# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 15:03:22 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(CCOc1ccc(cc1)C2=NCCCN2)CCOc3ccc(cc3)C4=NCCCN4
#
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
 5D0  5D0  2,2'-[pentane-1,5-diylbis(oxybenzene-4,1-diyl)]di-1,4,5,6-tetrahydropyrimidine  ligand  63  31  .  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_5D0
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
 5D0  C1   C  CH2   0  -0.171   -2.5031   0.4936   0.0333
 5D0  C2   C  CH2   0  -0.457   -1.2566   1.3529   0.0186
 5D0  C3   C  CH2   0  -0.440    0.0068   0.5004   0.0319
 5D0  C8   C  CR6   0   0.384    4.8804   0.8356   0.0268
 5D0  C9   C  CR16  0  -0.370    5.1608  -0.5265   0.1339
 5D0  C10  C  CR16  0  -0.266    6.4782  -0.9578   0.1786
 5D0  C11  C  CR6   0   0.016    7.5412  -0.0644   0.1076
 5D0  C12  C  CR16  0  -0.284    7.2456   1.2964   0.0026
 5D0  C13  C  CR16  0  -0.336    5.9389   1.7438  -0.0353
 5D0  C14  C  CR6   0   0.384   -4.8645   0.8194   0.0614
 5D0  C15  C  CR16  0  -0.336   -5.9326   1.7221   0.0921
 5D0  C16  C  CR16  0  -0.263   -7.2327   1.2631   0.1175
 5D0  C19  C  CR16  0  -0.371   -5.1328  -0.5467   0.0567
 5D0  C20  C  CR6   0   0.423    8.9376  -0.5654   0.1641
 5D0  C21  C  C     0   0.422   -8.9282  -0.5671   0.1407
 5D0  N23  N  NH1   0  -0.672   -9.1571  -1.7988  -0.3918
 5D0  N25  N  N     0  -0.467    9.1733  -1.6615   0.7825
 5D0  C27  C  CH2   0  -0.502  -11.5133  -1.2259  -0.4604
 5D0  C30  C  C     0  -0.502   11.3610  -1.6895  -0.4071
 5D0  C31  C  C     0  -0.315   10.5303  -2.1660   0.7767
 5D0  C4   C  CH2   0  -0.457    1.2702   1.3518  -0.0027
 5D0  C5   C  CH2   0  -0.171    2.5182   0.4952   0.0401
 5D0  O6   O  O2    0  -0.474    3.6439   1.3583  -0.0222
 5D0  O7   O  O2    0  -0.473   -3.6325   1.3543   0.0406
 5D0  C17  C  CR6   0   0.016   -7.5184  -0.1041   0.1030
 5D0  C18  C  CR16  0  -0.287   -6.4490  -0.9921   0.0762
 5D0  N22  N  N     0  -0.466   -9.8083   0.1872   0.6848
 5D0  N24  N  NR16  0  -0.673    9.8693   0.2234  -0.4381
 5D0  C26  C  CH2   0  -0.314  -11.1890  -0.2468   0.6601
 5D0  C28  C  CH2   0  -0.265  -10.4954  -2.3527  -0.4400
 5D0  C29  C  C     0  -0.263   11.2611  -0.1767  -0.5010
 5D0  H1   H  HCH2  0   0.223   -2.5244  -0.1572  -0.8486
 5D0  H2   H  HCH2  0   0.223   -2.5091  -0.1501   0.9207
 5D0  H3   H  HCH2  0   0.233   -1.2617   1.9893  -0.8711
 5D0  H4   H  HCH2  0   0.234   -1.2599   2.0162   0.8883
 5D0  H5   H  HCH2  0   0.227    0.0128  -0.1309   0.9266
 5D0  H6   H  HCH2  0   0.227    0.0002  -0.1804  -0.8255
 5D0  H7   H  HCR6  0   0.280    4.3715  -1.2639   0.1798
 5D0  H8   H  HCR6  0   0.252    6.6828  -2.0166   0.2648
 5D0  H9   H  HCR6  0   0.255    8.0399   2.0316  -0.0280
 5D0  H10  H  HCR6  0   0.263    5.7294   2.8040  -0.1060
 5D0  H11  H  HCR6  0   0.262   -5.7303   2.7861   0.0936
 5D0  H12  H  HCR6  0   0.250   -8.0484   1.9729   0.1438
 5D0  H13  H  HCR6  0   0.281   -4.3390  -1.2802   0.0457
 5D0  H15  H  HNH1  0   0.394   -8.4835  -2.1593  -1.0455
 5D0  H17  H  HCH2  0   0.242  -12.5220  -1.6246  -0.3442
 5D0  H18  H  HCH2  0   0.232  -11.4747  -0.7135  -1.4255
 5D0  H19  H  H     0   0.241   12.4027  -1.9930  -0.2936
 5D0  H20  H  H     0   0.232   10.9881  -2.1416  -1.3303
 5D0  H21  H  H     0   0.217   11.0303  -1.8759   1.7094
 5D0  H22  H  H     0   0.224   10.4923  -3.2585   0.7912
 5D0  H23  H  HCH2  0   0.233    1.2763   1.9617  -0.9108
 5D0  H24  H  HCH2  0   0.233    1.2723   2.0406   0.8470
 5D0  H25  H  HCH2  0   0.223    2.5396  -0.0960   0.9629
 5D0  H26  H  HCH2  0   0.223    2.5279  -0.2055  -0.8029
 5D0  H27  H  HCR6  0   0.257   -6.6199  -2.0614   0.0925
 5D0  H30  H  HNR6  0   0.393    9.5492   0.8896  -1.1197
 5D0  H31  H  HCH2  0   0.225  -11.8259   0.6380   0.5773
 5D0  H32  H  HCH2  0   0.217  -11.4450  -0.7011   1.6252
 5D0  H33  H  HCH2  0   0.251  -10.5771  -2.9808  -1.3263
 5D0  H34  H  HCH2  0   0.228  -10.6694  -2.9990   0.4263
 5D0  H35  H  H     0   0.228   11.8273   0.2855   0.3139
 5D0  H36  H  H     0   0.250   11.6852   0.1921  -1.4343

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
 5D0  C30  C29  single    1.519  0.020  1.519
 5D0  C30  C31  single    1.523  0.020  1.523
 5D0  C29  N24  single    1.450  0.020  1.450
 5D0  C26  N22  single    1.448  0.020  1.448
 5D0  C26  C27  single    1.523  0.020  1.523
 5D0  C31  N25  single    1.448  0.020  1.448
 5D0  N22  C21  double    1.280  0.020  1.280
 5D0  N24  C20  single    1.361  0.020  1.361
 5D0  N25  C20  double    1.280  0.020  1.280
 5D0  C27  C28  single    1.519  0.020  1.519
 5D0  C20  C11  single    1.485  0.020  1.485
 5D0  C18  C19  aromatic  1.390  0.020  1.390
 5D0  C18  C17  aromatic  1.390  0.020  1.390
 5D0  C10  C11  aromatic  1.390  0.020  1.390
 5D0  C10  C9   aromatic  1.387  0.020  1.387
 5D0  C19  C14  aromatic  1.392  0.020  1.392
 5D0  C11  C12  aromatic  1.397  0.020  1.397
 5D0  C21  C17  single    1.484  0.020  1.484
 5D0  C21  N23  single    1.361  0.020  1.361
 5D0  C9   C8   aromatic  1.395  0.020  1.395
 5D0  C17  C16  aromatic  1.397  0.020  1.397
 5D0  C28  N23  single    1.449  0.020  1.449
 5D0  C12  C13  aromatic  1.382  0.020  1.382
 5D0  C8   C13  aromatic  1.396  0.020  1.396
 5D0  C8   O6   single    1.343  0.020  1.343
 5D0  C14  O7   single    1.343  0.020  1.343
 5D0  C14  C15  aromatic  1.399  0.020  1.399
 5D0  C3   C2   single    1.524  0.020  1.524
 5D0  C3   C4   single    1.524  0.020  1.524
 5D0  C1   O7   single    1.420  0.020  1.420
 5D0  C1   C2   single    1.514  0.020  1.514
 5D0  O6   C5   single    1.420  0.020  1.420
 5D0  C5   C4   single    1.514  0.020  1.514
 5D0  C16  C15  aromatic  1.379  0.020  1.379
 5D0  C1   H1   single    0.970  0.020  1.090
 5D0  C1   H2   single    0.970  0.020  1.090
 5D0  C2   H3   single    0.970  0.020  1.090
 5D0  C2   H4   single    0.970  0.020  1.090
 5D0  C3   H5   single    0.970  0.020  1.090
 5D0  C3   H6   single    0.970  0.020  1.090
 5D0  C9   H7   single    0.930  0.020  1.080
 5D0  C10  H8   single    0.930  0.020  1.080
 5D0  C12  H9   single    0.930  0.020  1.080
 5D0  C13  H10  single    0.930  0.020  1.080
 5D0  C15  H11  single    0.930  0.020  1.080
 5D0  C16  H12  single    0.930  0.020  1.080
 5D0  C19  H13  single    0.930  0.020  1.080
 5D0  N23  H15  single    0.890  0.020  1.040
 5D0  C27  H17  single    0.970  0.020  1.090
 5D0  C27  H18  single    0.970  0.020  1.090
 5D0  C30  H19  single    0.970  0.020  1.090
 5D0  C30  H20  single    0.970  0.020  1.090
 5D0  C31  H21  single    0.970  0.020  1.090
 5D0  C31  H22  single    0.970  0.020  1.090
 5D0  C4   H23  single    0.970  0.020  1.090
 5D0  C4   H24  single    0.970  0.020  1.090
 5D0  C5   H25  single    0.970  0.020  1.090
 5D0  C5   H26  single    0.970  0.020  1.090
 5D0  C18  H27  single    0.930  0.020  1.080
 5D0  N24  H30  single    0.890  0.020  1.040
 5D0  C26  H31  single    0.970  0.020  1.090
 5D0  C26  H32  single    0.970  0.020  1.090
 5D0  C28  H33  single    0.970  0.020  1.090
 5D0  C28  H34  single    0.970  0.020  1.090
 5D0  C29  H35  single    0.970  0.020  1.090
 5D0  C29  H36  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
 5D0  H2   C1   H1   107.61  3.000
 5D0  H2   C1   O7   110.32  3.000
 5D0  H1   C1   O7   110.40  3.000
 5D0  H2   C1   C2   110.22  3.000
 5D0  H1   C1   C2   110.19  3.000
 5D0  O7   C1   C2   108.11  3.000
 5D0  H4   C2   H3   107.09  3.000
 5D0  H4   C2   C3   109.56  3.000
 5D0  H3   C2   C3   109.66  3.000
 5D0  H4   C2   C1   109.51  3.000
 5D0  H3   C2   C1   109.52  3.000
 5D0  C3   C2   C1   111.40  3.000
 5D0  H6   C3   H5   106.35  3.000
 5D0  H6   C3   C4   109.55  3.000
 5D0  H5   C3   C4   109.64  3.000
 5D0  H6   C3   C2   109.63  3.000
 5D0  H5   C3   C2   109.53  3.000
 5D0  C4   C3   C2   111.99  3.000
 5D0  O6   C8   C13  116.31  3.000
 5D0  O6   C8   C9   124.60  3.000
 5D0  C13  C8   C9   119.09  3.000
 5D0  H7   C9   C10  118.69  3.000
 5D0  H7   C9   C8   121.50  3.000
 5D0  C10  C9   C8   119.81  3.000
 5D0  H8   C10  C11  119.23  3.000
 5D0  H8   C10  C9   119.11  3.000
 5D0  C11  C10  C9   121.65  3.000
 5D0  C20  C11  C12  122.06  3.000
 5D0  C12  C11  C10  117.91  3.000
 5D0  C20  C11  C10  120.02  3.000
 5D0  H9   C12  C13  118.24  3.000
 5D0  H9   C12  C11  120.57  3.000
 5D0  C13  C12  C11  121.18  3.000
 5D0  H10  C13  C12  120.11  3.000
 5D0  H10  C13  C8   119.54  3.000
 5D0  C12  C13  C8   120.34  3.000
 5D0  O7   C14  C19  124.57  3.000
 5D0  O7   C14  C15  116.34  3.000
 5D0  C19  C14  C15  119.09  3.000
 5D0  H11  C15  C16  120.20  3.000
 5D0  H11  C15  C14  119.43  3.000
 5D0  C16  C15  C14  120.36  3.000
 5D0  H12  C16  C17  119.23  3.000
 5D0  H12  C16  C15  119.54  3.000
 5D0  C17  C16  C15  121.23  3.000
 5D0  H13  C19  C18  118.57  3.000
 5D0  H13  C19  C14  121.62  3.000
 5D0  C18  C19  C14  119.80  3.000
 5D0  N24  C20  N25  125.72  3.000
 5D0  N25  C20  C11  118.71  3.000
 5D0  N24  C20  C11  115.55  3.000
 5D0  N22  C21  C17  118.67  3.000
 5D0  C17  C21  N23  115.59  3.000
 5D0  N22  C21  N23  125.71  3.000
 5D0  H15  N23  C28  117.39  3.000
 5D0  H15  N23  C21  117.78  3.000
 5D0  C28  N23  C21  120.94  3.000
 5D0  C31  N25  C20  117.96  3.000
 5D0  H18  C27  H17  107.33  3.000
 5D0  H18  C27  C28  109.63  3.000
 5D0  H17  C27  C28  110.32  3.000
 5D0  H18  C27  C26  109.92  3.000
 5D0  H17  C27  C26  110.70  3.000
 5D0  C28  C27  C26  108.93  3.000
 5D0  H20  C30  H19  107.37  3.000
 5D0  H20  C30  C29  109.70  3.000
 5D0  H19  C30  C29  110.26  3.000
 5D0  H20  C30  C31  109.94  3.000
 5D0  H19  C30  C31  110.67  3.000
 5D0  C29  C30  C31  108.89  3.000
 5D0  H22  C31  H21  105.59  3.000
 5D0  H22  C31  C30  109.99  3.000
 5D0  H21  C31  C30  109.24  3.000
 5D0  H22  C31  N25  108.40  3.000
 5D0  H21  C31  N25  109.36  3.000
 5D0  C30  C31  N25  113.92  3.000
 5D0  H24  C4   H23  107.08  3.000
 5D0  H24  C4   C5   109.43  3.000
 5D0  H23  C4   C5   109.52  3.000
 5D0  H24  C4   C3   109.63  3.000
 5D0  H23  C4   C3   109.57  3.000
 5D0  C5   C4   C3   111.50  3.000
 5D0  H26  C5   H25  107.61  3.000
 5D0  H26  C5   O6   110.35  3.000
 5D0  H25  C5   O6   110.44  3.000
 5D0  H26  C5   C4   110.31  3.000
 5D0  H25  C5   C4   110.18  3.000
 5D0  O6   C5   C4   107.96  3.000
 5D0  C5   O6   C8   119.45  3.000
 5D0  C14  O7   C1   119.22  3.000
 5D0  C18  C17  C21  122.13  3.000
 5D0  C21  C17  C16  119.95  3.000
 5D0  C18  C17  C16  117.91  3.000
 5D0  H27  C18  C17  120.59  3.000
 5D0  H27  C18  C19  117.79  3.000
 5D0  C17  C18  C19  121.61  3.000
 5D0  C26  N22  C21  118.15  3.000
 5D0  H30  N24  C29  117.33  3.000
 5D0  H30  N24  C20  117.78  3.000
 5D0  C29  N24  C20  121.09  3.000
 5D0  H32  C26  H31  105.42  3.000
 5D0  H32  C26  N22  109.37  3.000
 5D0  H31  C26  N22  108.32  3.000
 5D0  H32  C26  C27  109.35  3.000
 5D0  H31  C26  C27  109.91  3.000
 5D0  N22  C26  C27  114.11  3.000
 5D0  H34  C28  H33  106.94  3.000
 5D0  H34  C28  C27  110.01  3.000
 5D0  H33  C28  C27  111.51  3.000
 5D0  H34  C28  N23  110.25  3.000
 5D0  H33  C28  N23  108.46  3.000
 5D0  C27  C28  N23  109.63  3.000
 5D0  H36  C29  H35  107.06  3.000
 5D0  H36  C29  N24  108.51  3.000
 5D0  H35  C29  N24  110.35  3.000
 5D0  H36  C29  C30  111.38  3.000
 5D0  H35  C29  C30  109.91  3.000
 5D0  N24  C29  C30  109.60  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
 5D0  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 5D0  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 5D0  CONST_03  C12  C11  C10  C9     0.00   0.0  0
 5D0  CONST_04  C12  C13  C8   C9     0.00   0.0  0
 5D0  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 5D0  CONST_06  C13  C8   C9   C10    0.00   0.0  0
 5D0  CONST_07  C17  C18  C19  C14    0.00   0.0  0
 5D0  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 5D0  CONST_09  C18  C19  C14  C15    0.00   0.0  0
 5D0  CONST_10  C18  C17  C16  C15    0.00   0.0  0
 5D0  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 5D0  CONST_12  C19  C14  C15  C16    0.00   0.0  0
 5D0  CONST_13  C20  C11  C10  C9   180.00   0.0  0
 5D0  CONST_14  C20  C11  C12  C13  180.00   0.0  0
 5D0  CONST_15  C21  C17  C16  C15  180.00   0.0  0
 5D0  CONST_16  C21  C17  C18  C19  180.00   0.0  0
 5D0  CONST_17  C29  N24  C20  C11  180.00   0.0  0
 5D0  CONST_18  C31  N25  C20  C11  180.00   0.0  0
 5D0  CONST_19  C26  N22  C21  N23    0.00   0.0  0
 5D0  CONST_20  C29  N24  C20  N25    0.00   0.0  0
 5D0  CONST_21  N24  C20  N25  C31    0.00   0.0  0
 5D0  CONST_22  C26  N22  C21  C17  180.00   0.0  0
 5D0  CONST_23  C28  N23  C21  C17  180.00   0.0  0
 5D0  CONST_24  C28  N23  C21  N22    0.00   0.0  0
 5D0  CONST_25  O6   C8   C9   C10  180.00   0.0  0
 5D0  CONST_26  O6   C8   C13  C12  180.00   0.0  0
 5D0  CONST_27  O7   C14  C15  C16  180.00   0.0  0
 5D0  CONST_28  C18  C19  C14  O7   180.00   0.0  0
 5D0  CONST_29  H8   C10  C9   C8   180.00   0.0  0
 5D0  CONST_30  H9   C12  C13  C8   180.00   0.0  0
 5D0  CONST_31  H10  C13  C8   C9   180.00   0.0  0
 5D0  CONST_32  H7   C9   C10  C11  180.00   0.0  0
 5D0  CONST_33  H27  C18  C19  C14  180.00   0.0  0
 5D0  CONST_34  H12  C16  C15  C14  180.00   0.0  0
 5D0  CONST_35  H13  C19  C14  C15  180.00   0.0  0
 5D0  CONST_36  H11  C15  C14  C19  180.00   0.0  0
 5D0  Var_01    N24  C20  C11  C10  154.06  30.0  2
 5D0  Var_02    N22  C21  C17  C16  -26.55  30.0  2
 5D0  Var_03    C30  C29  N24  C20   24.75  30.0  1
 5D0  Var_04    C30  C31  N25  C20  -24.77  30.0  1
 5D0  Var_05    C27  C26  N22  C21  -23.57  30.0  1
 5D0  Var_06    C27  C28  N23  C21   26.01  30.0  1
 5D0  Var_07    C26  C27  C28  N23  -49.74  30.0  1
 5D0  Var_08    C29  C30  C31  N25   51.39  30.0  1
 5D0  Var_09    N24  C29  C30  C31  -49.43  30.0  1
 5D0  Var_10    C28  C27  C26  N22   50.46  30.0  1
 5D0  Var_11    C19  C14  O7   C1    -1.00  30.0  3
 5D0  Var_12    C4   C5   O6   C8   178.69  30.0  3
 5D0  Var_13    H1   C1   O7   C14   59.76  30.0  1
 5D0  Var_14    C4   C3   C2   C1   179.19  30.0  1
 5D0  Var_15    C5   C4   C3   C2   178.81  30.0  3
 5D0  Var_16    O7   C1   C2   C3   179.11  30.0  1
 5D0  Var_17    O6   C5   C4   C3   178.86  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
 5D0  plan-1  C8   0.020
 5D0  plan-1  C9   0.020
 5D0  plan-1  C10  0.020
 5D0  plan-1  C11  0.020
 5D0  plan-1  C12  0.020
 5D0  plan-1  C13  0.020
 5D0  plan-1  C20  0.020
 5D0  plan-1  O6   0.020
 5D0  plan-1  H7   0.020
 5D0  plan-1  H8   0.020
 5D0  plan-1  H9   0.020
 5D0  plan-1  H10  0.020
 5D0  plan-2  C14  0.020
 5D0  plan-2  C15  0.020
 5D0  plan-2  C16  0.020
 5D0  plan-2  C19  0.020
 5D0  plan-2  C21  0.020
 5D0  plan-2  O7   0.020
 5D0  plan-2  C17  0.020
 5D0  plan-2  C18  0.020
 5D0  plan-2  H11  0.020
 5D0  plan-2  H12  0.020
 5D0  plan-2  H13  0.020
 5D0  plan-2  H27  0.020
 5D0  plan-3  C21  0.020
 5D0  plan-3  N23  0.020
 5D0  plan-3  C17  0.020
 5D0  plan-3  N22  0.020
 5D0  plan-3  C26  0.020
 5D0  plan-3  C28  0.020
 5D0  plan-3  H15  0.020
 5D0  plan-4  C11  0.020
 5D0  plan-4  C20  0.020
 5D0  plan-4  N25  0.020
 5D0  plan-4  C31  0.020
 5D0  plan-4  N24  0.020
 5D0  plan-4  C29  0.020
 5D0  plan-4  H30  0.020

