# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:27:14 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (1S)-1-cyclopropyl-2-[(2S)-4-(2,5-difluorophenyl)-2-phenyl-2,5-dihydro-1H-pyrrol-1-yl]-2-oxoethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C1CC1)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
 N4T  N4T  (1S)-1-cyclopropyl-2-[(2S)-4-(2,5-difluorophenyl)-2-phenyl-2,5-dihydro-1H-pyrrol-1-yl]-2-oxoethanamine  ligand  46  26  .  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_N4T
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
 N4T  C1    C  CR6   0   0.545  -5.0526  -0.3251   0.5742
 N4T  C2    C  CR16  0  -0.461  -3.7154  -0.4639   0.8811
 N4T  C3    C  CR6   0  -0.111  -2.7445   0.0780   0.0363
 N4T  C4    C  CR6   0   0.511  -3.1921   0.7497  -1.0953
 N4T  C5    C  CR16  0  -0.384  -4.5311   0.8914  -1.3998
 N4T  C6    C  CR16  0  -0.403  -5.4840   0.3463  -0.5534
 N4T  C10   C  CR5   0   0.069  -1.3230  -0.0861   0.3617
 N4T  C11   C  CH2   0  -0.313  -0.3097   1.0208   0.2627
 N4T  N12   N  NR5   0  -0.505   0.8802   0.4012   0.8304
 N4T  C13   C  CR15  0  -0.171   0.6859  -1.0053   1.1623
 N4T  C14   C  CR15  0  -0.265  -0.7700  -1.1853   0.8675
 N4T  C17   C  CR6   0   0.191   1.5495  -1.9360   0.3382
 N4T  C19   C  CR16  0  -0.295   1.6471  -1.7697  -1.0403
 N4T  C20   C  CR16  0  -0.241   2.4150  -2.6390  -1.8008
 N4T  C21   C  CR16  0  -0.269   3.0864  -3.6931  -1.1917
 N4T  C22   C  CR16  0  -0.242   2.9870  -3.8677   0.1815
 N4T  C23   C  CR16  0  -0.325   2.2247  -2.9885   0.9411
 N4T  C8    C  C     0   0.546   2.0449   1.0143   1.1126
 N4T  C7    C  CH1   0  -0.229   2.2298   2.4500   0.6139
 N4T  C35   C  CH1   0  -0.231   2.6764   2.3540  -0.8384
 N4T  F40   F  F     0  -0.304  -2.2898   1.2656  -1.9458
 N4T  F41   F  F     0  -0.313  -5.9635  -0.8487   1.4087
 N4T  O2    O  O     0  -0.486   2.9471   0.4297   1.6953
 N4T  C15   C  CH2   0  -0.483   3.3692   3.4960  -1.5074
 N4T  N1    N  NH2   0  -0.786   3.1589   3.2083   1.4185
 N4T  C12   C  CH2   0  -0.488   4.1256   2.2390  -1.1910
 N4T  H2    H  HCR6  0   0.289  -3.4175  -0.9737   1.7880
 N4T  H5    H  HCR6  0   0.295  -4.8291   1.4167  -2.2973
 N4T  H6    H  HCR6  0   0.294  -6.5384   0.4467  -0.7717
 N4T  H111  H  HCH2  0   0.275  -0.6314   1.8945   0.8371
 N4T  H112  H  HCH2  0   0.260  -0.1493   1.3487  -0.7666
 N4T  H13   H  HCR5  0   0.281   0.8915  -1.1837   2.2240
 N4T  H14   H  HCR5  0   0.280  -1.2709  -2.1273   1.0439
 N4T  H19   H  HCR6  0   0.245   1.1254  -0.9542  -1.5279
 N4T  H20   H  HCR6  0   0.255   2.4879  -2.4957  -2.8713
 N4T  H21   H  HCR6  0   0.256   3.6842  -4.3723  -1.7855
 N4T  H22   H  HCR6  0   0.256   3.5076  -4.6842   0.6651
 N4T  H23   H  HCR6  0   0.249   2.1576  -3.1234   2.0145
 N4T  H7    H  HCH1  0   0.263   1.2759   2.9839   0.6341
 N4T  H35   H  HCH1  0   0.261   2.0019   1.7840  -1.4699
 N4T  H151  H  HCH2  0   0.247   3.1217   3.7030  -2.5409
 N4T  H152  H  HCH2  0   0.245   3.5846   4.3703  -0.9075
 N4T  HN11  H  HNH2  0   0.357   2.7166   3.4640   2.2917
 N4T  HN12  H  HNH2  0   0.344   3.9503   2.6284   1.6694
 N4T  H121  H  HCH2  0   0.241   4.8594   2.2810  -0.3964
 N4T  H122  H  HCH2  0   0.250   4.3952   1.5774  -2.0041

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
 N4T  C1   C2    aromatic  1.379  0.020  1.379
 N4T  C1   C6    aromatic  1.381  0.020  1.381
 N4T  C1   F41   single    1.342  0.020  1.342
 N4T  C2   C3    aromatic  1.396  0.020  1.396
 N4T  C2   H2    single    0.930  0.020  1.080
 N4T  C3   C4    aromatic  1.390  0.020  1.390
 N4T  C3   C10   single    1.467  0.020  1.467
 N4T  C4   C5    aromatic  1.380  0.020  1.380
 N4T  C4   F40   single    1.343  0.020  1.343
 N4T  C5   C6    aromatic  1.386  0.020  1.386
 N4T  C5   H5    single    0.930  0.020  1.080
 N4T  C6   H6    single    0.930  0.020  1.080
 N4T  C10  C11   single    1.504  0.020  1.504
 N4T  C10  C14   double    1.330  0.020  1.330
 N4T  C11  N12   single    1.457  0.020  1.457
 N4T  C11  H111  single    0.970  0.020  1.090
 N4T  C11  H112  single    0.970  0.020  1.090
 N4T  N12  C13   single    1.458  0.020  1.458
 N4T  N12  C8    single    1.346  0.020  1.346
 N4T  C13  C14   single    1.496  0.020  1.496
 N4T  C13  C17   single    1.514  0.020  1.514
 N4T  C13  H13   single    0.970  0.020  1.090
 N4T  C14  H14   single    0.930  0.020  1.080
 N4T  C17  C19   aromatic  1.392  0.020  1.392
 N4T  C17  C23   aromatic  1.388  0.020  1.388
 N4T  C19  C20   aromatic  1.387  0.020  1.387
 N4T  C19  H19   single    0.930  0.020  1.080
 N4T  C20  C21   aromatic  1.390  0.020  1.390
 N4T  C20  H20   single    0.930  0.020  1.080
 N4T  C21  C22   aromatic  1.388  0.020  1.388
 N4T  C21  H21   single    0.930  0.020  1.080
 N4T  C22  C23   aromatic  1.390  0.020  1.390
 N4T  C22  H22   single    0.930  0.020  1.080
 N4T  C23  H23   single    0.930  0.020  1.080
 N4T  C8   C7    single    1.531  0.020  1.531
 N4T  C8   O2    double    1.223  0.020  1.223
 N4T  C7   C35   single    1.522  0.020  1.522
 N4T  C7   N1    single    1.444  0.020  1.444
 N4T  C7   H7    single    0.970  0.020  1.090
 N4T  C35  C15   single    1.494  0.020  1.494
 N4T  C35  C12   single    1.496  0.020  1.496
 N4T  C35  H35   single    0.970  0.020  1.090
 N4T  C15  C12   single    1.501  0.020  1.501
 N4T  C15  H151  single    0.970  0.020  1.090
 N4T  C15  H152  single    0.970  0.020  1.090
 N4T  N1   HN11  single    0.890  0.020  1.040
 N4T  N1   HN12  single    0.890  0.020  1.040
 N4T  C12  H121  single    0.970  0.020  1.090
 N4T  C12  H122  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
 N4T  F41   C1   C6    119.04  3.000
 N4T  F41   C1   C2    118.72  3.000
 N4T  C6    C1   C2    122.24  3.000
 N4T  H2    C2   C3    119.89  3.000
 N4T  H2    C2   C1    120.06  3.000
 N4T  C3    C2   C1    120.03  3.000
 N4T  C10   C3   C4    123.12  3.000
 N4T  C10   C3   C2    119.73  3.000
 N4T  C4    C3   C2    117.14  3.000
 N4T  F40   C4   C5    118.20  3.000
 N4T  F40   C4   C3    119.01  3.000
 N4T  C5    C4   C3    122.79  3.000
 N4T  H5    C5   C6    120.54  3.000
 N4T  H5    C5   C4    120.01  3.000
 N4T  C6    C5   C4    119.45  3.000
 N4T  H6    C6   C5    120.70  3.000
 N4T  H6    C6   C1    120.95  3.000
 N4T  C5    C6   C1    118.35  3.000
 N4T  C14   C10  C11   110.67  3.000
 N4T  C14   C10  C3    125.40  3.000
 N4T  C11   C10  C3    123.77  3.000
 N4T  H112  C11  H111  107.35  3.000
 N4T  H112  C11  N12   112.03  3.000
 N4T  H111  C11  N12   112.04  3.000
 N4T  H112  C11  C10   112.46  3.000
 N4T  H111  C11  C10   110.81  3.000
 N4T  N12   C11  C10   102.22  3.000
 N4T  C8    N12  C13   120.46  3.000
 N4T  C8    N12  C11   126.49  3.000
 N4T  C13   N12  C11   112.96  3.000
 N4T  H13   C13  C17   108.68  3.000
 N4T  H13   C13  C14   110.72  3.000
 N4T  C17   C13  C14   111.96  3.000
 N4T  H13   C13  N12   110.64  3.000
 N4T  C17   C13  N12   113.15  3.000
 N4T  C14   C13  N12   101.59  3.000
 N4T  H14   C14  C13   121.55  3.000
 N4T  H14   C14  C10   126.10  3.000
 N4T  C13   C14  C10   112.33  3.000
 N4T  C23   C17  C19   119.12  3.000
 N4T  C23   C17  C13   120.48  3.000
 N4T  C19   C17  C13   120.38  3.000
 N4T  H19   C19  C20   119.43  3.000
 N4T  H19   C19  C17   120.11  3.000
 N4T  C20   C19  C17   120.46  3.000
 N4T  H20   C20  C21   120.07  3.000
 N4T  H20   C20  C19   119.77  3.000
 N4T  C21   C20  C19   120.15  3.000
 N4T  H21   C21  C22   120.23  3.000
 N4T  H21   C21  C20   120.14  3.000
 N4T  C22   C21  C20   119.63  3.000
 N4T  H22   C22  C23   119.80  3.000
 N4T  H22   C22  C21   120.17  3.000
 N4T  C23   C22  C21   120.03  3.000
 N4T  H23   C23  C22   119.77  3.000
 N4T  H23   C23  C17   119.63  3.000
 N4T  C22   C23  C17   120.60  3.000
 N4T  O2    C8   C7    120.96  3.000
 N4T  O2    C8   N12   121.36  3.000
 N4T  C7    C8   N12   117.60  3.000
 N4T  H7    C7   N1    107.13  3.000
 N4T  H7    C7   C35   107.72  3.000
 N4T  N1    C7   C35   112.07  3.000
 N4T  H7    C7   C8    110.28  3.000
 N4T  N1    C7   C8    112.87  3.000
 N4T  C35   C7   C8    106.68  3.000
 N4T  H35   C35  C12   115.11  3.000
 N4T  H35   C35  C15   115.40  3.000
 N4T  C12   C35  C15    60.26  3.000
 N4T  H35   C35  C7    113.94  3.000
 N4T  C12   C35  C7    120.93  3.000
 N4T  C15   C35  C7    121.00  3.000
 N4T  H152  C15  H151  114.85  3.000
 N4T  H152  C15  C12   117.36  3.000
 N4T  H151  C15  C12   118.46  3.000
 N4T  H152  C15  C35   117.50  3.000
 N4T  H151  C15  C35   117.88  3.000
 N4T  C12   C15  C35    59.94  3.000
 N4T  HN12  N1   HN11  105.82  3.000
 N4T  HN12  N1   C7    109.88  3.000
 N4T  HN11  N1   C7    109.41  3.000
 N4T  H122  C12  H121  113.97  3.000
 N4T  H122  C12  C15   118.63  3.000
 N4T  H121  C12  C15   117.64  3.000
 N4T  H122  C12  C35   117.74  3.000
 N4T  H121  C12  C35   118.73  3.000
 N4T  C15   C12  C35    59.80  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
 N4T  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 N4T  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 N4T  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 N4T  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 N4T  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 N4T  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 N4T  CONST_07  C21   C20  C19  C17     0.00   0.0  0
 N4T  CONST_08  C21   C22  C23  C17     0.00   0.0  0
 N4T  CONST_09  C22   C23  C17  C19     0.00   0.0  0
 N4T  CONST_10  C22   C21  C20  C19     0.00   0.0  0
 N4T  CONST_11  C23   C17  C19  C20     0.00   0.0  0
 N4T  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 N4T  CONST_13  C10   C3   C2   C1    180.00   0.0  0
 N4T  CONST_14  C10   C3   C4   C5    180.00   0.0  0
 N4T  CONST_15  C20   C19  C17  C13   180.00   0.0  0
 N4T  CONST_16  C22   C23  C17  C13   180.00   0.0  0
 N4T  CONST_17  F40   C4   C3   C2    180.00   0.0  0
 N4T  CONST_18  F41   C1   C2   C3    180.00   0.0  0
 N4T  CONST_19  F41   C1   C6   C5    180.00   0.0  0
 N4T  CONST_20  F40   C4   C5   C6    180.00   0.0  0
 N4T  CONST_21  F40   C4   C3   C10     0.00   0.0  0
 N4T  CONST_22  H5    C5   C6   C1    180.00   0.0  0
 N4T  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 N4T  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 N4T  CONST_25  H19   C19  C17  C13     0.00   0.0  0
 N4T  CONST_26  H23   C23  C17  C13     0.00   0.0  0
 N4T  CONST_27  H20   C20  C19  C17   180.00   0.0  0
 N4T  CONST_28  H22   C22  C23  C17   180.00   0.0  0
 N4T  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 N4T  CONST_30  C7    C8   N12  C11     0.00   0.0  0
 N4T  CONST_31  O2    C8   N12  C11   180.00   0.0  0
 N4T  CONST_32  C7    C8   N12  C13   180.00   0.0  0
 N4T  CONST_33  O2    C8   N12  C13     0.00   0.0  0
 N4T  Var_01    C11   C10  C3   C2   -135.89  30.0  2
 N4T  Var_02    N12   C11  C10  C3    173.69  30.0  1
 N4T  Var_03    C13   C14  C10  C3   -176.59  30.0  1
 N4T  Var_04    C13   N12  C11  C10     4.37  30.0  1
 N4T  Var_05    C12   C15  C35  C7    110.32  30.0  1
 N4T  Var_06    H121  C12  C15  C35  -108.85  30.0  1

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
 N4T  chir_01  C13  N12  C14  C17  negativ
 N4T  chir_02  C7   N1   C8   C35  positiv
 N4T  chir_03  C35  C7   C15  C12  both

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
 N4T  plan-1  C1   0.020
 N4T  plan-1  C2   0.020
 N4T  plan-1  C3   0.020
 N4T  plan-1  C4   0.020
 N4T  plan-1  C5   0.020
 N4T  plan-1  C6   0.020
 N4T  plan-1  C10  0.020
 N4T  plan-1  F40  0.020
 N4T  plan-1  F41  0.020
 N4T  plan-1  H2   0.020
 N4T  plan-1  H5   0.020
 N4T  plan-1  H6   0.020
 N4T  plan-2  C13  0.020
 N4T  plan-2  C17  0.020
 N4T  plan-2  C19  0.020
 N4T  plan-2  C20  0.020
 N4T  plan-2  C21  0.020
 N4T  plan-2  C22  0.020
 N4T  plan-2  C23  0.020
 N4T  plan-2  H19  0.020
 N4T  plan-2  H20  0.020
 N4T  plan-2  H21  0.020
 N4T  plan-2  H22  0.020
 N4T  plan-2  H23  0.020
 N4T  plan-3  C11  0.020
 N4T  plan-3  N12  0.020
 N4T  plan-3  C13  0.020
 N4T  plan-3  C8   0.020
 N4T  plan-3  C7   0.020
 N4T  plan-3  O2   0.020

