# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:28:25 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-(5-chloro-2,4-dimethoxyphenyl)-3-(5-cyanopyrazin-2-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(NC(=O)Nc2cnc(cn2)C#N)cc1Cl
#
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
 A42  A42  1-(5-chloro-2,4-dimethoxyphenyl)-3-(5-cyanopyrazin-2-yl)urea  ligand  35  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A42
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
 A42  C1    C   CR6   0   0.135  -5.4578  -0.6793  -0.6971
 A42  N2    N   N     0  -0.360  -5.2757  -1.3303   0.4547
 A42  C3    C   CR16  0  -0.097  -4.0835  -1.2879   0.9836
 A42  C4    C   CR6   0   0.404  -3.0239  -0.5818   0.3681
 A42  N5    N   N     0  -0.294  -3.2177   0.0822  -0.7546
 A42  C6    C   CR16  0  -0.003  -4.4276   0.0307  -1.2893
 A42  C7    C   CSP   0   0.064  -6.7528  -0.7518  -1.2937
 A42  N8    N   NS    0  -0.188  -7.7967  -0.8033  -1.7753
 A42  N9    N   NH1   0  -0.755  -1.7976  -0.6068   0.9749
 A42  C10   C   C     0   0.766  -0.5907  -0.1095   0.4766
 A42  O11   O   O     0  -0.617  -0.4721   0.4335  -0.5873
 A42  N12   N   NH1   0  -0.694   0.4398  -0.2983   1.3602
 A42  C13   C   CR6   0   0.244   1.7711  -0.0408   0.9637
 A42  C14   C   CR16  0  -0.291   2.4314   1.0855   1.4204
 A42  C15   C   CR6   0  -0.119   3.7357   1.3474   1.0513
 A42  C16   C   CR6   0   0.396   4.4053   0.4740   0.1929
 A42  C17   C   CR16  0  -0.534   3.7459  -0.6610  -0.2744
 A42  C18   C   CR6   0   0.418   2.4338  -0.9243   0.1085
 A42  O19   O   O2    0  -0.511   1.7387  -2.0010  -0.2833
 A42  C20   C   CH3   0  -0.451   2.3033  -2.8689  -1.2373
 A42  O21   O   O2    0  -0.445   5.6630   0.7930  -0.1271
 A42  C22   C   CH3   0  -0.429   6.3707  -0.0255  -1.0261
 A42  CL1   CL  CL    0  -0.085   4.5416   2.7569   1.6284
 A42  H3    H   HCR6  0   0.304  -3.9349  -1.8212   1.9170
 A42  H6    H   HCR6  0   0.303  -4.5829   0.5708  -2.2150
 A42  HN9   H   HNH1  0   0.431  -1.7751  -1.1043   1.8497
 A42  HN12  H   HNH1  0   0.384   0.3114  -0.8884   2.1665
 A42  H14   H   HCR6  0   0.304   1.9075   1.7732   2.0700
 A42  H17   H   HCR6  0   0.313   4.2611  -1.3388  -0.9391
 A42  H201  H   HCH3  0   0.252   2.5488  -2.3491  -2.1674
 A42  H202  H   HCH3  0   0.229   3.2015  -3.3672  -0.8600
 A42  H203  H   HCH3  0   0.293   1.5529  -3.6261  -1.4499
 A42  H221  H   HCH3  0   0.211   5.8728  -0.0945  -1.9975
 A42  H222  H   HCH3  0   0.238   7.3420   0.4414  -1.1659
 A42  H223  H   HCH3  0   0.180   6.5235  -1.0350  -0.6323

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
 A42  C1   C6    aromatic  1.384  0.020  1.384
 A42  C1   N2    aromatic  1.335  0.020  1.335
 A42  C1   C7    single    1.428  0.020  1.428
 A42  N2   C3    aromatic  1.305  0.020  1.305
 A42  C3   C4    aromatic  1.414  0.020  1.414
 A42  C3   H3    single    0.930  0.020  1.080
 A42  C4   N9    single    1.368  0.020  1.368
 A42  C4   N5    aromatic  1.319  0.020  1.319
 A42  N5   C6    aromatic  1.324  0.020  1.324
 A42  C6   H6    single    0.930  0.020  1.080
 A42  C7   N8    triple    1.151  0.020  1.151
 A42  N9   C10   single    1.397  0.020  1.397
 A42  N9   HN9   single    0.860  0.020  1.020
 A42  C10  O11   double    1.200  0.020  1.200
 A42  C10  N12   single    1.371  0.020  1.371
 A42  N12  C13   single    1.413  0.020  1.413
 A42  N12  HN12  single    0.860  0.020  1.020
 A42  C13  C14   aromatic  1.383  0.020  1.383
 A42  C13  C18   aromatic  1.397  0.020  1.397
 A42  C14  C15   aromatic  1.381  0.020  1.381
 A42  C14  H14   single    0.930  0.020  1.080
 A42  C15  CL1   single    1.723  0.020  1.723
 A42  C15  C16   aromatic  1.396  0.020  1.396
 A42  C16  O21   single    1.336  0.020  1.336
 A42  C16  C17   aromatic  1.393  0.020  1.393
 A42  C17  C18   aromatic  1.392  0.020  1.392
 A42  C17  H17   single    0.930  0.020  1.080
 A42  C18  O19   single    1.340  0.020  1.340
 A42  O19  C20   single    1.408  0.020  1.408
 A42  C20  H201  single    0.970  0.020  1.090
 A42  C20  H202  single    0.970  0.020  1.090
 A42  C20  H203  single    0.970  0.020  1.090
 A42  O21  C22   single    1.407  0.020  1.407
 A42  C22  H221  single    0.970  0.020  1.090
 A42  C22  H222  single    0.970  0.020  1.090
 A42  C22  H223  single    0.970  0.020  1.090

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
 A42  C7    C1   C6    121.49  3.000
 A42  C7    C1   N2    117.34  3.000
 A42  C6    C1   N2    121.17  3.000
 A42  C3    N2   C1    117.27  3.000
 A42  H3    C3   C4    121.14  3.000
 A42  H3    C3   N2    117.24  3.000
 A42  C4    C3   N2    121.62  3.000
 A42  N9    C4   N5    121.22  3.000
 A42  N5    C4   C3    120.79  3.000
 A42  N9    C4   C3    117.99  3.000
 A42  C6    N5   C4    117.30  3.000
 A42  H6    C6   N5    117.19  3.000
 A42  H6    C6   C1    120.98  3.000
 A42  N5    C6   C1    121.82  3.000
 A42  N8    C7   C1    180.00  3.000
 A42  HN9   N9   C10   117.81  3.000
 A42  HN9   N9   C4    114.48  3.000
 A42  C10   N9   C4    127.55  3.000
 A42  N12   C10  O11   124.02  3.000
 A42  N12   C10  N9    111.75  3.000
 A42  O11   C10  N9    124.23  3.000
 A42  HN12  N12  C13   116.84  3.000
 A42  HN12  N12  C10   120.05  3.000
 A42  C13   N12  C10   120.17  3.000
 A42  C18   C13  C14   119.38  3.000
 A42  C18   C13  N12   120.24  3.000
 A42  C14   C13  N12   120.38  3.000
 A42  H14   C14  C15   119.84  3.000
 A42  H14   C14  C13   119.00  3.000
 A42  C15   C14  C13   121.15  3.000
 A42  CL1   C15  C16   119.57  3.000
 A42  C16   C15  C14   119.93  3.000
 A42  CL1   C15  C14   120.50  3.000
 A42  O21   C16  C17   124.02  3.000
 A42  C17   C16  C15   119.27  3.000
 A42  O21   C16  C15   116.71  3.000
 A42  H17   C17  C18   120.01  3.000
 A42  H17   C17  C16   119.46  3.000
 A42  C18   C17  C16   120.52  3.000
 A42  O19   C18  C17   124.09  3.000
 A42  O19   C18  C13   116.17  3.000
 A42  C17   C18  C13   119.74  3.000
 A42  C20   O19  C18   119.03  3.000
 A42  H203  C20  H202  108.48  3.000
 A42  H203  C20  H201  108.64  3.000
 A42  H202  C20  H201  108.99  3.000
 A42  H203  C20  O19   106.56  3.000
 A42  H202  C20  O19   112.11  3.000
 A42  H201  C20  O19   111.92  3.000
 A42  C22   O21  C16   119.18  3.000
 A42  H223  C22  H222  108.54  3.000
 A42  H223  C22  H221  108.96  3.000
 A42  H222  C22  H221  108.64  3.000
 A42  H223  C22  O21   112.15  3.000
 A42  H222  C22  O21   106.37  3.000
 A42  H221  C22  O21   112.04  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
 A42  CONST_01  C4    N5   C6   C1     0.00   0.0  0
 A42  CONST_02  C4    C3   N2   C1     0.00   0.0  0
 A42  CONST_03  N5    C6   C1   N2     0.00   0.0  0
 A42  CONST_04  N5    C4   C3   N2     0.00   0.0  0
 A42  CONST_05  C6    C1   N2   C3     0.00   0.0  0
 A42  CONST_06  C6    N5   C4   C3     0.00   0.0  0
 A42  CONST_07  C16   C15  C14  C13    0.00   0.0  0
 A42  CONST_08  C16   C17  C18  C13    0.00   0.0  0
 A42  CONST_09  C17   C18  C13  C14    0.00   0.0  0
 A42  CONST_10  C17   C16  C15  C14    0.00   0.0  0
 A42  CONST_11  C18   C13  C14  C15    0.00   0.0  0
 A42  CONST_12  C18   C17  C16  C15    0.00   0.0  0
 A42  CONST_13  N9    C4   C3   N2   180.00   0.0  0
 A42  CONST_14  C7    C1   N2   C3   180.00   0.0  0
 A42  CONST_15  C7    C1   C6   N5   180.00   0.0  0
 A42  CONST_16  N9    C4   N5   C6   180.00   0.0  0
 A42  CONST_17  C15   C14  C13  N12  180.00   0.0  0
 A42  CONST_18  C17   C18  C13  N12  180.00   0.0  0
 A42  CONST_19  CL1   C15  C14  C13  180.00   0.0  0
 A42  CONST_20  O19   C18  C13  C14  180.00   0.0  0
 A42  CONST_21  O21   C16  C15  C14  180.00   0.0  0
 A42  CONST_22  O19   C18  C17  C16  180.00   0.0  0
 A42  CONST_23  CL1   C15  C16  C17  180.00   0.0  0
 A42  CONST_24  O21   C16  C17  C18  180.00   0.0  0
 A42  CONST_25  H3    C3   N2   C1   180.00   0.0  0
 A42  CONST_26  H6    C6   C1   N2   180.00   0.0  0
 A42  CONST_27  H17   C17  C18  C13  180.00   0.0  0
 A42  CONST_28  H14   C14  C15  C16  180.00   0.0  0
 A42  CONST_29  C10   N9   C4   C3   180.00   0.0  0
 A42  CONST_30  C10   N9   C4   N5     0.00   0.0  0
 A42  CONST_33  HN9   N9   C4   C3     0.00   0.0  0
 A42  CONST_35  O11   C10  N9   C4     0.00   0.0  0
 A42  CONST_36  C13   N12  C10  O11    0.00   0.0  0
 A42  CONST_37  N12   C10  N9   C4   180.00   0.0  0
 A42  CONST_38  C13   N12  C10  N9   180.00   0.0  0
 A42  Var_01    H221  C22  O21  C16   59.25  30.0  3
 A42  Var_02    H201  C20  O19  C18  -57.91  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
 A42  plan-1  C1    0.020
 A42  plan-1  N2    0.020
 A42  plan-1  C3    0.020
 A42  plan-1  C4    0.020
 A42  plan-1  N5    0.020
 A42  plan-1  C6    0.020
 A42  plan-1  C7    0.020
 A42  plan-1  N8    0.020
 A42  plan-1  N9    0.020
 A42  plan-1  H3    0.020
 A42  plan-1  H6    0.020
 A42  plan-2  N12   0.020
 A42  plan-2  C13   0.020
 A42  plan-2  C14   0.020
 A42  plan-2  C15   0.020
 A42  plan-2  C16   0.020
 A42  plan-2  C17   0.020
 A42  plan-2  C18   0.020
 A42  plan-2  O19   0.020
 A42  plan-2  O21   0.020
 A42  plan-2  CL1   0.020
 A42  plan-2  H14   0.020
 A42  plan-2  H17   0.020
 A42  plan-3  C4    0.020
 A42  plan-3  N9    0.020
 A42  plan-3  C10   0.020
 A42  plan-3  O11   0.020
 A42  plan-3  N12   0.020
 A42  plan-3  C13   0.020
 A42  plan-3  HN9   0.020
 A42  plan-3  HN12  0.020

