# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:13:47 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-4-(2,5-difluorophenyl)-N,N-dimethyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)N1CC(=C[C@H]1c2ccccc2)c3cc(F)ccc3F
#
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
 N5T  N5T  (2S)-4-(2,5-difluorophenyl)-N,N-dimethyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxamide  ligand  42  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N5T
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
 N5T  C1    C  CR6   0   0.549  -4.6172   0.7145  -0.8671
 N5T  C2    C  CR16  0  -0.472  -3.2537   0.6114  -1.0385
 N5T  C3    C  CR6   0  -0.099  -2.4593   0.0378  -0.0415
 N5T  C4    C  CR6   0   0.507  -3.1152  -0.4188   1.0967
 N5T  C5    C  CR16  0  -0.384  -4.4824  -0.3214   1.2649
 N5T  C6    C  CR16  0  -0.404  -5.2546   0.2548   0.2695
 N5T  C10   C  CR5   0   0.073  -1.0068  -0.0493  -0.2319
 N5T  C11   C  CH2   0  -0.301  -0.1541  -1.1931   0.2471
 N5T  N12   N  NR5   0  -0.533   1.1567  -0.8649  -0.3025
 N5T  C13   C  CR15  0  -0.170   1.1606   0.4074  -1.0137
 N5T  C14   C  CR15  0  -0.270  -0.2690   0.8299  -0.9057
 N5T  C17   C  CR6   0   0.187   2.1188   1.4103  -0.4089
 N5T  C19   C  CR16  0  -0.325   3.0496   2.0676  -1.2024
 N5T  C20   C  CR16  0  -0.242   3.9178   3.0025  -0.6495
 N5T  C21   C  CR16  0  -0.268   3.8627   3.2830   0.7080
 N5T  C22   C  CR16  0  -0.241   2.9347   2.6255   1.5094
 N5T  C23   C  CR16  0  -0.301   2.0689   1.6966   0.9534
 N5T  C29   C  C     0   0.717   2.1226  -1.7871  -0.6030
 N5T  N30   N  NT    0  -0.477   2.1563  -2.9023   0.1826
 N5T  C31   C  CH3   0  -0.522   2.9740  -4.0124  -0.2588
 N5T  C35   C  CH3   0  -0.544   1.8852  -2.8586   1.6085
 N5T  O39   O  O     0  -0.525   2.8971  -1.6191  -1.5389
 N5T  F40   F  F     0  -0.305  -2.3993  -0.9662   2.0926
 N5T  F41   F  F     0  -0.314  -5.3499   1.2676  -1.8458
 N5T  H2    H  HCR6  0   0.288  -2.8002   0.9592  -1.9574
 N5T  H5    H  HCR6  0   0.294  -4.9404  -0.6913   2.1724
 N5T  H6    H  HCR6  0   0.294  -6.3273   0.3373   0.3788
 N5T  H111  H  HCH2  0   0.263  -0.5178  -2.1562  -0.1264
 N5T  H112  H  HCH2  0   0.249  -0.1425  -1.2534   1.3359
 N5T  H13   H  HCR5  0   0.273   1.4287   0.2669  -2.0666
 N5T  H14   H  HCR5  0   0.276  -0.6171   1.7563  -1.3419
 N5T  H19   H  HCR6  0   0.249   3.1017   1.8447  -2.2617
 N5T  H20   H  HCR6  0   0.255   4.6404   3.5050  -1.2795
 N5T  H21   H  HCR6  0   0.255   4.5384   4.0080   1.1433
 N5T  H22   H  HCR6  0   0.255   2.8864   2.8403   2.5692
 N5T  H23   H  HCR6  0   0.248   1.3491   1.1906   1.5868
 N5T  H311  H  HCH3  0   0.247   2.8947  -4.1500  -1.3340
 N5T  H312  H  HCH3  0   0.226   4.0299  -3.8857  -0.0021
 N5T  H313  H  HCH3  0   0.242   2.6159  -4.9219   0.2217
 N5T  H351  H  HCH3  0   0.249   1.8393  -1.8334   1.9690
 N5T  H352  H  HCH3  0   0.239   0.9576  -3.3683   1.8774
 N5T  H353  H  HCH3  0   0.260   2.7022  -3.3450   2.1433

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
 N5T  C1   C2    aromatic  1.378  0.020  1.378
 N5T  C1   C6    aromatic  1.382  0.020  1.382
 N5T  C1   F41   single    1.342  0.020  1.342
 N5T  C2   C3    aromatic  1.398  0.020  1.398
 N5T  C2   H2    single    0.930  0.020  1.080
 N5T  C3   C4    aromatic  1.391  0.020  1.391
 N5T  C3   C10   single    1.468  0.020  1.468
 N5T  C4   C5    aromatic  1.381  0.020  1.381
 N5T  C4   F40   single    1.343  0.020  1.343
 N5T  C5   C6    aromatic  1.385  0.020  1.385
 N5T  C5   H5    single    0.930  0.020  1.080
 N5T  C6   H6    single    0.930  0.020  1.080
 N5T  C10  C11   single    1.505  0.020  1.505
 N5T  C10  C14   double    1.331  0.020  1.331
 N5T  C11  N12   single    1.459  0.020  1.459
 N5T  C11  H111  single    0.970  0.020  1.090
 N5T  C11  H112  single    0.970  0.020  1.090
 N5T  N12  C13   single    1.458  0.020  1.458
 N5T  N12  C29   single    1.369  0.020  1.369
 N5T  C13  C14   single    1.495  0.020  1.495
 N5T  C13  C17   single    1.513  0.020  1.513
 N5T  C13  H13   single    0.970  0.020  1.090
 N5T  C14  H14   single    0.930  0.020  1.080
 N5T  C17  C19   aromatic  1.389  0.020  1.389
 N5T  C17  C23   aromatic  1.393  0.020  1.393
 N5T  C19  C20   aromatic  1.391  0.020  1.391
 N5T  C19  H19   single    0.930  0.020  1.080
 N5T  C20  C21   aromatic  1.387  0.020  1.387
 N5T  C20  H20   single    0.930  0.020  1.080
 N5T  C21  C22   aromatic  1.391  0.020  1.391
 N5T  C21  H21   single    0.930  0.020  1.080
 N5T  C22  C23   aromatic  1.386  0.020  1.386
 N5T  C22  H22   single    0.930  0.020  1.080
 N5T  C23  H23   single    0.930  0.020  1.080
 N5T  C29  N30   single    1.365  0.020  1.365
 N5T  C29  O39   double    1.226  0.020  1.226
 N5T  N30  C31   single    1.448  0.020  1.448
 N5T  N30  C35   single    1.452  0.020  1.452
 N5T  C31  H311  single    0.970  0.020  1.090
 N5T  C31  H312  single    0.970  0.020  1.090
 N5T  C31  H313  single    0.970  0.020  1.090
 N5T  C35  H351  single    0.970  0.020  1.090
 N5T  C35  H352  single    0.970  0.020  1.090
 N5T  C35  H353  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
 N5T  F41   C1   C6    119.02  3.000
 N5T  F41   C1   C2    118.71  3.000
 N5T  C6    C1   C2    122.26  3.000
 N5T  H2    C2   C3    119.96  3.000
 N5T  H2    C2   C1    119.75  3.000
 N5T  C3    C2   C1    120.28  3.000
 N5T  C10   C3   C4    123.60  3.000
 N5T  C10   C3   C2    119.62  3.000
 N5T  C4    C3   C2    116.77  3.000
 N5T  F40   C4   C5    117.78  3.000
 N5T  F40   C4   C3    119.30  3.000
 N5T  C5    C4   C3    122.92  3.000
 N5T  H5    C5   C6    120.60  3.000
 N5T  H5    C5   C4    119.82  3.000
 N5T  C6    C5   C4    119.58  3.000
 N5T  H6    C6   C5    120.80  3.000
 N5T  H6    C6   C1    121.02  3.000
 N5T  C5    C6   C1    118.18  3.000
 N5T  C14   C10  C11   110.43  3.000
 N5T  C14   C10  C3    125.11  3.000
 N5T  C11   C10  C3    124.38  3.000
 N5T  H112  C11  H111  107.18  3.000
 N5T  H112  C11  N12   112.27  3.000
 N5T  H111  C11  N12   111.58  3.000
 N5T  H112  C11  C10   111.46  3.000
 N5T  H111  C11  C10   111.82  3.000
 N5T  N12   C11  C10   102.61  3.000
 N5T  C29   N12  C13   118.62  3.000
 N5T  C29   N12  C11   124.42  3.000
 N5T  C13   N12  C11   112.49  3.000
 N5T  H13   C13  C17   108.32  3.000
 N5T  H13   C13  C14   109.86  3.000
 N5T  C17   C13  C14   112.92  3.000
 N5T  H13   C13  N12   110.95  3.000
 N5T  C17   C13  N12   112.66  3.000
 N5T  C14   C13  N12   102.06  3.000
 N5T  H14   C14  C13   121.39  3.000
 N5T  H14   C14  C10   126.27  3.000
 N5T  C13   C14  C10   112.34  3.000
 N5T  C23   C17  C19   119.05  3.000
 N5T  C23   C17  C13   120.29  3.000
 N5T  C19   C17  C13   120.65  3.000
 N5T  H19   C19  C20   119.79  3.000
 N5T  H19   C19  C17   119.56  3.000
 N5T  C20   C19  C17   120.64  3.000
 N5T  H20   C20  C21   120.15  3.000
 N5T  H20   C20  C19   119.84  3.000
 N5T  C21   C20  C19   120.01  3.000
 N5T  H21   C21  C22   120.08  3.000
 N5T  H21   C21  C20   120.27  3.000
 N5T  C22   C21  C20   119.65  3.000
 N5T  H22   C22  C23   119.85  3.000
 N5T  H22   C22  C21   120.00  3.000
 N5T  C23   C22  C21   120.15  3.000
 N5T  H23   C23  C22   119.55  3.000
 N5T  H23   C23  C17   119.95  3.000
 N5T  C22   C23  C17   120.50  3.000
 N5T  O39   C29  N30   122.40  3.000
 N5T  O39   C29  N12   121.39  3.000
 N5T  N30   C29  N12   116.21  3.000
 N5T  C35   N30  C31   115.33  3.000
 N5T  C35   N30  C29   122.42  3.000
 N5T  C31   N30  C29   117.72  3.000
 N5T  H313  C31  H312  108.09  3.000
 N5T  H313  C31  H311  107.86  3.000
 N5T  H312  C31  H311  108.49  3.000
 N5T  H313  C31  N30   108.67  3.000
 N5T  H312  C31  N30   112.63  3.000
 N5T  H311  C31  N30   110.95  3.000
 N5T  H353  C35  H352  107.89  3.000
 N5T  H353  C35  H351  106.82  3.000
 N5T  H352  C35  H351  108.81  3.000
 N5T  H353  C35  N30   109.16  3.000
 N5T  H352  C35  N30   112.73  3.000
 N5T  H351  C35  N30   111.21  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
 N5T  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 N5T  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 N5T  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 N5T  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 N5T  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 N5T  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 N5T  CONST_07  C21   C20  C19  C17     0.00   0.0  0
 N5T  CONST_08  C21   C22  C23  C17     0.00   0.0  0
 N5T  CONST_09  C22   C23  C17  C19     0.00   0.0  0
 N5T  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 N5T  CONST_11  C23   C17  C19  C20     0.00   0.0  0
 N5T  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 N5T  CONST_13  C10   C3   C2   C1    180.00   0.0  0
 N5T  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 N5T  CONST_15  C20   C19  C17  C13   180.00   0.0  0
 N5T  CONST_16  C22   C23  C17  C13   180.00   0.0  0
 N5T  CONST_17  F40   C4   C3   C2    180.00   0.0  0
 N5T  CONST_18  F41   C1   C2   C3    180.00   0.0  0
 N5T  CONST_19  F41   C1   C6   C5    180.00   0.0  0
 N5T  CONST_20  F40   C4   C5   C6    180.00   0.0  0
 N5T  CONST_21  F40   C4   C3   C10     0.00   0.0  0
 N5T  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 N5T  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 N5T  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 N5T  CONST_25  H19   C19  C17  C13     0.00   0.0  0
 N5T  CONST_26  H23   C23  C17  C13     0.00   0.0  0
 N5T  CONST_27  H20   C20  C19  C17   180.00   0.0  0
 N5T  CONST_28  H22   C22  C23  C17   180.00   0.0  0
 N5T  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 N5T  CONST_31  O39   C29  N12  C13     0.00   0.0  0
 N5T  CONST_33  N30   C29  N12  C13   180.00   0.0  0
 N5T  CONST_34  C31   N30  C29  N12   180.00   0.0  0
 N5T  CONST_36  O39   C29  N30  C31     0.00   0.0  0
 N5T  Var_01    C11   C10  C3   C2   -144.18  30.0  2
 N5T  Var_02    N12   C11  C10  C3    174.46  30.0  1
 N5T  Var_03    C13   C14  C10  C3   -175.43  30.0  1
 N5T  Var_04    C13   N12  C11  C10     2.62  30.0  1
 N5T  Var_05    H311  C31  N30  C29   -39.91  30.0  3
 N5T  Var_06    H351  C35  N30  C29   -10.23  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
 N5T  chir_01  C13  N12  C14  C17  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
 N5T  plan-1  C1   0.020
 N5T  plan-1  C2   0.020
 N5T  plan-1  C3   0.020
 N5T  plan-1  C4   0.020
 N5T  plan-1  C5   0.020
 N5T  plan-1  C6   0.020
 N5T  plan-1  C10  0.020
 N5T  plan-1  F40  0.020
 N5T  plan-1  F41  0.020
 N5T  plan-1  H2   0.020
 N5T  plan-1  H5   0.020
 N5T  plan-1  H6   0.020
 N5T  plan-2  C13  0.020
 N5T  plan-2  C17  0.020
 N5T  plan-2  C19  0.020
 N5T  plan-2  C20  0.020
 N5T  plan-2  C21  0.020
 N5T  plan-2  C22  0.020
 N5T  plan-2  C23  0.020
 N5T  plan-2  H19  0.020
 N5T  plan-2  H20  0.020
 N5T  plan-2  H21  0.020
 N5T  plan-2  H22  0.020
 N5T  plan-2  H23  0.020
 N5T  plan-3  C11  0.020
 N5T  plan-3  N12  0.020
 N5T  plan-3  C13  0.020
 N5T  plan-3  C29  0.020
 N5T  plan-3  N30  0.020
 N5T  plan-3  C31  0.020
 N5T  plan-3  C35  0.020
 N5T  plan-3  O39  0.020

