# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:31:01 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[(2,3-dihydro-1,4-benzodioxin-5-yl)methyl]-4-(pyridin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccc2OCCOc12)c3ccc(cc3)c4ccncc4
#
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
 J0P  J0P  N-[(2,3-dihydro-1,4-benzodioxin-5-yl)methyl]-4-(pyridin-4-yl)benzamide  ligand  44  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_J0P
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
 J0P  N1   N  N     0  -0.406  -7.3099   1.7016  -0.1059
 J0P  C4   C  CR16  0  -0.257   5.3449   0.2852  -2.2163
 J0P  C5   C  CR16  0  -0.370   5.4432   1.2429  -1.2208
 J0P  C6   C  CR6   0   0.324   4.6651   1.1381  -0.0744
 J0P  C7   C  CR6   0   0.309   3.7912   0.0575   0.0775
 J0P  C8   C  CH2   0  -0.223   3.4443   0.6982   2.2924
 J0P  C10  C  CR6   0  -0.048  -0.8584  -1.2187   0.1512
 J0P  C13  C  CR6   0   0.094  -3.4157  -0.0649   0.0474
 J0P  C15  C  CR16  0  -0.277  -1.4406  -0.8932  -1.0717
 J0P  C17  C  CR16  0  -0.377  -5.7514   0.1939   0.9053
 J0P  C20  C  CR16  0  -0.377  -5.0879   1.4954  -0.9691
 J0P  O    O  O     0  -0.488   0.7709  -2.5515   1.2334
 J0P  C14  C  CR16  0  -0.291  -2.7025  -0.3246  -1.1221
 J0P  C16  C  CR6   0   0.174  -4.7571   0.5439  -0.0063
 J0P  C19  C  CR16  0  -0.059  -6.3630   2.0374  -0.9746
 J0P  C18  C  CR16  0  -0.060  -6.9963   0.7946   0.8121
 J0P  C12  C  CR16  0  -0.293  -2.8329  -0.4016   1.2697
 J0P  C11  C  CR16  0  -0.255  -1.5761  -0.9774   1.3200
 J0P  N    N  NH1   0  -0.641   1.3457  -1.5949  -0.7357
 J0P  C1   C  CH2   0  -0.345   2.7191  -2.0490  -0.7728
 J0P  C2   C  CR6   0  -0.037   3.6794  -0.9009  -0.9314
 J0P  O1   O  O2    0  -0.466   3.0393  -0.0979   1.1906
 J0P  C9   C  CH2   0  -0.227   3.7376   2.1060   1.8356
 J0P  O2   O  O2    0  -0.481   4.7805   2.0995   0.8734
 J0P  C3   C  CR16  0  -0.327   4.4561  -0.7728  -2.0756
 J0P  H2   H  HCR6  0   0.266   6.1206   2.0820  -1.3215
 J0P  H3   H  HCH2  0   0.260   2.6268   0.6918   3.0116
 J0P  H4   H  HCH2  0   0.242   4.3279   0.2603   2.7689
 J0P  H5   H  HCR6  0   0.264  -0.9348  -1.1038  -2.0057
 J0P  H6   H  HCR6  0   0.271  -5.5765  -0.5509   1.6703
 J0P  H7   H  HCR6  0   0.271  -4.3629   1.8330  -1.6980
 J0P  H8   H  HCR6  0   0.266  -3.1414  -0.1061  -2.0869
 J0P  H9   H  HCR6  0   0.267  -6.6266   2.7828  -1.7169
 J0P  H10  H  HCR6  0   0.267  -7.7778   0.5232   1.5132
 J0P  H11  H  HCR6  0   0.264  -3.3561  -0.1981   2.1953
 J0P  H12  H  HCR6  0   0.264  -1.1448  -1.2279   2.2797
 J0P  H13  H  HNH1  0   0.406   1.0690  -0.9498  -1.4580
 J0P  H14  H  HCH2  0   0.267   2.9162  -2.6028   0.1439
 J0P  H15  H  HCH2  0   0.266   2.8546  -2.7452  -1.6033
 J0P  H16  H  HCH2  0   0.243   2.8376   2.5663   1.4135
 J0P  H17  H  HCH2  0   0.261   4.0750   2.7162   2.6724
 J0P  H18  H  HCR6  0   0.254   4.3666  -1.5147  -2.8594
 J0P  C    C  C     0   0.548   0.4938  -1.8511   0.2702
 J0P  H1   H  HCR6  0   0.255   5.9513   0.3723  -3.1079

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
 J0P  C9   O2   single    1.419  0.020  1.419
 J0P  C9   C8   single    1.509  0.020  1.509
 J0P  O2   C6   single    1.355  0.020  1.355
 J0P  C6   C5   aromatic  1.390  0.020  1.390
 J0P  C6   C7   aromatic  1.398  0.020  1.398
 J0P  C8   O1   single    1.418  0.020  1.418
 J0P  C5   C4   aromatic  1.385  0.020  1.385
 J0P  C7   O1   single    1.352  0.020  1.352
 J0P  C7   C2   aromatic  1.396  0.020  1.396
 J0P  C4   C3   aromatic  1.389  0.020  1.389
 J0P  C2   C3   aromatic  1.389  0.020  1.389
 J0P  C2   C1   single    1.505  0.020  1.505
 J0P  C1   N    single    1.447  0.020  1.447
 J0P  N    C    single    1.343  0.020  1.343
 J0P  C    O    double    1.223  0.020  1.223
 J0P  C    C10  single    1.498  0.020  1.498
 J0P  C15  C10  aromatic  1.393  0.020  1.393
 J0P  C15  C14  aromatic  1.385  0.020  1.385
 J0P  C10  C11  aromatic  1.393  0.020  1.393
 J0P  C14  C13  aromatic  1.394  0.020  1.394
 J0P  C11  C12  aromatic  1.383  0.020  1.383
 J0P  C13  C12  aromatic  1.395  0.020  1.395
 J0P  C13  C16  single    1.474  0.020  1.474
 J0P  C20  C16  aromatic  1.394  0.020  1.394
 J0P  C20  C19  aromatic  1.386  0.020  1.386
 J0P  C16  C17  aromatic  1.394  0.020  1.394
 J0P  C19  N1   aromatic  1.328  0.020  1.328
 J0P  C17  C18  aromatic  1.385  0.020  1.385
 J0P  N1   C18  aromatic  1.328  0.020  1.328
 J0P  C4   H1   single    0.930  0.020  1.080
 J0P  C5   H2   single    0.930  0.020  1.080
 J0P  C8   H3   single    0.970  0.020  1.090
 J0P  C8   H4   single    0.970  0.020  1.090
 J0P  C15  H5   single    0.930  0.020  1.080
 J0P  C17  H6   single    0.930  0.020  1.080
 J0P  C20  H7   single    0.930  0.020  1.080
 J0P  C14  H8   single    0.930  0.020  1.080
 J0P  C19  H9   single    0.930  0.020  1.080
 J0P  C18  H10  single    0.930  0.020  1.080
 J0P  C12  H11  single    0.930  0.020  1.080
 J0P  C11  H12  single    0.930  0.020  1.080
 J0P  N    H13  single    0.860  0.020  1.020
 J0P  C1   H14  single    0.970  0.020  1.090
 J0P  C1   H15  single    0.970  0.020  1.090
 J0P  C9   H16  single    0.970  0.020  1.090
 J0P  C9   H17  single    0.970  0.020  1.090
 J0P  C3   H18  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
 J0P  C18  N1   C19  117.15  3.000
 J0P  H1   C4   C3   120.23  3.000
 J0P  H1   C4   C5   119.80  3.000
 J0P  C3   C4   C5   119.96  3.000
 J0P  H2   C5   C6   119.04  3.000
 J0P  H2   C5   C4   120.89  3.000
 J0P  C6   C5   C4   120.08  3.000
 J0P  O2   C6   C7   121.71  3.000
 J0P  C7   C6   C5   119.87  3.000
 J0P  O2   C6   C5   118.42  3.000
 J0P  O1   C7   C2   118.13  3.000
 J0P  C2   C7   C6   120.15  3.000
 J0P  O1   C7   C6   121.73  3.000
 J0P  H4   C8   H3   108.42  3.000
 J0P  H4   C8   C9   110.36  3.000
 J0P  H3   C8   C9   110.57  3.000
 J0P  H4   C8   O1   110.11  3.000
 J0P  H3   C8   O1   107.19  3.000
 J0P  C9   C8   O1   110.12  3.000
 J0P  C11  C10  C    118.15  3.000
 J0P  C11  C10  C15  118.74  3.000
 J0P  C    C10  C15  123.08  3.000
 J0P  C12  C13  C16  120.77  3.000
 J0P  C16  C13  C14  120.79  3.000
 J0P  C12  C13  C14  118.43  3.000
 J0P  H5   C15  C14  118.30  3.000
 J0P  H5   C15  C10  121.10  3.000
 J0P  C14  C15  C10  120.58  3.000
 J0P  H6   C17  C18  119.43  3.000
 J0P  H6   C17  C16  121.34  3.000
 J0P  C18  C17  C16  119.22  3.000
 J0P  H7   C20  C19  119.47  3.000
 J0P  H7   C20  C16  121.30  3.000
 J0P  C19  C20  C16  119.22  3.000
 J0P  H8   C14  C15  119.00  3.000
 J0P  H8   C14  C13  120.18  3.000
 J0P  C15  C14  C13  120.80  3.000
 J0P  C20  C16  C17  117.01  3.000
 J0P  C17  C16  C13  121.45  3.000
 J0P  C20  C16  C13  121.54  3.000
 J0P  H9   C19  C20  119.69  3.000
 J0P  H9   C19  N1   116.62  3.000
 J0P  C20  C19  N1   123.69  3.000
 J0P  H10  C18  C17  119.70  3.000
 J0P  H10  C18  N1   116.60  3.000
 J0P  C17  C18  N1   123.70  3.000
 J0P  H11  C12  C11  119.09  3.000
 J0P  H11  C12  C13  120.12  3.000
 J0P  C11  C12  C13  120.78  3.000
 J0P  H12  C11  C12  119.40  3.000
 J0P  H12  C11  C10  119.94  3.000
 J0P  C12  C11  C10  120.65  3.000
 J0P  H13  N    C1   116.32  3.000
 J0P  H13  N    C    119.03  3.000
 J0P  C1   N    C    124.16  3.000
 J0P  H15  C1   H14  107.07  3.000
 J0P  H15  C1   C2   109.09  3.000
 J0P  H14  C1   C2   111.17  3.000
 J0P  H15  C1   N    109.71  3.000
 J0P  H14  C1   N    108.05  3.000
 J0P  C2   C1   N    111.65  3.000
 J0P  C3   C2   C1   120.93  3.000
 J0P  C1   C2   C7   119.91  3.000
 J0P  C3   C2   C7   119.16  3.000
 J0P  C8   O1   C7   114.59  3.000
 J0P  H17  C9   H16  108.37  3.000
 J0P  H17  C9   O2   107.21  3.000
 J0P  H16  C9   O2   110.15  3.000
 J0P  H17  C9   C8   110.51  3.000
 J0P  H16  C9   C8   110.42  3.000
 J0P  O2   C9   C8   110.11  3.000
 J0P  C9   O2   C6   114.52  3.000
 J0P  H18  C3   C2   119.13  3.000
 J0P  H18  C3   C4   120.10  3.000
 J0P  C2   C3   C4   120.77  3.000
 J0P  N    C    O    123.76  3.000
 J0P  O    C    C10  120.60  3.000
 J0P  N    C    C10  115.64  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
 J0P  CONST_01  C16  C20  C19  N1      0.00   0.0  0
 J0P  CONST_02  C16  C17  C18  N1      0.00   0.0  0
 J0P  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 J0P  CONST_04  C7   C2   C3   C4      0.00   0.0  0
 J0P  CONST_05  C2   C7   C6   C5      0.00   0.0  0
 J0P  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 J0P  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 J0P  CONST_08  C3   C2   C7   C6      0.00   0.0  0
 J0P  CONST_09  C13  C14  C15  C10     0.00   0.0  0
 J0P  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 J0P  CONST_11  C19  C20  C16  C13   180.00   0.0  0
 J0P  CONST_12  C18  C17  C16  C13   180.00   0.0  0
 J0P  CONST_13  C12  C11  C10  C15     0.00   0.0  0
 J0P  CONST_14  C12  C13  C14  C15     0.00   0.0  0
 J0P  CONST_15  C16  C13  C14  C15   180.00   0.0  0
 J0P  CONST_18  C19  C20  C16  C17     0.00   0.0  0
 J0P  CONST_19  C19  N1   C18  C17     0.00   0.0  0
 J0P  CONST_22  C18  C17  C16  C20     0.00   0.0  0
 J0P  CONST_23  C18  N1   C19  C20     0.00   0.0  0
 J0P  CONST_24  C11  C10  C15  C14     0.00   0.0  0
 J0P  CONST_25  C11  C12  C13  C14     0.00   0.0  0
 J0P  CONST_26  C11  C12  C13  C16   180.00   0.0  0
 J0P  CONST_27  C1   C2   C3   C4    180.00   0.0  0
 J0P  CONST_28  C1   C2   C7   C6    180.00   0.0  0
 J0P  CONST_29  C14  C15  C10  C     180.00   0.0  0
 J0P  CONST_30  C12  C11  C10  C     180.00   0.0  0
 J0P  CONST_31  O1   C7   C2   C1      0.00   0.0  0
 J0P  CONST_32  H7   C20  C19  N1    180.00   0.0  0
 J0P  CONST_33  H6   C17  C18  N1    180.00   0.0  0
 J0P  CONST_34  H18  C3   C4   C5    180.00   0.0  0
 J0P  CONST_35  H1   C4   C5   C6    180.00   0.0  0
 J0P  CONST_36  H2   C5   C6   C7    180.00   0.0  0
 J0P  CONST_37  H8   C14  C15  C10   180.00   0.0  0
 J0P  CONST_38  H11  C12  C11  C10   180.00   0.0  0
 J0P  CONST_39  H5   C15  C14  C13   180.00   0.0  0
 J0P  CONST_40  H12  C11  C12  C13   180.00   0.0  0
 J0P  CONST_41  H9   C19  C20  C16   180.00   0.0  0
 J0P  CONST_42  H10  C18  C17  C16   180.00   0.0  0
 J0P  CONST_43  C1   N    C    C10   180.00   0.0  0
 J0P  CONST_44  H13  N    C    C10     0.00   0.0  0
 J0P  CONST_45  C1   N    C    O       0.00   0.0  0
 J0P  Var_01    C8   C9   O2   C6     44.49  30.0  1
 J0P  Var_02    C9   C8   O1   C7     44.62  30.0  1
 J0P  Var_03    C2   C7   O1   C8    164.68  30.0  1
 J0P  Var_04    O2   C9   C8   O1    -60.23  30.0  1
 J0P  Var_05    N    C1   C2   C7     64.89  30.0  2
 J0P  Var_06    N    C    C10  C15    26.96  30.0  2
 J0P  Var_07    C2   C1   N    C    -123.28  30.0  1

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
 J0P  plan-1  C10  0.020
 J0P  plan-1  C13  0.020
 J0P  plan-1  C15  0.020
 J0P  plan-1  C14  0.020
 J0P  plan-1  C16  0.020
 J0P  plan-1  C12  0.020
 J0P  plan-1  C11  0.020
 J0P  plan-1  H5   0.020
 J0P  plan-1  H8   0.020
 J0P  plan-1  H11  0.020
 J0P  plan-1  H12  0.020
 J0P  plan-1  C    0.020
 J0P  plan-2  N1   0.020
 J0P  plan-2  C13  0.020
 J0P  plan-2  C17  0.020
 J0P  plan-2  C20  0.020
 J0P  plan-2  C16  0.020
 J0P  plan-2  C19  0.020
 J0P  plan-2  C18  0.020
 J0P  plan-2  H6   0.020
 J0P  plan-2  H7   0.020
 J0P  plan-2  H9   0.020
 J0P  plan-2  H10  0.020
 J0P  plan-3  C4   0.020
 J0P  plan-3  C5   0.020
 J0P  plan-3  C6   0.020
 J0P  plan-3  C7   0.020
 J0P  plan-3  C1   0.020
 J0P  plan-3  C2   0.020
 J0P  plan-3  O1   0.020
 J0P  plan-3  O2   0.020
 J0P  plan-3  C3   0.020
 J0P  plan-3  H2   0.020
 J0P  plan-3  H18  0.020
 J0P  plan-3  H1   0.020
 J0P  plan-4  C10  0.020
 J0P  plan-4  O    0.020
 J0P  plan-4  N    0.020
 J0P  plan-4  C1   0.020
 J0P  plan-4  H13  0.020
 J0P  plan-4  C    0.020

