# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 22:31:12 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N~2~-(3,4-difluorophenyl)-N-{2-methyl-5-[(piperazin-1-yl)methyl]phenyl}glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CN2CCNCC2)cc1NC(=O)CNc3ccc(F)c(F)c3
#
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
 7RS  7RS  N~2~-(3,4-difluorophenyl)-N-{2-methyl-5-[(piperazin-1-yl)methyl]phenyl}glycinamide  ligand  51  27  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7RS
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
 7RS  C10  C  CH2   0  -0.289   6.1425   1.9467  -1.1301
 7RS  N12  N  NH1   0  -0.579   6.2590   3.5379   0.7761
 7RS  C13  C  CH2   0  -0.323   5.2841   2.7027   1.4578
 7RS  C20  C  CR6   0   0.393  -4.3711   0.1822   0.0481
 7RS  C21  C  CR16  0  -0.518  -5.1022  -0.8590  -0.5378
 7RS  C22  C  CR6   0   0.427  -6.4620  -0.7141  -0.7318
 7RS  C24  C  CR16  0  -0.393  -6.4164   1.4756   0.2043
 7RS  C02  C  CR6   0   0.054   2.0657  -2.7275   0.6816
 7RS  C03  C  CR6   0   0.309   1.4504  -1.7330  -0.0810
 7RS  C04  C  CR16  0  -0.321   2.2070  -0.7534  -0.7168
 7RS  C05  C  CR6   0   0.085   3.5883  -0.7299  -0.5999
 7RS  C06  C  CR16  0  -0.282   4.2085  -1.7130   0.1660
 7RS  C07  C  CR16  0  -0.298   3.4555  -2.6975   0.7831
 7RS  N09  N  NT    0  -0.411   5.2167   1.1025  -0.3942
 7RS  C11  C  CH2   0  -0.325   7.0187   2.7471  -0.1771
 7RS  C14  C  CH2   0  -0.283   4.4043   1.8948   0.5131
 7RS  C16  C  C     0   0.523  -0.7608  -0.6842  -0.0004
 7RS  O17  O  O     0  -0.461  -0.3669   0.4116   0.3531
 7RS  C18  C  CH2   0  -0.407  -2.2294  -0.9648  -0.2709
 7RS  N19  N  NH1   0  -0.697  -3.0309   0.0748   0.3005
 7RS  C23  C  CR6   0   0.345  -7.1278   0.4382  -0.3677
 7RS  C25  C  CR16  0  -0.346  -5.0554   1.3535   0.4105
 7RS  F26  F  F     0  -0.317  -8.4520   0.5410  -0.5725
 7RS  F27  F  F     0  -0.312  -7.1516  -1.7164  -1.2910
 7RS  H1   H  HCH2  0   0.233   6.7693   1.3154  -1.7658
 7RS  H2   H  HCH2  0   0.186   5.6076   2.6448  -1.8005
 7RS  H3   H  HNH1  0   0.339   5.7695   4.2721   0.2759
 7RS  H5   H  HCH2  0   0.218   5.8233   2.0148   2.1174
 7RS  H6   H  HCH2  0   0.236   4.6557   3.3283   2.0940
 7RS  H7   H  HCR6  0   0.297  -4.6344  -1.7850  -0.8453
 7RS  H8   H  HCR6  0   0.288  -6.9301   2.3839   0.4913
 7RS  H9   H  HCH3  0   0.248   0.7349  -4.4328   0.6676
 7RS  H10  H  HCH3  0   0.256   1.9015  -4.4275   1.9783
 7RS  H11  H  HCH3  0   0.250   0.5064  -3.3516   2.0316
 7RS  H12  H  HCR6  0   0.254   1.7135  -0.0027  -1.3205
 7RS  H13  H  HCR6  0   0.245   5.2858  -1.7095   0.2773
 7RS  H14  H  HCR6  0   0.249   3.9541  -3.4610   1.3682
 7RS  H15  H  HCH2  0   0.247   5.0741  -0.1657  -2.0176
 7RS  H16  H  HCH2  0   0.210   3.7293   0.9628  -1.9005
 7RS  H18  H  HCH2  0   0.218   7.6617   2.0593   0.3817
 7RS  H19  H  HCH2  0   0.237   7.6757   3.4042  -0.7498
 7RS  H20  H  HCH2  0   0.238   3.7629   1.2303   1.0962
 7RS  H21  H  HCH2  0   0.184   3.7363   2.5798  -0.0417
 7RS  H22  H  HNH1  0   0.413  -0.3925  -2.6332  -0.4143
 7RS  H23  H  HCH2  0   0.272  -2.3529  -1.0472  -1.3612
 7RS  H24  H  HCH2  0   0.267  -2.4968  -1.9419   0.1438
 7RS  H25  H  HNH1  0   0.387  -2.5397   0.9383   0.4757
 7RS  H26  H  HCR6  0   0.272  -4.5120   2.1743   0.8608
 7RS  C08  C  CH2   0  -0.332   4.4016   0.3220  -1.3049
 7RS  N15  N  NH1   0  -0.746   0.0454  -1.7459  -0.2149
 7RS  C01  C  CH3   0  -0.738   1.2610  -3.7873   1.3747

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
 7RS  N12  C13  single    1.454  0.020  1.454
 7RS  N12  C11  single    1.453  0.020  1.453
 7RS  C13  C14  single    1.523  0.020  1.523
 7RS  C11  C10  single    1.522  0.020  1.522
 7RS  C14  N09  single    1.453  0.020  1.453
 7RS  C10  N09  single    1.453  0.020  1.453
 7RS  N09  C08  single    1.450  0.020  1.450
 7RS  C08  C05  single    1.505  0.020  1.505
 7RS  C05  C04  aromatic  1.386  0.020  1.386
 7RS  C05  C06  aromatic  1.392  0.020  1.392
 7RS  C04  C03  aromatic  1.392  0.020  1.392
 7RS  C06  C07  aromatic  1.385  0.020  1.385
 7RS  C03  N15  single    1.411  0.020  1.411
 7RS  C03  C02  aromatic  1.396  0.020  1.396
 7RS  N15  C16  single    1.350  0.020  1.350
 7RS  C07  C02  aromatic  1.394  0.020  1.394
 7RS  C02  C01  single    1.500  0.020  1.500
 7RS  C16  O17  double    1.217  0.020  1.217
 7RS  C16  C18  single    1.519  0.020  1.519
 7RS  C18  N19  single    1.432  0.020  1.432
 7RS  N19  C20  single    1.368  0.020  1.368
 7RS  C21  C20  aromatic  1.401  0.020  1.401
 7RS  C21  C22  aromatic  1.381  0.020  1.381
 7RS  C20  C25  aromatic  1.404  0.020  1.404
 7RS  C22  F27  single    1.339  0.020  1.339
 7RS  C22  C23  aromatic  1.380  0.020  1.380
 7RS  C25  C24  aromatic  1.382  0.020  1.382
 7RS  C23  C24  aromatic  1.382  0.020  1.382
 7RS  C23  F26  single    1.344  0.020  1.344
 7RS  C10  H1   single    0.970  0.020  1.090
 7RS  C10  H2   single    0.970  0.020  1.090
 7RS  N12  H3   single    0.890  0.020  1.040
 7RS  C13  H5   single    0.970  0.020  1.090
 7RS  C13  H6   single    0.970  0.020  1.090
 7RS  C21  H7   single    0.930  0.020  1.080
 7RS  C24  H8   single    0.930  0.020  1.080
 7RS  C01  H9   single    0.970  0.020  1.090
 7RS  C01  H10  single    0.970  0.020  1.090
 7RS  C01  H11  single    0.970  0.020  1.090
 7RS  C04  H12  single    0.930  0.020  1.080
 7RS  C06  H13  single    0.930  0.020  1.080
 7RS  C07  H14  single    0.930  0.020  1.080
 7RS  C08  H15  single    0.970  0.020  1.090
 7RS  C08  H16  single    0.970  0.020  1.090
 7RS  C11  H18  single    0.970  0.020  1.090
 7RS  C11  H19  single    0.970  0.020  1.090
 7RS  C14  H20  single    0.970  0.020  1.090
 7RS  C14  H21  single    0.970  0.020  1.090
 7RS  N15  H22  single    0.860  0.020  1.020
 7RS  C18  H23  single    0.970  0.020  1.090
 7RS  C18  H24  single    0.970  0.020  1.090
 7RS  N19  H25  single    0.890  0.020  1.040
 7RS  C25  H26  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
 7RS  H2   C10  H1   106.81  3.000
 7RS  H2   C10  C11  109.03  3.000
 7RS  H1   C10  C11  109.73  3.000
 7RS  H2   C10  N09  111.45  3.000
 7RS  H1   C10  N09  108.92  3.000
 7RS  C11  C10  N09  110.81  3.000
 7RS  H3   N12  C11  108.83  3.000
 7RS  H3   N12  C13  108.88  3.000
 7RS  C11  N12  C13  110.22  3.000
 7RS  H6   C13  H5   107.01  3.000
 7RS  H6   C13  C14  109.45  3.000
 7RS  H5   C13  C14  108.95  3.000
 7RS  H6   C13  N12  109.29  3.000
 7RS  H5   C13  N12  108.26  3.000
 7RS  C14  C13  N12  113.66  3.000
 7RS  C25  C20  N19  119.69  3.000
 7RS  C25  C20  C21  118.27  3.000
 7RS  N19  C20  C21  122.02  3.000
 7RS  H7   C21  C22  118.39  3.000
 7RS  H7   C21  C20  121.96  3.000
 7RS  C22  C21  C20  119.65  3.000
 7RS  F27  C22  C23  119.13  3.000
 7RS  C23  C22  C21  121.71  3.000
 7RS  F27  C22  C21  119.16  3.000
 7RS  H8   C24  C25  120.14  3.000
 7RS  H8   C24  C23  119.70  3.000
 7RS  C25  C24  C23  120.16  3.000
 7RS  C07  C02  C03  117.64  3.000
 7RS  C07  C02  C01  121.09  3.000
 7RS  C03  C02  C01  121.27  3.000
 7RS  N15  C03  C04  120.29  3.000
 7RS  N15  C03  C02  118.95  3.000
 7RS  C04  C03  C02  120.75  3.000
 7RS  H12  C04  C05  119.31  3.000
 7RS  H12  C04  C03  119.68  3.000
 7RS  C05  C04  C03  121.01  3.000
 7RS  C08  C05  C06  120.70  3.000
 7RS  C06  C05  C04  118.57  3.000
 7RS  C08  C05  C04  120.71  3.000
 7RS  H13  C06  C07  119.83  3.000
 7RS  H13  C06  C05  119.83  3.000
 7RS  C07  C06  C05  120.34  3.000
 7RS  H14  C07  C06  119.44  3.000
 7RS  H14  C07  C02  118.88  3.000
 7RS  C06  C07  C02  121.68  3.000
 7RS  C14  N09  C08  111.80  3.000
 7RS  C08  N09  C10  110.66  3.000
 7RS  C14  N09  C10  110.84  3.000
 7RS  H19  C11  H18  107.01  3.000
 7RS  H19  C11  N12  109.35  3.000
 7RS  H18  C11  N12  108.31  3.000
 7RS  H19  C11  C10  109.55  3.000
 7RS  H18  C11  C10  109.10  3.000
 7RS  N12  C11  C10  113.33  3.000
 7RS  H21  C14  H20  106.85  3.000
 7RS  H21  C14  N09  111.24  3.000
 7RS  H20  C14  N09  109.27  3.000
 7RS  H21  C14  C13  109.36  3.000
 7RS  H20  C14  C13  109.32  3.000
 7RS  N09  C14  C13  110.71  3.000
 7RS  C18  C16  O17  122.06  3.000
 7RS  C18  C16  N15  113.81  3.000
 7RS  O17  C16  N15  124.12  3.000
 7RS  H24  C18  H23  106.32  3.000
 7RS  H24  C18  N19  111.12  3.000
 7RS  H23  C18  N19  112.77  3.000
 7RS  H24  C18  C16  109.48  3.000
 7RS  H23  C18  C16  107.38  3.000
 7RS  N19  C18  C16  109.63  3.000
 7RS  H25  N19  C18  114.73  3.000
 7RS  H25  N19  C20  116.23  3.000
 7RS  C18  N19  C20  122.13  3.000
 7RS  F26  C23  C24  120.86  3.000
 7RS  F26  C23  C22  119.94  3.000
 7RS  C24  C23  C22  119.20  3.000
 7RS  H26  C25  C24  119.31  3.000
 7RS  H26  C25  C20  119.69  3.000
 7RS  C24  C25  C20  121.01  3.000
 7RS  H16  C08  H15  106.36  3.000
 7RS  H16  C08  N09  111.65  3.000
 7RS  H15  C08  N09  107.66  3.000
 7RS  H16  C08  C05  109.24  3.000
 7RS  H15  C08  C05  109.01  3.000
 7RS  N09  C08  C05  112.69  3.000
 7RS  H22  N15  C16  117.62  3.000
 7RS  H22  N15  C03  117.30  3.000
 7RS  C16  N15  C03  124.90  3.000
 7RS  H11  C01  H10  107.94  3.000
 7RS  H11  C01  H9   107.01  3.000
 7RS  H10  C01  H9   107.14  3.000
 7RS  H11  C01  C02  111.53  3.000
 7RS  H10  C01  C02  110.86  3.000
 7RS  H9   C01  C02  112.13  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
 7RS  CONST_01  C23  C22  C21  C20    0.00   0.0  0
 7RS  CONST_02  C23  C24  C25  C20    0.00   0.0  0
 7RS  CONST_03  C24  C25  C20  C21    0.00   0.0  0
 7RS  CONST_04  C24  C23  C22  C21    0.00   0.0  0
 7RS  CONST_05  C25  C20  C21  C22    0.00   0.0  0
 7RS  CONST_06  C25  C24  C23  C22    0.00   0.0  0
 7RS  CONST_07  C05  C04  C03  C02    0.00   0.0  0
 7RS  CONST_08  C05  C06  C07  C02    0.00   0.0  0
 7RS  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 7RS  CONST_10  C06  C07  C02  C03    0.00   0.0  0
 7RS  CONST_11  C07  C06  C05  C04    0.00   0.0  0
 7RS  CONST_12  C07  C02  C03  C04    0.00   0.0  0
 7RS  CONST_13  F27  C22  C21  C20  180.00   0.0  0
 7RS  CONST_14  F26  C23  C22  C21  180.00   0.0  0
 7RS  CONST_15  N19  C20  C21  C22  180.00   0.0  0
 7RS  CONST_16  N19  C20  C25  C24  180.00   0.0  0
 7RS  CONST_17  F27  C22  C23  C24  180.00   0.0  0
 7RS  CONST_18  C04  C03  C02  C01  180.00   0.0  0
 7RS  CONST_19  C06  C07  C02  C01  180.00   0.0  0
 7RS  CONST_20  C08  C05  C04  C03  180.00   0.0  0
 7RS  CONST_21  N15  C03  C04  C05  180.00   0.0  0
 7RS  CONST_22  C08  C05  C06  C07  180.00   0.0  0
 7RS  CONST_23  N15  C03  C02  C07  180.00   0.0  0
 7RS  CONST_24  F26  C23  C24  C25  180.00   0.0  0
 7RS  CONST_25  H8   C24  C25  C20  180.00   0.0  0
 7RS  CONST_26  H26  C25  C20  C21  180.00   0.0  0
 7RS  CONST_27  H12  C04  C03  C02  180.00   0.0  0
 7RS  CONST_28  H13  C06  C07  C02  180.00   0.0  0
 7RS  CONST_29  H14  C07  C02  C03  180.00   0.0  0
 7RS  CONST_30  H7   C21  C22  C23  180.00   0.0  0
 7RS  CONST_31  C18  N19  C20  C21    0.00   0.0  0
 7RS  CONST_34  C25  C20  N19  C18  180.00   0.0  0
 7RS  CONST_37  O17  C16  N15  C03    0.00   0.0  0
 7RS  CONST_38  C18  C16  N15  C03  180.00   0.0  0
 7RS  Var_01    C13  N12  C11  C10   51.91  30.0  1
 7RS  Var_02    C13  C14  N09  C10  -56.07  30.0  1
 7RS  Var_03    N09  C14  C13  N12   54.58  30.0  1
 7RS  Var_04    N09  C10  C11  N12  -55.20  30.0  1
 7RS  Var_05    C14  C13  N12  C11  -51.73  30.0  1
 7RS  Var_06    C14  N09  C10  C11   56.50  30.0  1
 7RS  Var_07    C05  C08  N09  C10  170.55  30.0  3
 7RS  Var_08    N09  C08  C05  C04  122.41  30.0  1
 7RS  Var_09    H9   C01  C02  C03   64.54  30.0  2
 7RS  Var_10    C16  C18  N19  C20  170.46  30.0  1
 7RS  Var_11    N19  C18  C16  N15  165.17  30.0  3

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
 7RS  plan-1  C20  0.020
 7RS  plan-1  C21  0.020
 7RS  plan-1  C22  0.020
 7RS  plan-1  C24  0.020
 7RS  plan-1  N19  0.020
 7RS  plan-1  C23  0.020
 7RS  plan-1  C25  0.020
 7RS  plan-1  F26  0.020
 7RS  plan-1  F27  0.020
 7RS  plan-1  H7   0.020
 7RS  plan-1  H8   0.020
 7RS  plan-1  H26  0.020
 7RS  plan-2  C02  0.020
 7RS  plan-2  C03  0.020
 7RS  plan-2  C04  0.020
 7RS  plan-2  C05  0.020
 7RS  plan-2  C06  0.020
 7RS  plan-2  C07  0.020
 7RS  plan-2  H12  0.020
 7RS  plan-2  H13  0.020
 7RS  plan-2  H14  0.020
 7RS  plan-2  C08  0.020
 7RS  plan-2  N15  0.020
 7RS  plan-2  C01  0.020
 7RS  plan-3  C20  0.020
 7RS  plan-3  C18  0.020
 7RS  plan-3  N19  0.020
 7RS  plan-3  H25  0.020
 7RS  plan-4  C03  0.020
 7RS  plan-4  C16  0.020
 7RS  plan-4  O17  0.020
 7RS  plan-4  C18  0.020
 7RS  plan-4  H22  0.020
 7RS  plan-4  N15  0.020

