# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 22:09:13 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-fluoro-N-({1-[(2R)-4-(hydroxyamino)-1-(naphthalen-2-yl)-4-oxobutan-2-yl]-1H-1,2,3-triazol-5-yl}methyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C[C@@H](Cc1ccc2ccccc2c1)n3nncc3CNC(=O)c4ccc(F)cc4
#
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
 3M9  3M9  4-fluoro-N-({1-[(2R)-4-(hydroxyamino)-1-(naphthalen-2-yl)-4-oxobutan-2-yl]-1H-1,2,3-triazol-5-yl}methyl)benzamide  ligand  55  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3M9
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
 3M9  C01  C  CH1   0  -0.109  -0.4752   1.5559  -0.4828
 3M9  N02  N  NR5   0  -0.318  -0.7966   1.0394  -1.8042
 3M9  C09  C  CR5   0   0.346  -0.7039  -0.2253  -2.2630
 3M9  C10  C  CR15  0  -0.231  -1.1925  -0.1367  -3.5413
 3M9  N11  N  N     0  -0.290  -1.5501   1.1412  -3.7759
 3M9  N12  N  N     0  -0.097  -1.3072   1.8413  -2.7223
 3M9  C23  C  CH2   0  -0.382  -0.1841  -1.3874  -1.4900
 3M9  N24  N  NH1   0  -0.647   1.1971  -1.2075  -1.1027
 3M9  C25  C  C     0   0.537   1.6382  -1.3592   0.1646
 3M9  C26  C  CR6   0  -0.030   3.0911  -1.0978   0.3743
 3M9  O27  O  O     0  -0.473   0.9093  -1.6828   1.0897
 3M9  C28  C  CR16  0  -0.261   3.7974  -0.1677  -0.3841
 3M9  C29  C  CR16  0  -0.399   5.1394   0.0753  -0.1395
 3M9  C30  C  CR6   0   0.532   5.7624  -0.6292   0.8723
 3M9  C31  C  CR16  0  -0.400   5.0900  -1.5535   1.6501
 3M9  C32  C  CR16  0  -0.252   3.7461  -1.7741   1.4005
 3M9  F33  F  F     0  -0.308   7.0613  -0.4057   1.1107
 3M9  C03  C  CH2   0  -0.514  -1.7574   1.9538   0.2551
 3M9  C13  C  CR6   0   0.120  -2.7400   0.8169   0.2679
 3M9  C14  C  CR16  0  -0.366  -2.5755  -0.2399   1.1269
 3M9  C15  C  CR66  0   0.134  -3.4424  -1.3554   1.0977
 3M9  C16  C  CR66  0   0.102  -4.5082  -1.3756   0.1615
 3M9  C17  C  CR16  0  -0.300  -4.6641  -0.2758  -0.7131
 3M9  C18  C  CR16  0  -0.293  -3.8039   0.7856  -0.6631
 3M9  C19  C  CR16  0  -0.315  -3.2750  -2.4567   1.9711
 3M9  C20  C  CR16  0  -0.258  -4.1285  -3.5246   1.9179
 3M9  C21  C  CR16  0  -0.260  -5.1913  -3.5426   0.9890
 3M9  C22  C  CR16  0  -0.311  -5.3762  -2.4925   0.1314
 3M9  C04  C  CH2   0  -0.599   0.5357   2.6908  -0.5939
 3M9  C05  C  C     0   0.533   1.1447   2.9962   0.7575
 3M9  N06  N  NH1   0  -0.375   1.2152   4.3126   1.0235
 3M9  O07  O  O     0  -0.457   1.5186   2.1256   1.5205
 3M9  O08  O  OH1   0  -0.541   1.9220   4.7522   2.1001
 3M9  H1   H  HCH1  0   0.303  -0.0101   0.7368   0.0626
 3M9  H2   H  HCR5  0   0.281  -1.2982  -0.9159  -4.2786
 3M9  H3   H  HCH2  0   0.293  -0.7763  -1.5472  -0.5891
 3M9  H4   H  HCH2  0   0.291  -0.2948  -2.2822  -2.1051
 3M9  H5   H  HNH1  0   0.409   1.8686  -1.1140  -1.8478
 3M9  H6   H  HCR6  0   0.263   3.3083   0.4024  -1.1635
 3M9  H7   H  HCR6  0   0.288   5.6873   0.8053  -0.7198
 3M9  H8   H  HCR6  0   0.286   5.6053  -2.0867   2.4377
 3M9  H9   H  HCR6  0   0.272   3.2067  -2.4892   2.0069
 3M9  H10  H  HCH2  0   0.275  -1.4861   2.2321   1.2754
 3M9  H11  H  HCH2  0   0.266  -2.1924   2.8395  -0.2127
 3M9  H12  H  HCR6  0   0.249  -1.7573  -0.2355   1.8394
 3M9  H13  H  HCR6  0   0.254  -5.4752  -0.2860  -1.4311
 3M9  H14  H  HCR6  0   0.251  -3.9351   1.6161  -1.3463
 3M9  H15  H  HCR6  0   0.253  -2.4586  -2.4422   2.6828
 3M9  H16  H  HCR6  0   0.258  -3.9912  -4.3622   2.5893
 3M9  H17  H  HCR6  0   0.258  -5.8588  -4.3937   0.9573
 3M9  H18  H  HCR6  0   0.255  -6.1914  -2.5064  -0.5823
 3M9  H19  H  HCH2  0   0.299   1.3540   2.3852  -1.2522
 3M9  H20  H  HCH2  0   0.281   0.0752   3.5710  -1.0457
 3M9  H21  H  HNH1  0   0.417   1.0258   5.0155   0.3230
 3M9  H22  H  HOH1  0   0.479   1.2733   4.9202   2.7960

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
 3M9  F33  C30  single    1.339  0.020  1.339
 3M9  C29  C30  aromatic  1.381  0.020  1.381
 3M9  C29  C28  aromatic  1.386  0.020  1.386
 3M9  C30  C31  aromatic  1.383  0.020  1.383
 3M9  C28  C26  aromatic  1.392  0.020  1.392
 3M9  C31  C32  aromatic  1.385  0.020  1.385
 3M9  O27  C25  double    1.221  0.020  1.221
 3M9  C26  C32  aromatic  1.393  0.020  1.393
 3M9  C26  C25  single    1.491  0.020  1.491
 3M9  C25  N24  single    1.350  0.020  1.350
 3M9  N24  C23  single    1.446  0.020  1.446
 3M9  C22  C21  aromatic  1.368  0.020  1.368
 3M9  C22  C16  aromatic  1.415  0.020  1.415
 3M9  C21  C20  aromatic  1.412  0.020  1.412
 3M9  C23  C09  single    1.489  0.020  1.489
 3M9  C17  C16  aromatic  1.414  0.020  1.414
 3M9  C17  C18  aromatic  1.367  0.020  1.367
 3M9  C16  C15  aromatic  1.419  0.020  1.419
 3M9  C18  C13  aromatic  1.414  0.020  1.414
 3M9  C20  C19  aromatic  1.368  0.020  1.368
 3M9  C09  C10  aromatic  1.371  0.020  1.371
 3M9  C09  N02  aromatic  1.349  0.020  1.349
 3M9  C10  N11  aromatic  1.348  0.020  1.348
 3M9  C15  C19  aromatic  1.415  0.020  1.415
 3M9  C15  C14  aromatic  1.413  0.020  1.413
 3M9  C13  C14  aromatic  1.372  0.020  1.372
 3M9  C13  C03  single    1.503  0.020  1.503
 3M9  N02  C01  single    1.455  0.020  1.455
 3M9  N02  N12  aromatic  1.322  0.020  1.322
 3M9  N11  N12  aromatic  1.288  0.020  1.288
 3M9  C01  C03  single    1.532  0.020  1.532
 3M9  C01  C04  single    1.524  0.020  1.524
 3M9  C04  C05  single    1.514  0.020  1.514
 3M9  C05  N06  single    1.345  0.020  1.345
 3M9  C05  O07  double    1.217  0.020  1.217
 3M9  N06  O08  single    1.361  0.020  1.361
 3M9  C01  H1   single    0.970  0.020  1.090
 3M9  C10  H2   single    0.930  0.020  1.080
 3M9  C23  H3   single    0.970  0.020  1.090
 3M9  C23  H4   single    0.970  0.020  1.090
 3M9  N24  H5   single    0.860  0.020  1.020
 3M9  C28  H6   single    0.930  0.020  1.080
 3M9  C29  H7   single    0.930  0.020  1.080
 3M9  C31  H8   single    0.930  0.020  1.080
 3M9  C32  H9   single    0.930  0.020  1.080
 3M9  C03  H10  single    0.970  0.020  1.090
 3M9  C03  H11  single    0.970  0.020  1.090
 3M9  C14  H12  single    0.930  0.020  1.080
 3M9  C17  H13  single    0.930  0.020  1.080
 3M9  C18  H14  single    0.930  0.020  1.080
 3M9  C19  H15  single    0.930  0.020  1.080
 3M9  C20  H16  single    0.930  0.020  1.080
 3M9  C21  H17  single    0.930  0.020  1.080
 3M9  C22  H18  single    0.930  0.020  1.080
 3M9  C04  H19  single    0.970  0.020  1.090
 3M9  C04  H20  single    0.970  0.020  1.090
 3M9  N06  H21  single    0.860  0.020  1.020
 3M9  O08  H22  single    0.850  0.020  0.980

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
 3M9  H1   C01  C04  108.27  3.000
 3M9  H1   C01  C03  108.17  3.000
 3M9  C04  C01  C03  113.38  3.000
 3M9  H1   C01  N02  106.40  3.000
 3M9  C04  C01  N02  110.17  3.000
 3M9  C03  C01  N02  110.17  3.000
 3M9  N12  N02  C09  111.05  3.000
 3M9  N12  N02  C01  120.06  3.000
 3M9  C09  N02  C01  128.82  3.000
 3M9  C23  C09  C10  131.19  3.000
 3M9  C10  C09  N02  103.42  3.000
 3M9  C23  C09  N02  125.39  3.000
 3M9  H2   C10  N11  122.71  3.000
 3M9  H2   C10  C09  128.74  3.000
 3M9  N11  C10  C09  108.55  3.000
 3M9  N12  N11  C10  108.84  3.000
 3M9  N11  N12  N02  108.13  3.000
 3M9  H4   C23  H3   106.89  3.000
 3M9  H4   C23  N24  110.48  3.000
 3M9  H3   C23  N24  108.42  3.000
 3M9  H4   C23  C09  108.17  3.000
 3M9  H3   C23  C09  110.72  3.000
 3M9  N24  C23  C09  112.05  3.000
 3M9  H5   N24  C25  119.13  3.000
 3M9  H5   N24  C23  116.76  3.000
 3M9  C25  N24  C23  123.33  3.000
 3M9  O27  C25  C26  121.43  3.000
 3M9  C26  C25  N24  115.50  3.000
 3M9  O27  C25  N24  123.07  3.000
 3M9  C32  C26  C28  119.15  3.000
 3M9  C32  C26  C25  118.48  3.000
 3M9  C28  C26  C25  122.33  3.000
 3M9  H6   C28  C29  118.19  3.000
 3M9  H6   C28  C26  120.98  3.000
 3M9  C29  C28  C26  120.81  3.000
 3M9  H7   C29  C30  120.58  3.000
 3M9  H7   C29  C28  120.95  3.000
 3M9  C30  C29  C28  118.47  3.000
 3M9  F33  C30  C31  118.88  3.000
 3M9  C31  C30  C29  122.26  3.000
 3M9  F33  C30  C29  118.86  3.000
 3M9  H8   C31  C32  121.01  3.000
 3M9  H8   C31  C30  120.50  3.000
 3M9  C32  C31  C30  118.49  3.000
 3M9  H9   C32  C31  119.22  3.000
 3M9  H9   C32  C26  119.97  3.000
 3M9  C31  C32  C26  120.80  3.000
 3M9  H11  C03  H10  107.02  3.000
 3M9  H11  C03  C13  110.90  3.000
 3M9  H10  C03  C13  110.32  3.000
 3M9  H11  C03  C01  109.74  3.000
 3M9  H10  C03  C01  107.96  3.000
 3M9  C13  C03  C01  110.78  3.000
 3M9  C18  C13  C14  119.04  3.000
 3M9  C14  C13  C03  120.65  3.000
 3M9  C18  C13  C03  120.21  3.000
 3M9  H12  C14  C15  118.65  3.000
 3M9  H12  C14  C13  119.91  3.000
 3M9  C15  C14  C13  121.44  3.000
 3M9  C19  C15  C16  119.00  3.000
 3M9  C19  C15  C14  121.93  3.000
 3M9  C16  C15  C14  119.06  3.000
 3M9  C22  C16  C17  122.23  3.000
 3M9  C17  C16  C15  118.69  3.000
 3M9  C22  C16  C15  119.09  3.000
 3M9  H13  C17  C18  120.17  3.000
 3M9  H13  C17  C16  119.03  3.000
 3M9  C18  C17  C16  120.79  3.000
 3M9  H14  C18  C17  119.73  3.000
 3M9  H14  C18  C13  119.30  3.000
 3M9  C17  C18  C13  120.98  3.000
 3M9  H15  C19  C20  120.41  3.000
 3M9  H15  C19  C15  118.95  3.000
 3M9  C20  C19  C15  120.64  3.000
 3M9  H16  C20  C21  119.60  3.000
 3M9  H16  C20  C19  120.06  3.000
 3M9  C21  C20  C19  120.34  3.000
 3M9  H17  C21  C22  120.13  3.000
 3M9  H17  C21  C20  119.58  3.000
 3M9  C22  C21  C20  120.29  3.000
 3M9  H18  C22  C21  120.31  3.000
 3M9  H18  C22  C16  119.06  3.000
 3M9  C21  C22  C16  120.64  3.000
 3M9  H20  C04  H19  106.97  3.000
 3M9  H20  C04  C05  112.13  3.000
 3M9  H19  C04  C05  107.02  3.000
 3M9  H20  C04  C01  110.55  3.000
 3M9  H19  C04  C01  109.39  3.000
 3M9  C05  C04  C01  110.62  3.000
 3M9  O07  C05  N06  124.09  3.000
 3M9  O07  C05  C04  122.63  3.000
 3M9  N06  C05  C04  113.28  3.000
 3M9  H21  N06  O08  114.91  3.000
 3M9  H21  N06  C05  122.29  3.000
 3M9  O08  N06  C05  119.99  3.000
 3M9  H22  O08  N06  106.10  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
 3M9  CONST_01  N11  C10  C09  N02     0.00   0.0  0
 3M9  CONST_02  C10  N11  N12  N02     0.00   0.0  0
 3M9  CONST_03  N12  N11  C10  C09     0.00   0.0  0
 3M9  CONST_04  N11  N12  N02  C09     0.00   0.0  0
 3M9  CONST_05  N12  N02  C09  C10     0.00   0.0  0
 3M9  CONST_06  C30  C29  C28  C26     0.00   0.0  0
 3M9  CONST_07  C30  C31  C32  C26     0.00   0.0  0
 3M9  CONST_08  C31  C30  C29  C28     0.00   0.0  0
 3M9  CONST_09  C31  C32  C26  C28     0.00   0.0  0
 3M9  CONST_10  C32  C31  C30  C29     0.00   0.0  0
 3M9  CONST_11  C32  C26  C28  C29     0.00   0.0  0
 3M9  CONST_12  C16  C17  C18  C13     0.00   0.0  0
 3M9  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 3M9  CONST_14  C19  C15  C14  C13   180.00   0.0  0
 3M9  CONST_15  C22  C16  C15  C14   180.00   0.0  0
 3M9  CONST_16  C17  C16  C15  C14     0.00   0.0  0
 3M9  CONST_17  C20  C19  C15  C14   180.00   0.0  0
 3M9  CONST_18  C17  C18  C13  C14     0.00   0.0  0
 3M9  CONST_19  C21  C22  C16  C15     0.00   0.0  0
 3M9  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 3M9  CONST_21  C21  C20  C19  C15     0.00   0.0  0
 3M9  CONST_22  C18  C13  C14  C15     0.00   0.0  0
 3M9  CONST_23  C20  C21  C22  C16     0.00   0.0  0
 3M9  CONST_24  C20  C19  C15  C16     0.00   0.0  0
 3M9  CONST_25  C21  C22  C16  C17   180.00   0.0  0
 3M9  CONST_26  C19  C15  C16  C17   180.00   0.0  0
 3M9  CONST_27  C22  C16  C17  C18   180.00   0.0  0
 3M9  CONST_28  C22  C21  C20  C19     0.00   0.0  0
 3M9  CONST_29  C22  C16  C15  C19     0.00   0.0  0
 3M9  CONST_30  C10  C09  N02  C01   180.00   0.0  0
 3M9  CONST_31  N11  N12  N02  C01   180.00   0.0  0
 3M9  CONST_32  C23  C09  C10  N11   180.00   0.0  0
 3M9  CONST_33  C23  C09  N02  N12   180.00   0.0  0
 3M9  CONST_34  C29  C28  C26  C25   180.00   0.0  0
 3M9  CONST_35  C31  C32  C26  C25   180.00   0.0  0
 3M9  CONST_36  F33  C30  C29  C28   180.00   0.0  0
 3M9  CONST_37  F33  C30  C31  C32   180.00   0.0  0
 3M9  CONST_38  C17  C18  C13  C03   180.00   0.0  0
 3M9  CONST_39  C15  C14  C13  C03   180.00   0.0  0
 3M9  CONST_40  H2   C10  C09  N02   180.00   0.0  0
 3M9  CONST_41  H7   C29  C28  C26   180.00   0.0  0
 3M9  CONST_42  H8   C31  C32  C26   180.00   0.0  0
 3M9  CONST_43  H9   C32  C26  C28   180.00   0.0  0
 3M9  CONST_44  H6   C28  C29  C30   180.00   0.0  0
 3M9  CONST_45  H13  C17  C18  C13   180.00   0.0  0
 3M9  CONST_46  H15  C19  C15  C14     0.00   0.0  0
 3M9  CONST_47  H14  C18  C13  C14   180.00   0.0  0
 3M9  CONST_48  H18  C22  C16  C15   180.00   0.0  0
 3M9  CONST_49  H16  C20  C19  C15   180.00   0.0  0
 3M9  CONST_50  H17  C21  C22  C16   180.00   0.0  0
 3M9  CONST_51  H12  C14  C15  C16   180.00   0.0  0
 3M9  CONST_52  C26  C25  N24  C23   180.00   0.0  0
 3M9  CONST_53  H5   N24  C25  C26     0.00   0.0  0
 3M9  CONST_54  O27  C25  N24  C23     0.00   0.0  0
 3M9  CONST_55  O08  N06  C05  C04   180.00   0.0  0
 3M9  CONST_56  O08  N06  C05  O07     0.00   0.0  0
 3M9  CONST_57  H21  N06  C05  C04     0.00   0.0  0
 3M9  Var_01    C18  C13  C03  C01   -99.14  30.0  2
 3M9  Var_02    N24  C23  C09  N02   -61.58  30.0  1
 3M9  Var_03    C28  C26  C25  N24    31.44  30.0  2
 3M9  Var_04    C25  N24  C23  C09   128.53  30.0  2
 3M9  Var_05    N06  C05  C04  C01  -135.21  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
 3M9  chir_01  C01  N02  C03  C04  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
 3M9  plan-1  C01  0.020
 3M9  plan-1  N02  0.020
 3M9  plan-1  C09  0.020
 3M9  plan-1  C10  0.020
 3M9  plan-1  N11  0.020
 3M9  plan-1  N12  0.020
 3M9  plan-1  C23  0.020
 3M9  plan-1  H2   0.020
 3M9  plan-2  C25  0.020
 3M9  plan-2  C26  0.020
 3M9  plan-2  C28  0.020
 3M9  plan-2  C29  0.020
 3M9  plan-2  C30  0.020
 3M9  plan-2  C31  0.020
 3M9  plan-2  C32  0.020
 3M9  plan-2  F33  0.020
 3M9  plan-2  H6   0.020
 3M9  plan-2  H7   0.020
 3M9  plan-2  H8   0.020
 3M9  plan-2  H9   0.020
 3M9  plan-3  C03  0.020
 3M9  plan-3  C13  0.020
 3M9  plan-3  C14  0.020
 3M9  plan-3  C15  0.020
 3M9  plan-3  C16  0.020
 3M9  plan-3  C17  0.020
 3M9  plan-3  C18  0.020
 3M9  plan-3  C19  0.020
 3M9  plan-3  C20  0.020
 3M9  plan-3  C21  0.020
 3M9  plan-3  C22  0.020
 3M9  plan-3  H12  0.020
 3M9  plan-3  H13  0.020
 3M9  plan-3  H14  0.020
 3M9  plan-3  H15  0.020
 3M9  plan-3  H16  0.020
 3M9  plan-3  H17  0.020
 3M9  plan-3  H18  0.020
 3M9  plan-4  C23  0.020
 3M9  plan-4  N24  0.020
 3M9  plan-4  C25  0.020
 3M9  plan-4  C26  0.020
 3M9  plan-4  O27  0.020
 3M9  plan-4  H5   0.020
 3M9  plan-5  C04  0.020
 3M9  plan-5  C05  0.020
 3M9  plan-5  N06  0.020
 3M9  plan-5  O07  0.020
 3M9  plan-5  O08  0.020
 3M9  plan-5  H21  0.020

