# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:48:59 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-(5-methyl-1,2-oxazol-3-yl)-N'-[3-(4-phenylpiperazin-1-yl)propyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(NC(=O)NCCCN2CCN(CC2)c3ccccc3)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
 N64  N64  N-(5-methyl-1,2-oxazol-3-yl)-N'-[3-(4-phenylpiperazin-1-yl)propyl]urea  ligand  50  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N64
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
 N64  N1   N  NH1   0  -0.690   2.4840   0.7432   0.1106
 N64  N3   N  NT    0  -0.512  -4.7766   0.3783   0.1718
 N64  C4   C  C     0   0.752   3.6489   0.2043  -0.2932
 N64  C5   C  CH2   0  -0.228   1.2427   0.4839  -0.5884
 N64  C6   C  CH2   0  -0.491   0.1078   1.2716   0.0458
 N64  C7   C  CH2   0  -0.270  -1.2100   1.0034  -0.6696
 N64  C8   C  CH2   0  -0.332  -2.7968   1.4513   1.1399
 N64  C10  C  CH2   0  -0.311  -4.3045   0.7609  -1.1547
 N64  C13  C  CR16  0  -0.335  -6.9548  -0.3768  -0.5963
 N64  C15  C  CR16  0  -0.292  -8.0383  -2.2926   0.3970
 N64  C17  C  CR16  0  -0.361  -5.8506  -1.5929   1.1487
 N64  N    N  NH1   0  -0.775   4.7298   0.5563   0.4902
 N64  O    O  O     0  -0.517   3.7491  -0.5303  -1.2636
 N64  C1   C  CR5   0   0.439   7.9105  -0.6584  -0.4384
 N64  C11  C  CH2   0  -0.331  -3.4042   1.9864  -1.0720
 N64  C12  C  CR6   0   0.368  -5.8344  -0.5271   0.2383
 N64  C14  C  CR16  0  -0.244  -8.0300  -1.2444  -0.5167
 N64  C16  C  CR16  0  -0.242  -6.9402  -2.4517   1.2267
 N64  C2   C  CR15  0  -0.523   6.5978  -0.6095  -0.7678
 N64  C3   C  CR5   0   0.495   6.0266   0.1601   0.2826
 N64  C9   C  CH2   0  -0.317  -3.6927   0.2165   1.1236
 N64  N2   N  NT    0  -0.412  -2.2861   1.8384  -0.1613
 N64  N4   N  N     0  -0.234   6.9316   0.5281   1.1508
 N64  O1   O  O     0  -0.342   8.1148   0.0131   0.6951
 N64  H1   H  HNH1  0   0.403   2.4600   1.3602   0.9062
 N64  H2   H  HCH2  0   0.232   1.3402   0.7642  -1.6409
 N64  H3   H  HCH2  0   0.232   1.0131  -0.5855  -0.5640
 N64  H4   H  HCH2  0   0.237   0.0306   1.0048   1.1039
 N64  H5   H  HCH2  0   0.236   0.3239   2.3421  -0.0008
 N64  H6   H  HCH2  0   0.233  -1.0823   1.2435  -1.7288
 N64  H7   H  HCH2  0   0.204  -1.4277  -0.0749  -0.6286
 N64  H8   H  HCH2  0   0.236  -3.3734   2.2904   1.5420
 N64  H9   H  HCH2  0   0.246  -1.9738   1.2797   1.8351
 N64  H10  H  HCH2  0   0.218  -3.7691  -0.0744  -1.6300
 N64  H11  H  HCH2  0   0.255  -5.1443   1.0070  -1.8012
 N64  H12  H  HCR6  0   0.259  -7.0044   0.4401  -1.3034
 N64  H13  H  HCR6  0   0.247  -8.8835  -2.9647   0.4602
 N64  H14  H  HCR6  0   0.265  -5.0117  -1.7763   1.8050
 N64  H15  H  HNH1  0   0.411   4.5778   1.1329   1.3050
 N64  H16  H  HCH3  0   0.269   9.8720  -0.5792  -1.2742
 N64  H17  H  HCH3  0   0.270   9.4885  -2.0910  -0.4544
 N64  H18  H  HCH3  0   0.267   8.7794  -1.7422  -2.0319
 N64  H19  H  HCH2  0   0.244  -3.0334   2.2265  -2.0705
 N64  H20  H  HCH2  0   0.235  -4.0059   2.8396  -0.7410
 N64  H21  H  HCR6  0   0.250  -8.8776  -1.0894  -1.1726
 N64  H22  H  HCR6  0   0.251  -6.9148  -3.2628   1.9436
 N64  H23  H  HCR5  0   0.287   6.1208  -1.0499  -1.6222
 N64  H24  H  HCH2  0   0.252  -4.1062   0.0994   2.1267
 N64  H25  H  HCH2  0   0.213  -3.1001  -0.6877   0.9168
 N64  C    C  CH3   0  -0.747   9.0771  -1.3010  -1.0841

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
 N64  C    C1   single    1.480  0.020  1.480
 N64  O1   C1   aromatic  1.333  0.020  1.333
 N64  O1   N4   aromatic  1.368  0.020  1.368
 N64  C1   C2   aromatic  1.354  0.020  1.354
 N64  N4   C3   aromatic  1.307  0.020  1.307
 N64  C2   C3   aromatic  1.422  0.020  1.422
 N64  C3   N    single    1.372  0.020  1.372
 N64  N    C4   single    1.381  0.020  1.381
 N64  O    C4   double    1.221  0.020  1.221
 N64  C4   N1   single    1.346  0.020  1.346
 N64  N1   C5   single    1.448  0.020  1.448
 N64  C6   C5   single    1.520  0.020  1.520
 N64  C6   C7   single    1.523  0.020  1.523
 N64  C11  C10  single    1.523  0.020  1.523
 N64  C11  N2   single    1.450  0.020  1.450
 N64  C7   N2   single    1.454  0.020  1.454
 N64  C10  N3   single    1.459  0.020  1.459
 N64  C13  C14  aromatic  1.384  0.020  1.384
 N64  C13  C12  aromatic  1.405  0.020  1.405
 N64  N2   C8   single    1.450  0.020  1.450
 N64  C14  C15  aromatic  1.390  0.020  1.390
 N64  N3   C9   single    1.452  0.020  1.452
 N64  N3   C12  single    1.394  0.020  1.394
 N64  C9   C8   single    1.526  0.020  1.526
 N64  C12  C17  aromatic  1.402  0.020  1.402
 N64  C15  C16  aromatic  1.385  0.020  1.385
 N64  C17  C16  aromatic  1.390  0.020  1.390
 N64  N1   H1   single    0.860  0.020  1.020
 N64  C5   H2   single    0.970  0.020  1.090
 N64  C5   H3   single    0.970  0.020  1.090
 N64  C6   H4   single    0.970  0.020  1.090
 N64  C6   H5   single    0.970  0.020  1.090
 N64  C7   H6   single    0.970  0.020  1.090
 N64  C7   H7   single    0.970  0.020  1.090
 N64  C8   H8   single    0.970  0.020  1.090
 N64  C8   H9   single    0.970  0.020  1.090
 N64  C10  H10  single    0.970  0.020  1.090
 N64  C10  H11  single    0.970  0.020  1.090
 N64  C13  H12  single    0.930  0.020  1.080
 N64  C15  H13  single    0.930  0.020  1.080
 N64  C17  H14  single    0.930  0.020  1.080
 N64  N    H15  single    0.860  0.020  1.020
 N64  C    H16  single    0.970  0.020  1.090
 N64  C    H17  single    0.970  0.020  1.090
 N64  C    H18  single    0.970  0.020  1.090
 N64  C11  H19  single    0.970  0.020  1.090
 N64  C11  H20  single    0.970  0.020  1.090
 N64  C14  H21  single    0.930  0.020  1.080
 N64  C16  H22  single    0.930  0.020  1.080
 N64  C2   H23  single    0.930  0.020  1.080
 N64  C9   H24  single    0.970  0.020  1.090
 N64  C9   H25  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
 N64  H1   N1   C5   118.08  3.000
 N64  H1   N1   C4   120.20  3.000
 N64  C5   N1   C4   121.71  3.000
 N64  C9   N3   C12  117.58  3.000
 N64  C12  N3   C10  117.34  3.000
 N64  C9   N3   C10  112.57  3.000
 N64  O    C4   N    122.69  3.000
 N64  O    C4   N1   123.40  3.000
 N64  N    C4   N1   113.92  3.000
 N64  H3   C5   H2   106.90  3.000
 N64  H3   C5   C6   109.91  3.000
 N64  H2   C5   C6   109.59  3.000
 N64  H3   C5   N1   110.13  3.000
 N64  H2   C5   N1   110.02  3.000
 N64  C6   C5   N1   110.23  3.000
 N64  H5   C6   H4   107.10  3.000
 N64  H5   C6   C7   108.87  3.000
 N64  H4   C6   C7   110.50  3.000
 N64  H5   C6   C5   110.01  3.000
 N64  H4   C6   C5   109.26  3.000
 N64  C7   C6   C5   111.02  3.000
 N64  H7   C7   H6   105.92  3.000
 N64  H7   C7   N2   113.78  3.000
 N64  H6   C7   N2   107.39  3.000
 N64  H7   C7   C6   109.03  3.000
 N64  H6   C7   C6   108.37  3.000
 N64  N2   C7   C6   112.02  3.000
 N64  H9   C8   H8   106.49  3.000
 N64  H9   C8   N2   110.36  3.000
 N64  H8   C8   N2   108.08  3.000
 N64  H9   C8   C9   108.81  3.000
 N64  H8   C8   C9   108.37  3.000
 N64  N2   C8   C9   114.41  3.000
 N64  H11  C10  H10  106.90  3.000
 N64  H11  C10  C11  107.86  3.000
 N64  H10  C10  C11  110.29  3.000
 N64  H11  C10  N3   110.47  3.000
 N64  H10  C10  N3   110.55  3.000
 N64  C11  C10  N3   110.67  3.000
 N64  H12  C13  C14  118.39  3.000
 N64  H12  C13  C12  120.38  3.000
 N64  C14  C13  C12  121.22  3.000
 N64  H13  C15  C16  120.86  3.000
 N64  H13  C15  C14  120.76  3.000
 N64  C16  C15  C14  118.38  3.000
 N64  H14  C17  C16  118.02  3.000
 N64  H14  C17  C12  120.96  3.000
 N64  C16  C17  C12  121.02  3.000
 N64  H15  N    C3   115.43  3.000
 N64  H15  N    C4   119.06  3.000
 N64  C3   N    C4   125.49  3.000
 N64  O1   C1   C2   109.71  3.000
 N64  C2   C1   C    132.34  3.000
 N64  O1   C1   C    117.95  3.000
 N64  H20  C11  H19  106.95  3.000
 N64  H20  C11  N2   108.27  3.000
 N64  H19  C11  N2   109.57  3.000
 N64  H20  C11  C10  108.57  3.000
 N64  H19  C11  C10  109.15  3.000
 N64  N2   C11  C10  114.08  3.000
 N64  C17  C12  C13  117.25  3.000
 N64  C17  C12  N3   122.25  3.000
 N64  C13  C12  N3   120.48  3.000
 N64  H21  C14  C15  120.08  3.000
 N64  H21  C14  C13  118.92  3.000
 N64  C15  C14  C13  121.00  3.000
 N64  H22  C16  C17  118.80  3.000
 N64  H22  C16  C15  120.07  3.000
 N64  C17  C16  C15  121.13  3.000
 N64  H23  C2   C3   129.18  3.000
 N64  H23  C2   C1   127.57  3.000
 N64  C3   C2   C1   103.25  3.000
 N64  N4   C3   C2   111.40  3.000
 N64  C2   C3   N    130.38  3.000
 N64  N4   C3   N    118.21  3.000
 N64  H25  C9   H24  106.77  3.000
 N64  H25  C9   C8   110.53  3.000
 N64  H24  C9   C8   107.43  3.000
 N64  H25  C9   N3   111.74  3.000
 N64  H24  C9   N3   109.38  3.000
 N64  C8   C9   N3   110.81  3.000
 N64  C11  N2   C8   108.61  3.000
 N64  C8   N2   C7   114.90  3.000
 N64  C11  N2   C7   114.20  3.000
 N64  O1   N4   C3   105.76  3.000
 N64  N4   O1   C1   109.89  3.000
 N64  H18  C    H17  108.22  3.000
 N64  H18  C    H16  108.44  3.000
 N64  H17  C    H16  107.77  3.000
 N64  H18  C    C1   109.92  3.000
 N64  H17  C    C1   111.09  3.000
 N64  H16  C    C1   111.30  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
 N64  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 N64  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 N64  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 N64  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 N64  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 N64  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 N64  CONST_07  C3   N4   O1   C1      0.00   0.0  0
 N64  CONST_08  N4   C3   C2   C1      0.00   0.0  0
 N64  CONST_09  N4   O1   C1   C2      0.00   0.0  0
 N64  CONST_10  O1   N4   C3   C2      0.00   0.0  0
 N64  CONST_11  O1   C1   C2   C3      0.00   0.0  0
 N64  CONST_12  C14  C13  C12  N3    180.00   0.0  0
 N64  CONST_13  C16  C17  C12  N3    180.00   0.0  0
 N64  CONST_14  O1   N4   C3   N     180.00   0.0  0
 N64  CONST_15  C1   C2   C3   N     180.00   0.0  0
 N64  CONST_16  N4   O1   C1   C     180.00   0.0  0
 N64  CONST_17  C3   C2   C1   C     180.00   0.0  0
 N64  CONST_18  H12  C13  C12  N3      0.00   0.0  0
 N64  CONST_19  H14  C17  C12  N3      0.00   0.0  0
 N64  CONST_20  H13  C15  C14  C13   180.00   0.0  0
 N64  CONST_21  H21  C14  C13  C12   180.00   0.0  0
 N64  CONST_22  H22  C16  C17  C12   180.00   0.0  0
 N64  CONST_23  H23  C2   C3   N4    180.00   0.0  0
 N64  CONST_24  N4   C3   N    C4    180.00   0.0  0
 N64  CONST_25  C2   C3   N    C4      0.00   0.0  0
 N64  CONST_26  H15  N    C3   C2    180.00   0.0  0
 N64  CONST_27  C3   N    C4   O       0.00   0.0  0
 N64  CONST_28  C3   N    C4   N1    180.00   0.0  0
 N64  CONST_29  O    C4   N1   C5      0.00   0.0  0
 N64  CONST_30  N    C4   N1   C5    180.00   0.0  0
 N64  CONST_31  H1   N1   C4   O     180.00   0.0  0
 N64  Var_01    N2   C11  C10  N3     54.81  30.0  1
 N64  Var_02    N2   C8   C9   N3    -53.88  30.0  1
 N64  Var_03    C10  C11  N2   C8    -54.34  30.0  1
 N64  Var_04    C10  N3   C9   C8     52.21  30.0  1
 N64  Var_05    C13  C12  N3   C10   -44.82  30.0  2
 N64  Var_06    C9   C8   N2   C11    53.87  30.0  1
 N64  Var_07    C11  N2   C7   C6    159.23  30.0  3
 N64  Var_08    H16  C    C1   C2    125.06  30.0  2
 N64  Var_09    N2   C7   C6   C5   -174.68  30.0  3
 N64  Var_10    C7   C6   C5   N1   -179.56  30.0  2
 N64  Var_11    C6   C5   N1   C4   -177.29  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
 N64  plan-1  N    0.020
 N64  plan-1  C1   0.020
 N64  plan-1  C2   0.020
 N64  plan-1  C3   0.020
 N64  plan-1  N4   0.020
 N64  plan-1  O1   0.020
 N64  plan-1  H23  0.020
 N64  plan-1  C    0.020
 N64  plan-2  N3   0.020
 N64  plan-2  C13  0.020
 N64  plan-2  C15  0.020
 N64  plan-2  C17  0.020
 N64  plan-2  C12  0.020
 N64  plan-2  C14  0.020
 N64  plan-2  C16  0.020
 N64  plan-2  H12  0.020
 N64  plan-2  H13  0.020
 N64  plan-2  H14  0.020
 N64  plan-2  H21  0.020
 N64  plan-2  H22  0.020
 N64  plan-3  N1   0.020
 N64  plan-3  C4   0.020
 N64  plan-3  C5   0.020
 N64  plan-3  N    0.020
 N64  plan-3  O    0.020
 N64  plan-3  C3   0.020
 N64  plan-3  H1   0.020
 N64  plan-3  H15  0.020

