# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:57:04 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S)-4-(2,5-difluorophenyl)-N-methyl-2-phenyl-N-piperidin-4-yl-2,5-dihydro-1H-pyrrole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1CCNCC1)C(=O)N2CC(=C[C@H]2c3ccccc3)c4cc(F)ccc4F
#
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
 N2T  N2T  (2S)-4-(2,5-difluorophenyl)-N-methyl-2-phenyl-N-piperidin-4-yl-2,5-dihydro-1H-pyrrole-1-carboxamide  ligand  54  29  .  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_N2T
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
 N2T  C1    C  CR6   0   0.546   5.3158   1.5193  -1.1274
 N2T  C2    C  CR16  0  -0.466   4.1115   0.8596  -1.2487
 N2T  C3    C  CR6   0  -0.105   3.1773   0.9071  -0.2100
 N2T  C4    C  CR6   0   0.507   3.5255   1.6447   0.9164
 N2T  C5    C  CR16  0  -0.383   4.7291   2.3107   1.0342
 N2T  C6    C  CR16  0  -0.404   5.6460   2.2514  -0.0031
 N2T  C10   C  CR5   0   0.072   1.9060   0.1851  -0.3415
 N2T  C11   C  CH2   0  -0.299   0.5779   0.7213   0.1161
 N2T  N12   N  NR5   0  -0.551  -0.3513  -0.3237  -0.3051
 N2T  C13   C  CR15  0  -0.150   0.3171  -1.4057  -1.0168
 N2T  C14   C  CR15  0  -0.271   1.7515  -0.9909  -0.9432
 N2T  C17   C  CR6   0   0.172   0.0639  -2.7632  -0.4008
 N2T  C19   C  CR16  0  -0.301   0.1015  -2.9347   0.9800
 N2T  C20   C  CR16  0  -0.241  -0.1013  -4.1881   1.5387
 N2T  C21   C  CR16  0  -0.268  -0.3400  -5.2875   0.7212
 N2T  C22   C  CR16  0  -0.242  -0.3767  -5.1230  -0.6563
 N2T  C23   C  CR16  0  -0.322  -0.1782  -3.8647  -1.2117
 N2T  C8    C  C     0   0.727  -1.6854  -0.1209  -0.5532
 N2T  N1    N  NT    0  -0.486  -2.3176   0.8068   0.2223
 N2T  C35   C  CH1   0  -0.091  -3.6323   1.2754  -0.2041
 N2T  F40   F  F     0  -0.305   2.6705   1.7037   1.9506
 N2T  F41   F  F     0  -0.314   6.1910   1.4574  -2.1427
 N2T  O2    O  O     0  -0.526  -2.2621  -0.7481  -1.4360
 N2T  C15   C  CH2   0  -0.427  -4.7889   0.4773   0.3986
 N2T  C26   C  CH3   0  -0.567  -1.9377   1.0546   1.6008
 N2T  C12   C  CH2   0  -0.422  -3.8131   2.7649   0.0815
 N2T  C9    C  CH2   0  -0.295  -6.1210   1.0317  -0.0888
 N2T  C16   C  CH2   0  -0.296  -5.1836   3.2196  -0.4022
 N2T  N2    N  NH1   0  -0.595  -6.2229   2.4408   0.2460
 N2T  H2    H  HCR6  0   0.288   3.8809   0.3191  -2.1577
 N2T  H5    H  HCR6  0   0.294   4.9520   2.8685   1.9340
 N2T  H6    H  HCR6  0   0.294   6.5931   2.7691   0.0655
 N2T  H111  H  HCH2  0   0.260   0.3474   1.6831  -0.3559
 N2T  H112  H  HCH2  0   0.251   0.5607   0.8803   1.1936
 N2T  H13   H  HCR5  0   0.271   0.0043  -1.4441  -2.0669
 N2T  H14   H  HCR5  0   0.276   2.5406  -1.6025  -1.3590
 N2T  H19   H  HCR6  0   0.247   0.2811  -2.0816   1.6239
 N2T  H20   H  HCR6  0   0.255  -0.0740  -4.3086   2.6141
 N2T  H21   H  HCR6  0   0.255  -0.5009  -6.2650   1.1572
 N2T  H22   H  HCR6  0   0.255  -0.5687  -5.9718  -1.3000
 N2T  H23   H  HCR6  0   0.249  -0.2179  -3.7390  -2.2875
 N2T  H35   H  HCH1  0   0.240  -3.6748   1.1492  -1.2881
 N2T  H151  H  HCH2  0   0.237  -4.6977  -0.5744   0.1211
 N2T  H152  H  HCH2  0   0.216  -4.7624   0.5314   1.4911
 N2T  H261  H  HCH3  0   0.257  -1.3540   0.2253   1.9959
 N2T  H262  H  HCH3  0   0.241  -1.3691   1.9772   1.7313
 N2T  H263  H  HCH3  0   0.264  -2.8322   1.1290   2.2175
 N2T  H121  H  HCH2  0   0.224  -3.7311   2.9662   1.1534
 N2T  H122  H  HCH2  0   0.235  -3.0311   3.3394  -0.4205
 N2T  H91   H  HCH2  0   0.188  -6.2065   0.8500  -1.1735
 N2T  H92   H  HCH2  0   0.233  -6.9440   0.4939   0.3860
 N2T  H161  H  HCH2  0   0.188  -5.2171   3.1344  -1.5015
 N2T  H162  H  HCH2  0   0.235  -5.3286   4.2749  -0.1633
 N2T  HN2   H  HNH1  0   0.352  -7.1297   2.7898  -0.0354

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
 N2T  C1   C2    aromatic  1.378  0.020  1.378
 N2T  C1   C6    aromatic  1.382  0.020  1.382
 N2T  C1   F41   single    1.342  0.020  1.342
 N2T  C2   C3    aromatic  1.398  0.020  1.398
 N2T  C2   H2    single    0.930  0.020  1.080
 N2T  C3   C4    aromatic  1.391  0.020  1.391
 N2T  C3   C10   single    1.468  0.020  1.468
 N2T  C4   C5    aromatic  1.381  0.020  1.381
 N2T  C4   F40   single    1.343  0.020  1.343
 N2T  C5   C6    aromatic  1.386  0.020  1.386
 N2T  C5   H5    single    0.930  0.020  1.080
 N2T  C6   H6    single    0.930  0.020  1.080
 N2T  C10  C11   single    1.504  0.020  1.504
 N2T  C10  C14   double    1.330  0.020  1.330
 N2T  C11  N12   single    1.460  0.020  1.460
 N2T  C11  H111  single    0.970  0.020  1.090
 N2T  C11  H112  single    0.970  0.020  1.090
 N2T  N12  C13   single    1.457  0.020  1.457
 N2T  N12  C8    single    1.372  0.020  1.372
 N2T  C13  C14   single    1.495  0.020  1.495
 N2T  C13  C17   single    1.512  0.020  1.512
 N2T  C13  H13   single    0.970  0.020  1.090
 N2T  C14  H14   single    0.930  0.020  1.080
 N2T  C17  C19   aromatic  1.392  0.020  1.392
 N2T  C17  C23   aromatic  1.389  0.020  1.389
 N2T  C19  C20   aromatic  1.387  0.020  1.387
 N2T  C19  H19   single    0.930  0.020  1.080
 N2T  C20  C21   aromatic  1.391  0.020  1.391
 N2T  C20  H20   single    0.930  0.020  1.080
 N2T  C21  C22   aromatic  1.388  0.020  1.388
 N2T  C21  H21   single    0.930  0.020  1.080
 N2T  C22  C23   aromatic  1.390  0.020  1.390
 N2T  C22  H22   single    0.930  0.020  1.080
 N2T  C23  H23   single    0.930  0.020  1.080
 N2T  C8   N1    single    1.364  0.020  1.364
 N2T  C8   O2    double    1.227  0.020  1.227
 N2T  N1   C35   single    1.459  0.020  1.459
 N2T  N1   C26   single    1.451  0.020  1.451
 N2T  C35  C15   single    1.529  0.020  1.529
 N2T  C35  C12   single    1.527  0.020  1.527
 N2T  C35  H35   single    0.970  0.020  1.090
 N2T  C15  C9    single    1.523  0.020  1.523
 N2T  C15  H151  single    0.970  0.020  1.090
 N2T  C15  H152  single    0.970  0.020  1.090
 N2T  C26  H261  single    0.970  0.020  1.090
 N2T  C26  H262  single    0.970  0.020  1.090
 N2T  C26  H263  single    0.970  0.020  1.090
 N2T  C12  C16   single    1.523  0.020  1.523
 N2T  C12  H121  single    0.970  0.020  1.090
 N2T  C12  H122  single    0.970  0.020  1.090
 N2T  C9   N2    single    1.452  0.020  1.452
 N2T  C9   H91   single    0.970  0.020  1.090
 N2T  C9   H92   single    0.970  0.020  1.090
 N2T  C16  N2    single    1.452  0.020  1.452
 N2T  C16  H161  single    0.970  0.020  1.090
 N2T  C16  H162  single    0.970  0.020  1.090
 N2T  N2   HN2   single    0.890  0.020  1.040

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
 N2T  F41   C1   C6    118.96  3.000
 N2T  F41   C1   C2    118.76  3.000
 N2T  C6    C1   C2    122.27  3.000
 N2T  H2    C2   C3    119.91  3.000
 N2T  H2    C2   C1    119.93  3.000
 N2T  C3    C2   C1    120.15  3.000
 N2T  C10   C3   C4    123.38  3.000
 N2T  C10   C3   C2    119.71  3.000
 N2T  C4    C3   C2    116.91  3.000
 N2T  F40   C4   C5    117.91  3.000
 N2T  F40   C4   C3    119.18  3.000
 N2T  C5    C4   C3    122.90  3.000
 N2T  H5    C5   C6    120.56  3.000
 N2T  H5    C5   C4    119.95  3.000
 N2T  C6    C5   C4    119.49  3.000
 N2T  H6    C6   C5    120.76  3.000
 N2T  H6    C6   C1    120.97  3.000
 N2T  C5    C6   C1    118.27  3.000
 N2T  C14   C10  C11   110.51  3.000
 N2T  C14   C10  C3    125.17  3.000
 N2T  C11   C10  C3    124.22  3.000
 N2T  H112  C11  H111  107.13  3.000
 N2T  H112  C11  N12   112.32  3.000
 N2T  H111  C11  N12   111.71  3.000
 N2T  H112  C11  C10   111.54  3.000
 N2T  H111  C11  C10   111.57  3.000
 N2T  N12   C11  C10   102.65  3.000
 N2T  C8    N12  C13   117.87  3.000
 N2T  C8    N12  C11   124.41  3.000
 N2T  C13   N12  C11   112.35  3.000
 N2T  H13   C13  C17   108.12  3.000
 N2T  H13   C13  C14   109.30  3.000
 N2T  C17   C13  C14   112.94  3.000
 N2T  H13   C13  N12   111.27  3.000
 N2T  C17   C13  N12   113.01  3.000
 N2T  C14   C13  N12   102.12  3.000
 N2T  H14   C14  C13   121.62  3.000
 N2T  H14   C14  C10   126.10  3.000
 N2T  C13   C14  C10   112.27  3.000
 N2T  C23   C17  C19   119.09  3.000
 N2T  C23   C17  C13   120.22  3.000
 N2T  C19   C17  C13   120.68  3.000
 N2T  H19   C19  C20   119.74  3.000
 N2T  H19   C19  C17   119.80  3.000
 N2T  C20   C19  C17   120.46  3.000
 N2T  H20   C20  C21   120.02  3.000
 N2T  H20   C20  C19   119.80  3.000
 N2T  C21   C20  C19   120.18  3.000
 N2T  H21   C21  C22   120.19  3.000
 N2T  H21   C21  C20   120.18  3.000
 N2T  C22   C21  C20   119.63  3.000
 N2T  H22   C22  C23   119.84  3.000
 N2T  H22   C22  C21   120.14  3.000
 N2T  C23   C22  C21   120.02  3.000
 N2T  H23   C23  C22   119.77  3.000
 N2T  H23   C23  C17   119.60  3.000
 N2T  C22   C23  C17   120.63  3.000
 N2T  O2    C8   N1    122.59  3.000
 N2T  O2    C8   N12   120.77  3.000
 N2T  N1    C8   N12   116.63  3.000
 N2T  C26   N1   C35   117.30  3.000
 N2T  C26   N1   C8    122.32  3.000
 N2T  C35   N1   C8    118.01  3.000
 N2T  H35   C35  C12   107.08  3.000
 N2T  H35   C35  C15   107.55  3.000
 N2T  C12   C35  C15   110.23  3.000
 N2T  H35   C35  N1    106.74  3.000
 N2T  C12   C35  N1    111.42  3.000
 N2T  C15   C35  N1    113.49  3.000
 N2T  H152  C15  H151  107.43  3.000
 N2T  H152  C15  C9    108.83  3.000
 N2T  H151  C15  C9    110.03  3.000
 N2T  H152  C15  C35   110.45  3.000
 N2T  H151  C15  C35   109.85  3.000
 N2T  C9    C15  C35   110.21  3.000
 N2T  H263  C26  H262  107.60  3.000
 N2T  H263  C26  H261  106.67  3.000
 N2T  H262  C26  H261  108.74  3.000
 N2T  H263  C26  N1    109.54  3.000
 N2T  H262  C26  N1    113.23  3.000
 N2T  H261  C26  N1    110.80  3.000
 N2T  H122  C12  H121  107.45  3.000
 N2T  H122  C12  C16   109.95  3.000
 N2T  H121  C12  C16   108.89  3.000
 N2T  H122  C12  C35   110.01  3.000
 N2T  H121  C12  C35   110.73  3.000
 N2T  C16   C12  C35   109.77  3.000
 N2T  H92   C9   H91   106.74  3.000
 N2T  H92   C9   N2    108.96  3.000
 N2T  H91   C9   N2    112.41  3.000
 N2T  H92   C9   C15   109.93  3.000
 N2T  H91   C9   C15   108.81  3.000
 N2T  N2    C9   C15   109.94  3.000
 N2T  H162  C16  H161  106.78  3.000
 N2T  H162  C16  N2    109.01  3.000
 N2T  H161  C16  N2    112.45  3.000
 N2T  H162  C16  C12   109.80  3.000
 N2T  H161  C16  C12   108.72  3.000
 N2T  N2    C16  C12   110.02  3.000
 N2T  HN2   N2   C16   109.42  3.000
 N2T  HN2   N2   C9    109.49  3.000
 N2T  C16   N2   C9    111.56  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
 N2T  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 N2T  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 N2T  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 N2T  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 N2T  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 N2T  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 N2T  CONST_07  C21   C20  C19  C17     0.00   0.0  0
 N2T  CONST_08  C21   C22  C23  C17     0.00   0.0  0
 N2T  CONST_09  C22   C23  C17  C19     0.00   0.0  0
 N2T  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 N2T  CONST_11  C23   C17  C19  C20     0.00   0.0  0
 N2T  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 N2T  CONST_13  C10   C3   C2   C1    180.00   0.0  0
 N2T  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 N2T  CONST_15  C20   C19  C17  C13   180.00   0.0  0
 N2T  CONST_16  C22   C23  C17  C13   180.00   0.0  0
 N2T  CONST_17  F40   C4   C3   C2    180.00   0.0  0
 N2T  CONST_18  F41   C1   C2   C3    180.00   0.0  0
 N2T  CONST_19  F41   C1   C6   C5    180.00   0.0  0
 N2T  CONST_20  F40   C4   C5   C6    180.00   0.0  0
 N2T  CONST_21  F40   C4   C3   C10     0.00   0.0  0
 N2T  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 N2T  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 N2T  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 N2T  CONST_25  H19   C19  C17  C13     0.00   0.0  0
 N2T  CONST_26  H23   C23  C17  C13     0.00   0.0  0
 N2T  CONST_27  H20   C20  C19  C17   180.00   0.0  0
 N2T  CONST_28  H22   C22  C23  C17   180.00   0.0  0
 N2T  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 N2T  CONST_31  O2    C8   N12  C13     0.00   0.0  0
 N2T  CONST_33  C35   N1   C8   N12   180.00   0.0  0
 N2T  CONST_34  N1    C8   N12  C13   180.00   0.0  0
 N2T  CONST_35  O2    C8   N1   C35     0.00   0.0  0
 N2T  Var_01    C11   C10  C3   C2   -139.97  30.0  2
 N2T  Var_02    N12   C11  C10  C3    176.87  30.0  1
 N2T  Var_03    C13   C14  C10  C3   -174.96  30.0  1
 N2T  Var_04    C13   N12  C11  C10    -2.14  30.0  1
 N2T  Var_05    N2    C9   C15  C35   -57.01  30.0  1
 N2T  Var_06    N2    C16  C12  C35    57.83  30.0  1
 N2T  Var_07    C16   N2   C9   C15    61.79  30.0  1
 N2T  Var_08    C9    N2   C16  C12   -62.35  30.0  1
 N2T  Var_09    H261  C26  N1   C35   143.87  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
 N2T  chir_01  C13  N12  C14  C17  negativ
 N2T  chir_02  C35  N1   C15  C12  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
 N2T  plan-1  C1   0.020
 N2T  plan-1  C2   0.020
 N2T  plan-1  C3   0.020
 N2T  plan-1  C4   0.020
 N2T  plan-1  C5   0.020
 N2T  plan-1  C6   0.020
 N2T  plan-1  C10  0.020
 N2T  plan-1  F40  0.020
 N2T  plan-1  F41  0.020
 N2T  plan-1  H2   0.020
 N2T  plan-1  H5   0.020
 N2T  plan-1  H6   0.020
 N2T  plan-2  C13  0.020
 N2T  plan-2  C17  0.020
 N2T  plan-2  C19  0.020
 N2T  plan-2  C20  0.020
 N2T  plan-2  C21  0.020
 N2T  plan-2  C22  0.020
 N2T  plan-2  C23  0.020
 N2T  plan-2  H19  0.020
 N2T  plan-2  H20  0.020
 N2T  plan-2  H21  0.020
 N2T  plan-2  H22  0.020
 N2T  plan-2  H23  0.020
 N2T  plan-3  C11  0.020
 N2T  plan-3  N12  0.020
 N2T  plan-3  C13  0.020
 N2T  plan-3  C8   0.020
 N2T  plan-3  N1   0.020
 N2T  plan-3  C35  0.020
 N2T  plan-3  O2   0.020
 N2T  plan-3  C26  0.020

