# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:13:17 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (3S,4R)-N-(7-chloro-1-oxo-1,4-dihydroisoquinolin-6-yl)-4-(4-chlorophenyl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)[C@@H]2CNC[C@H]2C(=O)Nc3cc4CC=NC(=O)c4cc3Cl
#
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
 3ND  3ND  (3S,4R)-N-(7-chloro-1-oxo-1,4-dihydroisoquinolin-6-yl)-4-(4-chlorophenyl)pyrrolidine-3-carboxamide  ligand  44  27  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3ND
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
 3ND  C1    C   CR16  0   0.014   5.9162   0.3457   1.6440
 3ND  N2    N   N     0  -0.416   5.9216  -0.9030   1.8936
 3ND  C3    C   CR6   0   0.456   4.7923  -1.6747   1.5792
 3ND  C4    C   C     0  -0.601   4.8244   1.1387   1.0332
 3ND  C5    C   CR66  0   0.170   3.6166   0.3361   0.6970
 3ND  C6    C   CR66  0  -0.141   3.6191  -1.0278   0.9641
 3ND  C7    C   CR16  0  -0.226   2.4951  -1.7887   0.6449
 3ND  C8    C   CR6   0  -0.142   1.3998  -1.1881   0.0762
 3ND  C9    C   CR6   0   0.487   1.3740   0.1960  -0.1972
 3ND  C10   C   CR16  0  -0.371   2.5067   0.9402   0.1230
 3ND  N11   N   NH1   0  -0.748   0.2341   0.7277  -0.7716
 3ND  C12   C   C     0   0.572  -0.1124   2.0378  -0.9717
 3ND  C13   C   CH1   0  -0.449  -1.5280   2.1798  -1.4817
 3ND  C14   C   CH2   0  -0.290  -1.8833   3.5559  -2.0910
 3ND  N15   N   NH1   0  -0.581  -3.0353   4.0820  -1.3619
 3ND  C16   C   CH2   0  -0.288  -3.6787   2.9265  -0.7652
 3ND  C17   C   CH1   0  -0.369  -2.5284   2.0167  -0.3070
 3ND  C18   C   CR6   0   0.169  -2.8868   0.5965   0.0208
 3ND  C19   C   CR16  0  -0.320  -2.6097   0.0722   1.2797
 3ND  C20   C   CR16  0  -0.187  -2.9158  -1.2423   1.6002
 3ND  C21   C   CR6   0  -0.055  -3.5057  -2.0470   0.6412
 3ND  C22   C   CR16  0  -0.192  -3.7939  -1.5561  -0.6230
 3ND  C23   C   CR16  0  -0.321  -3.4836  -0.2390  -0.9231
 3ND  CL24  CL  CL    0  -0.133  -3.8832  -3.6963   1.0214
 3ND  O25   O   O     0  -0.403   4.8149  -2.8607   1.8266
 3ND  CL26  CL  CL    0  -0.093   0.0172  -2.1640  -0.3011
 3ND  O27   O   O     0  -0.437   0.6152   2.9753  -0.7192
 3ND  H1    H   HCR6  0   0.287   6.8140   0.9019   1.9049
 3ND  H4    H   H     0   0.315   4.5798   1.9602   1.7159
 3ND  H4A   H   H     0   0.315   5.2305   1.6346   0.1442
 3ND  H7    H   HCR6  0   0.288   2.4820  -2.8511   0.8463
 3ND  H10   H   HCR6  0   0.296   2.5308   1.9992  -0.0777
 3ND  HN11  H   HNH1  0   0.413  -0.4819   0.0539  -1.0052
 3ND  H13   H   HCH1  0   0.296  -1.7101   1.3957  -2.2222
 3ND  H14   H   HCH2  0   0.250  -1.0555   4.2615  -2.0492
 3ND  H14A  H   HCH2  0   0.237  -2.1381   3.4175  -3.1433
 3ND  HN15  H   HNH1  0   0.352  -2.7014   4.6790  -0.6158
 3ND  H16   H   HCH2  0   0.258  -4.3321   3.2172   0.0573
 3ND  H16A  H   HCH2  0   0.230  -4.2917   2.4120  -1.5129
 3ND  H17   H   HCH1  0   0.275  -2.0940   2.4762   0.5881
 3ND  H19   H   HCR6  0   0.262  -2.1384   0.6963   2.0293
 3ND  H20   H   HCR6  0   0.278  -2.6874  -1.6314   2.5831
 3ND  H22   H   HCR6  0   0.280  -4.2556  -2.1899  -1.3680
 3ND  H23   H   HCR6  0   0.264  -3.7134   0.1330  -1.9148

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
 3ND  N2    C1    double    1.273  0.020  1.273
 3ND  C4    C1    single    1.481  0.020  1.481
 3ND  C1    H1    single    0.930  0.020  1.080
 3ND  C3    N2    single    1.403  0.020  1.403
 3ND  O25   C3    double    1.212  0.020  1.212
 3ND  C6    C3    single    1.474  0.020  1.474
 3ND  C5    C4    single    1.489  0.020  1.489
 3ND  C4    H4    single    0.970  0.020  1.090
 3ND  C4    H4A   single    0.970  0.020  1.090
 3ND  C6    C5    aromatic  1.390  0.020  1.390
 3ND  C10   C5    aromatic  1.388  0.020  1.388
 3ND  C7    C6    aromatic  1.394  0.020  1.394
 3ND  C8    C7    aromatic  1.372  0.020  1.372
 3ND  C7    H7    single    0.930  0.020  1.080
 3ND  CL26  C8    single    1.734  0.020  1.734
 3ND  C8    C9    aromatic  1.411  0.020  1.411
 3ND  N11   C9    single    1.383  0.020  1.383
 3ND  C9    C10   aromatic  1.393  0.020  1.393
 3ND  C10   H10   single    0.930  0.020  1.080
 3ND  C12   N11   single    1.370  0.020  1.370
 3ND  N11   HN11  single    0.860  0.020  1.020
 3ND  O27   C12   double    1.213  0.020  1.213
 3ND  C13   C12   single    1.511  0.020  1.511
 3ND  C14   C13   single    1.546  0.020  1.546
 3ND  C13   C17   single    1.552  0.020  1.552
 3ND  C13   H13   single    0.970  0.020  1.090
 3ND  N15   C14   single    1.461  0.020  1.461
 3ND  C14   H14   single    0.970  0.020  1.090
 3ND  C14   H14A  single    0.970  0.020  1.090
 3ND  N15   C16   single    1.451  0.020  1.451
 3ND  N15   HN15  single    0.890  0.020  1.040
 3ND  C16   C17   single    1.537  0.020  1.537
 3ND  C16   H16   single    0.970  0.020  1.090
 3ND  C16   H16A  single    0.970  0.020  1.090
 3ND  C17   C18   single    1.501  0.020  1.501
 3ND  C17   H17   single    0.970  0.020  1.090
 3ND  C18   C19   aromatic  1.392  0.020  1.392
 3ND  C18   C23   aromatic  1.395  0.020  1.395
 3ND  C19   C20   aromatic  1.387  0.020  1.387
 3ND  C19   H19   single    0.930  0.020  1.080
 3ND  C20   C21   aromatic  1.384  0.020  1.384
 3ND  C20   H20   single    0.930  0.020  1.080
 3ND  C22   C21   aromatic  1.387  0.020  1.387
 3ND  C21   CL24  single    1.734  0.020  1.734
 3ND  C23   C22   aromatic  1.386  0.020  1.386
 3ND  C22   H22   single    0.930  0.020  1.080
 3ND  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
 3ND  H1    C1   C4   115.69  3.000
 3ND  H1    C1   N2   116.80  3.000
 3ND  C4    C1   N2   127.51  3.000
 3ND  C3    N2   C1   119.47  3.000
 3ND  O25   C3   C6   121.97  3.000
 3ND  C6    C3   N2   119.51  3.000
 3ND  O25   C3   N2   118.52  3.000
 3ND  H4A   C4   H4   104.41  3.000
 3ND  H4A   C4   C5   111.18  3.000
 3ND  H4    C4   C5   111.34  3.000
 3ND  H4A   C4   C1   107.67  3.000
 3ND  H4    C4   C1   108.00  3.000
 3ND  C5    C4   C1   113.74  3.000
 3ND  C10   C5   C6   120.53  3.000
 3ND  C10   C5   C4   120.50  3.000
 3ND  C6    C5   C4   118.96  3.000
 3ND  C7    C6   C5   119.34  3.000
 3ND  C7    C6   C3   119.85  3.000
 3ND  C5    C6   C3   120.81  3.000
 3ND  H7    C7   C8   119.83  3.000
 3ND  H7    C7   C6   120.21  3.000
 3ND  C8    C7   C6   119.96  3.000
 3ND  CL26  C8   C9   119.69  3.000
 3ND  C9    C8   C7   121.60  3.000
 3ND  CL26  C8   C7   118.70  3.000
 3ND  N11   C9   C10  124.09  3.000
 3ND  C10   C9   C8   117.70  3.000
 3ND  N11   C9   C8   118.21  3.000
 3ND  H10   C10  C9   120.02  3.000
 3ND  H10   C10  C5   119.12  3.000
 3ND  C9    C10  C5   120.86  3.000
 3ND  HN11  N11  C12  115.13  3.000
 3ND  HN11  N11  C9   115.07  3.000
 3ND  C12   N11  C9   129.57  3.000
 3ND  O27   C12  C13  124.01  3.000
 3ND  C13   C12  N11  112.09  3.000
 3ND  O27   C12  N11  123.84  3.000
 3ND  H13   C13  C17  109.26  3.000
 3ND  H13   C13  C14  109.45  3.000
 3ND  C17   C13  C14  104.10  3.000
 3ND  H13   C13  C12  108.49  3.000
 3ND  C17   C13  C12  109.79  3.000
 3ND  C14   C13  C12  115.58  3.000
 3ND  H14A  C14  H14  107.26  3.000
 3ND  H14A  C14  N15  110.04  3.000
 3ND  H14   C14  N15  110.30  3.000
 3ND  H14A  C14  C13  108.70  3.000
 3ND  H14   C14  C13  112.77  3.000
 3ND  N15   C14  C13  107.76  3.000
 3ND  HN15  N15  C16  108.23  3.000
 3ND  HN15  N15  C14  108.67  3.000
 3ND  C16   N15  C14  105.54  3.000
 3ND  H16A  C16  H16  107.75  3.000
 3ND  H16A  C16  C17  110.15  3.000
 3ND  H16   C16  C17  112.44  3.000
 3ND  H16A  C16  N15  109.97  3.000
 3ND  H16   C16  N15  111.33  3.000
 3ND  C17   C16  N15  105.21  3.000
 3ND  H17   C17  C18  108.25  3.000
 3ND  H17   C17  C16  106.98  3.000
 3ND  C18   C17  C16  116.53  3.000
 3ND  H17   C17  C13  108.58  3.000
 3ND  C18   C17  C13  114.76  3.000
 3ND  C16   C17  C13  101.22  3.000
 3ND  C23   C18  C19  118.14  3.000
 3ND  C23   C18  C17  121.42  3.000
 3ND  C19   C18  C17  120.43  3.000
 3ND  H19   C19  C20  118.81  3.000
 3ND  H19   C19  C18  119.71  3.000
 3ND  C20   C19  C18  121.47  3.000
 3ND  H20   C20  C21  120.70  3.000
 3ND  H20   C20  C19  120.29  3.000
 3ND  C21   C20  C19  119.01  3.000
 3ND  CL24  C21  C22  119.43  3.000
 3ND  CL24  C21  C20  119.60  3.000
 3ND  C22   C21  C20  120.97  3.000
 3ND  H22   C22  C23  120.22  3.000
 3ND  H22   C22  C21  120.62  3.000
 3ND  C23   C22  C21  119.16  3.000
 3ND  H23   C23  C22  118.48  3.000
 3ND  H23   C23  C18  120.28  3.000
 3ND  C22   C23  C18  121.24  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
 3ND  CONST_01  C8    C7   C6   C5     0.00   0.0  0
 3ND  CONST_02  C8    C9   C10  C5     0.00   0.0  0
 3ND  CONST_03  C9    C10  C5   C6     0.00   0.0  0
 3ND  CONST_04  C9    C8   C7   C6     0.00   0.0  0
 3ND  CONST_05  C10   C5   C6   C7     0.00   0.0  0
 3ND  CONST_06  C10   C9   C8   C7     0.00   0.0  0
 3ND  CONST_07  C21   C20  C19  C18    0.00   0.0  0
 3ND  CONST_08  C21   C22  C23  C18    0.00   0.0  0
 3ND  CONST_09  C22   C23  C18  C19    0.00   0.0  0
 3ND  CONST_10  C22   C21  C20  C19    0.00   0.0  0
 3ND  CONST_11  C23   C18  C19  C20    0.00   0.0  0
 3ND  CONST_12  C23   C22  C21  C20    0.00   0.0  0
 3ND  CONST_13  C20   C19  C18  C17  180.00   0.0  0
 3ND  CONST_14  C22   C23  C18  C17  180.00   0.0  0
 3ND  CONST_15  N11   C9   C10  C5   180.00   0.0  0
 3ND  CONST_16  CL26  C8   C7   C6   180.00   0.0  0
 3ND  CONST_17  N11   C9   C8   C7   180.00   0.0  0
 3ND  CONST_18  CL26  C8   C9   C10  180.00   0.0  0
 3ND  CONST_19  CL24  C21  C20  C19  180.00   0.0  0
 3ND  CONST_20  CL24  C21  C22  C23  180.00   0.0  0
 3ND  CONST_21  H7    C7   C6   C3     0.00   0.0  0
 3ND  CONST_22  H10   C10  C5   C4     0.00   0.0  0
 3ND  CONST_23  H19   C19  C18  C17    0.00   0.0  0
 3ND  CONST_24  H23   C23  C18  C17    0.00   0.0  0
 3ND  CONST_25  H20   C20  C19  C18  180.00   0.0  0
 3ND  CONST_26  H22   C22  C23  C18  180.00   0.0  0
 3ND  CONST_27  C13   C12  N11  C9   180.00   0.0  0
 3ND  CONST_28  C12   N11  C9   C8   180.00   0.0  0
 3ND  CONST_29  C12   N11  C9   C10    0.00   0.0  0
 3ND  CONST_30  HN11  N11  C9   C8     0.00   0.0  0
 3ND  CONST_31  O27   C12  N11  C9     0.00   0.0  0
 3ND  Var_01    C6    C3   N2   C1     0.07  30.0  1
 3ND  Var_02    C6    C5   C4   C1    -0.41  30.0  1
 3ND  Var_03    C5    C4   C1   N2     0.26  30.0  1
 3ND  Var_04    C5    C6   C3   N2    -0.25  30.0  1
 3ND  Var_05    C4    C1   N2   C3    -0.09  30.0  1
 3ND  Var_06    C16   N15  C14  C13  -22.02  30.0  1
 3ND  Var_07    C17   C16  N15  C14   38.77  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
 3ND  chir_01  C13  C12  C14  C17  positiv
 3ND  chir_02  C17  C13  C16  C18  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
 3ND  plan-1  C17   0.020
 3ND  plan-1  C18   0.020
 3ND  plan-1  C19   0.020
 3ND  plan-1  C20   0.020
 3ND  plan-1  C21   0.020
 3ND  plan-1  C22   0.020
 3ND  plan-1  C23   0.020
 3ND  plan-1  CL24  0.020
 3ND  plan-1  H19   0.020
 3ND  plan-1  H20   0.020
 3ND  plan-1  H22   0.020
 3ND  plan-1  H23   0.020
 3ND  plan-2  C3    0.020
 3ND  plan-2  C4    0.020
 3ND  plan-2  C5    0.020
 3ND  plan-2  C6    0.020
 3ND  plan-2  C7    0.020
 3ND  plan-2  C8    0.020
 3ND  plan-2  C9    0.020
 3ND  plan-2  C10   0.020
 3ND  plan-2  N11   0.020
 3ND  plan-2  CL26  0.020
 3ND  plan-2  H7    0.020
 3ND  plan-2  H10   0.020
 3ND  plan-3  C9    0.020
 3ND  plan-3  N11   0.020
 3ND  plan-3  C12   0.020
 3ND  plan-3  C13   0.020
 3ND  plan-3  O27   0.020
 3ND  plan-3  HN11  0.020
 3ND  plan-4  N2    0.020
 3ND  plan-4  C3    0.020
 3ND  plan-4  C6    0.020
 3ND  plan-4  O25   0.020

