# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:11:40 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-[3-chloro-4-(4-chloro-2-hydroxyphenoxy)phenyl]morpholine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(Cl)ccc1Oc2ccc(NC(=O)N3CCOCC3)cc2Cl
#
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
 JP1  JP1  N-[3-chloro-4-(4-chloro-2-hydroxyphenoxy)phenyl]morpholine-4-carboxamide  ligand  41  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JP1
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
 JP1  C2    C   CR6   0   0.244   3.5882   0.5746   0.3292
 JP1  C3    C   CR16  0  -0.312   4.3695   0.2831   1.4298
 JP1  C4    C   CR16  0  -0.244   5.4814  -0.5404   1.3109
 JP1  C5    C   CR6   0  -0.029   5.7785  -1.0689   0.0674
 JP1  C10   C   CR6   0   0.430   1.2718   0.9459   0.4242
 JP1  C11   C   CR6   0  -0.135   0.2312   1.8602   0.3051
 JP1  C12   C   CR16  0  -0.262  -1.0955   1.4651   0.3002
 JP1  C15   C   CR16  0  -0.336   0.9513  -0.3984   0.5391
 JP1  C19   C   C     0   0.747  -3.8234   0.1813  -0.1448
 JP1  C23   C   CH2   0  -0.180  -6.2383  -2.6304   0.1208
 JP1  C25   C   CH2   0  -0.194  -7.2362  -0.8519  -0.9591
 JP1  C26   C   CH2   0  -0.308  -6.2237   0.1297  -0.4061
 JP1  O20   O   O     0  -0.522  -3.7764   1.2765  -0.6871
 JP1  N21   N   NT    0  -0.516  -4.9755  -0.5527  -0.0922
 JP1  O24   O   O2    0  -0.480  -7.4428  -1.9357  -0.0823
 JP1  C22   C   CH2   0  -0.339  -5.1576  -1.7456   0.7204
 JP1  C13   C   CR6   0   0.357  -1.4120   0.1107   0.3952
 JP1  CL16  CL  CL    0  -0.107   0.6079   3.5423   0.1758
 JP1  C14   C   CR16  0  -0.336  -0.3704  -0.8075   0.5145
 JP1  O9    O   O2    0  -0.492   2.5358   1.4412   0.4501
 JP1  C1    C   CR6   0   0.326   3.8974   0.0386  -0.9250
 JP1  O7    O   OH1   0  -0.609   3.0947   0.3611  -1.9475
 JP1  C6    C   CR16  0  -0.343   5.0037  -0.7928  -1.0492
 JP1  CL27  CL  CL    0  -0.122   7.1561  -2.1023  -0.1128
 JP1  H3    H   HCR6  0   0.285   4.1124   0.7104   2.3905
 JP1  H4    H   HCR6  0   0.283   6.0937  -0.7630   2.1729
 JP1  H12   H   HCR6  0   0.293  -1.8650   2.2158   0.2291
 JP1  H15   H   HCR6  0   0.289   1.7281  -1.1443   0.6440
 JP1  H232  H   HCH2  0   0.211  -5.8724  -3.0515  -0.8264
 JP1  H251  H   HCH2  0   0.246  -8.1936  -0.3477  -1.0943
 JP1  H252  H   HCH2  0   0.209  -6.9005  -1.2121  -1.9417
 JP1  H261  H   HCH2  0   0.236  -6.6264   0.6112   0.4936
 JP1  H262  H   HCH2  0   0.268  -6.0453   0.9057  -1.1455
 JP1  H221  H   HCH2  0   0.258  -4.2556  -2.3552   0.7489
 JP1  H222  H   HCH2  0   0.250  -5.4130  -1.4767   1.7520
 JP1  H14   H   HCR6  0   0.279  -0.5876  -1.8656   0.5935
 JP1  HO7   H   HOH1  0   0.485   3.3972  -0.0506  -2.7648
 JP1  H6    H   HCR6  0   0.300   5.2604  -1.2168  -2.0122
 JP1  N17   N   NH1   0  -0.796  -2.7186  -0.3852   0.4358
 JP1  H231  H   HCH2  0   0.250  -6.4395  -3.4584   0.8012
 JP1  H17   H   HNH1  0   0.414  -2.7870  -1.3188   0.8024

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
 JP1  C2   C3    aromatic  1.381  0.020  1.381
 JP1  C2   O9    single    1.369  0.020  1.369
 JP1  C2   C1    aromatic  1.399  0.020  1.399
 JP1  C3   C4    aromatic  1.389  0.020  1.389
 JP1  C3   H3    single    0.930  0.020  1.080
 JP1  C4   C5    aromatic  1.383  0.020  1.383
 JP1  C4   H4    single    0.930  0.020  1.080
 JP1  C5   C6    aromatic  1.387  0.020  1.387
 JP1  C5   CL27  single    1.731  0.020  1.731
 JP1  C10  C11   aromatic  1.390  0.020  1.390
 JP1  C10  C15   aromatic  1.387  0.020  1.387
 JP1  C10  O9    single    1.358  0.020  1.358
 JP1  C11  C12   aromatic  1.384  0.020  1.384
 JP1  C11  CL16  single    1.729  0.020  1.729
 JP1  C12  C13   aromatic  1.394  0.020  1.394
 JP1  C12  H12   single    0.930  0.020  1.080
 JP1  C15  C14   aromatic  1.384  0.020  1.384
 JP1  C15  H15   single    0.930  0.020  1.080
 JP1  C19  O20   double    1.223  0.020  1.223
 JP1  C19  N21   single    1.367  0.020  1.367
 JP1  C19  N17   single    1.371  0.020  1.371
 JP1  C23  O24   single    1.405  0.020  1.405
 JP1  C23  C22   single    1.520  0.020  1.520
 JP1  C23  H231  single    0.970  0.020  1.090
 JP1  C23  H232  single    0.970  0.020  1.090
 JP1  C25  C26   single    1.515  0.020  1.515
 JP1  C25  O24   single    1.409  0.020  1.409
 JP1  C25  H251  single    0.970  0.020  1.090
 JP1  C25  H252  single    0.970  0.020  1.090
 JP1  C26  N21   single    1.457  0.020  1.457
 JP1  C26  H261  single    0.970  0.020  1.090
 JP1  C26  H262  single    0.970  0.020  1.090
 JP1  N21  C22   single    1.455  0.020  1.455
 JP1  C22  H221  single    0.970  0.020  1.090
 JP1  C22  H222  single    0.970  0.020  1.090
 JP1  N17  C13   single    1.398  0.020  1.398
 JP1  N17  H17   single    0.860  0.020  1.020
 JP1  C13  C14   aromatic  1.394  0.020  1.394
 JP1  C14  H14   single    0.930  0.020  1.080
 JP1  C1   O7    single    1.339  0.020  1.339
 JP1  C1   C6    aromatic  1.390  0.020  1.390
 JP1  O7   HO7   single    0.850  0.020  0.980
 JP1  C6   H6    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
 JP1  C1    C2   O9    119.47  3.000
 JP1  C1    C2   C3    120.58  3.000
 JP1  O9    C2   C3    119.89  3.000
 JP1  H3    C3   C4    120.02  3.000
 JP1  H3    C3   C2    119.32  3.000
 JP1  C4    C3   C2    120.66  3.000
 JP1  H4    C4   C5    121.11  3.000
 JP1  H4    C4   C3    120.50  3.000
 JP1  C5    C4   C3    118.39  3.000
 JP1  CL27  C5   C6    118.65  3.000
 JP1  CL27  C5   C4    119.50  3.000
 JP1  C6    C5   C4    121.85  3.000
 JP1  O9    C10  C15   124.55  3.000
 JP1  O9    C10  C11   117.29  3.000
 JP1  C15   C10  C11   118.14  3.000
 JP1  CL16  C11  C12   119.10  3.000
 JP1  CL16  C11  C10   118.90  3.000
 JP1  C12   C11  C10   122.00  3.000
 JP1  H12   C12  C13   121.29  3.000
 JP1  H12   C12  C11   119.07  3.000
 JP1  C13   C12  C11   119.64  3.000
 JP1  H15   C15  C14   118.93  3.000
 JP1  H15   C15  C10   120.69  3.000
 JP1  C14   C15  C10   120.38  3.000
 JP1  N17   C19  N21   116.17  3.000
 JP1  N17   C19  O20   121.81  3.000
 JP1  N21   C19  O20   122.02  3.000
 JP1  H232  C23  H231  107.95  3.000
 JP1  H232  C23  C22   109.05  3.000
 JP1  H231  C23  C22   109.09  3.000
 JP1  H232  C23  O24   110.50  3.000
 JP1  H231  C23  O24   107.90  3.000
 JP1  C22   C23  O24   112.25  3.000
 JP1  H252  C25  H251  107.99  3.000
 JP1  H252  C25  O24   110.42  3.000
 JP1  H251  C25  O24   107.70  3.000
 JP1  H252  C25  C26   109.55  3.000
 JP1  H251  C25  C26   109.42  3.000
 JP1  O24   C25  C26   111.67  3.000
 JP1  H262  C26  H261  107.75  3.000
 JP1  H262  C26  N21   109.91  3.000
 JP1  H261  C26  N21   110.08  3.000
 JP1  H262  C26  C25   108.91  3.000
 JP1  H261  C26  C25   109.79  3.000
 JP1  N21   C26  C25   110.35  3.000
 JP1  C22   N21  C26   113.41  3.000
 JP1  C22   N21  C19   124.55  3.000
 JP1  C26   N21  C19   117.53  3.000
 JP1  C25   O24  C23   110.14  3.000
 JP1  H222  C22  H221  107.80  3.000
 JP1  H222  C22  N21   110.71  3.000
 JP1  H221  C22  N21   111.71  3.000
 JP1  H222  C22  C23   110.39  3.000
 JP1  H221  C22  C23   105.86  3.000
 JP1  N21   C22  C23   110.24  3.000
 JP1  C14   C13  N17   117.53  3.000
 JP1  C14   C13  C12   118.44  3.000
 JP1  N17   C13  C12   123.97  3.000
 JP1  H14   C14  C13   120.00  3.000
 JP1  H14   C14  C15   118.62  3.000
 JP1  C13   C14  C15   121.37  3.000
 JP1  C10   O9   C2    118.89  3.000
 JP1  C6    C1   O7    123.58  3.000
 JP1  C6    C1   C2    119.04  3.000
 JP1  O7    C1   C2    117.38  3.000
 JP1  HO7   O7   C1    110.88  3.000
 JP1  H6    C6   C1    120.16  3.000
 JP1  H6    C6   C5    120.37  3.000
 JP1  C1    C6   C5    119.47  3.000
 JP1  H17   N17  C13   113.80  3.000
 JP1  H17   N17  C19   118.91  3.000
 JP1  C13   N17  C19   126.46  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
 JP1  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 JP1  CONST_02  C5    C6   C1   C2      0.00   0.0  0
 JP1  CONST_03  C6    C1   C2   C3      0.00   0.0  0
 JP1  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 JP1  CONST_05  C1    C2   C3   C4      0.00   0.0  0
 JP1  CONST_06  C1    C6   C5   C4      0.00   0.0  0
 JP1  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 JP1  CONST_08  C13   C14  C15  C10     0.00   0.0  0
 JP1  CONST_09  C14   C15  C10  C11     0.00   0.0  0
 JP1  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 JP1  CONST_11  C15   C10  C11  C12     0.00   0.0  0
 JP1  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 JP1  CONST_13  O7    C1   C2   C3    180.00   0.0  0
 JP1  CONST_14  CL27  C5   C4   C3    180.00   0.0  0
 JP1  CONST_15  O9    C2   C3   C4    180.00   0.0  0
 JP1  CONST_16  O7    C1   C6   C5    180.00   0.0  0
 JP1  CONST_17  N17   C13  C12  C11   180.00   0.0  0
 JP1  CONST_18  O9    C10  C11  C12   180.00   0.0  0
 JP1  CONST_19  CL16  C11  C10  C15   180.00   0.0  0
 JP1  CONST_20  N17   C13  C14  C15   180.00   0.0  0
 JP1  CONST_21  CL16  C11  C12  C13   180.00   0.0  0
 JP1  CONST_22  O9    C10  C15  C14   180.00   0.0  0
 JP1  CONST_23  C6    C1   C2   O9    180.00   0.0  0
 JP1  CONST_24  CL27  C5   C6   C1    180.00   0.0  0
 JP1  CONST_25  H4    C4   C3   C2    180.00   0.0  0
 JP1  CONST_26  H6    C6   C1   C2    180.00   0.0  0
 JP1  CONST_27  H3    C3   C4   C5    180.00   0.0  0
 JP1  CONST_28  H12   C12  C11  C10   180.00   0.0  0
 JP1  CONST_29  H14   C14  C15  C10   180.00   0.0  0
 JP1  CONST_30  H15   C15  C10  C11   180.00   0.0  0
 JP1  CONST_31  O20   C19  N21  C26     0.00   0.0  0
 JP1  CONST_32  C22   N21  C19  O20   180.00   0.0  0
 JP1  CONST_35  C13   N17  C19  N21   180.00   0.0  0
 JP1  CONST_36  N17   C19  N21  C26   180.00   0.0  0
 JP1  CONST_37  N17   C19  N21  C22     0.00   0.0  0
 JP1  CONST_39  C13   N17  C19  O20     0.00   0.0  0
 JP1  Var_01    C26   C25  O24  C23   -60.29  30.0  1
 JP1  Var_02    C26   N21  C22  C23    49.53  30.0  1
 JP1  Var_03    C22   N21  C26  C25   -50.33  30.0  1
 JP1  Var_04    C22   C23  O24  C25    59.82  30.0  1
 JP1  Var_05    O24   C25  C26  N21    55.22  30.0  1
 JP1  Var_06    O24   C23  C22  N21   -54.05  30.0  1
 JP1  Var_07    C11   C10  O9   C2   -168.63  30.0  2
 JP1  Var_08    C1    C2   O9   C10    75.66  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
 JP1  plan-1  C2    0.020
 JP1  plan-1  C3    0.020
 JP1  plan-1  C4    0.020
 JP1  plan-1  C5    0.020
 JP1  plan-1  O9    0.020
 JP1  plan-1  C1    0.020
 JP1  plan-1  O7    0.020
 JP1  plan-1  C6    0.020
 JP1  plan-1  CL27  0.020
 JP1  plan-1  H3    0.020
 JP1  plan-1  H4    0.020
 JP1  plan-1  H6    0.020
 JP1  plan-2  C10   0.020
 JP1  plan-2  C11   0.020
 JP1  plan-2  C12   0.020
 JP1  plan-2  C15   0.020
 JP1  plan-2  C13   0.020
 JP1  plan-2  CL16  0.020
 JP1  plan-2  C14   0.020
 JP1  plan-2  O9    0.020
 JP1  plan-2  H12   0.020
 JP1  plan-2  H15   0.020
 JP1  plan-2  H14   0.020
 JP1  plan-2  N17   0.020
 JP1  plan-3  C19   0.020
 JP1  plan-3  C26   0.020
 JP1  plan-3  O20   0.020
 JP1  plan-3  N21   0.020
 JP1  plan-3  C22   0.020
 JP1  plan-3  C13   0.020
 JP1  plan-3  N17   0.020
 JP1  plan-3  H17   0.020

