# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 02:27:08 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (3R,5S)-N-{4-chloro-3-[(pyridin-3-yloxy)methyl]phenyl}-3-fluoro-5-morpholin-4-ylcyclohex-1-ene-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: F[C@@H]1C[C@H](CC(=C1)C(=O)Nc2ccc(Cl)c(COc3cccnc3)c2)N4CCOCC4
#
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
 L11  L11  (3R,5S)-N-{4-chloro-3-[(pyridin-3-yloxy)methyl]phenyl}-3-fluoro-5-morpholin-4-ylcyclohex-1-ene-1-carboxamide  ligand  56  31  .  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_L11
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
 L11  CL15  CL  CL    0  -0.125  -5.1419  -2.9521   1.4336
 L11  C14   C   CR6   0  -0.119  -3.5023  -2.5537   1.0277
 L11  C13   C   CR16  0  -0.186  -2.5113  -3.4938   1.2414
 L11  C12   C   CR16  0  -0.325  -1.1932  -3.2077   0.9253
 L11  C16   C   CR6   0   0.138  -3.2076  -1.2992   0.5004
 L11  C17   C   CH2   0  -0.198  -4.3114  -0.3038   0.2820
 L11  O18   O   O2    0  -0.478  -3.7639   0.8830  -0.2407
 L11  C19   C   CR6   0   0.338  -4.5889   1.9136  -0.5018
 L11  C24   C   CR16  0  -0.182  -5.9709   1.8898  -0.3251
 L11  N23   N   N     0  -0.388  -6.7461   2.9335  -0.6014
 L11  C22   C   CR16  0  -0.090  -6.1891   4.0422  -1.0614
 L11  C21   C   CR16  0  -0.306  -4.8196   4.1611  -1.2681
 L11  C20   C   CR16  0  -0.255  -4.0054   3.0827  -0.9846
 L11  C25   C   CR16  0  -0.439  -1.8867  -1.0245   0.1825
 L11  C11   C   CR6   0   0.431  -0.8754  -1.9642   0.3852
 L11  N10   N   NH1   0  -0.770   0.4268  -1.5729   0.0576
 L11  C8    C   C     0   0.522   1.4628  -2.3737  -0.3063
 L11  O9    O   O     0  -0.456   1.3834  -3.5881  -0.3551
 L11  C6    C   C     0  -0.006   2.7191  -1.6400  -0.6684
 L11  C7    C   C1    0  -0.288   3.6003  -2.2819  -1.4339
 L11  C2    C   CH1   0   0.179   4.8557  -1.6419  -1.9191
 L11  F1    F   F     0  -0.385   5.9361  -2.2849  -1.2894
 L11  C5    C   CH2   0  -0.586   2.9446  -0.2446  -0.1522
 L11  C4    C   CH1   0  -0.015   4.4118   0.1785  -0.2404
 L11  C3    C   CH2   0  -0.534   4.9102  -0.1586  -1.6433
 L11  N26   N   NT    0  -0.446   4.5823   1.6005   0.0485
 L11  C31   C   CH2   0  -0.317   5.9918   1.9601   0.1468
 L11  C30   C   CH2   0  -0.186   6.1555   3.4443   0.4089
 L11  O29   O   O2    0  -0.483   5.4927   3.8468   1.5849
 L11  C28   C   CH2   0  -0.183   4.1276   3.5092   1.5085
 L11  C27   C   CH2   0  -0.319   3.9175   2.0248   1.2739
 L11  H13   H   HCR6  0   0.285  -2.7621  -4.4578   1.6625
 L11  H12   H   HCR6  0   0.284  -0.4367  -3.9508   1.1164
 L11  H171  H   HCH2  0   0.257  -5.0533  -0.7272  -0.4060
 L11  H172  H   HCH2  0   0.257  -4.8240  -0.1068   1.2314
 L11  H24   H   HCR6  0   0.280  -6.4792   1.0080   0.0476
 L11  H22   H   HCR6  0   0.263  -6.8530   4.8711  -1.2775
 L11  H21   H   HCR6  0   0.276  -4.4005   5.0843  -1.6435
 L11  H20   H   HCR6  0   0.283  -2.9339   3.1345  -1.1321
 L11  H25   H   HCR6  0   0.277  -1.6267  -0.0605  -0.2350
 L11  H10   H   HNH1  0   0.430   0.5507  -0.5787  -0.0586
 L11  H7    H   H     0   0.272   3.4097  -3.3008  -1.7492
 L11  H2    H   HCH1  0   0.236   4.9719  -1.8244  -2.9899
 L11  H51   H   HCH2  0   0.281   2.6052  -0.2057   0.8851
 L11  H52   H   HCH2  0   0.267   2.3350   0.4762  -0.7126
 L11  H41   H   HCH1  0   0.214   4.9746  -0.4269   0.4930
 L11  H3C1  H   HCH2  0   0.269   5.9304   0.1813  -1.8207
 L11  H3C2  H   HCH2  0   0.249   4.2794   0.3519  -2.3772
 L11  H311  H   HCH2  0   0.201   6.4949   1.3847   0.9432
 L11  H312  H   HCH2  0   0.247   6.5111   1.7357  -0.7845
 L11  H301  H   HCH2  0   0.238   7.2136   3.6811   0.5299
 L11  H302  H   HCH2  0   0.200   5.7792   4.0080  -0.4570
 L11  H281  H   HCH2  0   0.238   3.6619   3.8007   2.4511
 L11  H282  H   HCH2  0   0.200   3.6387   4.0733   0.7012
 L11  H271  H   HCH2  0   0.251   2.8418   1.8631   1.2011
 L11  H272  H   HCH2  0   0.201   4.2759   1.4577   2.1506

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
 L11  CL15  C14   single    1.736  0.020  1.736
 L11  C14   C13   aromatic  1.383  0.020  1.383
 L11  C14   C16   aromatic  1.392  0.020  1.392
 L11  C13   C12   aromatic  1.385  0.020  1.385
 L11  C13   H13   single    0.930  0.020  1.080
 L11  C12   C11   aromatic  1.392  0.020  1.392
 L11  C12   H12   single    0.930  0.020  1.080
 L11  C16   C17   single    1.502  0.020  1.502
 L11  C16   C25   aromatic  1.386  0.020  1.386
 L11  C17   O18   single    1.408  0.020  1.408
 L11  C17   H171  single    0.970  0.020  1.090
 L11  C17   H172  single    0.970  0.020  1.090
 L11  O18   C19   single    1.346  0.020  1.346
 L11  C19   C24   aromatic  1.393  0.020  1.393
 L11  C19   C20   aromatic  1.393  0.020  1.393
 L11  C24   N23   aromatic  1.329  0.020  1.329
 L11  C24   H24   single    0.930  0.020  1.080
 L11  N23   C22   aromatic  1.323  0.020  1.323
 L11  C22   C21   aromatic  1.390  0.020  1.390
 L11  C22   H22   single    0.930  0.020  1.080
 L11  C21   C20   aromatic  1.381  0.020  1.381
 L11  C21   H21   single    0.930  0.020  1.080
 L11  C20   H20   single    0.930  0.020  1.080
 L11  C25   C11   aromatic  1.395  0.020  1.395
 L11  C25   H25   single    0.930  0.020  1.080
 L11  C11   N10   single    1.399  0.020  1.399
 L11  N10   C8    single    1.359  0.020  1.359
 L11  N10   H10   single    0.860  0.020  1.020
 L11  C8    O9    double    1.218  0.020  1.218
 L11  C8    C6    single    1.499  0.020  1.499
 L11  C6    C7    double    1.332  0.020  1.332
 L11  C6    C5    single    1.505  0.020  1.505
 L11  C7    C2    single    1.490  0.020  1.490
 L11  C7    H7    single    0.930  0.020  1.080
 L11  C2    F1    single    1.406  0.020  1.406
 L11  C2    C3    single    1.510  0.020  1.510
 L11  C2    H2    single    0.970  0.020  1.090
 L11  C5    C4    single    1.530  0.020  1.530
 L11  C5    H51   single    0.970  0.020  1.090
 L11  C5    H52   single    0.970  0.020  1.090
 L11  C4    C3    single    1.526  0.020  1.526
 L11  C4    N26   single    1.461  0.020  1.461
 L11  C4    H41   single    0.970  0.020  1.090
 L11  C3    H3C1  single    0.970  0.020  1.090
 L11  C3    H3C2  single    0.970  0.020  1.090
 L11  N26   C31   single    1.458  0.020  1.458
 L11  N26   C27   single    1.457  0.020  1.457
 L11  C31   C30   single    1.516  0.020  1.516
 L11  C31   H311  single    0.970  0.020  1.090
 L11  C31   H312  single    0.970  0.020  1.090
 L11  C30   O29   single    1.409  0.020  1.409
 L11  C30   H301  single    0.970  0.020  1.090
 L11  C30   H302  single    0.970  0.020  1.090
 L11  O29   C28   single    1.408  0.020  1.408
 L11  C28   C27   single    1.518  0.020  1.518
 L11  C28   H281  single    0.970  0.020  1.090
 L11  C28   H282  single    0.970  0.020  1.090
 L11  C27   H271  single    0.970  0.020  1.090
 L11  C27   H272  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
 L11  C16   C14  C13   121.30  3.000
 L11  C16   C14  CL15  119.69  3.000
 L11  C13   C14  CL15  119.01  3.000
 L11  H13   C13  C12   119.58  3.000
 L11  H13   C13  C14   120.01  3.000
 L11  C12   C13  C14   120.41  3.000
 L11  H12   C12  C11   121.63  3.000
 L11  H12   C12  C13   119.01  3.000
 L11  C11   C12  C13   119.35  3.000
 L11  C25   C16  C17   122.38  3.000
 L11  C25   C16  C14   117.84  3.000
 L11  C17   C16  C14   119.77  3.000
 L11  H172  C17  H171  107.23  3.000
 L11  H172  C17  O18   110.60  3.000
 L11  H171  C17  O18   110.83  3.000
 L11  H172  C17  C16   109.67  3.000
 L11  H171  C17  C16   109.41  3.000
 L11  O18   C17  C16   109.08  3.000
 L11  C19   O18  C17   118.64  3.000
 L11  C20   C19  C24   118.28  3.000
 L11  C20   C19  O18   116.95  3.000
 L11  C24   C19  O18   124.77  3.000
 L11  H24   C24  N23   115.90  3.000
 L11  H24   C24  C19   121.50  3.000
 L11  N23   C24  C19   122.59  3.000
 L11  C22   N23  C24   118.99  3.000
 L11  H22   C22  C21   120.56  3.000
 L11  H22   C22  N23   116.89  3.000
 L11  C21   C22  N23   122.55  3.000
 L11  H21   C21  C20   120.65  3.000
 L11  H21   C21  C22   120.43  3.000
 L11  C20   C21  C22   118.93  3.000
 L11  H20   C20  C21   121.21  3.000
 L11  H20   C20  C19   120.12  3.000
 L11  C21   C20  C19   118.66  3.000
 L11  H25   C25  C11   118.80  3.000
 L11  H25   C25  C16   119.60  3.000
 L11  C11   C25  C16   121.60  3.000
 L11  N10   C11  C25   116.90  3.000
 L11  N10   C11  C12   123.58  3.000
 L11  C25   C11  C12   119.50  3.000
 L11  H10   N10  C8    117.15  3.000
 L11  H10   N10  C11   114.66  3.000
 L11  C8    N10  C11   127.41  3.000
 L11  C6    C8   O9    122.20  3.000
 L11  C6    C8   N10   114.52  3.000
 L11  O9    C8   N10   123.27  3.000
 L11  C5    C6   C7    123.01  3.000
 L11  C5    C6   C8    119.77  3.000
 L11  C7    C6   C8    117.22  3.000
 L11  H7    C7   C2    117.21  3.000
 L11  H7    C7   C6    120.26  3.000
 L11  C2    C7   C6    122.51  3.000
 L11  H2    C2   C3    109.84  3.000
 L11  H2    C2   F1    106.31  3.000
 L11  C3    C2   F1    109.86  3.000
 L11  H2    C2   C7    109.69  3.000
 L11  C3    C2   C7    113.13  3.000
 L11  F1    C2   C7    107.76  3.000
 L11  H52   C5   H51   106.79  3.000
 L11  H52   C5   C4    108.76  3.000
 L11  H51   C5   C4    110.06  3.000
 L11  H52   C5   C6    110.52  3.000
 L11  H51   C5   C6    108.19  3.000
 L11  C4    C5   C6    112.36  3.000
 L11  H41   C4   N26   110.03  3.000
 L11  H41   C4   C3    108.83  3.000
 L11  N26   C4   C3    111.01  3.000
 L11  H41   C4   C5    107.38  3.000
 L11  N26   C4   C5    111.70  3.000
 L11  C3    C4   C5    107.77  3.000
 L11  H3C2  C3   H3C1  106.56  3.000
 L11  H3C2  C3   C4    108.97  3.000
 L11  H3C1  C3   C4    112.73  3.000
 L11  H3C2  C3   C2    108.37  3.000
 L11  H3C1  C3   C2    108.09  3.000
 L11  C4    C3   C2    111.90  3.000
 L11  C27   N26  C31   108.21  3.000
 L11  C27   N26  C4    113.36  3.000
 L11  C31   N26  C4    111.48  3.000
 L11  H312  C31  H311  106.98  3.000
 L11  H312  C31  C30   107.33  3.000
 L11  H311  C31  C30   109.66  3.000
 L11  H312  C31  N26   110.62  3.000
 L11  H311  C31  N26   111.14  3.000
 L11  C30   C31  N26   110.95  3.000
 L11  H302  C30  H301  107.93  3.000
 L11  H302  C30  O29   110.48  3.000
 L11  H301  C30  O29   107.56  3.000
 L11  H302  C30  C31   109.20  3.000
 L11  H301  C30  C31   109.65  3.000
 L11  O29   C30  C31   111.92  3.000
 L11  C28   O29  C30   110.02  3.000
 L11  H282  C28  H281  107.91  3.000
 L11  H282  C28  C27   109.07  3.000
 L11  H281  C28  C27   109.62  3.000
 L11  H282  C28  O29   110.36  3.000
 L11  H281  C28  O29   107.63  3.000
 L11  C27   C28  O29   112.16  3.000
 L11  H272  C27  H271  107.29  3.000
 L11  H272  C27  C28   109.56  3.000
 L11  H271  C27  C28   106.98  3.000
 L11  H272  C27  N26   111.72  3.000
 L11  H271  C27  N26   110.54  3.000
 L11  C28   C27  N26   110.59  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
 L11  CONST_01  C11  C12  C13  C14      0.00   0.0  0
 L11  CONST_02  C11  C25  C16  C14      0.00   0.0  0
 L11  CONST_03  C25  C16  C14  C13      0.00   0.0  0
 L11  CONST_04  C25  C11  C12  C13      0.00   0.0  0
 L11  CONST_05  C16  C14  C13  C12      0.00   0.0  0
 L11  CONST_06  C16  C25  C11  C12      0.00   0.0  0
 L11  CONST_07  C22  N23  C24  C19      0.00   0.0  0
 L11  CONST_08  C22  C21  C20  C19      0.00   0.0  0
 L11  CONST_09  C21  C20  C19  C24      0.00   0.0  0
 L11  CONST_10  C21  C22  N23  C24      0.00   0.0  0
 L11  CONST_11  C20  C19  C24  N23      0.00   0.0  0
 L11  CONST_12  C20  C21  C22  N23      0.00   0.0  0
 L11  CONST_13  C12  C13  C14  CL15   180.00   0.0  0
 L11  CONST_14  C25  C16  C14  CL15   180.00   0.0  0
 L11  CONST_15  C17  C16  C14  C13    180.00   0.0  0
 L11  CONST_16  N10  C11  C12  C13    180.00   0.0  0
 L11  CONST_17  N10  C11  C25  C16    180.00   0.0  0
 L11  CONST_18  C11  C25  C16  C17    180.00   0.0  0
 L11  CONST_19  N23  C24  C19  O18    180.00   0.0  0
 L11  CONST_20  C21  C20  C19  O18    180.00   0.0  0
 L11  CONST_21  H12  C12  C13  C14    180.00   0.0  0
 L11  CONST_22  H25  C25  C16  C14    180.00   0.0  0
 L11  CONST_23  H13  C13  C14  C16    180.00   0.0  0
 L11  CONST_24  H21  C21  C20  C19    180.00   0.0  0
 L11  CONST_25  H20  C20  C19  C24    180.00   0.0  0
 L11  CONST_26  H22  C22  N23  C24    180.00   0.0  0
 L11  CONST_27  H24  C24  N23  C22    180.00   0.0  0
 L11  CONST_28  C6   C8   N10  C11    180.00   0.0  0
 L11  CONST_32  O9   C8   N10  C11      0.00   0.0  0
 L11  Var_01    C4   C5   C6   C7     -16.98  30.0  1
 L11  Var_02    C5   C6   C7   C2      -3.89  30.0  1
 L11  Var_03    C30  C31  N26  C4     178.44  30.0  1
 L11  Var_04    C28  C27  N26  C4    -179.67  30.0  1
 L11  Var_05    O29  C30  C31  N26     57.81  30.0  1
 L11  Var_06    O29  C28  C27  N26    -58.00  30.0  1
 L11  Var_07    C27  C28  O29  C30     57.11  30.0  1
 L11  Var_08    O18  C17  C16  C14    179.35  30.0  2
 L11  Var_09    C24  C19  O18  C17     -1.72  30.0  2
 L11  Var_10    C7   C6   C8   N10   -158.40  30.0  2

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
 L11  chir_01  C2  C7   F1  C3  positiv
 L11  chir_02  C4  N26  C5  C3  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
 L11  plan-1  CL15  0.020
 L11  plan-1  C14   0.020
 L11  plan-1  C13   0.020
 L11  plan-1  C12   0.020
 L11  plan-1  C16   0.020
 L11  plan-1  C17   0.020
 L11  plan-1  C25   0.020
 L11  plan-1  C11   0.020
 L11  plan-1  N10   0.020
 L11  plan-1  H13   0.020
 L11  plan-1  H12   0.020
 L11  plan-1  H25   0.020
 L11  plan-2  O18   0.020
 L11  plan-2  C19   0.020
 L11  plan-2  C24   0.020
 L11  plan-2  N23   0.020
 L11  plan-2  C22   0.020
 L11  plan-2  C21   0.020
 L11  plan-2  C20   0.020
 L11  plan-2  H24   0.020
 L11  plan-2  H22   0.020
 L11  plan-2  H21   0.020
 L11  plan-2  H20   0.020
 L11  plan-3  C11   0.020
 L11  plan-3  N10   0.020
 L11  plan-3  C8    0.020
 L11  plan-3  O9    0.020
 L11  plan-3  C6    0.020
 L11  plan-3  H10   0.020

