# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:53:40 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2R,3S,4R)-3-(2'-fluoro[1,1'-biphenyl]-4-yl)-4-(hydroxymethyl)azetidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1N[C@@H](C#N)[C@@H]1c2ccc(cc2)c3ccccc3F
#
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
 79V  79V  (2R,3S,4R)-3-(2'-fluoro[1,1'-biphenyl]-4-yl)-4-(hydroxymethyl)azetidine-2-carbonitrile  ligand  36  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_79V
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
 79V  C19  C  CH2   0  -0.159  -2.7343   2.0422  -0.4903
 79V  C17  C  CSP   0   0.132  -4.1595  -1.8738   1.0620
 79V  C16  C  C     0  -0.142  -3.5905  -0.5716   0.7265
 79V  C14  C  C     0  -0.083  -3.4245   0.7546  -0.8819
 79V  C10  C  CR6   0   0.155  -1.1608  -0.5071  -0.3406
 79V  C11  C  CR16  0  -0.285  -0.3745  -0.7571  -1.4643
 79V  C12  C  CR16  0  -0.284   1.0071  -0.7159  -1.3948
 79V  C13  C  C     0  -0.378  -2.6478  -0.5317  -0.4966
 79V  C01  C  CR16  0  -0.256   5.2477  -1.5060  -0.6535
 79V  C02  C  CR16  0  -0.247   5.9376  -0.4548  -0.0647
 79V  C03  C  CR16  0  -0.402   5.2387   0.6097   0.4860
 79V  C04  C  CR6   0   0.514   3.8585   0.5970   0.4396
 79V  C05  C  CR6   0  -0.139   3.1296  -0.4379  -0.1339
 79V  C06  C  CR16  0  -0.281   3.8618  -1.4911  -0.6856
 79V  C07  C  CR6   0   0.084   1.6538  -0.4319  -0.1917
 79V  C08  C  CR16  0  -0.276   0.8704  -0.1902   0.9349
 79V  C09  C  CR16  0  -0.315  -0.5141  -0.2272   0.8594
 79V  N15  N  N     0  -0.594  -4.5027   0.3252   0.0241
 79V  O20  O  OH1   0  -0.669  -3.6704   3.0852  -0.6393
 79V  F21  F  F     0  -0.307   3.1985   1.6468   0.9569
 79V  H1   H  HCH2  0   0.204  -2.3671   1.9781   0.5428
 79V  H2   H  HCH2  0   0.208  -1.8547   2.1832  -1.1318
 79V  H3   H  H     0   0.308  -3.1440  -0.1534   1.6339
 79V  H4   H  H     0   0.255  -3.7314   0.8064  -1.9300
 79V  H5   H  HCR6  0   0.257  -0.8498  -0.9887  -2.4102
 79V  H6   H  HCR6  0   0.259   1.5887  -0.9018  -2.2891
 79V  H7   H  H     0   0.297  -2.9188  -1.3256  -1.1945
 79V  H8   H  HCR6  0   0.263   5.7860  -2.3401  -1.0826
 79V  H9   H  HCR6  0   0.269   7.0189  -0.4580  -0.0326
 79V  H10  H  HCR6  0   0.280   5.7557   1.4450   0.9399
 79V  H11  H  HCR6  0   0.267   3.3286  -2.3200  -1.1340
 79V  H12  H  HCR6  0   0.255   1.3345   0.0036   1.8927
 79V  H13  H  HCR6  0   0.251  -1.0810  -0.0452   1.7636
 79V  H14  H  H     0   0.363  -4.9163   1.0511   0.5969
 79V  H16  H  HOH1  0   0.459  -3.2864   3.8900  -0.2801
 79V  N18  N  NS    0  -0.264  -4.6046  -2.9057   1.3080

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
 79V  C02  C01  aromatic  1.388  0.020  1.388
 79V  C02  C03  aromatic  1.387  0.020  1.387
 79V  C01  C06  aromatic  1.386  0.020  1.386
 79V  C03  C04  aromatic  1.381  0.020  1.381
 79V  C06  C05  aromatic  1.396  0.020  1.396
 79V  C04  C05  aromatic  1.390  0.020  1.390
 79V  C04  F21  single    1.344  0.020  1.344
 79V  C05  C07  single    1.477  0.020  1.477
 79V  C07  C12  aromatic  1.395  0.020  1.395
 79V  C07  C08  aromatic  1.393  0.020  1.393
 79V  C12  C11  aromatic  1.384  0.020  1.384
 79V  C08  C09  aromatic  1.387  0.020  1.387
 79V  C11  C10  aromatic  1.394  0.020  1.394
 79V  O20  C19  single    1.409  0.020  1.409
 79V  C09  C10  aromatic  1.392  0.020  1.392
 79V  C10  C13  single    1.495  0.020  1.495
 79V  C19  C14  single    1.513  0.020  1.513
 79V  C13  C14  single    1.551  0.020  1.551
 79V  C13  C16  single    1.545  0.020  1.545
 79V  C14  N15  single    1.472  0.020  1.472
 79V  C16  N15  single    1.459  0.020  1.459
 79V  C16  C17  single    1.460  0.020  1.460
 79V  C17  N18  triple    1.150  0.020  1.150
 79V  C19  H1   single    0.970  0.020  1.090
 79V  C19  H2   single    0.970  0.020  1.090
 79V  C16  H3   single    0.970  0.020  1.090
 79V  C14  H4   single    0.970  0.020  1.090
 79V  C11  H5   single    0.930  0.020  1.080
 79V  C12  H6   single    0.930  0.020  1.080
 79V  C13  H7   single    0.970  0.020  1.090
 79V  C01  H8   single    0.930  0.020  1.080
 79V  C02  H9   single    0.930  0.020  1.080
 79V  C03  H10  single    0.930  0.020  1.080
 79V  C06  H11  single    0.930  0.020  1.080
 79V  C08  H12  single    0.930  0.020  1.080
 79V  C09  H13  single    0.930  0.020  1.080
 79V  N15  H14  single    0.890  0.020  1.040
 79V  O20  H16  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
 79V  H2   C19  H1   106.81  3.000
 79V  H2   C19  O20  112.05  3.000
 79V  H1   C19  O20  111.39  3.000
 79V  H2   C19  C14  108.89  3.000
 79V  H1   C19  C14  110.27  3.000
 79V  O20  C19  C14  107.43  3.000
 79V  N18  C17  C16  180.00  3.000
 79V  H3   C16  N15  114.78  3.000
 79V  H3   C16  C13  113.43  3.000
 79V  N15  C16  C13   89.11  3.000
 79V  H3   C16  C17  108.02  3.000
 79V  N15  C16  C17  114.52  3.000
 79V  C13  C16  C17  116.28  3.000
 79V  H4   C14  N15  113.46  3.000
 79V  H4   C14  C13  114.71  3.000
 79V  N15  C14  C13   88.40  3.000
 79V  H4   C14  C19  109.63  3.000
 79V  N15  C14  C19  115.03  3.000
 79V  C13  C14  C19  114.40  3.000
 79V  C09  C10  C13  123.74  3.000
 79V  C13  C10  C11  118.28  3.000
 79V  C09  C10  C11  117.97  3.000
 79V  H5   C11  C12  119.22  3.000
 79V  H5   C11  C10  119.64  3.000
 79V  C12  C11  C10  121.14  3.000
 79V  H6   C12  C07  119.88  3.000
 79V  H6   C12  C11  119.31  3.000
 79V  C07  C12  C11  120.81  3.000
 79V  H7   C13  C10  109.00  3.000
 79V  H7   C13  C14  108.67  3.000
 79V  C10  C13  C14  120.68  3.000
 79V  H7   C13  C16  109.64  3.000
 79V  C14  C13  C16   84.98  3.000
 79V  C10  C13  C16  121.64  3.000
 79V  H8   C01  C06  119.78  3.000
 79V  H8   C01  C02  120.32  3.000
 79V  C06  C01  C02  119.89  3.000
 79V  H9   C02  C03  119.61  3.000
 79V  H9   C02  C01  120.46  3.000
 79V  C03  C02  C01  119.93  3.000
 79V  H10  C03  C04  119.91  3.000
 79V  H10  C03  C02  121.20  3.000
 79V  C04  C03  C02  118.89  3.000
 79V  F21  C04  C05  118.89  3.000
 79V  F21  C04  C03  118.09  3.000
 79V  C05  C04  C03  123.02  3.000
 79V  C07  C05  C06  120.77  3.000
 79V  C07  C05  C04  122.49  3.000
 79V  C06  C05  C04  116.73  3.000
 79V  H11  C06  C05  118.86  3.000
 79V  H11  C06  C01  119.58  3.000
 79V  C05  C06  C01  121.55  3.000
 79V  C08  C07  C05  122.07  3.000
 79V  C08  C07  C12  118.16  3.000
 79V  C05  C07  C12  119.74  3.000
 79V  H12  C08  C09  118.77  3.000
 79V  H12  C08  C07  120.38  3.000
 79V  C09  C08  C07  120.84  3.000
 79V  H13  C09  C08  118.21  3.000
 79V  H13  C09  C10  120.71  3.000
 79V  C08  C09  C10  121.08  3.000
 79V  H14  N15  C14  115.98  3.000
 79V  H14  N15  C16  115.05  3.000
 79V  C14  N15  C16   91.01  3.000
 79V  H16  O20  C19  108.35  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
 79V  CONST_01  C07  C12  C11  C10    0.00  0.0  0
 79V  CONST_02  C07  C08  C09  C10    0.00  0.0  0
 79V  CONST_03  C05  C07  C12  C11  180.00  0.0  0
 79V  CONST_04  C08  C07  C12  C11    0.00  0.0  0
 79V  CONST_05  C08  C09  C10  C11    0.00  0.0  0
 79V  CONST_08  C09  C08  C07  C12    0.00  0.0  0
 79V  CONST_09  C09  C10  C11  C12    0.00  0.0  0
 79V  CONST_10  C04  C03  C02  C01    0.00  0.0  0
 79V  CONST_11  C04  C05  C06  C01    0.00  0.0  0
 79V  CONST_12  C07  C05  C06  C01  180.00  0.0  0
 79V  CONST_13  C05  C06  C01  C02    0.00  0.0  0
 79V  CONST_14  C05  C04  C03  C02    0.00  0.0  0
 79V  CONST_15  C06  C01  C02  C03    0.00  0.0  0
 79V  CONST_16  C06  C05  C04  C03    0.00  0.0  0
 79V  CONST_17  C07  C05  C04  C03  180.00  0.0  0
 79V  CONST_19  C09  C08  C07  C05  180.00  0.0  0
 79V  CONST_21  C13  C10  C11  C12  180.00  0.0  0
 79V  CONST_22  C08  C09  C10  C13  180.00  0.0  0
 79V  CONST_23  F21  C04  C03  C02  180.00  0.0  0
 79V  CONST_24  F21  C04  C05  C06  180.00  0.0  0
 79V  CONST_25  F21  C04  C05  C07    0.00  0.0  0
 79V  CONST_26  H6   C12  C11  C10  180.00  0.0  0
 79V  CONST_27  H12  C08  C09  C10  180.00  0.0  0
 79V  CONST_28  H13  C09  C10  C11  180.00  0.0  0
 79V  CONST_29  H5   C11  C10  C13    0.00  0.0  0
 79V  CONST_30  H10  C03  C02  C01  180.00  0.0  0
 79V  CONST_31  H11  C06  C01  C02  180.00  0.0  0
 79V  CONST_32  H8   C01  C02  C03  180.00  0.0  0
 79V  CONST_33  H9   C02  C03  C04  180.00  0.0  0

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
 79V  chir_01  C16  C13  N15  C17  negativ
 79V  chir_02  C14  N15  C13  C19  positiv
 79V  chir_03  C13  C16  C14  C10  negativ

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
 79V  plan-1  C01  0.020
 79V  plan-1  C02  0.020
 79V  plan-1  C03  0.020
 79V  plan-1  C04  0.020
 79V  plan-1  C05  0.020
 79V  plan-1  C06  0.020
 79V  plan-1  C07  0.020
 79V  plan-1  F21  0.020
 79V  plan-1  H8   0.020
 79V  plan-1  H9   0.020
 79V  plan-1  H10  0.020
 79V  plan-1  H11  0.020
 79V  plan-2  C10  0.020
 79V  plan-2  C11  0.020
 79V  plan-2  C12  0.020
 79V  plan-2  C13  0.020
 79V  plan-2  C05  0.020
 79V  plan-2  C07  0.020
 79V  plan-2  C08  0.020
 79V  plan-2  C09  0.020
 79V  plan-2  H5   0.020
 79V  plan-2  H6   0.020
 79V  plan-2  H12  0.020
 79V  plan-2  H13  0.020

