# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:30:05 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-{3-[(2,4-diaminopyrimidin-5-yl)methyl]-4-methoxyphenoxy}pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCCCCC(O)=O)cc1Cc2cnc(N)nc2N
#
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
 DH1  DH1  '5-{3-[(2,4-diaminopyrimidin-5-yl)methyl]-4-methoxyphenoxy}pentanoic acid'  ligand  46  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DH1
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
 DH1  C16   C  CH3    0  -0.471   2.9573   3.5119   1.1108
 DH1  O1    O  O2     0  -0.451   2.8326   2.4762   0.1630
 DH1  C2'   C  CR6    0   0.315   1.6202   1.9135  -0.0258
 DH1  C3'   C  CR16   0  -0.388   0.4594   2.3099   0.6223
 DH1  C4'   C  CR16   0  -0.485  -0.7634   1.6922   0.3544
 DH1  C5'   C  CR6    0   0.467  -0.8312   0.6702  -0.5771
 DH1  O5'   O  O2     0  -0.472  -1.9502  -0.0111  -0.9058
 DH1  C52   C  CH2    0  -0.193  -3.1645   0.3010  -0.2339
 DH1  C1    C  CH2    0  -0.443  -4.2602  -0.6209  -0.7504
 DH1  C3    C  CH2    0  -0.439  -5.5826  -0.3874  -0.0230
 DH1  C7    C  CH2    0  -0.557  -6.6908  -1.2807  -0.5371
 DH1  C8    C  C      0   0.413  -8.0538  -1.1063   0.1637
 DH1  O9    O  OC    -1  -0.678  -8.9658  -1.8517  -0.2211
 DH1  O10   O  O      0  -0.668  -8.0946  -0.2317   1.0544
 DH1  C6'   C  CR16   0  -0.421   0.3438   0.2752  -1.2200
 DH1  C1'   C  CR6    0   0.155   1.5685   0.8577  -0.9522
 DH1  C51   C  CH2    0  -0.661   2.8166   0.3830  -1.6539
 DH1  C5    C  CR6    0  -0.127   3.8390  -0.2416  -0.7443
 DH1  C6    C  CR16   0  -0.012   5.0481   0.3643  -0.4854
 DH1  N1    N  N      0  -0.572   6.0061  -0.1422   0.2849
 DH1  C2    C  CR6    0   0.493   5.7252  -1.3231   0.8352
 DH1  N2    N  NH2    0  -0.824   6.6803  -1.8860   1.6157
 DH1  N3    N  N      0  -0.439   4.5981  -2.0117   0.6778
 DH1  C4    C  CR6    0   0.478   3.6573  -1.4851  -0.1002
 DH1  N4    N  NH2    0  -0.771   2.5445  -2.2305  -0.2879
 DH1  H161  H  HCH3   0   0.226   4.0074   3.8032   1.1417
 DH1  H162  H  HCH3   0   0.194   2.3703   4.3925   0.8329
 DH1  H163  H  HCH3   0   0.245   2.6502   3.1927   2.1112
 DH1  H3'   H  HCR6   0   0.301   0.4697   3.1141   1.3453
 DH1  H4'   H  HCR6   0   0.263  -1.6376   2.0341   0.8915
 DH1  H521  H  HCH2   0   0.282  -3.0500   0.1737   0.8511
 DH1  H522  H  HCH2   0   0.172  -3.4376   1.3495  -0.4106
 DH1  H11   H  HCH2   0   0.267  -4.3982  -0.4583  -1.8244
 DH1  H12   H  HCH2   0   0.209  -3.9490  -1.6627  -0.6251
 DH1  H31   H  HCH2   0   0.199  -5.4424  -0.5536   1.0484
 DH1  H32   H  HCH2   0   0.192  -5.8779   0.6598  -0.1298
 DH1  H71   H  HCH2   0   0.265  -6.8321  -1.1155  -1.6123
 DH1  H72   H  HCH2   0   0.268  -6.3966  -2.3337  -0.4565
 DH1  H6'   H  HCR6   0   0.246   0.2835  -0.5221  -1.9543
 DH1  H511  H  HCH2   0   0.266   2.5259  -0.3228  -2.4385
 DH1  H512  H  HCH2   0   0.284   3.2881   1.2231  -2.1710
 DH1  H6    H  HCR6   0   0.263   5.2652   1.3266  -0.9406
 DH1  HN21  H  HNH2   0   0.398   7.4260  -1.2976   1.9420
 DH1  HN22  H  HNH2   0   0.381   6.4047  -2.6392   2.2204
 DH1  HN41  H  HNH2   0   0.411   2.4273  -3.0298   0.3077
 DH1  HN42  H  HNH2   0   0.421   1.6956  -1.7929  -0.5996

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
 DH1  C16  O1    single    1.410  0.020  1.410
 DH1  C16  H161  single    0.970  0.020  1.090
 DH1  C16  H162  single    0.970  0.020  1.090
 DH1  C16  H163  single    0.970  0.020  1.090
 DH1  O1   C2'   single    1.350  0.020  1.350
 DH1  C2'  C3'   aromatic  1.387  0.020  1.387
 DH1  C2'  C1'   aromatic  1.406  0.020  1.406
 DH1  C3'  C4'   aromatic  1.396  0.020  1.396
 DH1  C3'  H3'   single    0.930  0.020  1.080
 DH1  C4'  C5'   aromatic  1.385  0.020  1.385
 DH1  C4'  H4'   single    0.930  0.020  1.080
 DH1  C5'  O5'   single    1.351  0.020  1.351
 DH1  C5'  C6'   aromatic  1.396  0.020  1.396
 DH1  O5'  C52   single    1.422  0.020  1.422
 DH1  C52  C1    single    1.522  0.020  1.522
 DH1  C52  H521  single    0.970  0.020  1.090
 DH1  C52  H522  single    0.970  0.020  1.090
 DH1  C1   C3    single    1.527  0.020  1.527
 DH1  C1   H11   single    0.970  0.020  1.090
 DH1  C1   H12   single    0.970  0.020  1.090
 DH1  C3   C7    single    1.513  0.020  1.513
 DH1  C3   H31   single    0.970  0.020  1.090
 DH1  C3   H32   single    0.970  0.020  1.090
 DH1  C7   C8    single    1.543  0.020  1.543
 DH1  C7   H71   single    0.970  0.020  1.090
 DH1  C7   H72   single    0.970  0.020  1.090
 DH1  C8   O9    deloc     1.239  0.020  1.239
 DH1  C8   O10   deloc     1.249  0.020  1.249
 DH1  C6'  C1'   aromatic  1.382  0.020  1.382
 DH1  C6'  H6'   single    0.930  0.020  1.080
 DH1  C1'  C51   single    1.508  0.020  1.508
 DH1  C51  C5    single    1.504  0.020  1.504
 DH1  C51  H511  single    0.970  0.020  1.090
 DH1  C51  H512  single    0.970  0.020  1.090
 DH1  C5   C6    aromatic  1.377  0.020  1.377
 DH1  C5   C4    aromatic  1.412  0.020  1.412
 DH1  C6   N1    aromatic  1.330  0.020  1.330
 DH1  C6   H6    single    0.930  0.020  1.080
 DH1  N1   C2    aromatic  1.333  0.020  1.333
 DH1  C2   N2    single    1.356  0.020  1.356
 DH1  C2   N3    aromatic  1.330  0.020  1.330
 DH1  N2   HN21  single    0.890  0.020  1.040
 DH1  N2   HN22  single    0.890  0.020  1.040
 DH1  N3   C4    aromatic  1.330  0.020  1.330
 DH1  C4   N4    single    1.352  0.020  1.352
 DH1  N4   HN41  single    0.890  0.020  1.040
 DH1  N4   HN42  single    0.890  0.020  1.040

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
 DH1  H163  C16  H162  108.45  3.000
 DH1  H163  C16  H161  108.81  3.000
 DH1  H162  C16  H161  108.00  3.000
 DH1  H163  C16  O1    112.06  3.000
 DH1  H162  C16  O1    111.91  3.000
 DH1  H161  C16  O1    107.49  3.000
 DH1  C2'   O1   C16   118.67  3.000
 DH1  C1'   C2'  C3'   119.46  3.000
 DH1  C1'   C2'  O1    116.00  3.000
 DH1  C3'   C2'  O1    124.55  3.000
 DH1  H3'   C3'  C4'   117.75  3.000
 DH1  H3'   C3'  C2'   121.12  3.000
 DH1  C4'   C3'  C2'   121.12  3.000
 DH1  H4'   C4'  C5'   121.87  3.000
 DH1  H4'   C4'  C3'   118.22  3.000
 DH1  C5'   C4'  C3'   119.91  3.000
 DH1  C6'   C5'  O5'   116.25  3.000
 DH1  C6'   C5'  C4'   118.52  3.000
 DH1  O5'   C5'  C4'   125.22  3.000
 DH1  C52   O5'  C5'   118.79  3.000
 DH1  H522  C52  H521  107.19  3.000
 DH1  H522  C52  C1    110.17  3.000
 DH1  H521  C52  C1    109.88  3.000
 DH1  H522  C52  O5'   110.24  3.000
 DH1  H521  C52  O5'   110.62  3.000
 DH1  C1    C52  O5'   108.74  3.000
 DH1  H12   C1   H11   106.83  3.000
 DH1  H12   C1   C3    109.70  3.000
 DH1  H11   C1   C3    109.59  3.000
 DH1  H12   C1   C52   109.45  3.000
 DH1  H11   C1   C52   109.49  3.000
 DH1  C3    C1   C52   111.66  3.000
 DH1  H32   C3   H31   106.02  3.000
 DH1  H32   C3   C7    109.54  3.000
 DH1  H31   C3   C7    109.70  3.000
 DH1  H32   C3   C1    109.50  3.000
 DH1  H31   C3   C1    109.42  3.000
 DH1  C7    C3   C1    112.46  3.000
 DH1  H72   C7   H71   104.56  3.000
 DH1  H72   C7   C8    108.20  3.000
 DH1  H71   C7   C8    108.33  3.000
 DH1  H72   C7   C3    110.21  3.000
 DH1  H71   C7   C3    109.78  3.000
 DH1  C8    C7   C3    115.21  3.000
 DH1  O10   C8   O9    128.22  3.000
 DH1  O10   C8   C7    115.60  3.000
 DH1  O9    C8   C7    116.18  3.000
 DH1  H6'   C6'  C1'   119.32  3.000
 DH1  H6'   C6'  C5'   118.20  3.000
 DH1  C1'   C6'  C5'   122.49  3.000
 DH1  C51   C1'  C6'   120.69  3.000
 DH1  C51   C1'  C2'   120.83  3.000
 DH1  C6'   C1'  C2'   118.48  3.000
 DH1  H512  C51  H511  105.72  3.000
 DH1  H512  C51  C5    108.18  3.000
 DH1  H511  C51  C5    110.25  3.000
 DH1  H512  C51  C1'   109.58  3.000
 DH1  H511  C51  C1'   108.46  3.000
 DH1  C5    C51  C1'   114.32  3.000
 DH1  C4    C5   C6    114.50  3.000
 DH1  C4    C5   C51   123.64  3.000
 DH1  C6    C5   C51   121.86  3.000
 DH1  H6    C6   N1    115.86  3.000
 DH1  H6    C6   C5    119.11  3.000
 DH1  N1    C6   C5    125.03  3.000
 DH1  C2    N1   C6    115.15  3.000
 DH1  N3    C2   N2    116.75  3.000
 DH1  N3    C2   N1    126.04  3.000
 DH1  N2    C2   N1    117.20  3.000
 DH1  HN22  N2   HN21  116.58  3.000
 DH1  HN22  N2   C2    117.68  3.000
 DH1  HN21  N2   C2    117.83  3.000
 DH1  C4    N3   C2    117.64  3.000
 DH1  N4    C4   N3    116.43  3.000
 DH1  N4    C4   C5    121.86  3.000
 DH1  N3    C4   C5    121.64  3.000
 DH1  HN42  N4   HN41  115.62  3.000
 DH1  HN42  N4   C4    119.88  3.000
 DH1  HN41  N4   C4    116.91  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
 DH1  CONST_01  C5'   C4'  C3'  C2'     0.00   0.0  0
 DH1  CONST_02  C5'   C6'  C1'  C2'     0.00   0.0  0
 DH1  CONST_03  C6'   C1'  C2'  C3'     0.00   0.0  0
 DH1  CONST_04  C6'   C5'  C4'  C3'     0.00   0.0  0
 DH1  CONST_05  C1'   C2'  C3'  C4'     0.00   0.0  0
 DH1  CONST_06  C1'   C6'  C5'  C4'     0.00   0.0  0
 DH1  CONST_07  C2    N1   C6   C5      0.00   0.0  0
 DH1  CONST_08  C2    N3   C4   C5      0.00   0.0  0
 DH1  CONST_09  N3    C4   C5   C6      0.00   0.0  0
 DH1  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 DH1  CONST_11  C4    C5   C6   N1      0.00   0.0  0
 DH1  CONST_12  C4    N3   C2   N1      0.00   0.0  0
 DH1  CONST_13  C4'   C3'  C2'  O1    180.00   0.0  0
 DH1  CONST_14  C6'   C1'  C2'  O1    180.00   0.0  0
 DH1  CONST_15  C51   C1'  C2'  C3'   180.00   0.0  0
 DH1  CONST_16  O5'   C5'  C4'  C3'   180.00   0.0  0
 DH1  CONST_17  C51   C1'  C6'  C5'   180.00   0.0  0
 DH1  CONST_18  C1'   C6'  C5'  O5'   180.00   0.0  0
 DH1  CONST_19  N1    C6   C5   C51   180.00   0.0  0
 DH1  CONST_20  N3    C4   C5   C51   180.00   0.0  0
 DH1  CONST_21  N4    C4   C5   C6    180.00   0.0  0
 DH1  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 DH1  CONST_23  N4    C4   N3   C2    180.00   0.0  0
 DH1  CONST_24  C4    N3   C2   N2    180.00   0.0  0
 DH1  CONST_25  H4'   C4'  C3'  C2'   180.00   0.0  0
 DH1  CONST_26  H6'   C6'  C1'  C2'   180.00   0.0  0
 DH1  CONST_27  H3'   C3'  C4'  C5'   180.00   0.0  0
 DH1  CONST_28  H6    C6   N1   C2    180.00   0.0  0
 DH1  CONST_29  HN41  N4   C4   C5    180.00   0.0  0
 DH1  Var_01    C5    C51  C1'  C2'    65.65  30.0  2
 DH1  Var_02    C6    C5   C51  C1'  -111.47  30.0  2
 DH1  Var_03    C3'   C2'  O1   C16     2.10  30.0  2
 DH1  Var_04    C6'   C5'  O5'  C52   176.86  30.0  1
 DH1  Var_05    C1    C52  O5'  C5'  -178.49  30.0  3
 DH1  Var_06    H161  C16  O1   C2'   177.90  30.0  3
 DH1  Var_07    C3    C1   C52  O5'   177.26  30.0  3
 DH1  Var_08    C7    C3   C1   C52   179.13  30.0  3
 DH1  Var_09    C8    C7   C3   C1    179.46  30.0  3
 DH1  Var_10    O9    C8   C7   C3   -178.31  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
 DH1  plan-1  O1    0.020
 DH1  plan-1  C2'   0.020
 DH1  plan-1  C3'   0.020
 DH1  plan-1  C4'   0.020
 DH1  plan-1  C5'   0.020
 DH1  plan-1  O5'   0.020
 DH1  plan-1  C6'   0.020
 DH1  plan-1  C1'   0.020
 DH1  plan-1  C51   0.020
 DH1  plan-1  H3'   0.020
 DH1  plan-1  H4'   0.020
 DH1  plan-1  H6'   0.020
 DH1  plan-2  C51   0.020
 DH1  plan-2  C5    0.020
 DH1  plan-2  C6    0.020
 DH1  plan-2  N1    0.020
 DH1  plan-2  C2    0.020
 DH1  plan-2  N2    0.020
 DH1  plan-2  N3    0.020
 DH1  plan-2  C4    0.020
 DH1  plan-2  N4    0.020
 DH1  plan-2  H6    0.020
 DH1  plan-3  C2    0.020
 DH1  plan-3  N2    0.020
 DH1  plan-3  HN21  0.020
 DH1  plan-3  HN22  0.020
 DH1  plan-4  C4    0.020
 DH1  plan-4  N4    0.020
 DH1  plan-4  HN41  0.020
 DH1  plan-4  HN42  0.020
 DH1  plan-5  C7    0.020
 DH1  plan-5  C8    0.020
 DH1  plan-5  O9    0.020
 DH1  plan-5  O10   0.020

