# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:05:38 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-tert-butyl-3-quinoxalin-6-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)Nc1ccc2nccnc2c1
#
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
 Z0O  Z0O  1-tert-butyl-3-quinoxalin-6-ylurea  ligand  34  18  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z0O
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
 Z0O  O     O  O     0  -0.514   1.8498  -1.2876  -0.4948
 Z0O  C     C  C     0   0.740   1.9205  -0.1721  -0.0029
 Z0O  N3    N  NH1   0  -0.695   3.0675   0.5033   0.2105
 Z0O  C9    C  CT    0   0.104   4.4125   0.0627  -0.1765
 Z0O  C12   C  CH3   0  -0.644   4.5107  -0.1347  -1.6898
 Z0O  C11   C  CH3   0  -0.682   5.3541   1.1919   0.2410
 Z0O  C10   C  CH3   0  -0.639   4.8054  -1.2195   0.5590
 Z0O  N     N  NH1   0  -0.787   0.7965   0.5330   0.4010
 Z0O  C1    C  CR6   0   0.394  -0.5168   0.0971   0.2857
 Z0O  C8    C  CR16  0  -0.289  -0.8738  -1.2664   0.4748
 Z0O  C7    C  CR16  0  -0.300  -2.1787  -1.6593   0.3987
 Z0O  C6    C  CR66  0   0.212  -3.2043  -0.7235   0.1469
 Z0O  C3    C  CR66  0   0.250  -2.8545   0.6384  -0.0168
 Z0O  C2    C  CR16  0  -0.419  -1.5047   1.0268   0.0503
 Z0O  N2    N  N     0  -0.376  -4.4905  -1.1284   0.0753
 Z0O  C5    C  CR16  0  -0.126  -5.3872  -0.2093  -0.1548
 Z0O  C4    C  CR16  0  -0.116  -5.0396   1.1517  -0.3217
 Z0O  N1    N  N     0  -0.389  -3.8072   1.5716  -0.2541
 Z0O  H3    H  HNH1  0   0.398   3.0103   1.3955   0.6754
 Z0O  H     H  HNH1  0   0.409   0.9039   1.5282   0.5307
 Z0O  H121  H  HCH3  0   0.227   4.2288   0.7776  -2.2181
 Z0O  H122  H  HCH3  0   0.226   5.5378  -0.3789  -1.9648
 Z0O  H123  H  HCH3  0   0.239   3.8724  -0.9453  -2.0362
 Z0O  H111  H  HCH3  0   0.238   5.3201   1.3590   1.3195
 Z0O  H112  H  HCH3  0   0.243   6.3807   0.9434  -0.0265
 Z0O  H113  H  HCH3  0   0.238   5.0957   2.1276  -0.2593
 Z0O  H101  H  HCH3  0   0.238   4.1747  -2.0581   0.2699
 Z0O  H102  H  HCH3  0   0.224   5.8389  -1.4808   0.3251
 Z0O  H103  H  HCH3  0   0.226   4.7280  -1.0868   1.6393
 Z0O  H8    H  HCR6  0   0.279  -0.1137  -1.9988   0.6946
 Z0O  H2    H  HCR6  0   0.273  -1.2619   2.0729  -0.0950
 Z0O  H7    H  HCR6  0   0.270  -2.4467  -2.6974   0.5473
 Z0O  H5    H  HCR6  0   0.274  -6.4257  -0.5135  -0.2168
 Z0O  H4    H  HCR6  0   0.275  -5.8148   1.8850  -0.5135

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
 Z0O  O    C     double    1.221  0.020  1.221
 Z0O  C    N3    single    1.348  0.020  1.348
 Z0O  C    N     single    1.387  0.020  1.387
 Z0O  N3   C9    single    1.467  0.020  1.467
 Z0O  C9   C12   single    1.529  0.020  1.529
 Z0O  C9   C11   single    1.528  0.020  1.528
 Z0O  C9   C10   single    1.530  0.020  1.530
 Z0O  N    C1    single    1.389  0.020  1.389
 Z0O  C1   C8    aromatic  1.422  0.020  1.422
 Z0O  C1   C2    aromatic  1.377  0.020  1.377
 Z0O  C8   C7    aromatic  1.365  0.020  1.365
 Z0O  C7   C6    aromatic  1.411  0.020  1.411
 Z0O  C6   C3    aromatic  1.416  0.020  1.416
 Z0O  C6   N2    aromatic  1.350  0.020  1.350
 Z0O  C3   C2    aromatic  1.406  0.020  1.406
 Z0O  C3   N1    aromatic  1.354  0.020  1.354
 Z0O  N2   C5    aromatic  1.305  0.020  1.305
 Z0O  C5   C4    aromatic  1.415  0.020  1.415
 Z0O  C4   N1    aromatic  1.304  0.020  1.304
 Z0O  N3   H3    single    0.860  0.020  1.020
 Z0O  N    H     single    0.860  0.020  1.020
 Z0O  C12  H121  single    0.970  0.020  1.090
 Z0O  C12  H122  single    0.970  0.020  1.090
 Z0O  C12  H123  single    0.970  0.020  1.090
 Z0O  C11  H111  single    0.970  0.020  1.090
 Z0O  C11  H112  single    0.970  0.020  1.090
 Z0O  C11  H113  single    0.970  0.020  1.090
 Z0O  C10  H101  single    0.970  0.020  1.090
 Z0O  C10  H102  single    0.970  0.020  1.090
 Z0O  C10  H103  single    0.970  0.020  1.090
 Z0O  C8   H8    single    0.930  0.020  1.080
 Z0O  C2   H2    single    0.930  0.020  1.080
 Z0O  C7   H7    single    0.930  0.020  1.080
 Z0O  C5   H5    single    0.930  0.020  1.080
 Z0O  C4   H4    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
 Z0O  N     C    N3    112.87  3.000
 Z0O  N     C    O     122.33  3.000
 Z0O  N3    C    O     124.80  3.000
 Z0O  H3    N3   C9    116.08  3.000
 Z0O  H3    N3   C     117.93  3.000
 Z0O  C9    N3   C     126.00  3.000
 Z0O  C10   C9   C11   109.26  3.000
 Z0O  C10   C9   C12   110.56  3.000
 Z0O  C11   C9   C12   109.03  3.000
 Z0O  C10   C9   N3    111.12  3.000
 Z0O  C11   C9   N3    105.71  3.000
 Z0O  C12   C9   N3    111.02  3.000
 Z0O  H123  C12  H122  107.77  3.000
 Z0O  H123  C12  H121  108.48  3.000
 Z0O  H122  C12  H121  107.96  3.000
 Z0O  H123  C12  C9    111.93  3.000
 Z0O  H122  C12  C9    109.81  3.000
 Z0O  H121  C12  C9    110.77  3.000
 Z0O  H113  C11  H112  107.81  3.000
 Z0O  H113  C11  H111  108.30  3.000
 Z0O  H112  C11  H111  107.86  3.000
 Z0O  H113  C11  C9    111.23  3.000
 Z0O  H112  C11  C9    110.17  3.000
 Z0O  H111  C11  C9    111.33  3.000
 Z0O  H103  C10  H102  107.97  3.000
 Z0O  H103  C10  H101  108.39  3.000
 Z0O  H102  C10  H101  107.90  3.000
 Z0O  H103  C10  C9    110.85  3.000
 Z0O  H102  C10  C9    109.93  3.000
 Z0O  H101  C10  C9    111.67  3.000
 Z0O  H     N    C1    114.88  3.000
 Z0O  H     N    C     116.91  3.000
 Z0O  C1    N    C     125.64  3.000
 Z0O  C2    C1   C8    119.34  3.000
 Z0O  C2    C1   N     118.74  3.000
 Z0O  C8    C1   N     121.83  3.000
 Z0O  H8    C8   C7    119.33  3.000
 Z0O  H8    C8   C1    120.09  3.000
 Z0O  C7    C8   C1    120.57  3.000
 Z0O  H7    C7   C6    118.72  3.000
 Z0O  H7    C7   C8    120.34  3.000
 Z0O  C6    C7   C8    120.93  3.000
 Z0O  N2    C6   C3    121.18  3.000
 Z0O  N2    C6   C7    120.19  3.000
 Z0O  C3    C6   C7    118.63  3.000
 Z0O  N1    C3   C2    119.55  3.000
 Z0O  N1    C3   C6    120.61  3.000
 Z0O  C2    C3   C6    119.83  3.000
 Z0O  H2    C2   C3    118.38  3.000
 Z0O  H2    C2   C1    120.93  3.000
 Z0O  C3    C2   C1    120.69  3.000
 Z0O  C5    N2   C6    116.92  3.000
 Z0O  H5    C5   C4    119.91  3.000
 Z0O  H5    C5   N2    118.10  3.000
 Z0O  C4    C5   N2    121.99  3.000
 Z0O  H4    C4   N1    117.86  3.000
 Z0O  H4    C4   C5    119.73  3.000
 Z0O  N1    C4   C5    122.41  3.000
 Z0O  C4    N1   C3    116.88  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
 Z0O  CONST_01  C6    C7   C8  C1    0.00   0.0  0
 Z0O  CONST_02  C6    C3   C2  C1    0.00   0.0  0
 Z0O  CONST_03  N1    C3   C2  C1  180.00   0.0  0
 Z0O  CONST_04  C3    C2   C1  C8    0.00   0.0  0
 Z0O  CONST_05  C3    C6   C7  C8    0.00   0.0  0
 Z0O  CONST_06  N2    C6   C7  C8  180.00   0.0  0
 Z0O  CONST_07  C2    C1   C8  C7    0.00   0.0  0
 Z0O  CONST_08  C2    C3   C6  C7    0.00   0.0  0
 Z0O  CONST_09  N1    C3   C6  C7  180.00   0.0  0
 Z0O  CONST_10  C5    N2   C6  C7  180.00   0.0  0
 Z0O  CONST_11  C4    N1   C3  C6    0.00   0.0  0
 Z0O  CONST_12  C4    C5   N2  C6    0.00   0.0  0
 Z0O  CONST_13  C5    N2   C6  C3    0.00   0.0  0
 Z0O  CONST_14  C5    C4   N1  C3    0.00   0.0  0
 Z0O  CONST_15  N2    C6   C3  C2  180.00   0.0  0
 Z0O  CONST_16  C4    N1   C3  C2  180.00   0.0  0
 Z0O  CONST_17  N1    C3   C6  N2    0.00   0.0  0
 Z0O  CONST_18  N1    C4   C5  N2    0.00   0.0  0
 Z0O  CONST_19  C7    C8   C1  N   180.00   0.0  0
 Z0O  CONST_20  C3    C2   C1  N   180.00   0.0  0
 Z0O  CONST_21  H7    C7   C8  C1  180.00   0.0  0
 Z0O  CONST_22  H2    C2   C1  C8  180.00   0.0  0
 Z0O  CONST_23  H8    C8   C7  C6  180.00   0.0  0
 Z0O  CONST_24  H5    C5   N2  C6  180.00   0.0  0
 Z0O  CONST_25  H4    C4   N1  C3  180.00   0.0  0
 Z0O  CONST_29  C1    N    C   O     0.00   0.0  0
 Z0O  CONST_30  C1    N    C   N3  180.00   0.0  0
 Z0O  CONST_31  C9    N3   C   O     0.00   0.0  0
 Z0O  CONST_32  N     C    N3  C9  180.00   0.0  0
 Z0O  CONST_33  H3    N3   C   O   180.00   0.0  0
 Z0O  Var_01    C12   C9   N3  C    60.02  30.0  3
 Z0O  Var_02    H121  C12  C9  N3   56.06  30.0  3
 Z0O  Var_03    H111  C11  C9  N3   61.09  30.0  3
 Z0O  Var_04    H101  C10  C9  N3   65.25  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
 Z0O  plan-1  N   0.020
 Z0O  plan-1  C1  0.020
 Z0O  plan-1  C8  0.020
 Z0O  plan-1  C7  0.020
 Z0O  plan-1  C6  0.020
 Z0O  plan-1  C3  0.020
 Z0O  plan-1  C2  0.020
 Z0O  plan-1  N2  0.020
 Z0O  plan-1  C5  0.020
 Z0O  plan-1  C4  0.020
 Z0O  plan-1  N1  0.020
 Z0O  plan-1  H8  0.020
 Z0O  plan-1  H2  0.020
 Z0O  plan-1  H7  0.020
 Z0O  plan-1  H5  0.020
 Z0O  plan-1  H4  0.020
 Z0O  plan-2  O   0.020
 Z0O  plan-2  C   0.020
 Z0O  plan-2  N3  0.020
 Z0O  plan-2  C9  0.020
 Z0O  plan-2  N   0.020
 Z0O  plan-2  C1  0.020
 Z0O  plan-2  H3  0.020
 Z0O  plan-2  H   0.020

