# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 08:19:10 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Oc2cc(Cl)cc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
#
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
 494  494  (2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile  ligand  45  30  .  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_494
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
 494  C00  C   CR16  0  -0.338   1.2642   3.4317   0.3547
 494  C01  C   CR6   0  -0.029   0.8451   4.5162  -0.4054
 494  C02  C   CR16  0  -0.244   0.1302   4.3582  -1.5767
 494  C03  C   CR16  0  -0.318  -0.1704   3.0686  -1.9982
 494  C04  C   CR6   0   0.229   0.2451   1.9755  -1.2671
 494  C05  C   CR6   0   0.378   0.9598   2.1450  -0.0722
 494  CL7  CL  CL    0  -0.120   1.2414   6.1111   0.1427
 494  O0A  O   O2    0  -0.498   0.0331   0.7197  -1.7649
 494  O0B  O   O2    0  -0.452   1.2893   1.0248   0.5823
 494  C0C  C   CR6   0   0.413  -0.7724  -0.1529  -1.1077
 494  C0D  C   CR16  0  -0.312  -0.6625  -1.4810  -1.4951
 494  C0E  C   CR6   0   0.005  -1.4710  -2.4175  -0.8755
 494  C0F  C   CR16  0  -0.285  -2.3838  -2.0744   0.1004
 494  C0G  C   CR6   0   0.156  -2.4911  -0.7343   0.4722
 494  C0H  C   CR16  0  -0.386  -1.6831   0.2267  -0.1337
 494  CL0  CL  CL    0  -0.111  -1.2988  -4.0822  -1.3232
 494  C0M  C   C1    0  -0.207  -3.4302  -0.2804   1.4921
 494  C0O  C   CH2   0  -0.209   2.1951   1.0986   1.6656
 494  C0P  C   CH2   0  -0.355   2.3437  -0.2965   2.2380
 494  N0S  N   NR6   0  -0.524   2.6422  -1.2879   1.2132
 494  C0V  C   CR6   0   0.744   1.7038  -2.2556   0.9138
 494  N0W  N   NR16  0  -0.734   2.0444  -3.0676  -0.1398
 494  C0X  C   CR6   0   0.564   3.2004  -3.0441  -0.9039
 494  C0Y  C   CR16  0  -0.509   4.1353  -2.0256  -0.4946
 494  C0Z  C   CR16  0   0.105   3.8145  -1.2093   0.5234
 494  O10  O   O     0  -0.462   0.6694  -2.3997   1.5264
 494  O12  O   O     0  -0.466   3.3543  -3.8348  -1.8168
 494  C15  C   C1    0  -0.348  -4.3089  -1.0491   2.1498
 494  C17  C   CSP   0   0.089  -5.1746  -0.4947   3.1280
 494  N19  N   NS    0  -0.265  -5.8868  -0.0623   3.9259
 494  H1   H   HCR6  0   0.307   1.8243   3.6024   1.2634
 494  H2   H   HCR6  0   0.285  -0.1883   5.2120  -2.1574
 494  H3   H   HCR6  0   0.286  -0.7197   2.9128  -2.9176
 494  H4   H   HCR6  0   0.299   0.0466  -1.7678  -2.2601
 494  H5   H   HCR6  0   0.281  -2.9908  -2.8383   0.5660
 494  H6   H   HCR6  0   0.290  -1.7826   1.2645   0.1595
 494  H7   H   H     0   0.295  -3.3966   0.7786   1.7225
 494  H8   H   HCH2  0   0.246   3.1553   1.5011   1.3252
 494  H9   H   HCH2  0   0.266   1.8251   1.7496   2.4638
 494  H10  H   HCH2  0   0.292   3.1409  -0.2870   2.9820
 494  H11  H   HCH2  0   0.294   1.4294  -0.5986   2.7387
 494  H12  H   HNR6  0   0.407   1.3603  -3.7792  -0.3666
 494  H13  H   HCR6  0   0.293   5.0816  -1.9269  -1.0030
 494  H14  H   HCR6  0   0.323   4.4971  -0.4383   0.8543
 494  H15  H   H     0   0.324  -4.4134  -2.1131   1.9786

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
 494  CL7  C01  single    1.732  0.020  1.732
 494  C01  C02  aromatic  1.381  0.020  1.381
 494  C01  C00  aromatic  1.389  0.020  1.389
 494  C02  C03  aromatic  1.390  0.020  1.390
 494  C00  C05  aromatic  1.389  0.020  1.389
 494  O10  C0V  double    1.211  0.020  1.211
 494  C03  C04  aromatic  1.379  0.020  1.379
 494  C05  C04  aromatic  1.403  0.020  1.403
 494  C05  O0B  single    1.339  0.020  1.339
 494  N0W  C0V  single    1.373  0.020  1.373
 494  N0W  C0X  single    1.386  0.020  1.386
 494  C0V  N0S  single    1.381  0.020  1.381
 494  C04  O0A  single    1.367  0.020  1.367
 494  O0B  C0O  single    1.414  0.020  1.414
 494  O12  C0X  double    1.217  0.020  1.217
 494  C0X  C0Y  single    1.442  0.020  1.442
 494  N0S  C0P  single    1.457  0.020  1.457
 494  N0S  C0Z  single    1.363  0.020  1.363
 494  O0A  C0C  single    1.357  0.020  1.357
 494  C0O  C0P  single    1.515  0.020  1.515
 494  C0Y  C0Z  double    1.344  0.020  1.344
 494  C0D  C0C  aromatic  1.388  0.020  1.388
 494  C0D  C0E  aromatic  1.384  0.020  1.384
 494  C0C  C0H  aromatic  1.387  0.020  1.387
 494  CL0  C0E  single    1.732  0.020  1.732
 494  C0E  C0F  aromatic  1.380  0.020  1.380
 494  C0H  C0G  aromatic  1.394  0.020  1.394
 494  C0F  C0G  aromatic  1.395  0.020  1.395
 494  C0G  C0M  single    1.459  0.020  1.459
 494  C0M  C15  double    1.340  0.020  1.340
 494  C15  C17  single    1.419  0.020  1.419
 494  C17  N19  triple    1.154  0.020  1.154
 494  C00  H1   single    0.930  0.020  1.080
 494  C02  H2   single    0.930  0.020  1.080
 494  C03  H3   single    0.930  0.020  1.080
 494  C0D  H4   single    0.930  0.020  1.080
 494  C0F  H5   single    0.930  0.020  1.080
 494  C0H  H6   single    0.930  0.020  1.080
 494  C0M  H7   single    0.930  0.020  1.080
 494  C0O  H8   single    0.970  0.020  1.090
 494  C0O  H9   single    0.970  0.020  1.090
 494  C0P  H10  single    0.970  0.020  1.090
 494  C0P  H11  single    0.970  0.020  1.090
 494  N0W  H12  single    0.860  0.020  1.020
 494  C0Y  H13  single    0.930  0.020  1.080
 494  C0Z  H14  single    0.930  0.020  1.080
 494  C15  H15  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
 494  H1   C00  C05  121.20  3.000
 494  H1   C00  C01  119.53  3.000
 494  C05  C00  C01  119.26  3.000
 494  CL7  C01  C02  119.47  3.000
 494  C02  C01  C00  122.06  3.000
 494  CL7  C01  C00  118.47  3.000
 494  H2   C02  C03  120.43  3.000
 494  H2   C02  C01  121.19  3.000
 494  C03  C02  C01  118.38  3.000
 494  H3   C03  C04  119.28  3.000
 494  H3   C03  C02  120.07  3.000
 494  C04  C03  C02  120.63  3.000
 494  O0A  C04  C05  120.00  3.000
 494  O0A  C04  C03  119.22  3.000
 494  C05  C04  C03  120.62  3.000
 494  O0B  C05  C04  116.16  3.000
 494  O0B  C05  C00  124.81  3.000
 494  C04  C05  C00  119.03  3.000
 494  C0C  O0A  C04  120.41  3.000
 494  C0O  O0B  C05  119.25  3.000
 494  C0H  C0C  C0D  120.67  3.000
 494  C0H  C0C  O0A  123.64  3.000
 494  C0D  C0C  O0A  115.67  3.000
 494  H4   C0D  C0E  121.34  3.000
 494  H4   C0D  C0C  120.20  3.000
 494  C0E  C0D  C0C  118.46  3.000
 494  CL0  C0E  C0F  119.18  3.000
 494  C0F  C0E  C0D  122.34  3.000
 494  CL0  C0E  C0D  118.46  3.000
 494  H5   C0F  C0G  121.39  3.000
 494  H5   C0F  C0E  120.03  3.000
 494  C0G  C0F  C0E  118.58  3.000
 494  C0M  C0G  C0H  117.55  3.000
 494  C0M  C0G  C0F  122.33  3.000
 494  C0H  C0G  C0F  120.12  3.000
 494  H6   C0H  C0G  119.32  3.000
 494  H6   C0H  C0C  120.86  3.000
 494  C0G  C0H  C0C  119.82  3.000
 494  H7   C0M  C15  118.45  3.000
 494  H7   C0M  C0G  115.62  3.000
 494  C15  C0M  C0G  125.93  3.000
 494  H9   C0O  H8   107.73  3.000
 494  H9   C0O  C0P  107.78  3.000
 494  H8   C0O  C0P  111.70  3.000
 494  H9   C0O  O0B  111.92  3.000
 494  H8   C0O  O0B  110.03  3.000
 494  C0P  C0O  O0B  107.71  3.000
 494  H11  C0P  H10  107.67  3.000
 494  H11  C0P  N0S  107.92  3.000
 494  H10  C0P  N0S  109.64  3.000
 494  H11  C0P  C0O  110.36  3.000
 494  H10  C0P  C0O  108.75  3.000
 494  N0S  C0P  C0O  112.39  3.000
 494  C0Z  N0S  C0V  121.02  3.000
 494  C0Z  N0S  C0P  119.55  3.000
 494  C0V  N0S  C0P  119.36  3.000
 494  O10  C0V  N0W  121.99  3.000
 494  N0W  C0V  N0S  114.35  3.000
 494  O10  C0V  N0S  123.66  3.000
 494  H12  N0W  C0X  116.86  3.000
 494  H12  N0W  C0V  114.82  3.000
 494  C0X  N0W  C0V  128.31  3.000
 494  O12  C0X  C0Y  126.13  3.000
 494  C0Y  C0X  N0W  113.34  3.000
 494  O12  C0X  N0W  120.52  3.000
 494  H13  C0Y  C0Z  120.73  3.000
 494  H13  C0Y  C0X  119.97  3.000
 494  C0Z  C0Y  C0X  119.30  3.000
 494  H14  C0Z  C0Y  120.94  3.000
 494  H14  C0Z  N0S  115.41  3.000
 494  C0Y  C0Z  N0S  123.64  3.000
 494  H15  C15  C17  115.72  3.000
 494  H15  C15  C0M  123.33  3.000
 494  C17  C15  C0M  120.95  3.000
 494  N19  C17  C15  180.00  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
 494  CONST_01  C03  C02  C01  C00     0.00   0.0  0
 494  CONST_02  C03  C04  C05  C00     0.00   0.0  0
 494  CONST_03  C04  C03  C02  C01     0.00   0.0  0
 494  CONST_04  C04  C05  C00  C01     0.00   0.0  0
 494  CONST_05  C05  C00  C01  C02     0.00   0.0  0
 494  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 494  CONST_07  C0F  C0E  C0D  C0C     0.00   0.0  0
 494  CONST_08  C0F  C0G  C0H  C0C     0.00   0.0  0
 494  CONST_09  C0G  C0H  C0C  C0D     0.00   0.0  0
 494  CONST_10  C0G  C0F  C0E  C0D     0.00   0.0  0
 494  CONST_11  C0H  C0C  C0D  C0E     0.00   0.0  0
 494  CONST_12  C0H  C0G  C0F  C0E     0.00   0.0  0
 494  CONST_13  C0X  N0W  C0V  N0S     0.00   0.0  0
 494  CONST_14  C0Y  C0X  N0W  C0V     0.00   0.0  0
 494  CONST_15  C0Z  N0S  C0V  N0W     0.00   0.0  0
 494  CONST_16  O0A  C04  C05  C00   180.00   0.0  0
 494  CONST_17  O0B  C05  C00  C01   180.00   0.0  0
 494  CONST_18  O0A  C04  C03  C02   180.00   0.0  0
 494  CONST_19  CL7  C01  C02  C03   180.00   0.0  0
 494  CONST_20  O0B  C05  C04  C03   180.00   0.0  0
 494  CONST_21  CL7  C01  C00  C05   180.00   0.0  0
 494  CONST_22  C0E  C0D  C0C  O0A   180.00   0.0  0
 494  CONST_23  C0G  C0H  C0C  O0A   180.00   0.0  0
 494  CONST_24  CL0  C0E  C0D  C0C   180.00   0.0  0
 494  CONST_25  C0M  C0G  C0H  C0C   180.00   0.0  0
 494  CONST_26  C0M  C0G  C0F  C0E   180.00   0.0  0
 494  CONST_27  CL0  C0E  C0F  C0G   180.00   0.0  0
 494  CONST_28  N0W  C0V  N0S  C0P   180.00   0.0  0
 494  CONST_29  O12  C0X  N0W  C0V   180.00   0.0  0
 494  CONST_30  O10  C0V  N0W  C0X   180.00   0.0  0
 494  CONST_31  O10  C0V  N0S  C0Z   180.00   0.0  0
 494  CONST_32  H2   C02  C01  C00   180.00   0.0  0
 494  CONST_33  H3   C03  C02  C01   180.00   0.0  0
 494  CONST_34  H1   C00  C01  C02   180.00   0.0  0
 494  CONST_35  H6   C0H  C0C  C0D   180.00   0.0  0
 494  CONST_36  H5   C0F  C0E  C0D   180.00   0.0  0
 494  CONST_37  H4   C0D  C0E  C0F   180.00   0.0  0
 494  CONST_38  H12  N0W  C0V  N0S   180.00   0.0  0
 494  CONST_39  O10  C0V  N0S  C0P     0.00   0.0  0
 494  CONST_40  C17  C15  C0M  C0G   180.00   0.0  0
 494  CONST_41  H15  C15  C0M  C0G     0.00   0.0  0
 494  CONST_42  H7   C0M  C15  C17     0.00   0.0  0
 494  Var_01    C0D  C0C  O0A  C04  -164.48  30.0  2
 494  Var_02    C15  C0M  C0G  C0F    -2.24  30.0  2
 494  Var_03    C0V  N0S  C0P  C0O  -112.62  30.0  2
 494  Var_04    C0P  C0O  O0B  C05   178.12  30.0  3
 494  Var_05    N0S  C0P  C0O  O0B    50.60  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
 494  plan-1  C00  0.020
 494  plan-1  C01  0.020
 494  plan-1  C02  0.020
 494  plan-1  C03  0.020
 494  plan-1  C04  0.020
 494  plan-1  C05  0.020
 494  plan-1  CL7  0.020
 494  plan-1  O0A  0.020
 494  plan-1  O0B  0.020
 494  plan-1  H1   0.020
 494  plan-1  H2   0.020
 494  plan-1  H3   0.020
 494  plan-2  O0A  0.020
 494  plan-2  C0C  0.020
 494  plan-2  C0D  0.020
 494  plan-2  C0E  0.020
 494  plan-2  C0F  0.020
 494  plan-2  C0G  0.020
 494  plan-2  C0H  0.020
 494  plan-2  CL0  0.020
 494  plan-2  C0M  0.020
 494  plan-2  H4   0.020
 494  plan-2  H5   0.020
 494  plan-2  H6   0.020
 494  plan-3  C0P  0.020
 494  plan-3  N0S  0.020
 494  plan-3  C0V  0.020
 494  plan-3  N0W  0.020
 494  plan-3  C0X  0.020
 494  plan-3  C0Y  0.020
 494  plan-3  C0Z  0.020
 494  plan-3  O10  0.020
 494  plan-3  O12  0.020
 494  plan-3  H12  0.020
 494  plan-3  H13  0.020
 494  plan-3  H14  0.020
 494  plan-4  C0G  0.020
 494  plan-4  C0M  0.020
 494  plan-4  C15  0.020
 494  plan-4  C17  0.020
 494  plan-4  H7   0.020
 494  plan-4  H15  0.020

