# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:38:54 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (1R)-2-{[6-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrimidin-4-yl]amino}-1-phenylethan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CNc1cc(ncn1)c2ccc3OCCOc3c2)c4ccccc4
#
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
 JXV  JXV  (1R)-2-{[6-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrimidin-4-yl]amino}-1-phenylethan-1-ol  ligand  45  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JXV
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
 JXV  C1   C  CR6   0   0.054   2.3711   0.3593  -0.1950
 JXV  C2   C  CR16  0  -0.411   3.6817   0.6976   0.1363
 JXV  C3   C  CR16  0  -0.329   2.0912  -0.9616  -0.5488
 JXV  C4   C  CR6   0   0.348   4.6910  -0.2505   0.1207
 JXV  C5   C  CR16  0  -0.348   3.0966  -1.9102  -0.5829
 JXV  C6   C  CR6   0   0.317   4.4021  -1.5688  -0.2526
 JXV  C11  C  CR6   0   0.281   1.3203   1.3951  -0.1597
 JXV  C15  C  CR16  0  -0.455  -0.0231   1.0727  -0.1060
 JXV  C18  C  CH2   0  -0.283  -2.9126   0.6602   0.0677
 JXV  C19  C  CH1   0  -0.088  -4.4125   0.7815  -0.1912
 JXV  C21  C  CR16  0  -0.238  -5.9820  -2.5395  -1.1570
 JXV  C23  C  CR16  0  -0.309  -5.4039  -1.2792  -1.2354
 JXV  C24  C  CR16  0  -0.321  -5.3176  -1.1609   1.1569
 JXV  O26  O  OH1   0  -0.653  -5.0112   1.7564   0.6323
 JXV  C10  C  CH2   0  -0.229   6.8151  -0.9488   0.7731
 JXV  C13  C  CR6   0   0.541  -0.9446   2.1334  -0.0933
 JXV  C14  C  CR16  0   0.049   0.7840   3.5913  -0.1313
 JXV  C20  C  CR16  0  -0.267  -6.2329  -3.1118   0.0823
 JXV  C22  C  CR16  0  -0.239  -5.8975  -2.4190   1.2390
 JXV  C25  C  CR6   0   0.132  -5.0656  -0.5778  -0.0828
 JXV  C9   C  CH2   0  -0.227   6.6874  -2.0270  -0.2746
 JXV  N12  N  N     0  -0.463  -0.5209   3.4057  -0.1020
 JXV  N16  N  N     0  -0.465   1.7312   2.6726  -0.1670
 JXV  N17  N  NH1   0  -0.659  -2.2738   1.9440  -0.0771
 JXV  O7   O  O2    0  -0.475   5.3552  -2.5224  -0.3051
 JXV  O8   O  O2    0  -0.481   5.9415   0.1299   0.4739
 JXV  H1   H  HCR6  0   0.266   3.9233   1.7139   0.4194
 JXV  H2   H  HCR6  0   0.253   1.0918  -1.2619  -0.8320
 JXV  H3   H  HCR6  0   0.272   2.8771  -2.9289  -0.8768
 JXV  H4   H  HCR6  0   0.274  -0.3540   0.0465  -0.0536
 JXV  H5   H  HCH2  0   0.243  -2.7350   0.2354   1.0653
 JXV  H6   H  HCH2  0   0.259  -2.5003  -0.0475  -0.6551
 JXV  H7   H  HCH1  0   0.262  -4.5465   1.1450  -1.2139
 JXV  H9   H  HCR6  0   0.255  -5.2145  -0.8348  -2.2057
 JXV  H10  H  HCR6  0   0.246  -5.0634  -0.6460   2.0766
 JXV  H11  H  HOH1  0   0.454  -4.8349   1.5503   1.5568
 JXV  H12  H  HCH2  0   0.245   6.5886  -1.3523   1.7657
 JXV  H13  H  HCH2  0   0.263   7.8277  -0.5486   0.7867
 JXV  H14  H  HCR6  0   0.251   1.1172   4.6248  -0.1284
 JXV  H15  H  HCR6  0   0.258  -6.6883  -4.0915   0.1483
 JXV  H16  H  HCR6  0   0.259  -6.0883  -2.8596   2.2089
 JXV  H17  H  HCH2  0   0.247   6.9636  -1.6389  -1.2603
 JXV  H18  H  HCH2  0   0.264   7.3377  -2.8680  -0.0394
 JXV  H19  H  HNH1  0   0.389  -2.8337   2.7665   0.0901
 JXV  H8   H  HCR6  0   0.258  -6.2401  -3.0698  -2.0645

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
 JXV  C20  C22  aromatic  1.389  0.020  1.389
 JXV  C20  C21  aromatic  1.388  0.020  1.388
 JXV  C22  C24  aromatic  1.388  0.020  1.388
 JXV  C21  C23  aromatic  1.389  0.020  1.389
 JXV  C24  C25  aromatic  1.393  0.020  1.393
 JXV  C23  C25  aromatic  1.391  0.020  1.391
 JXV  C25  C19  single    1.512  0.020  1.512
 JXV  C19  C18  single    1.527  0.020  1.527
 JXV  C19  O26  single    1.410  0.020  1.410
 JXV  C18  N17  single    1.441  0.020  1.441
 JXV  N12  C14  aromatic  1.318  0.020  1.318
 JXV  N12  C13  aromatic  1.341  0.020  1.341
 JXV  C14  N16  aromatic  1.320  0.020  1.320
 JXV  N17  C13  single    1.343  0.020  1.343
 JXV  C13  C15  aromatic  1.405  0.020  1.405
 JXV  N16  C11  aromatic  1.342  0.020  1.342
 JXV  C15  C11  aromatic  1.383  0.020  1.383
 JXV  C11  C1   single    1.476  0.020  1.476
 JXV  C1   C3   aromatic  1.396  0.020  1.396
 JXV  C1   C2   aromatic  1.393  0.020  1.393
 JXV  C3   C5   aromatic  1.383  0.020  1.383
 JXV  C2   C4   aromatic  1.385  0.020  1.385
 JXV  C5   C6   aromatic  1.389  0.020  1.389
 JXV  C4   C6   aromatic  1.400  0.020  1.400
 JXV  C4   O8   single    1.354  0.020  1.354
 JXV  C6   O7   single    1.349  0.020  1.349
 JXV  O8   C10  single    1.420  0.020  1.420
 JXV  O7   C9   single    1.422  0.020  1.422
 JXV  C10  C9   single    1.509  0.020  1.509
 JXV  C2   H1   single    0.930  0.020  1.080
 JXV  C3   H2   single    0.930  0.020  1.080
 JXV  C5   H3   single    0.930  0.020  1.080
 JXV  C15  H4   single    0.930  0.020  1.080
 JXV  C18  H5   single    0.970  0.020  1.090
 JXV  C18  H6   single    0.970  0.020  1.090
 JXV  C19  H7   single    0.970  0.020  1.090
 JXV  C21  H8   single    0.930  0.020  1.080
 JXV  C23  H9   single    0.930  0.020  1.080
 JXV  C24  H10  single    0.930  0.020  1.080
 JXV  O26  H11  single    0.850  0.020  0.980
 JXV  C10  H12  single    0.970  0.020  1.090
 JXV  C10  H13  single    0.970  0.020  1.090
 JXV  C14  H14  single    0.930  0.020  1.080
 JXV  C20  H15  single    0.930  0.020  1.080
 JXV  C22  H16  single    0.930  0.020  1.080
 JXV  C9   H17  single    0.970  0.020  1.090
 JXV  C9   H18  single    0.970  0.020  1.090
 JXV  N17  H19  single    0.860  0.020  1.020

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
 JXV  C11  C1   C3   121.83  3.000
 JXV  C3   C1   C2   118.60  3.000
 JXV  C11  C1   C2   119.57  3.000
 JXV  H1   C2   C4   118.89  3.000
 JXV  H1   C2   C1   120.01  3.000
 JXV  C4   C2   C1   121.10  3.000
 JXV  H2   C3   C5   118.36  3.000
 JXV  H2   C3   C1   120.97  3.000
 JXV  C5   C3   C1   120.64  3.000
 JXV  O8   C4   C6   121.64  3.000
 JXV  O8   C4   C2   118.54  3.000
 JXV  C6   C4   C2   119.82  3.000
 JXV  H3   C5   C6   119.10  3.000
 JXV  H3   C5   C3   120.32  3.000
 JXV  C6   C5   C3   120.58  3.000
 JXV  O7   C6   C5   118.75  3.000
 JXV  O7   C6   C4   122.01  3.000
 JXV  C5   C6   C4   119.25  3.000
 JXV  N16  C11  C15  121.31  3.000
 JXV  C15  C11  C1   121.94  3.000
 JXV  N16  C11  C1   116.74  3.000
 JXV  H4   C15  C13  121.07  3.000
 JXV  H4   C15  C11  121.42  3.000
 JXV  C13  C15  C11  117.49  3.000
 JXV  H6   C18  H5   106.81  3.000
 JXV  H6   C18  N17  110.08  3.000
 JXV  H5   C18  N17  111.34  3.000
 JXV  H6   C18  C19  108.06  3.000
 JXV  H5   C18  C19  110.09  3.000
 JXV  N17  C18  C19  110.34  3.000
 JXV  H7   C19  C25  108.24  3.000
 JXV  H7   C19  O26  105.33  3.000
 JXV  C25  C19  O26  113.35  3.000
 JXV  H7   C19  C18  107.77  3.000
 JXV  O26  C19  C18  111.91  3.000
 JXV  C25  C19  C18  109.92  3.000
 JXV  H8   C21  C20  120.24  3.000
 JXV  H8   C21  C23  119.77  3.000
 JXV  C20  C21  C23  119.99  3.000
 JXV  H9   C23  C25  119.51  3.000
 JXV  H9   C23  C21  119.69  3.000
 JXV  C25  C23  C21  120.80  3.000
 JXV  H10  C24  C25  120.91  3.000
 JXV  H10  C24  C22  118.58  3.000
 JXV  C25  C24  C22  120.51  3.000
 JXV  H11  O26  C19  109.56  3.000
 JXV  H13  C10  H12  108.45  3.000
 JXV  H13  C10  O8   107.19  3.000
 JXV  H12  C10  O8   110.10  3.000
 JXV  H13  C10  C9   110.49  3.000
 JXV  H12  C10  C9   110.40  3.000
 JXV  O8   C10  C9   110.15  3.000
 JXV  N17  C13  N12  116.53  3.000
 JXV  N17  C13  C15  122.88  3.000
 JXV  N12  C13  C15  120.59  3.000
 JXV  H14  C14  N16  116.25  3.000
 JXV  H14  C14  N12  115.95  3.000
 JXV  N16  C14  N12  127.79  3.000
 JXV  H15  C20  C22  120.14  3.000
 JXV  H15  C20  C21  120.25  3.000
 JXV  C22  C20  C21  119.61  3.000
 JXV  H16  C22  C20  120.04  3.000
 JXV  H16  C22  C24  119.72  3.000
 JXV  C20  C22  C24  120.25  3.000
 JXV  C24  C25  C23  118.84  3.000
 JXV  C23  C25  C19  119.93  3.000
 JXV  C24  C25  C19  121.22  3.000
 JXV  H18  C9   H17  108.52  3.000
 JXV  H18  C9   O7   107.17  3.000
 JXV  H17  C9   O7   109.92  3.000
 JXV  H18  C9   C10  110.57  3.000
 JXV  H17  C9   C10  110.52  3.000
 JXV  O7   C9   C10  110.08  3.000
 JXV  C14  N12  C13  116.52  3.000
 JXV  C14  N16  C11  116.28  3.000
 JXV  H19  N17  C13  115.87  3.000
 JXV  H19  N17  C18  117.61  3.000
 JXV  C13  N17  C18  124.45  3.000
 JXV  C9   O7   C6   114.51  3.000
 JXV  C10  O8   C4   114.19  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
 JXV  CONST_01  C14  N16  C11  C1    180.00   0.0  0
 JXV  CONST_02  C13  C15  C11  C1    180.00   0.0  0
 JXV  CONST_03  C6   C5   C3   C1      0.00   0.0  0
 JXV  CONST_04  C6   C4   C2   C1      0.00   0.0  0
 JXV  CONST_07  C5   C3   C1   C2      0.00   0.0  0
 JXV  CONST_08  C5   C6   C4   C2      0.00   0.0  0
 JXV  CONST_11  C4   C2   C1   C3      0.00   0.0  0
 JXV  CONST_12  C4   C6   C5   C3      0.00   0.0  0
 JXV  CONST_13  C11  C1   C2   C4    180.00   0.0  0
 JXV  CONST_14  C11  C1   C3   C5    180.00   0.0  0
 JXV  CONST_15  N12  C14  N16  C11     0.00   0.0  0
 JXV  CONST_16  N12  C13  C15  C11     0.00   0.0  0
 JXV  CONST_17  C14  N12  C13  C15     0.00   0.0  0
 JXV  CONST_18  C14  N16  C11  C15     0.00   0.0  0
 JXV  CONST_19  C24  C22  C20  C21     0.00   0.0  0
 JXV  CONST_20  C24  C25  C23  C21     0.00   0.0  0
 JXV  CONST_21  C22  C20  C21  C23     0.00   0.0  0
 JXV  CONST_22  C22  C24  C25  C23     0.00   0.0  0
 JXV  CONST_23  N16  C14  N12  C13     0.00   0.0  0
 JXV  CONST_24  N16  C11  C15  C13     0.00   0.0  0
 JXV  CONST_25  C25  C24  C22  C20     0.00   0.0  0
 JXV  CONST_26  C25  C23  C21  C20     0.00   0.0  0
 JXV  CONST_27  N17  C13  C15  C11   180.00   0.0  0
 JXV  CONST_28  C22  C24  C25  C19   180.00   0.0  0
 JXV  CONST_29  C21  C23  C25  C19   180.00   0.0  0
 JXV  CONST_30  N17  C13  N12  C14   180.00   0.0  0
 JXV  CONST_31  H4   C15  C11  C1      0.00   0.0  0
 JXV  CONST_32  H3   C5   C3   C1    180.00   0.0  0
 JXV  CONST_33  H2   C3   C1   C2    180.00   0.0  0
 JXV  CONST_34  H1   C2   C1   C3    180.00   0.0  0
 JXV  CONST_35  H14  C14  N16  C11   180.00   0.0  0
 JXV  CONST_36  H16  C22  C20  C21   180.00   0.0  0
 JXV  CONST_37  H15  C20  C21  C23   180.00   0.0  0
 JXV  CONST_38  H10  C24  C25  C23   180.00   0.0  0
 JXV  CONST_39  H9   C23  C25  C24   180.00   0.0  0
 JXV  CONST_40  H8   C21  C20  C22   180.00   0.0  0
 JXV  CONST_41  C18  N17  C13  C15     0.00   0.0  0
 JXV  CONST_42  N12  C13  N17  C18   180.00   0.0  0
 JXV  CONST_43  H19  N17  C13  C15   180.00   0.0  0
 JXV  Var_01    C9   C10  O8   C4     45.41  30.0  1
 JXV  Var_02    C10  C9   O7   C6     44.01  30.0  1
 JXV  Var_03    O8   C10  C9   O7    -60.48  30.0  1
 JXV  Var_04    C13  N17  C18  C19  -170.47  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JXV  chir_01  C19  C25  C18  O26  positiv

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
 JXV  plan-1  C19  0.020
 JXV  plan-1  C21  0.020
 JXV  plan-1  C23  0.020
 JXV  plan-1  C24  0.020
 JXV  plan-1  C20  0.020
 JXV  plan-1  C22  0.020
 JXV  plan-1  C25  0.020
 JXV  plan-1  H9   0.020
 JXV  plan-1  H10  0.020
 JXV  plan-1  H15  0.020
 JXV  plan-1  H16  0.020
 JXV  plan-1  H8   0.020
 JXV  plan-2  C1   0.020
 JXV  plan-2  C11  0.020
 JXV  plan-2  C15  0.020
 JXV  plan-2  C13  0.020
 JXV  plan-2  C14  0.020
 JXV  plan-2  N12  0.020
 JXV  plan-2  N16  0.020
 JXV  plan-2  N17  0.020
 JXV  plan-2  H4   0.020
 JXV  plan-2  H14  0.020
 JXV  plan-3  C1   0.020
 JXV  plan-3  C2   0.020
 JXV  plan-3  C3   0.020
 JXV  plan-3  C4   0.020
 JXV  plan-3  C5   0.020
 JXV  plan-3  C6   0.020
 JXV  plan-3  C11  0.020
 JXV  plan-3  O7   0.020
 JXV  plan-3  O8   0.020
 JXV  plan-3  H1   0.020
 JXV  plan-3  H2   0.020
 JXV  plan-3  H3   0.020
 JXV  plan-4  C18  0.020
 JXV  plan-4  C13  0.020
 JXV  plan-4  N17  0.020
 JXV  plan-4  H19  0.020

