# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:13:25 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: methyl (3S)-3-[(4-chloro-3-fluorophenyl)carbamoyl]piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CCC[C@@H](C1)C(=O)Nc2ccc(Cl)c(F)c2
#
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
 MVY  MVY  'methyl (3S)-3-[(4-chloro-3-fluorophenyl)carbamoyl]piperidine-1-carboxylate'  ligand  37  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MVY
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
 MVY  C11  C   CR16  0  -0.494  -2.7671  -0.4404  -0.5199
 MVY  C12  C   CR6   0   0.654  -4.1152  -0.1443  -0.5118
 MVY  C14  C   CR6   0  -0.259  -4.6573   0.8296   0.3061
 MVY  C16  C   CR16  0  -0.198  -3.8104   1.5310   1.1508
 MVY  C17  C   CR16  0  -0.365  -2.4574   1.2539   1.1631
 MVY  C18  C   CH2   0  -0.428   2.2092  -2.1040   0.4988
 MVY  C19  C   CH2   0  -0.442   3.7163  -2.0866   0.7354
 MVY  C20  C   CH2   0  -0.320   4.4532  -1.5529  -0.4870
 MVY  C01  C   CH3   0  -0.411   6.5264   1.9489   0.1444
 MVY  C03  C   C     0   0.756   4.5318   0.9306  -0.5695
 MVY  C05  C   CH2   0  -0.290   2.5187  -0.2624  -1.1782
 MVY  C06  C   CH1   0  -0.416   1.7105  -0.7286   0.0422
 MVY  C07  C   C     0   0.580   0.2408  -0.7800  -0.3164
 MVY  C10  C   CR6   0   0.406  -1.9189   0.2684   0.3304
 MVY  F13  F   F     0  -0.297  -4.9229  -0.8294  -1.3240
 MVY  N04  N   NT    0  -0.484   3.9308  -0.2462  -0.8595
 MVY  N09  N   NH1   0  -0.748  -0.5452   0.0543   0.4135
 MVY  O02  O   O2    0  -0.478   5.7837   0.7681  -0.1381
 MVY  O08  O   O     0  -0.463  -0.1787  -1.5100  -1.1969
 MVY  O21  O   O     0  -0.526   4.0149   2.0230  -0.7059
 MVY  CL1  CL  CL    0  -0.096  -6.3493   1.1493   0.2630
 MVY  H1   H   HCR6  0   0.311  -2.4029  -1.2127  -1.1778
 MVY  H2   H   HCR6  0   0.294  -4.2105   2.2972   1.8005
 MVY  H3   H   HCR6  0   0.287  -1.8109   1.8111   1.8289
 MVY  H4   H   HCH2  0   0.234   1.9759  -2.8428  -0.2736
 MVY  H5   H   HCH2  0   0.255   1.6853  -2.4114   1.4062
 MVY  H6   H   HCH2  0   0.231   3.9594  -1.4680   1.6043
 MVY  H7   H   HCH2  0   0.247   4.0668  -3.0970   0.9552
 MVY  H8   H   HCH2  0   0.273   5.5237  -1.5049  -0.3140
 MVY  H9   H   HCH2  0   0.244   4.2952  -2.2261  -1.3348
 MVY  H10  H   HCH3  0   0.247   7.5015   1.6103   0.4832
 MVY  H11  H   HCH3  0   0.234   6.6525   2.5688  -0.7433
 MVY  H12  H   HCH3  0   0.234   6.0614   2.5412   0.9324
 MVY  H13  H   HCH2  0   0.254   2.3610  -0.9576  -2.0071
 MVY  H14  H   HCH2  0   0.279   2.2015   0.7241  -1.5077
 MVY  H15  H   HCH1  0   0.272   1.8734  -0.0072   0.8499
 MVY  H16  H   HNH1  0   0.424  -0.0731   0.6061   1.1140

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
 MVY  CL1  C14  single    1.722  0.020  1.722
 MVY  C14  C16  aromatic  1.387  0.020  1.387
 MVY  C14  C12  aromatic  1.382  0.020  1.382
 MVY  C16  C17  aromatic  1.381  0.020  1.381
 MVY  C12  F13  single    1.335  0.020  1.335
 MVY  C12  C11  aromatic  1.380  0.020  1.380
 MVY  C17  C10  aromatic  1.398  0.020  1.398
 MVY  C11  C10  aromatic  1.395  0.020  1.395
 MVY  C10  N09  single    1.393  0.020  1.393
 MVY  N09  C07  single    1.359  0.020  1.359
 MVY  C07  O08  double    1.218  0.020  1.218
 MVY  C07  C06  single    1.514  0.020  1.514
 MVY  C06  C18  single    1.533  0.020  1.533
 MVY  C06  C05  single    1.536  0.020  1.536
 MVY  C18  C19  single    1.526  0.020  1.526
 MVY  C19  C20  single    1.524  0.020  1.524
 MVY  C05  N04  single    1.448  0.020  1.448
 MVY  C20  N04  single    1.456  0.020  1.456
 MVY  N04  C03  single    1.353  0.020  1.353
 MVY  C03  O21  double    1.216  0.020  1.216
 MVY  C03  O02  single    1.334  0.020  1.334
 MVY  C01  O02  single    1.423  0.020  1.423
 MVY  C11  H1   single    0.930  0.020  1.080
 MVY  C16  H2   single    0.930  0.020  1.080
 MVY  C17  H3   single    0.930  0.020  1.080
 MVY  C18  H4   single    0.970  0.020  1.090
 MVY  C18  H5   single    0.970  0.020  1.090
 MVY  C19  H6   single    0.970  0.020  1.090
 MVY  C19  H7   single    0.970  0.020  1.090
 MVY  C20  H8   single    0.970  0.020  1.090
 MVY  C20  H9   single    0.970  0.020  1.090
 MVY  C01  H10  single    0.970  0.020  1.090
 MVY  C01  H11  single    0.970  0.020  1.090
 MVY  C01  H12  single    0.970  0.020  1.090
 MVY  C05  H13  single    0.970  0.020  1.090
 MVY  C05  H14  single    0.970  0.020  1.090
 MVY  C06  H15  single    0.970  0.020  1.090
 MVY  N09  H16  single    0.860  0.020  1.020

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
 MVY  H1   C11  C10  122.06  3.000
 MVY  H1   C11  C12  119.16  3.000
 MVY  C10  C11  C12  118.78  3.000
 MVY  F13  C12  C14  118.97  3.000
 MVY  F13  C12  C11  118.51  3.000
 MVY  C14  C12  C11  122.52  3.000
 MVY  CL1  C14  C16  121.42  3.000
 MVY  C16  C14  C12  118.50  3.000
 MVY  CL1  C14  C12  120.07  3.000
 MVY  H2   C16  C17  119.95  3.000
 MVY  H2   C16  C14  119.90  3.000
 MVY  C17  C16  C14  120.15  3.000
 MVY  H3   C17  C10  119.95  3.000
 MVY  H3   C17  C16  119.16  3.000
 MVY  C10  C17  C16  120.89  3.000
 MVY  H5   C18  H4   107.11  3.000
 MVY  H5   C18  C06  110.13  3.000
 MVY  H4   C18  C06  109.04  3.000
 MVY  H5   C18  C19  110.38  3.000
 MVY  H4   C18  C19  109.14  3.000
 MVY  C06  C18  C19  110.94  3.000
 MVY  H7   C19  H6   106.98  3.000
 MVY  H7   C19  C20  109.29  3.000
 MVY  H6   C19  C20  109.37  3.000
 MVY  H7   C19  C18  109.75  3.000
 MVY  H6   C19  C18  110.43  3.000
 MVY  C20  C19  C18  110.93  3.000
 MVY  H9   C20  H8   107.05  3.000
 MVY  H9   C20  N04  107.59  3.000
 MVY  H8   C20  N04  110.79  3.000
 MVY  H9   C20  C19  109.65  3.000
 MVY  H8   C20  C19  111.38  3.000
 MVY  N04  C20  C19  110.25  3.000
 MVY  H12  C01  H11  109.22  3.000
 MVY  H12  C01  H10  109.08  3.000
 MVY  H11  C01  H10  109.11  3.000
 MVY  H12  C01  O02  111.82  3.000
 MVY  H11  C01  O02  111.75  3.000
 MVY  H10  C01  O02  105.76  3.000
 MVY  O21  C03  O02  122.99  3.000
 MVY  O02  C03  N04  112.35  3.000
 MVY  O21  C03  N04  124.64  3.000
 MVY  H14  C05  H13  107.76  3.000
 MVY  H14  C05  N04  109.94  3.000
 MVY  H13  C05  N04  108.34  3.000
 MVY  H14  C05  C06  111.26  3.000
 MVY  H13  C05  C06  109.48  3.000
 MVY  N04  C05  C06  109.98  3.000
 MVY  H15  C06  C07  109.97  3.000
 MVY  H15  C06  C05  107.92  3.000
 MVY  C07  C06  C05  109.45  3.000
 MVY  H15  C06  C18  108.84  3.000
 MVY  C05  C06  C18  109.75  3.000
 MVY  C07  C06  C18  110.86  3.000
 MVY  O08  C07  N09  123.84  3.000
 MVY  O08  C07  C06  121.73  3.000
 MVY  N09  C07  C06  114.43  3.000
 MVY  N09  C10  C17  116.92  3.000
 MVY  N09  C10  C11  123.93  3.000
 MVY  C17  C10  C11  119.16  3.000
 MVY  C05  N04  C03  119.36  3.000
 MVY  C03  N04  C20  124.51  3.000
 MVY  C05  N04  C20  113.35  3.000
 MVY  H16  N09  C10  114.76  3.000
 MVY  H16  N09  C07  115.98  3.000
 MVY  C10  N09  C07  129.26  3.000
 MVY  C03  O02  C01  116.92  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
 MVY  CONST_01  C16  C14  C12  C11     0.00   0.0  0
 MVY  CONST_02  C16  C17  C10  C11     0.00   0.0  0
 MVY  CONST_03  C17  C16  C14  C12     0.00   0.0  0
 MVY  CONST_04  C17  C10  C11  C12     0.00   0.0  0
 MVY  CONST_05  C10  C17  C16  C14     0.00   0.0  0
 MVY  CONST_06  C10  C11  C12  C14     0.00   0.0  0
 MVY  CONST_07  CL1  C14  C12  C11   180.00   0.0  0
 MVY  CONST_08  N09  C10  C11  C12   180.00   0.0  0
 MVY  CONST_09  F13  C12  C14  C16   180.00   0.0  0
 MVY  CONST_10  N09  C10  C17  C16   180.00   0.0  0
 MVY  CONST_11  CL1  C14  C16  C17   180.00   0.0  0
 MVY  CONST_12  F13  C12  C11  C10   180.00   0.0  0
 MVY  CONST_13  H3   C17  C10  C11   180.00   0.0  0
 MVY  CONST_14  H2   C16  C14  C12   180.00   0.0  0
 MVY  CONST_15  H1   C11  C12  C14   180.00   0.0  0
 MVY  CONST_16  C10  N09  C07  C06   180.00   0.0  0
 MVY  CONST_17  C07  N09  C10  C11     0.00   0.0  0
 MVY  CONST_18  C07  N09  C10  C17   180.00   0.0  0
 MVY  CONST_19  H16  N09  C10  C11   180.00   0.0  0
 MVY  CONST_20  O08  C07  N09  C10     0.00   0.0  0
 MVY  Var_01    N04  C20  C19  C18    54.59  30.0  1
 MVY  Var_02    C05  N04  C20  C19   -59.57  30.0  1
 MVY  Var_03    C06  C18  C19  C20   -53.10  30.0  1
 MVY  Var_04    C06  C05  N04  C20    60.69  30.0  1
 MVY  Var_05    O21  C03  N04  C20  -168.97  30.0  2
 MVY  Var_06    N04  C03  O02  C01   177.55  30.0  1
 MVY  Var_07    H10  C01  O02  C03   179.63  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
 MVY  chir_01  C06  C07  C18  C05  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
 MVY  plan-1  C11  0.020
 MVY  plan-1  C12  0.020
 MVY  plan-1  C14  0.020
 MVY  plan-1  C16  0.020
 MVY  plan-1  C17  0.020
 MVY  plan-1  C10  0.020
 MVY  plan-1  F13  0.020
 MVY  plan-1  N09  0.020
 MVY  plan-1  CL1  0.020
 MVY  plan-1  H1   0.020
 MVY  plan-1  H2   0.020
 MVY  plan-1  H3   0.020
 MVY  plan-2  C06  0.020
 MVY  plan-2  C07  0.020
 MVY  plan-2  C10  0.020
 MVY  plan-2  N09  0.020
 MVY  plan-2  O08  0.020
 MVY  plan-2  H16  0.020
 MVY  plan-3  C03  0.020
 MVY  plan-3  N04  0.020
 MVY  plan-3  O02  0.020
 MVY  plan-3  O21  0.020

