# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:41:48 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: ~{N}2-methyl-~{N}4-[(1~{R},5~{S})-3-oxabicyclo[3.1.0]hexan-6-yl]-6-[(1~{S})-1-phenylethyl]pyridine-2,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc(n1)[C@@H](C)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
 ULN  ULN  ~{N}2-methyl-~{N}4-[(1~{R},5~{S})-3-oxabicyclo[3.1.0]hexan-6-yl]-6-[(1~{S})-1-phenylethyl]pyridine-2,4-dicarboxamide  ligand  50  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ULN
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
 ULN  C13  C  CR6   0   0.165  41.1111  18.6585  11.7334
 ULN  C15  C  CR16  0  -0.237  40.0401  16.7186  12.6970
 ULN  C17  C  CR16  0  -0.237  40.9027  18.4375  14.1321
 ULN  C22  C  CH1   0  -0.029  48.3224  16.6074   9.8459
 ULN  C24  C  CH2   0  -0.150  50.1448  16.7343  11.6212
 ULN  C26  C  CH2   0  -0.147  50.2892  15.0152  10.0916
 ULN  C01  C  CH3   0  -0.515  40.4289  15.9226   5.5378
 ULN  N02  N  NH1   0  -0.636  41.1251  16.5773   6.6172
 ULN  O04  O  O     0  -0.478  43.1592  15.7169   6.1386
 ULN  C05  C  CR6   0   0.125  42.9754  17.1845   8.0036
 ULN  C06  C  CR16  0  -0.361  44.3203  17.0914   8.3152
 ULN  C07  C  CR6   0   0.086  44.7935  17.8210   9.4014
 ULN  C08  C  CR16  0  -0.346  43.8984  18.6076  10.1071
 ULN  C09  C  CR6   0   0.305  42.5571  18.6319   9.7276
 ULN  N10  N  N     0  -0.455  42.1218  17.9308   8.6937
 ULN  C11  C  CH1   0  -0.411  41.5598  19.4465  10.5186
 ULN  C12  C  CH3   0  -0.641  40.3723  19.9148   9.6809
 ULN  C14  C  CR16  0  -0.292  40.4646  17.4321  11.5859
 ULN  C16  C  CR16  0  -0.268  40.2566  17.2197  13.9754
 ULN  C18  C  CR16  0  -0.325  41.3271  19.1498  13.0165
 ULN  O20  O  O     0  -0.462  46.7177  18.8017  10.3735
 ULN  N21  N  NH1   0  -0.675  46.9341  16.7156   9.5426
 ULN  C23  C  CR15  0  -0.304  48.7201  16.3813  11.2737
 ULN  O25  O  O     0  -0.492  50.9369  16.1728  10.5885
 ULN  C27  C  CR15  0  -0.351  48.8134  15.2646  10.2816
 ULN  H1   H  HCR6  0   0.252  39.5392  15.7679  12.5655
 ULN  H2   H  HCR6  0   0.253  41.0779  18.8367  15.1230
 ULN  H3   H  HCH1  0   0.273  48.9715  17.2175   9.2212
 ULN  H4   H  HCH2  0   0.215  50.3976  16.3150  12.6036
 ULN  H5   H  HCH2  0   0.231  50.3404  17.8086  11.6500
 ULN  H6   H  HCH2  0   0.216  50.5812  14.1144  10.6467
 ULN  H7   H  HCH2  0   0.232  50.5869  14.8837   9.0491
 ULN  H8   H  HCH3  0   0.252  39.3811  16.2047   5.5825
 ULN  H9   H  HCH3  0   0.240  40.8237  16.2199   4.5655
 ULN  H10  H  HCH3  0   0.240  40.4962  14.8369   5.6157
 ULN  H11  H  HNH1  0   0.409  40.6195  17.1818   7.2461
 ULN  H12  H  HCR6  0   0.275  44.9678  16.4837   7.6979
 ULN  H13  H  HCR6  0   0.275  44.2292  19.1976  10.9519
 ULN  H14  H  HCH1  0   0.273  42.0894  20.3326  10.8801
 ULN  H15  H  HCH3  0   0.238  39.7387  20.5722  10.2759
 ULN  H16  H  HCH3  0   0.235  40.7070  20.4711   8.8050
 ULN  H17  H  HCH3  0   0.233  39.7617  19.0815   9.3366
 ULN  H18  H  HCR6  0   0.250  40.2937  17.0277  10.5949
 ULN  H19  H  HCR6  0   0.253  39.9248  16.6628  14.8420
 ULN  H20  H  HCR6  0   0.250  41.8315  20.1002  13.1467
 ULN  H21  H  HNH1  0   0.414  46.4788  15.9280   9.1095
 ULN  H22  H  HCR5  0   0.276  47.9616  16.3992  12.0455
 ULN  H23  H  HCR5  0   0.280  48.1311  14.4229  10.2986
 ULN  C19  C  C     0   0.538  46.2360  17.8297   9.8160
 ULN  C03  C  C     0   0.533  42.4321  16.4204   6.8274

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
 ULN  C01  N02  single    1.442  0.020  1.442
 ULN  O04  C03  double    1.224  0.020  1.224
 ULN  N02  C03  single    1.333  0.020  1.333
 ULN  C03  C05  single    1.504  0.020  1.504
 ULN  C05  C06  aromatic  1.384  0.020  1.384
 ULN  C05  N10  aromatic  1.327  0.020  1.327
 ULN  C06  C07  aromatic  1.391  0.020  1.391
 ULN  N10  C09  aromatic  1.323  0.020  1.323
 ULN  C26  C27  single    1.509  0.020  1.509
 ULN  C26  O25  single    1.416  0.020  1.416
 ULN  C07  C19  single    1.501  0.020  1.501
 ULN  C07  C08  aromatic  1.385  0.020  1.385
 ULN  C12  C11  single    1.527  0.020  1.527
 ULN  C27  C22  single    1.495  0.020  1.495
 ULN  C27  C23  single    1.497  0.020  1.497
 ULN  N21  C19  single    1.343  0.020  1.343
 ULN  N21  C22  single    1.425  0.020  1.425
 ULN  C09  C08  aromatic  1.394  0.020  1.394
 ULN  C09  C11  single    1.511  0.020  1.511
 ULN  C19  O20  double    1.220  0.020  1.220
 ULN  C22  C23  single    1.499  0.020  1.499
 ULN  C11  C13  single    1.516  0.020  1.516
 ULN  O25  C24  single    1.417  0.020  1.417
 ULN  C23  C24  single    1.508  0.020  1.508
 ULN  C14  C13  aromatic  1.394  0.020  1.394
 ULN  C14  C15  aromatic  1.387  0.020  1.387
 ULN  C13  C18  aromatic  1.391  0.020  1.391
 ULN  C15  C16  aromatic  1.390  0.020  1.390
 ULN  C18  C17  aromatic  1.390  0.020  1.390
 ULN  C16  C17  aromatic  1.387  0.020  1.387
 ULN  C15  H1   single    0.930  0.020  1.080
 ULN  C17  H2   single    0.930  0.020  1.080
 ULN  C22  H3   single    0.970  0.020  1.090
 ULN  C24  H4   single    0.970  0.020  1.090
 ULN  C24  H5   single    0.970  0.020  1.090
 ULN  C26  H6   single    0.970  0.020  1.090
 ULN  C26  H7   single    0.970  0.020  1.090
 ULN  C01  H8   single    0.970  0.020  1.090
 ULN  C01  H9   single    0.970  0.020  1.090
 ULN  C01  H10  single    0.970  0.020  1.090
 ULN  N02  H11  single    0.860  0.020  1.020
 ULN  C06  H12  single    0.930  0.020  1.080
 ULN  C08  H13  single    0.930  0.020  1.080
 ULN  C11  H14  single    0.970  0.020  1.090
 ULN  C12  H15  single    0.970  0.020  1.090
 ULN  C12  H16  single    0.970  0.020  1.090
 ULN  C12  H17  single    0.970  0.020  1.090
 ULN  C14  H18  single    0.930  0.020  1.080
 ULN  C16  H19  single    0.930  0.020  1.080
 ULN  C18  H20  single    0.930  0.020  1.080
 ULN  N21  H21  single    0.860  0.020  1.020
 ULN  C23  H22  single    0.970  0.020  1.090
 ULN  C27  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
 ULN  C18  C13  C14  118.71  3.000
 ULN  C18  C13  C11  120.64  3.000
 ULN  C14  C13  C11  120.65  3.000
 ULN  H1   C15  C16  120.03  3.000
 ULN  H1   C15  C14  119.74  3.000
 ULN  C16  C15  C14  120.24  3.000
 ULN  H2   C17  C18  119.75  3.000
 ULN  H2   C17  C16  120.16  3.000
 ULN  C18  C17  C16  120.09  3.000
 ULN  H3   C22  C27  118.37  3.000
 ULN  H3   C22  C23  118.23  3.000
 ULN  C27  C22  C23   59.99  3.000
 ULN  H3   C22  N21  114.61  3.000
 ULN  C23  C22  N21  118.20  3.000
 ULN  C27  C22  N21  116.76  3.000
 ULN  H5   C24  H4   108.11  3.000
 ULN  H5   C24  O25  107.98  3.000
 ULN  H4   C24  O25  111.84  3.000
 ULN  H5   C24  C23  113.92  3.000
 ULN  H4   C24  C23  109.53  3.000
 ULN  O25  C24  C23  105.50  3.000
 ULN  H7   C26  H6   108.14  3.000
 ULN  H7   C26  C27  114.00  3.000
 ULN  H6   C26  C27  109.40  3.000
 ULN  H7   C26  O25  107.98  3.000
 ULN  H6   C26  O25  111.82  3.000
 ULN  C27  C26  O25  105.55  3.000
 ULN  H10  C01  H9   108.22  3.000
 ULN  H10  C01  H8   108.37  3.000
 ULN  H9   C01  H8   108.37  3.000
 ULN  H10  C01  N02  111.64  3.000
 ULN  H9   C01  N02  111.64  3.000
 ULN  H8   C01  N02  108.49  3.000
 ULN  H11  N02  C03  117.64  3.000
 ULN  H11  N02  C01  119.81  3.000
 ULN  C03  N02  C01  122.55  3.000
 ULN  N10  C05  C06  123.08  3.000
 ULN  N10  C05  C03  117.38  3.000
 ULN  C06  C05  C03  119.54  3.000
 ULN  H12  C06  C07  122.46  3.000
 ULN  H12  C06  C05  119.42  3.000
 ULN  C07  C06  C05  118.10  3.000
 ULN  C19  C07  C08  118.50  3.000
 ULN  C08  C07  C06  118.42  3.000
 ULN  C19  C07  C06  123.06  3.000
 ULN  H13  C08  C09  119.80  3.000
 ULN  H13  C08  C07  120.66  3.000
 ULN  C09  C08  C07  119.54  3.000
 ULN  C11  C09  N10  118.53  3.000
 ULN  C11  C09  C08  120.12  3.000
 ULN  N10  C09  C08  121.34  3.000
 ULN  C09  N10  C05  119.52  3.000
 ULN  H14  C11  C12  108.03  3.000
 ULN  H14  C11  C09  106.87  3.000
 ULN  C12  C11  C09  113.05  3.000
 ULN  H14  C11  C13  107.43  3.000
 ULN  C09  C11  C13  109.55  3.000
 ULN  C12  C11  C13  111.65  3.000
 ULN  H17  C12  H16  107.97  3.000
 ULN  H17  C12  H15  107.95  3.000
 ULN  H16  C12  H15  108.02  3.000
 ULN  H17  C12  C11  112.01  3.000
 ULN  H16  C12  C11  111.01  3.000
 ULN  H15  C12  C11  109.74  3.000
 ULN  H18  C14  C15  119.48  3.000
 ULN  H18  C14  C13  119.87  3.000
 ULN  C15  C14  C13  120.65  3.000
 ULN  H19  C16  C17  120.26  3.000
 ULN  H19  C16  C15  120.21  3.000
 ULN  C17  C16  C15  119.53  3.000
 ULN  H20  C18  C17  119.68  3.000
 ULN  H20  C18  C13  119.53  3.000
 ULN  C17  C18  C13  120.80  3.000
 ULN  H21  N21  C19  120.08  3.000
 ULN  H21  N21  C22  118.18  3.000
 ULN  C19  N21  C22  121.75  3.000
 ULN  H22  C23  C27  121.92  3.000
 ULN  H22  C23  C24  119.59  3.000
 ULN  C27  C23  C24  105.57  3.000
 ULN  H22  C23  C22  119.39  3.000
 ULN  C24  C23  C22  115.77  3.000
 ULN  C27  C23  C22   59.85  3.000
 ULN  C26  O25  C24  108.90  3.000
 ULN  H23  C27  C23  122.00  3.000
 ULN  H23  C27  C26  119.31  3.000
 ULN  C23  C27  C26  105.53  3.000
 ULN  H23  C27  C22  119.71  3.000
 ULN  C23  C27  C22   60.16  3.000
 ULN  C26  C27  C22  115.66  3.000
 ULN  N21  C19  O20  123.29  3.000
 ULN  O20  C19  C07  120.70  3.000
 ULN  N21  C19  C07  116.01  3.000
 ULN  C05  C03  O04  121.16  3.000
 ULN  C05  C03  N02  114.69  3.000
 ULN  O04  C03  N02  124.15  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
 ULN  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 ULN  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 ULN  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 ULN  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 ULN  CONST_05  C14  C13  C18  C17     0.00   0.0  0
 ULN  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 ULN  CONST_07  C08  C07  C06  C05     0.00   0.0  0
 ULN  CONST_08  C08  C09  N10  C05     0.00   0.0  0
 ULN  CONST_09  C09  N10  C05  C06     0.00   0.0  0
 ULN  CONST_10  C09  C08  C07  C06     0.00   0.0  0
 ULN  CONST_11  N10  C05  C06  C07     0.00   0.0  0
 ULN  CONST_12  N10  C09  C08  C07     0.00   0.0  0
 ULN  CONST_13  C11  C13  C14  C15   180.00   0.0  0
 ULN  CONST_14  C11  C13  C18  C17   180.00   0.0  0
 ULN  CONST_15  C07  C06  C05  C03   180.00   0.0  0
 ULN  CONST_16  C09  N10  C05  C03   180.00   0.0  0
 ULN  CONST_17  C19  C07  C06  C05   180.00   0.0  0
 ULN  CONST_18  C11  C09  N10  C05   180.00   0.0  0
 ULN  CONST_19  C11  C09  C08  C07   180.00   0.0  0
 ULN  CONST_20  C19  C07  C08  C09   180.00   0.0  0
 ULN  CONST_21  H1   C15  C14  C13   180.00   0.0  0
 ULN  CONST_22  H2   C17  C18  C13   180.00   0.0  0
 ULN  CONST_23  H13  C08  C07  C06   180.00   0.0  0
 ULN  CONST_24  H12  C06  C07  C08   180.00   0.0  0
 ULN  CONST_25  H20  C18  C13  C14   180.00   0.0  0
 ULN  CONST_26  H19  C16  C15  C14   180.00   0.0  0
 ULN  CONST_27  H18  C14  C15  C16   180.00   0.0  0
 ULN  CONST_28  C07  C19  N21  C22   180.00   0.0  0
 ULN  CONST_29  O20  C19  N21  C22     0.00   0.0  0
 ULN  CONST_30  C05  C03  N02  C01   180.00   0.0  0
 ULN  CONST_31  H11  N02  C03  C05     0.00   0.0  0
 ULN  CONST_32  H21  N21  C19  C07     0.00   0.0  0
 ULN  CONST_33  O04  C03  N02  C01     0.00   0.0  0
 ULN  Var_01    O25  C26  C27  C22    46.50  30.0  1
 ULN  Var_02    C24  C23  C27  C22  -111.10  30.0  1
 ULN  Var_03    O25  C24  C23  C22   -46.08  30.0  1
 ULN  Var_04    C27  C26  O25  C24    29.84  30.0  1
 ULN  Var_05    C23  C24  O25  C26   -29.88  30.0  1
 ULN  Var_06    C06  C05  C03  N02   179.84  30.0  2
 ULN  Var_07    N21  C19  C07  C06   -29.36  30.0  2
 ULN  Var_08    H8   C01  N02  C03   179.72  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
 ULN  chir_02  C11  C12  C09  C13  positiv
 ULN  chir_03  C22  C27  N21  C23  both
 ULN  chir_04  C23  C27  C22  C24  both
 ULN  chir_05  C27  C23  C22  C26  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
 ULN  plan-1  C05  0.020
 ULN  plan-1  C06  0.020
 ULN  plan-1  C07  0.020
 ULN  plan-1  C08  0.020
 ULN  plan-1  C09  0.020
 ULN  plan-1  N10  0.020
 ULN  plan-1  C11  0.020
 ULN  plan-1  H12  0.020
 ULN  plan-1  H13  0.020
 ULN  plan-1  C19  0.020
 ULN  plan-1  C03  0.020
 ULN  plan-2  C13  0.020
 ULN  plan-2  C15  0.020
 ULN  plan-2  C17  0.020
 ULN  plan-2  C11  0.020
 ULN  plan-2  C14  0.020
 ULN  plan-2  C16  0.020
 ULN  plan-2  C18  0.020
 ULN  plan-2  H1   0.020
 ULN  plan-2  H2   0.020
 ULN  plan-2  H18  0.020
 ULN  plan-2  H19  0.020
 ULN  plan-2  H20  0.020
 ULN  plan-3  C22  0.020
 ULN  plan-3  C07  0.020
 ULN  plan-3  O20  0.020
 ULN  plan-3  N21  0.020
 ULN  plan-3  H21  0.020
 ULN  plan-3  C19  0.020
 ULN  plan-4  C01  0.020
 ULN  plan-4  N02  0.020
 ULN  plan-4  O04  0.020
 ULN  plan-4  C05  0.020
 ULN  plan-4  H11  0.020
 ULN  plan-4  C03  0.020

