# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:26:57 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)C2=CNC(=O)C(=C2)CNc3cccc(c3)C(=O)N4CCOCC4
#
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
 L7Y  L7Y  5-(4-chlorophenyl)-3-({[3-(morpholine-4-carbonyl)phenyl]amino}methyl)pyridin-2(1H)-one  ligand  52  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L7Y
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
 L7Y  CL   CL  CL    0  -0.129  -8.5274  -2.5823   0.2410
 L7Y  C02  C   CR6   0  -0.057  -7.1355  -1.5706   0.0347
 L7Y  C03  C   CR16  0  -0.193  -6.7208  -1.2288  -1.2429
 L7Y  C04  C   CR16  0  -0.324  -5.6038  -0.4243  -1.3995
 L7Y  C05  C   CR6   0   0.108  -4.8989   0.0604  -0.2963
 L7Y  C06  C   CR16  0  -0.325  -5.3395  -0.3040   0.9768
 L7Y  C07  C   CR16  0  -0.193  -6.4490  -1.1162   1.1493
 L7Y  C08  C   CR6   0  -0.044  -3.7279   0.9347  -0.4652
 L7Y  C09  C   CR16  0   0.017  -3.6516   1.8399  -1.4808
 L7Y  N10  N   NR16  0  -0.660  -2.5756   2.6398  -1.6226
 L7Y  C11  C   CR6   0   0.536  -1.4686   2.6542  -0.7993
 L7Y  O12  O   O     0  -0.488  -0.5438   3.4321  -1.0093
 L7Y  C13  C   CR6   0  -0.155  -1.5350   1.7015   0.2869
 L7Y  C14  C   CH2   0  -0.328  -0.3666   1.6235   1.2195
 L7Y  N15  N   NH1   0  -0.683   0.7390   0.9490   0.5755
 L7Y  C16  C   CR6   0   0.391   1.9587   0.8111   1.1887
 L7Y  C17  C   CR16  0  -0.353   2.3326   1.5614   2.3112
 L7Y  C18  C   CR16  0  -0.236   3.5913   1.4007   2.8739
 L7Y  C19  C   CR16  0  -0.315   4.5007   0.4901   2.3616
 L7Y  C20  C   CR6   0  -0.058   4.1413  -0.2520   1.2382
 L7Y  C21  C   CR16  0  -0.355   2.8919  -0.0955   0.6612
 L7Y  C22  C   C     0   0.509   5.0790  -1.3054   0.7357
 L7Y  O23  O   O     0  -0.489   5.4647  -2.1775   1.5047
 L7Y  N24  N   NT    0  -0.456   5.4279  -1.2664  -0.5663
 L7Y  C25  C   CH2   0  -0.334   6.2538  -2.3112  -1.1502
 L7Y  C26  C   CH2   0  -0.183   7.6022  -1.7425  -1.5563
 L7Y  O27  O   O2    0  -0.482   7.4504  -0.6458  -2.4317
 L7Y  C28  C   CH2   0  -0.174   6.6809   0.3777  -1.8428
 L7Y  C29  C   CH2   0  -0.333   5.2973  -0.1106  -1.4397
 L7Y  C30  C   CR16  0  -0.194  -2.6197   0.8926   0.4248
 L7Y  H1   H   HCR6  0   0.282  -7.2522  -1.5934  -2.1115
 L7Y  H2   H   HCR6  0   0.265  -5.2715  -0.1910  -2.4031
 L7Y  H3   H   HCR6  0   0.266  -4.8268   0.0613   1.8576
 L7Y  H4   H   HCR6  0   0.282  -6.7778  -1.3800   2.1452
 L7Y  H6   H   HCR6  0   0.311  -4.4371   1.9874  -2.2082
 L7Y  H7   H   HCH2  0   0.250  -0.0610   2.6356   1.4919
 L7Y  H8   H   HCH2  0   0.240  -0.6706   1.1227   2.1471
 L7Y  H9   H   HNH1  0   0.381   0.4686   0.1692  -0.0039
 L7Y  H10  H   HCR6  0   0.268   1.6499   2.2704   2.7591
 L7Y  H11  H   HCR6  0   0.256   3.8565   1.9937   3.7401
 L7Y  H12  H   HCR6  0   0.251   5.4733   0.3650   2.8185
 L7Y  H13  H   HCR6  0   0.265   2.6191  -0.6827  -0.2095
 L7Y  H14  H   HCH2  0   0.270   6.3839  -3.1256  -0.4425
 L7Y  H15  H   HCH2  0   0.253   5.7364  -2.7067  -2.0296
 L7Y  H16  H   HCH2  0   0.211   8.1592  -1.4447  -0.6569
 L7Y  H17  H   HCH2  0   0.245   8.1856  -2.5014  -2.0793
 L7Y  H18  H   HCH2  0   0.207   7.1905   0.7811  -0.9564
 L7Y  H19  H   HCH2  0   0.247   6.5876   1.1813  -2.5743
 L7Y  H20  H   HCH2  0   0.251   4.7207  -0.3926  -2.3256
 L7Y  H21  H   HCH2  0   0.279   4.7671   0.6961  -0.9404
 L7Y  H22  H   HCR6  0   0.272  -2.6282   0.1766   1.2392
 L7Y  H5   H   HNR6  0   0.427  -2.5761   3.3013  -2.3879

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
 L7Y  O23  C22  double    1.225  0.020  1.225
 L7Y  N15  C14  single    1.446  0.020  1.446
 L7Y  N15  C16  single    1.372  0.020  1.372
 L7Y  C21  C16  aromatic  1.404  0.020  1.404
 L7Y  C21  C20  aromatic  1.385  0.020  1.385
 L7Y  C22  C20  single    1.497  0.020  1.497
 L7Y  C22  N24  single    1.349  0.020  1.349
 L7Y  C14  C13  single    1.497  0.020  1.497
 L7Y  C16  C17  aromatic  1.401  0.020  1.401
 L7Y  C25  N24  single    1.454  0.020  1.454
 L7Y  C25  C26  single    1.519  0.020  1.519
 L7Y  C20  C19  aromatic  1.394  0.020  1.394
 L7Y  N24  C29  single    1.455  0.020  1.455
 L7Y  C13  C30  double    1.360  0.020  1.360
 L7Y  C13  C11  single    1.446  0.020  1.446
 L7Y  C26  O27  single    1.411  0.020  1.411
 L7Y  C30  C08  single    1.422  0.020  1.422
 L7Y  C17  C18  aromatic  1.388  0.020  1.388
 L7Y  C03  C04  aromatic  1.385  0.020  1.385
 L7Y  C03  C02  aromatic  1.386  0.020  1.386
 L7Y  C04  C05  aromatic  1.396  0.020  1.396
 L7Y  C19  C18  aromatic  1.385  0.020  1.385
 L7Y  CL   C02  single    1.733  0.020  1.733
 L7Y  C11  O12  double    1.227  0.020  1.227
 L7Y  C11  N10  single    1.380  0.020  1.380
 L7Y  C02  C07  aromatic  1.386  0.020  1.386
 L7Y  C05  C08  single    1.471  0.020  1.471
 L7Y  C05  C06  aromatic  1.396  0.020  1.396
 L7Y  C08  C09  double    1.363  0.020  1.363
 L7Y  C29  C28  single    1.522  0.020  1.522
 L7Y  O27  C28  single    1.409  0.020  1.409
 L7Y  C07  C06  aromatic  1.386  0.020  1.386
 L7Y  N10  C09  single    1.348  0.020  1.348
 L7Y  C03  H1   single    0.930  0.020  1.080
 L7Y  C04  H2   single    0.930  0.020  1.080
 L7Y  C06  H3   single    0.930  0.020  1.080
 L7Y  C07  H4   single    0.930  0.020  1.080
 L7Y  C09  H6   single    0.930  0.020  1.080
 L7Y  C14  H7   single    0.970  0.020  1.090
 L7Y  C14  H8   single    0.970  0.020  1.090
 L7Y  N15  H9   single    0.890  0.020  1.040
 L7Y  C17  H10  single    0.930  0.020  1.080
 L7Y  C18  H11  single    0.930  0.020  1.080
 L7Y  C19  H12  single    0.930  0.020  1.080
 L7Y  C21  H13  single    0.930  0.020  1.080
 L7Y  C25  H14  single    0.970  0.020  1.090
 L7Y  C25  H15  single    0.970  0.020  1.090
 L7Y  C26  H16  single    0.970  0.020  1.090
 L7Y  C26  H17  single    0.970  0.020  1.090
 L7Y  C28  H18  single    0.970  0.020  1.090
 L7Y  C28  H19  single    0.970  0.020  1.090
 L7Y  C29  H20  single    0.970  0.020  1.090
 L7Y  C29  H21  single    0.970  0.020  1.090
 L7Y  C30  H22  single    0.930  0.020  1.080
 L7Y  N10  H5   single    0.860  0.020  1.020

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
 L7Y  C07  C02  C03  120.82  3.000
 L7Y  C07  C02  CL   119.58  3.000
 L7Y  C03  C02  CL   119.60  3.000
 L7Y  H1   C03  C04  120.08  3.000
 L7Y  H1   C03  C02  120.67  3.000
 L7Y  C04  C03  C02  119.25  3.000
 L7Y  H2   C04  C05  120.19  3.000
 L7Y  H2   C04  C03  118.51  3.000
 L7Y  C05  C04  C03  121.29  3.000
 L7Y  C08  C05  C06  120.74  3.000
 L7Y  C06  C05  C04  118.09  3.000
 L7Y  C08  C05  C04  121.17  3.000
 L7Y  H3   C06  C07  118.40  3.000
 L7Y  H3   C06  C05  120.30  3.000
 L7Y  C07  C06  C05  121.29  3.000
 L7Y  H4   C07  C06  120.06  3.000
 L7Y  H4   C07  C02  120.68  3.000
 L7Y  C06  C07  C02  119.25  3.000
 L7Y  C30  C08  C09  116.27  3.000
 L7Y  C09  C08  C05  121.66  3.000
 L7Y  C30  C08  C05  122.07  3.000
 L7Y  H6   C09  N10  115.36  3.000
 L7Y  H6   C09  C08  123.48  3.000
 L7Y  N10  C09  C08  121.14  3.000
 L7Y  H5   N10  C11  116.42  3.000
 L7Y  H5   N10  C09  117.85  3.000
 L7Y  C11  N10  C09  125.72  3.000
 L7Y  C13  C11  O12  125.52  3.000
 L7Y  O12  C11  N10  120.62  3.000
 L7Y  C13  C11  N10  113.85  3.000
 L7Y  C30  C13  C14  121.89  3.000
 L7Y  C30  C13  C11  120.30  3.000
 L7Y  C14  C13  C11  117.80  3.000
 L7Y  H8   C14  H7   106.85  3.000
 L7Y  H8   C14  N15  112.05  3.000
 L7Y  H7   C14  N15  109.23  3.000
 L7Y  H8   C14  C13  109.53  3.000
 L7Y  H7   C14  C13  109.00  3.000
 L7Y  N15  C14  C13  110.09  3.000
 L7Y  H9   N15  C16  114.67  3.000
 L7Y  H9   N15  C14  114.30  3.000
 L7Y  C16  N15  C14  121.83  3.000
 L7Y  C21  C16  C17  118.00  3.000
 L7Y  C17  C16  N15  122.78  3.000
 L7Y  C21  C16  N15  119.20  3.000
 L7Y  H10  C17  C18  118.71  3.000
 L7Y  H10  C17  C16  120.96  3.000
 L7Y  C18  C17  C16  120.32  3.000
 L7Y  H11  C18  C19  119.68  3.000
 L7Y  H11  C18  C17  118.88  3.000
 L7Y  C19  C18  C17  121.43  3.000
 L7Y  H12  C19  C20  120.71  3.000
 L7Y  H12  C19  C18  120.67  3.000
 L7Y  C20  C19  C18  118.61  3.000
 L7Y  C22  C20  C21  120.31  3.000
 L7Y  C22  C20  C19  118.93  3.000
 L7Y  C21  C20  C19  120.55  3.000
 L7Y  H13  C21  C20  119.99  3.000
 L7Y  H13  C21  C16  118.94  3.000
 L7Y  C20  C21  C16  121.07  3.000
 L7Y  N24  C22  O23  123.04  3.000
 L7Y  N24  C22  C20  117.75  3.000
 L7Y  O23  C22  C20  119.18  3.000
 L7Y  C29  N24  C25  112.38  3.000
 L7Y  C29  N24  C22  125.42  3.000
 L7Y  C25  N24  C22  120.92  3.000
 L7Y  H15  C25  H14  108.01  3.000
 L7Y  H15  C25  C26  109.89  3.000
 L7Y  H14  C25  C26  110.40  3.000
 L7Y  H15  C25  N24  108.29  3.000
 L7Y  H14  C25  N24  110.18  3.000
 L7Y  C26  C25  N24  110.03  3.000
 L7Y  H17  C26  H16  108.04  3.000
 L7Y  H17  C26  O27  107.50  3.000
 L7Y  H16  C26  O27  110.59  3.000
 L7Y  H17  C26  C25  110.03  3.000
 L7Y  H16  C26  C25  109.43  3.000
 L7Y  O27  C26  C25  111.18  3.000
 L7Y  C28  O27  C26  111.33  3.000
 L7Y  H19  C28  H18  108.06  3.000
 L7Y  H19  C28  C29  109.66  3.000
 L7Y  H18  C28  C29  109.01  3.000
 L7Y  H19  C28  O27  107.55  3.000
 L7Y  H18  C28  O27  110.51  3.000
 L7Y  C29  C28  O27  111.97  3.000
 L7Y  H21  C29  H20  107.83  3.000
 L7Y  H21  C29  C28  109.09  3.000
 L7Y  H20  C29  C28  110.33  3.000
 L7Y  H21  C29  N24  110.96  3.000
 L7Y  H20  C29  N24  109.20  3.000
 L7Y  C28  C29  N24  109.42  3.000
 L7Y  H22  C30  C13  118.37  3.000
 L7Y  H22  C30  C08  118.91  3.000
 L7Y  C13  C30  C08  122.71  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
 L7Y  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 L7Y  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 L7Y  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 L7Y  CONST_04  C06  C07  C02  C03     0.00   0.0  0
 L7Y  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 L7Y  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 L7Y  CONST_07  C19  C20  C21  C16     0.00   0.0  0
 L7Y  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 L7Y  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 L7Y  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 L7Y  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 L7Y  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 L7Y  CONST_13  C08  C05  C04  C03   180.00   0.0  0
 L7Y  CONST_14  C08  C05  C06  C07   180.00   0.0  0
 L7Y  CONST_15  C13  C11  N10  C09     0.00   0.0  0
 L7Y  CONST_16  C04  C03  C02  CL    180.00   0.0  0
 L7Y  CONST_17  C06  C07  C02  CL    180.00   0.0  0
 L7Y  CONST_18  C20  C21  C16  N15   180.00   0.0  0
 L7Y  CONST_19  C18  C17  C16  N15   180.00   0.0  0
 L7Y  CONST_20  C22  C20  C21  C16   180.00   0.0  0
 L7Y  CONST_21  C22  C20  C19  C18   180.00   0.0  0
 L7Y  CONST_22  C25  N24  C22  C20   180.00   0.0  0
 L7Y  CONST_24  O12  C11  N10  C09   180.00   0.0  0
 L7Y  CONST_25  H2   C04  C03  C02   180.00   0.0  0
 L7Y  CONST_26  H3   C06  C07  C02   180.00   0.0  0
 L7Y  CONST_27  H4   C07  C02  C03   180.00   0.0  0
 L7Y  CONST_28  H1   C03  C04  C05   180.00   0.0  0
 L7Y  CONST_29  H11  C18  C17  C16   180.00   0.0  0
 L7Y  CONST_30  H13  C21  C16  C17   180.00   0.0  0
 L7Y  CONST_31  H12  C19  C18  C17   180.00   0.0  0
 L7Y  CONST_32  H10  C17  C18  C19   180.00   0.0  0
 L7Y  CONST_33  H5   N10  C11  C13   180.00   0.0  0
 L7Y  CONST_34  C25  N24  C22  O23     0.00   0.0  0
 L7Y  CONST_36  C21  C16  N15  C14   180.00   0.0  0
 L7Y  Var_01    C30  C08  C05  C04  -146.27  30.0  2
 L7Y  Var_02    O27  C26  C25  N24   -55.67  30.0  1
 L7Y  Var_03    O27  C28  C29  N24    55.17  30.0  1
 L7Y  Var_04    C28  C29  N24  C25   -53.49  30.0  1
 L7Y  Var_05    C29  N24  C25  C26    54.14  30.0  1
 L7Y  Var_06    C29  C28  O27  C26   -58.45  30.0  1
 L7Y  Var_07    N24  C22  C20  C19  -127.45  30.0  2
 L7Y  Var_08    N15  C14  C13  C11   -74.47  30.0  2
 L7Y  Var_09    C16  N15  C14  C13   176.32  30.0  1

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
 L7Y  plan-1  CL   0.020
 L7Y  plan-1  C02  0.020
 L7Y  plan-1  C03  0.020
 L7Y  plan-1  C04  0.020
 L7Y  plan-1  C05  0.020
 L7Y  plan-1  C06  0.020
 L7Y  plan-1  C07  0.020
 L7Y  plan-1  C08  0.020
 L7Y  plan-1  H1   0.020
 L7Y  plan-1  H2   0.020
 L7Y  plan-1  H3   0.020
 L7Y  plan-1  H4   0.020
 L7Y  plan-2  C05  0.020
 L7Y  plan-2  C08  0.020
 L7Y  plan-2  C09  0.020
 L7Y  plan-2  N10  0.020
 L7Y  plan-2  C11  0.020
 L7Y  plan-2  O12  0.020
 L7Y  plan-2  C13  0.020
 L7Y  plan-2  C14  0.020
 L7Y  plan-2  C30  0.020
 L7Y  plan-2  H6   0.020
 L7Y  plan-2  H22  0.020
 L7Y  plan-2  H5   0.020
 L7Y  plan-3  N15  0.020
 L7Y  plan-3  C16  0.020
 L7Y  plan-3  C17  0.020
 L7Y  plan-3  C18  0.020
 L7Y  plan-3  C19  0.020
 L7Y  plan-3  C20  0.020
 L7Y  plan-3  C21  0.020
 L7Y  plan-3  C22  0.020
 L7Y  plan-3  H10  0.020
 L7Y  plan-3  H11  0.020
 L7Y  plan-3  H12  0.020
 L7Y  plan-3  H13  0.020
 L7Y  plan-4  C20  0.020
 L7Y  plan-4  C22  0.020
 L7Y  plan-4  O23  0.020
 L7Y  plan-4  N24  0.020
 L7Y  plan-4  C25  0.020
 L7Y  plan-4  C29  0.020
 L7Y  plan-5  C14  0.020
 L7Y  plan-5  N15  0.020
 L7Y  plan-5  C16  0.020
 L7Y  plan-5  H9   0.020

