  C20  N4   C15  C16    0.00   0.0  0
 XL7  CONST_48  H15  N4   C15  C14    0.00   0.0  0
 XL7  CONST_49  O4   C20  N4   C15    0.00   0.0  0
 XL7  CONST_50  C21  C20  N4   C15  180.00   0.0  0
 XL7  Var_01    C14  N3   C12  N1   162.18  30.0  1
 XL7  Var_02    C19  C14  N3   C12  -80.14  30.0  2
 XL7  Var_03    O3   C9   C3   C2    98.57  30.0  2
 XL7  Var_04    C11  C10  O3   C9     0.48  30.0  3
 XL7  Var_05    H2   C7   O1   C1   -61.85  30.0  3
 XL7  Var_06    H5   C8   O2   C5   -61.99  30.0  3
 XL7  Var_07    C22  C21  C20  N4   177.91  30.0  3
 XL7  Var_08    H18  C22  C21  C20  -61.25  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
 XL7  plan-1  C1   0.020
 XL7  plan-1  C2   0.020
 XL7  plan-1  C3   0.020
 XL7  plan-1  C4   0.020
 XL7  plan-1  C5   0.020
 XL7  plan-1  C6   0.020
 XL7  plan-1  O1   0.020
 XL7  plan-1  O2   0.020
 XL7  plan-1  C9   0.020
 XL7  plan-1  CL1  0.020
 XL7  plan-1  CL2  0.020
 XL7  plan-1  H1   0.020
 XL7  plan-2  O3   0.020
 XL7  plan-2  C10  0.020
 XL7  plan-2  C11  0.020
 XL7  plan-2  N1   0.020
 XL7  plan-2  C12  0.020
 XL7  plan-2  N2   0.020
 XL7  plan-2  C13  0.020
 XL7  plan-2  N3   0.020
 XL7  plan-2  H10  0.020
 XL7  plan-2  H11  0.020
 XL7  plan-3  N3   0.020
 XL7  plan-3  C14  0.020
 XL7  plan-3  C15  0.020
 XL7  plan-3  C16  0.020
 XL7  plan-3  C17  0.020
 XL7  plan-3  C18  0.020
 XL7  plan-3  C19  0.020
 XL7  plan-3  CL3  0.020
 XL7  plan-3  F1   0.020
 XL7  plan-3  N4   0.020
 XL7  plan-3  H13  0.020
 XL7  plan-3  H14  0.020
 XL7  plan-4  C15  0.020
 XL7  plan-4  N4   0.020
 XL7  plan-4  C20  0.020
 XL7  plan-4  C21  0.020
 XL7  plan-4  O4   0.020
 XL7  plan-4  H15  0.020

