# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 17:45:07 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-[(~{S})-methoxy(phenyl)methyl]-~{N}2-methyl-~{N}4-[(1~{S},5~{R})-3-oxabicyclo[3.1.0]hexan-6-yl]pyridine-2,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc(n1)[C@@H](OC)c2ccccc2)C(=O)NC3[C@H]4COC[C@@H]34
#
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
 ULQ  ULQ  6-[(~{S})-methoxy(phenyl)methyl]-~{N}2-methyl-~{N}4-[(1~{S},5~{R})-3-oxabicyclo[3.1.0]hexan-6-yl]pyridine-2,4-dicarboxamide  ligand  51  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ULQ
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
 ULQ  C15  C  CR6   0   0.083  40.5205  18.4110  11.2364
 ULQ  C17  C  CR16  0  -0.238  39.2983  16.5960  12.2470
 ULQ  C20  C  CR16  0  -0.307  40.9478  18.8084  12.4967
 ULQ  C24  C  CH1   0  -0.032  47.6741  16.2095   9.6355
 ULQ  C26  C  CH1   0  -0.348  48.0763  14.9613  10.3555
 ULQ  C28  C  CH2   0  -0.146  49.5321  14.5784  10.2517
 ULQ  C01  C  CH3   0  -0.515  39.7892  15.2854   5.3170
 ULQ  N02  N  NH1   0  -0.635  40.5006  16.0166   6.3357
 ULQ  O04  O  O     0  -0.477  42.5372  15.1512   5.8733
 ULQ  C05  C  CR6   0   0.127  42.3678  16.7346   7.6431
 ULQ  C06  C  CR16  0  -0.355  43.7161  16.6621   7.9530
 ULQ  C07  C  CR6   0   0.088  44.1981  17.4760   8.9723
 ULQ  C08  C  CR16  0  -0.346  43.3125  18.3264   9.6146
 ULQ  C09  C  CR6   0   0.235  41.9713  18.3095   9.2475
 ULQ  N10  N  N     0  -0.442  41.5189  17.5273   8.2838
 ULQ  C11  C  CH1   0  -0.043  40.9738  19.1625   9.9985
 ULQ  O13  O  O2    0  -0.472  39.9221  19.4743   9.1341
 ULQ  C14  C  CH3   0  -0.405  39.0385  20.4416   9.6527
 ULQ  C16  C  CR16  0  -0.279  39.6889  17.2995  11.1178
 ULQ  C18  C  CR16  0  -0.262  39.7365  16.9928  13.5057
 ULQ  C19  C  CR16  0  -0.238  40.5619  18.1007  13.6291
 ULQ  O22  O  O     0  -0.461  46.1571  18.5432   9.7643
 ULQ  N23  N  NH1   0  -0.669  46.2938  16.3350   9.3014
 ULQ  O29  O  O2    0  -0.493  50.2590  15.7668  10.5077
 ULQ  C30  C  CH2   0  -0.149  49.4992  16.5953  11.3714
 ULQ  C31  C  CH1   0  -0.304  48.0551  16.2677  11.0843
 ULQ  H1   H  HCR6  0   0.255  38.6513  15.7341  12.1460
 ULQ  H2   H  HCR6  0   0.254  41.5864  19.6786  12.5974
 ULQ  H3   H  HCH1  0   0.273  48.3600  16.6312   8.9032
 ULQ  H4   H  HCH1  0   0.281  47.3382  14.1897  10.5389
 ULQ  H5   H  HCH2  0   0.216  49.7546  13.7968  10.9895
 ULQ  H6   H  HCH2  0   0.231  49.8252  14.2084   9.2667
 ULQ  H7   H  HCH3  0   0.253  38.7400  15.5619   5.3640
 ULQ  H8   H  HCH3  0   0.240  40.1617  15.5193   4.3190
 ULQ  H9   H  HCH3  0   0.240  39.8673  14.2080   5.4663
 ULQ  H10  H  HNH1  0   0.409  40.0011  16.6579   6.9323
 ULQ  H11  H  HCR6  0   0.280  44.3615  16.0037   7.3876
 ULQ  H12  H  HCR6  0   0.278  43.6523  18.9888  10.4002
 ULQ  H13  H  HCH1  0   0.251  41.4924  20.0766  10.3275
 ULQ  H14  H  HCH3  0   0.240  38.2918  20.6441   8.8866
 ULQ  H15  H  HCH3  0   0.213  38.5234  20.0976  10.5552
 ULQ  H16  H  HCH3  0   0.210  39.5557  21.3778   9.8915
 ULQ  H17  H  HCR6  0   0.255  39.3475  16.9788  10.1410
 ULQ  H18  H  HCR6  0   0.256  39.4315  16.4411  14.3855
 ULQ  H19  H  HCR6  0   0.256  40.9014  18.4201  14.6059
 ULQ  H20  H  HNH1  0   0.414  45.8014  15.5086   8.9995
 ULQ  H21  H  HCH2  0   0.215  49.7177  16.3915  12.4275
 ULQ  H22  H  HCH2  0   0.231  49.7665  17.6339  11.1638
 ULQ  H23  H  HCH1  0   0.277  47.2993  16.5005  11.8231
 ULQ  C21  C  C     0   0.530  45.6430  17.5073   9.3782
 ULQ  C03  C  C     0   0.530  41.8131  15.8879   6.5295

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
 ULQ  C01  N02  single    1.442  0.020  1.442
 ULQ  O04  C03  double    1.224  0.020  1.224
 ULQ  N02  C03  single    1.333  0.020  1.333
 ULQ  C03  C05  single    1.505  0.020  1.505
 ULQ  C05  C06  aromatic  1.385  0.020  1.385
 ULQ  C05  N10  aromatic  1.326  0.020  1.326
 ULQ  C06  C07  aromatic  1.391  0.020  1.391
 ULQ  N10  C09  aromatic  1.321  0.020  1.321
 ULQ  O13  C14  single    1.409  0.020  1.409
 ULQ  O13  C11  single    1.397  0.020  1.397
 ULQ  C07  C21  single    1.501  0.020  1.501
 ULQ  C07  C08  aromatic  1.386  0.020  1.386
 ULQ  C09  C08  aromatic  1.391  0.020  1.391
 ULQ  C09  C11  single    1.512  0.020  1.512
 ULQ  C28  C26  single    1.509  0.020  1.509
 ULQ  C28  O29  single    1.416  0.020  1.416
 ULQ  N23  C21  single    1.343  0.020  1.343
 ULQ  N23  C24  single    1.426  0.020  1.426
 ULQ  C26  C24  single    1.496  0.020  1.496
 ULQ  C26  C31  single    1.496  0.020  1.496
 ULQ  C21  O22  double    1.219  0.020  1.219
 ULQ  C24  C31  single    1.499  0.020  1.499
 ULQ  C11  C15  single    1.517  0.020  1.517
 ULQ  O29  C30  single    1.418  0.020  1.418
 ULQ  C31  C30  single    1.508  0.020  1.508
 ULQ  C16  C15  aromatic  1.393  0.020  1.393
 ULQ  C16  C17  aromatic  1.387  0.020  1.387
 ULQ  C15  C20  aromatic  1.389  0.020  1.389
 ULQ  C17  C18  aromatic  1.391  0.020  1.391
 ULQ  C20  C19  aromatic  1.390  0.020  1.390
 ULQ  C18  C19  aromatic  1.387  0.020  1.387
 ULQ  C17  H1   single    0.930  0.020  1.080
 ULQ  C20  H2   single    0.930  0.020  1.080
 ULQ  C24  H3   single    0.970  0.020  1.090
 ULQ  C26  H4   single    0.970  0.020  1.090
 ULQ  C28  H5   single    0.970  0.020  1.090
 ULQ  C28  H6   single    0.970  0.020  1.090
 ULQ  C01  H7   single    0.970  0.020  1.090
 ULQ  C01  H8   single    0.970  0.020  1.090
 ULQ  C01  H9   single    0.970  0.020  1.090
 ULQ  N02  H10  single    0.860  0.020  1.020
 ULQ  C06  H11  single    0.930  0.020  1.080
 ULQ  C08  H12  single    0.930  0.020  1.080
 ULQ  C11  H13  single    0.970  0.020  1.090
 ULQ  C14  H14  single    0.970  0.020  1.090
 ULQ  C14  H15  single    0.970  0.020  1.090
 ULQ  C14  H16  single    0.970  0.020  1.090
 ULQ  C16  H17  single    0.930  0.020  1.080
 ULQ  C18  H18  single    0.930  0.020  1.080
 ULQ  C19  H19  single    0.930  0.020  1.080
 ULQ  N23  H20  single    0.860  0.020  1.020
 ULQ  C30  H21  single    0.970  0.020  1.090
 ULQ  C30  H22  single    0.970  0.020  1.090
 ULQ  C31  H23  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
 ULQ  C16  C15  C11  120.26  3.000
 ULQ  C16  C15  C20  119.29  3.000
 ULQ  C11  C15  C20  120.44  3.000
 ULQ  H1   C17  C18  120.00  3.000
 ULQ  H1   C17  C16  119.76  3.000
 ULQ  C18  C17  C16  120.24  3.000
 ULQ  H2   C20  C19  119.78  3.000
 ULQ  H2   C20  C15  119.68  3.000
 ULQ  C19  C20  C15  120.54  3.000
 ULQ  H3   C24  C31  118.36  3.000
 ULQ  H3   C24  N23  114.73  3.000
 ULQ  C31  C24  N23  117.98  3.000
 ULQ  H3   C24  C26  118.53  3.000
 ULQ  C31  C24  C26   59.93  3.000
 ULQ  N23  C24  C26  116.52  3.000
 ULQ  H4   C26  C31  121.99  3.000
 ULQ  H4   C26  C28  119.22  3.000
 ULQ  C31  C26  C28  105.59  3.000
 ULQ  H4   C26  C24  119.50  3.000
 ULQ  C31  C26  C24   60.14  3.000
 ULQ  C28  C26  C24  115.98  3.000
 ULQ  H6   C28  H5   108.09  3.000
 ULQ  H6   C28  O29  108.03  3.000
 ULQ  H5   C28  O29  111.83  3.000
 ULQ  H6   C28  C26  114.01  3.000
 ULQ  H5   C28  C26  109.27  3.000
 ULQ  O29  C28  C26  105.66  3.000
 ULQ  H9   C01  H8   108.22  3.000
 ULQ  H9   C01  H7   108.35  3.000
 ULQ  H8   C01  H7   108.36  3.000
 ULQ  H9   C01  N02  111.65  3.000
 ULQ  H8   C01  N02  111.67  3.000
 ULQ  H7   C01  N02  108.48  3.000
 ULQ  H10  N02  C03  117.59  3.000
 ULQ  H10  N02  C01  119.75  3.000
 ULQ  C03  N02  C01  122.66  3.000
 ULQ  N10  C05  C06  123.09  3.000
 ULQ  N10  C05  C03  117.25  3.000
 ULQ  C06  C05  C03  119.66  3.000
 ULQ  H11  C06  C07  122.18  3.000
 ULQ  H11  C06  C05  119.71  3.000
 ULQ  C07  C06  C05  118.08  3.000
 ULQ  C08  C07  C06  118.52  3.000
 ULQ  C08  C07  C21  118.49  3.000
 ULQ  C06  C07  C21  122.96  3.000
 ULQ  H12  C08  C09  120.12  3.000
 ULQ  H12  C08  C07  120.76  3.000
 ULQ  C09  C08  C07  119.12  3.000
 ULQ  C11  C09  N10  118.06  3.000
 ULQ  C11  C09  C08  119.88  3.000
 ULQ  N10  C09  C08  122.01  3.000
 ULQ  C09  N10  C05  119.15  3.000
 ULQ  H13  C11  O13  110.74  3.000
 ULQ  H13  C11  C09  107.82  3.000
 ULQ  O13  C11  C09  108.38  3.000
 ULQ  H13  C11  C15  107.94  3.000
 ULQ  C09  C11  C15  108.84  3.000
 ULQ  O13  C11  C15  112.99  3.000
 ULQ  C14  O13  C11  113.43  3.000
 ULQ  H16  C14  H15  108.11  3.000
 ULQ  H16  C14  H14  108.55  3.000
 ULQ  H15  C14  H14  108.41  3.000
 ULQ  H16  C14  O13  111.75  3.000
 ULQ  H15  C14  O13  112.51  3.000
 ULQ  H14  C14  O13  107.39  3.000
 ULQ  H17  C16  C17  119.69  3.000
 ULQ  H17  C16  C15  120.07  3.000
 ULQ  C17  C16  C15  120.24  3.000
 ULQ  H18  C18  C19  120.16  3.000
 ULQ  H18  C18  C17  120.10  3.000
 ULQ  C19  C18  C17  119.73  3.000
 ULQ  H19  C19  C18  120.18  3.000
 ULQ  H19  C19  C20  119.86  3.000
 ULQ  C18  C19  C20  119.96  3.000
 ULQ  H20  N23  C24  118.09  3.000
 ULQ  H20  N23  C21  119.73  3.000
 ULQ  C24  N23  C21  122.18  3.000
 ULQ  C30  O29  C28  108.99  3.000
 ULQ  H22  C30  H21  108.10  3.000
 ULQ  H22  C30  C31  113.87  3.000
 ULQ  H21  C30  C31  109.47  3.000
 ULQ  H22  C30  O29  107.99  3.000
 ULQ  H21  C30  O29  111.78  3.000
 ULQ  C31  C30  O29  105.68  3.000
 ULQ  H23  C31  C30  119.47  3.000
 ULQ  H23  C31  C26  122.02  3.000
 ULQ  C30  C31  C26  105.59  3.000
 ULQ  H23  C31  C24  119.38  3.000
 ULQ  C30  C31  C24  115.83  3.000
 ULQ  C26  C31  C24   59.93  3.000
 ULQ  N23  C21  O22  123.74  3.000
 ULQ  O22  C21  C07  120.61  3.000
 ULQ  N23  C21  C07  115.64  3.000
 ULQ  C05  C03  O04  121.16  3.000
 ULQ  C05  C03  N02  114.59  3.000
 ULQ  O04  C03  N02  124.25  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
 ULQ  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 ULQ  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 ULQ  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 ULQ  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 ULQ  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 ULQ  CONST_06  C08  C09  N10  C05     0.00   0.0  0
 ULQ  CONST_07  C09  N10  C05  C06     0.00   0.0  0
 ULQ  CONST_08  C09  C08  C07  C06     0.00   0.0  0
 ULQ  CONST_09  N10  C05  C06  C07     0.00   0.0  0
 ULQ  CONST_10  N10  C09  C08  C07     0.00   0.0  0
 ULQ  CONST_11  C19  C20  C15  C16     0.00   0.0  0
 ULQ  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 ULQ  CONST_13  C11  C15  C16  C17   180.00   0.0  0
 ULQ  CONST_14  C05  C06  C07  C21   180.00   0.0  0
 ULQ  CONST_15  C09  C08  C07  C21   180.00   0.0  0
 ULQ  CONST_16  C07  C06  C05  C03   180.00   0.0  0
 ULQ  CONST_17  C09  N10  C05  C03   180.00   0.0  0
 ULQ  CONST_18  C11  C09  N10  C05   180.00   0.0  0
 ULQ  CONST_19  C11  C09  C08  C07   180.00   0.0  0
 ULQ  CONST_20  C19  C20  C15  C11   180.00   0.0  0
 ULQ  CONST_21  H1   C17  C16  C15   180.00   0.0  0
 ULQ  CONST_22  H19  C19  C20  C15   180.00   0.0  0
 ULQ  CONST_23  H17  C16  C15  C20   180.00   0.0  0
 ULQ  CONST_24  H18  C18  C19  C20   180.00   0.0  0
 ULQ  CONST_25  H12  C08  C07  C06   180.00   0.0  0
 ULQ  CONST_26  H11  C06  C07  C08   180.00   0.0  0
 ULQ  CONST_27  H2   C20  C15  C16   180.00   0.0  0
 ULQ  CONST_28  C07  C21  N23  C24   180.00   0.0  0
 ULQ  CONST_29  O22  C21  N23  C24     0.00   0.0  0
 ULQ  CONST_30  C05  C03  N02  C01   180.00   0.0  0
 ULQ  CONST_31  H10  N02  C03  C05     0.00   0.0  0
 ULQ  CONST_32  H20  N23  C21  C07     0.00   0.0  0
 ULQ  CONST_33  O04  C03  N02  C01     0.00   0.0  0
 ULQ  Var_01    O29  C28  C26  C24    46.74  30.0  1
 ULQ  Var_02    C30  C31  C26  C24  -111.17  30.0  1
 ULQ  Var_03    O29  C30  C31  C24   -46.82  30.0  1
 ULQ  Var_04    C31  C30  O29  C28   -29.04  30.0  1
 ULQ  Var_05    C26  C24  N23  C21   141.56  30.0  3
 ULQ  Var_06    C06  C05  C03  N02   178.69  30.0  2
 ULQ  Var_07    N23  C21  C07  C06   -34.91  30.0  2
 ULQ  Var_08    H7   C01  N02  C03   179.86  30.0  3
 ULQ  Var_09    H14  C14  O13  C11   177.30  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
 ULQ  chir_03  C11  O13  C09  C15  positiv
 ULQ  chir_04  C24  N23  C26  C31  both
 ULQ  chir_05  C26  C31  C24  C28  both
 ULQ  chir_06  C31  C26  C24  C30  both

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
 ULQ  plan-1  C05  0.020
 ULQ  plan-1  C06  0.020
 ULQ  plan-1  C07  0.020
 ULQ  plan-1  C08  0.020
 ULQ  plan-1  C09  0.020
 ULQ  plan-1  N10  0.020
 ULQ  plan-1  C11  0.020
 ULQ  plan-1  H11  0.020
 ULQ  plan-1  H12  0.020
 ULQ  plan-1  C21  0.020
 ULQ  plan-1  C03  0.020
 ULQ  plan-2  C15  0.020
 ULQ  plan-2  C17  0.020
 ULQ  plan-2  C20  0.020
 ULQ  plan-2  C11  0.020
 ULQ  plan-2  C16  0.020
 ULQ  plan-2  C18  0.020
 ULQ  plan-2  C19  0.020
 ULQ  plan-2  H1   0.020
 ULQ  plan-2  H2   0.020
 ULQ  plan-2  H17  0.020
 ULQ  plan-2  H18  0.020
 ULQ  plan-2  H19  0.020
 ULQ  plan-3  C24  0.020
 ULQ  plan-3  C07  0.020
 ULQ  plan-3  O22  0.020
 ULQ  plan-3  N23  0.020
 ULQ  plan-3  H20  0.020
 ULQ  plan-3  C21  0.020
 ULQ  plan-4  C01  0.020
 ULQ  plan-4  N02  0.020
 ULQ  plan-4  O04  0.020
 ULQ  plan-4  C05  0.020
 ULQ  plan-4  H10  0.020
 ULQ  plan-4  C03  0.020

