# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:05:58 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-N-[(2S,3E)-1-(4'-cyanobiphenyl-4-yl)-3-iminopropan-2-yl]piperidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C[C@H](Cc1ccc(cc1)c2ccc(cc2)C#N)NC(=O)[C@@H]3CCCCN3
#
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
 GDI  GDI  (2S)-N-[(2S,3E)-1-(4'-cyanobiphenyl-4-yl)-3-iminopropan-2-yl]piperidine-2-carboxamide  ligand  51  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GDI
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
 GDI  N1    N  NH1   0  -0.581  -2.6819  -2.5571   0.2648
 GDI  C2    C  CH2   0  -0.439  -4.7491  -3.9049  -0.1365
 GDI  C3    C  CH2   0  -0.316  -3.2350  -3.7860  -0.2859
 GDI  C4    C  CH1   0  -0.229  -3.3340  -1.3792  -0.2715
 GDI  C5    C  CH2   0  -0.433  -4.8654  -1.3986  -0.1204
 GDI  C6    C  CH2   0  -0.442  -5.4383  -2.6771  -0.7217
 GDI  C7    C  C     0   0.561  -2.7947  -0.1305   0.4051
 GDI  O8    O  O     0  -0.489  -2.4151  -0.1353   1.5665
 GDI  N9    N  NH1   0  -0.619  -2.8339   0.9704  -0.3651
 GDI  C10   C  CH1   0  -0.130  -2.6164   2.3058   0.1124
 GDI  C11   C  C1    0  -0.028  -3.8719   3.1334   0.0440
 GDI  C12   C  CH2   0  -0.540  -1.4936   3.0102  -0.6719
 GDI  C13   C  CR6   0   0.148  -0.1731   2.3207  -0.5024
 GDI  C14   C  CR16  0  -0.284   0.2285   1.3112  -1.3723
 GDI  C15   C  CR16  0  -0.292   1.4373   0.6572  -1.1964
 GDI  C16   C  CR6   0   0.072   2.2874   0.9973  -0.1439
 GDI  C17   C  CR16  0  -0.291   1.8845   2.0090   0.7286
 GDI  C18   C  CR16  0  -0.289   0.6720   2.6548   0.5522
 GDI  C19   C  CR6   0   0.106   3.5817   0.3143   0.0336
 GDI  C20   C  CR16  0  -0.302   4.7056   1.0178   0.4749
 GDI  C21   C  CR16  0  -0.301   3.7128  -1.0497  -0.2400
 GDI  C22   C  CR16  0  -0.222   5.9235   0.3855   0.6379
 GDI  C23   C  CR16  0  -0.223   4.9247  -1.6948  -0.0820
 GDI  C24   C  CR6   0  -0.011   6.0361  -0.9761   0.3580
 GDI  C25   C  CSP   0   0.054   7.2909  -1.6341   0.5208
 GDI  N26   N  NS    0  -0.253   8.3064  -2.1642   0.6479
 GDI  N27   N  N     0  -0.532  -4.9454   2.6854  -0.4423
 GDI  H11   H  H     0   0.234  -3.7595   4.1467   0.4395
 GDI  H1    H  HNH1  0   0.338  -2.7940  -2.5630   1.2727
 GDI  H31C  H  HCH2  0   0.214  -2.9723  -3.8322  -1.3488
 GDI  H32C  H  HCH2  0   0.236  -2.7342  -4.6300   0.1927
 GDI  H4    H  HCH1  0   0.246  -3.1027  -1.3302  -1.3433
 GDI  H21C  H  HCH2  0   0.228  -5.1025  -4.8155  -0.6267
 GDI  H22C  H  HCH2  0   0.214  -5.0005  -3.9994   0.9255
 GDI  H61C  H  HCH2  0   0.217  -5.2934  -2.6619  -1.8074
 GDI  H62C  H  HCH2  0   0.236  -6.5164  -2.7209  -0.5528
 GDI  H51C  H  HCH2  0   0.223  -5.1160  -1.3452   0.9450
 GDI  H52C  H  HCH2  0   0.237  -5.3034  -0.5154  -0.5930
 GDI  H9    H  HNH1  0   0.396  -3.2223   0.8812  -1.2915
 GDI  H10   H  HCH1  0   0.286  -2.3125   2.2456   1.1606
 GDI  H121  H  HCH2  0   0.267  -1.7691   3.0492  -1.7290
 GDI  H122  H  HCH2  0   0.266  -1.4214   4.0433  -0.3244
 GDI  H27   H  H     0   0.350  -5.6736   3.3932  -0.4088
 GDI  H14   H  HCR6  0   0.248  -0.4039   1.0399  -2.2085
 GDI  H18   H  HCR6  0   0.251   0.3821   3.4341   1.2475
 GDI  H15   H  HCR6  0   0.256   1.7303  -0.1068  -1.9059
 GDI  H17   H  HCR6  0   0.256   2.5121   2.2888   1.5657
 GDI  H20   H  HCR6  0   0.271   4.6366   2.0793   0.6734
 GDI  H21   H  HCR6  0   0.271   2.8527  -1.6223  -0.5614
 GDI  H22   H  HCR6  0   0.282   6.7867   0.9459   0.9703
 GDI  H23   H  HCR6  0   0.283   5.0085  -2.7527  -0.2905

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
 GDI  N1   C3    single    1.456  0.020  1.456
 GDI  N1   C4    single    1.449  0.020  1.449
 GDI  C2   C3    single    1.526  0.020  1.526
 GDI  C2   C6    single    1.525  0.020  1.525
 GDI  C4   C5    single    1.539  0.020  1.539
 GDI  C4   C7    single    1.519  0.020  1.519
 GDI  C5   C6    single    1.525  0.020  1.525
 GDI  C7   O8    double    1.222  0.020  1.222
 GDI  C7   N9    single    1.344  0.020  1.344
 GDI  N9   C10   single    1.435  0.020  1.435
 GDI  C10  C11   single    1.505  0.020  1.505
 GDI  C10  C12   single    1.540  0.020  1.540
 GDI  C11  N27   double    1.261  0.020  1.261
 GDI  C11  H11   single    0.930  0.020  1.080
 GDI  C12  C13   single    1.499  0.020  1.499
 GDI  C13  C14   aromatic  1.392  0.020  1.392
 GDI  C13  C18   aromatic  1.392  0.020  1.392
 GDI  C14  C15   aromatic  1.386  0.020  1.386
 GDI  C15  C16   aromatic  1.395  0.020  1.395
 GDI  C16  C17   aromatic  1.395  0.020  1.395
 GDI  C16  C19   single    1.474  0.020  1.474
 GDI  C17  C18   aromatic  1.385  0.020  1.385
 GDI  C19  C20   aromatic  1.397  0.020  1.397
 GDI  C19  C21   aromatic  1.397  0.020  1.397
 GDI  C20  C22   aromatic  1.382  0.020  1.382
 GDI  C21  C23   aromatic  1.382  0.020  1.382
 GDI  C22  C24   aromatic  1.395  0.020  1.395
 GDI  C23  C24   aromatic  1.395  0.020  1.395
 GDI  C24  C25   single    1.426  0.020  1.426
 GDI  C25  N26   triple    1.153  0.020  1.153
 GDI  N1   H1    single    0.890  0.020  1.040
 GDI  C3   H31C  single    0.970  0.020  1.090
 GDI  C3   H32C  single    0.970  0.020  1.090
 GDI  C4   H4    single    0.970  0.020  1.090
 GDI  C2   H21C  single    0.970  0.020  1.090
 GDI  C2   H22C  single    0.970  0.020  1.090
 GDI  C6   H61C  single    0.970  0.020  1.090
 GDI  C6   H62C  single    0.970  0.020  1.090
 GDI  C5   H51C  single    0.970  0.020  1.090
 GDI  C5   H52C  single    0.970  0.020  1.090
 GDI  N9   H9    single    0.860  0.020  1.020
 GDI  C10  H10   single    0.970  0.020  1.090
 GDI  C12  H121  single    0.970  0.020  1.090
 GDI  C12  H122  single    0.970  0.020  1.090
 GDI  N27  H27   single    0.890  0.020  1.040
 GDI  C14  H14   single    0.930  0.020  1.080
 GDI  C18  H18   single    0.930  0.020  1.080
 GDI  C15  H15   single    0.930  0.020  1.080
 GDI  C17  H17   single    0.930  0.020  1.080
 GDI  C20  H20   single    0.930  0.020  1.080
 GDI  C21  H21   single    0.930  0.020  1.080
 GDI  C22  H22   single    0.930  0.020  1.080
 GDI  C23  H23   single    0.930  0.020  1.080

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
 GDI  H1    N1   C4    108.83  3.000
 GDI  H1    N1   C3    109.21  3.000
 GDI  C4    N1   C3    112.04  3.000
 GDI  H22C  C2   H21C  106.78  3.000
 GDI  H22C  C2   C6    109.75  3.000
 GDI  H21C  C2   C6    110.65  3.000
 GDI  H22C  C2   C3    109.22  3.000
 GDI  H21C  C2   C3    109.99  3.000
 GDI  C6    C2   C3    110.38  3.000
 GDI  H32C  C3   H31C  106.42  3.000
 GDI  H32C  C3   C2    110.61  3.000
 GDI  H31C  C3   C2    109.24  3.000
 GDI  H32C  C3   N1    108.21  3.000
 GDI  H31C  C3   N1    108.14  3.000
 GDI  C2    C3   N1    113.93  3.000
 GDI  H4    C4   C7    108.87  3.000
 GDI  H4    C4   C5    107.82  3.000
 GDI  C7    C4   C5    108.66  3.000
 GDI  H4    C4   N1    107.63  3.000
 GDI  C7    C4   N1    110.09  3.000
 GDI  C5    C4   N1    113.65  3.000
 GDI  H52C  C5   H51C  106.81  3.000
 GDI  H52C  C5   C6    110.88  3.000
 GDI  H51C  C5   C6    109.78  3.000
 GDI  H52C  C5   C4    110.24  3.000
 GDI  H51C  C5   C4    108.81  3.000
 GDI  C6    C5   C4    110.23  3.000
 GDI  H62C  C6   H61C  106.53  3.000
 GDI  H62C  C6   C5    110.09  3.000
 GDI  H61C  C6   C5    109.24  3.000
 GDI  H62C  C6   C2    110.77  3.000
 GDI  H61C  C6   C2    109.38  3.000
 GDI  C5    C6   C2    110.73  3.000
 GDI  N9    C7   O8    123.84  3.000
 GDI  N9    C7   C4    114.06  3.000
 GDI  O8    C7   C4    122.03  3.000
 GDI  H9    N9   C10   116.51  3.000
 GDI  H9    N9   C7    117.72  3.000
 GDI  C10   N9   C7    124.55  3.000
 GDI  H10   C10  C12   108.11  3.000
 GDI  H10   C10  C11   107.80  3.000
 GDI  C12   C10  C11   109.48  3.000
 GDI  H10   C10  N9    108.06  3.000
 GDI  C12   C10  N9    111.52  3.000
 GDI  C11   C10  N9    111.73  3.000
 GDI  H11   C11  N27   123.80  3.000
 GDI  H11   C11  C10   114.04  3.000
 GDI  N27   C11  C10   122.16  3.000
 GDI  H122  C12  H121  106.89  3.000
 GDI  H122  C12  C13   109.92  3.000
 GDI  H121  C12  C13   110.35  3.000
 GDI  H122  C12  C10   108.59  3.000
 GDI  H121  C12  C10   108.97  3.000
 GDI  C13   C12  C10   111.97  3.000
 GDI  C18   C13  C14   118.19  3.000
 GDI  C18   C13  C12   120.66  3.000
 GDI  C14   C13  C12   121.14  3.000
 GDI  H14   C14  C15   119.29  3.000
 GDI  H14   C14  C13   119.72  3.000
 GDI  C15   C14  C13   120.98  3.000
 GDI  H15   C15  C16   120.09  3.000
 GDI  H15   C15  C14   119.07  3.000
 GDI  C16   C15  C14   120.82  3.000
 GDI  C19   C16  C17   120.94  3.000
 GDI  C19   C16  C15   120.86  3.000
 GDI  C17   C16  C15   118.20  3.000
 GDI  H17   C17  C18   119.03  3.000
 GDI  H17   C17  C16   120.22  3.000
 GDI  C18   C17  C16   120.74  3.000
 GDI  H18   C18  C17   119.19  3.000
 GDI  H18   C18  C13   119.75  3.000
 GDI  C17   C18  C13   121.06  3.000
 GDI  C21   C19  C20   118.54  3.000
 GDI  C21   C19  C16   120.74  3.000
 GDI  C20   C19  C16   120.72  3.000
 GDI  H20   C20  C22   118.91  3.000
 GDI  H20   C20  C19   120.03  3.000
 GDI  C22   C20  C19   121.04  3.000
 GDI  H21   C21  C23   118.94  3.000
 GDI  H21   C21  C19   120.01  3.000
 GDI  C23   C21  C19   121.04  3.000
 GDI  H22   C22  C24   120.21  3.000
 GDI  H22   C22  C20   120.17  3.000
 GDI  C24   C22  C20   119.62  3.000
 GDI  H23   C23  C24   120.20  3.000
 GDI  H23   C23  C21   120.17  3.000
 GDI  C24   C23  C21   119.62  3.000
 GDI  C25   C24  C23   119.96  3.000
 GDI  C25   C24  C22   119.91  3.000
 GDI  C23   C24  C22   120.13  3.000
 GDI  N26   C25  C24   180.00  3.000
 GDI  H27   N27  C11   110.48  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
 GDI  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 GDI  CONST_02  C16  C17  C18  C13    0.00   0.0  0
 GDI  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 GDI  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 GDI  CONST_05  C19  C16  C15  C14  180.00   0.0  0
 GDI  CONST_06  C18  C13  C14  C15    0.00   0.0  0
 GDI  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 GDI  CONST_10  C22  C20  C19  C16  180.00   0.0  0
 GDI  CONST_11  C23  C21  C19  C16  180.00   0.0  0
 GDI  CONST_14  C19  C16  C17  C18  180.00   0.0  0
 GDI  CONST_15  C24  C22  C20  C19    0.00   0.0  0
 GDI  CONST_16  C24  C23  C21  C19    0.00   0.0  0
 GDI  CONST_17  C23  C21  C19  C20    0.00   0.0  0
 GDI  CONST_18  C23  C24  C22  C20    0.00   0.0  0
 GDI  CONST_19  C22  C20  C19  C21    0.00   0.0  0
 GDI  CONST_20  C22  C24  C23  C21    0.00   0.0  0
 GDI  CONST_21  C15  C14  C13  C12  180.00   0.0  0
 GDI  CONST_22  C17  C18  C13  C12  180.00   0.0  0
 GDI  CONST_23  C25  C24  C22  C20  180.00   0.0  0
 GDI  CONST_24  C25  C24  C23  C21  180.00   0.0  0
 GDI  CONST_25  H15  C15  C14  C13  180.00   0.0  0
 GDI  CONST_26  H17  C17  C18  C13  180.00   0.0  0
 GDI  CONST_27  H18  C18  C13  C14  180.00   0.0  0
 GDI  CONST_28  H14  C14  C15  C16  180.00   0.0  0
 GDI  CONST_29  H20  C20  C19  C16    0.00   0.0  0
 GDI  CONST_30  H21  C21  C19  C16    0.00   0.0  0
 GDI  CONST_31  H22  C22  C20  C19  180.00   0.0  0
 GDI  CONST_32  H23  C23  C21  C19  180.00   0.0  0
 GDI  CONST_33  C10  N9   C7   C4   180.00   0.0  0
 GDI  CONST_34  H9   N9   C7   C4     0.00   0.0  0
 GDI  CONST_35  C10  N9   C7   O8     0.00   0.0  0
 GDI  Var_01    C6   C2   C3   N1    53.96  30.0  1
 GDI  Var_02    C4   N1   C3   C2   -53.91  30.0  1
 GDI  Var_03    C4   C5   C6   C2    53.30  30.0  1
 GDI  Var_04    C5   C6   C2   C3   -53.39  30.0  1
 GDI  Var_05    C14  C13  C12  C10   90.25  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
 GDI  chir_01  C4   N1  C5   C7   negativ
 GDI  chir_02  C10  N9  C11  C12  positiv

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
 GDI  plan-1  C12  0.020
 GDI  plan-1  C13  0.020
 GDI  plan-1  C14  0.020
 GDI  plan-1  C15  0.020
 GDI  plan-1  C16  0.020
 GDI  plan-1  C17  0.020
 GDI  plan-1  C18  0.020
 GDI  plan-1  C19  0.020
 GDI  plan-1  H14  0.020
 GDI  plan-1  H18  0.020
 GDI  plan-1  H15  0.020
 GDI  plan-1  H17  0.020
 GDI  plan-2  C16  0.020
 GDI  plan-2  C19  0.020
 GDI  plan-2  C20  0.020
 GDI  plan-2  C21  0.020
 GDI  plan-2  C22  0.020
 GDI  plan-2  C23  0.020
 GDI  plan-2  C24  0.020
 GDI  plan-2  C25  0.020
 GDI  plan-2  N26  0.020
 GDI  plan-2  H20  0.020
 GDI  plan-2  H21  0.020
 GDI  plan-2  H22  0.020
 GDI  plan-2  H23  0.020
 GDI  plan-3  C4   0.020
 GDI  plan-3  C7   0.020
 GDI  plan-3  O8   0.020
 GDI  plan-3  N9   0.020
 GDI  plan-3  C10  0.020
 GDI  plan-3  H9   0.020
 GDI  plan-4  C10  0.020
 GDI  plan-4  C11  0.020
 GDI  plan-4  N27  0.020
 GDI  plan-4  H11  0.020
 GDI  plan-4  H27  0.020

