# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:25:51 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (2S)-2-(3-{2-bromo-5-[(2,4-diaminopyrimidin-1-ium-5-yl)methyl]-3-methoxyphenoxy}propyl)pentanedioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cc2c[nH+]c(N)nc2N)cc(OCCC[C@@H](CCC([O-])=O)C([O-])=O)c1Br
#
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
 BDM  BDM  (2S)-2-(3-{2-bromo-5-[(2,4-diaminopyrimidin-1-ium-5-yl)methyl]-3-methoxyphenoxy}propyl)pentanedioate  ligand  55  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BDM
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
 BDM  N1    N   NR16   1  -0.658    5.7496  -4.3628  -0.6244
 BDM  C2    C   CR6    0   0.736    5.4457  -4.7629   0.6318
 BDM  N2    N   NH2    0  -0.814    6.3222  -5.5004   1.2951
 BDM  N3    N   N      0  -0.498    4.3045  -4.4296   1.1991
 BDM  C4    C   CR6    0   0.532    3.4296  -3.6887   0.5231
 BDM  N4    N   NH2    0  -0.794    2.2986  -3.3830   1.1358
 BDM  C5    C   CR6    0  -0.063    3.6852  -3.2391  -0.8187
 BDM  C6    C   CR16   0   0.047    4.8745  -3.6124  -1.3367
 BDM  C7    C   CH2    0  -0.600    2.6965  -2.4235  -1.5937
 BDM  C8    C   CR6    0   0.147    2.4369  -1.0602  -0.9939
 BDM  C9    C   CR16   0  -0.505    1.1311  -0.6150  -0.8512
 BDM  C10   C   CR6    0   0.488    0.8758   0.6550  -0.3294
 BDM  O10   O   O2     0  -0.458   -0.3474   1.1646  -0.1700
 BDM  C11   C   CR6    0  -0.380    1.9512   1.4558   0.0556
 BDM  BR11  BR  BR     0  -0.023    1.6244   3.1603   0.7710
 BDM  C12   C   CR6    0   0.482    3.2678   1.0061  -0.0790
 BDM  O12   O   O2     0  -0.454    4.2301   1.8431   0.3206
 BDM  C13   C   CR16   0  -0.441    3.5039  -0.2603  -0.6078
 BDM  C14   C   CH3    0  -0.441    5.5798   1.4173   0.2535
 BDM  C15   C   CH2    0  -0.175   -1.4813   0.3580  -0.4785
 BDM  C16   C   CH2    0  -0.459   -2.7309   1.1741  -0.2324
 BDM  C17   C   CH2    0  -0.414   -3.9823   0.3364  -0.4729
 BDM  C18   C   CH1    0  -0.318   -5.2839   1.1330  -0.3887
 BDM  C19   C   CH2    0  -0.390   -6.4773   0.2298  -0.7043
 BDM  C20   C   CH2    0  -0.589   -7.8062   0.9663  -0.7529
 BDM  C21   C   C      0   0.406   -5.4351   1.7839   0.9989
 BDM  OXV   O   O      0  -0.621   -5.5077   3.0289   1.0545
 BDM  OXW   O   OC    -1  -0.622   -5.4782   1.0024   1.9738
 BDM  C22   C   C      0   0.410   -9.0337   0.1167  -1.1262
 BDM  OX5   O   O      0  -0.611   -8.8861  -1.1182  -1.2190
 BDM  OX6   O   OC    -1  -0.637  -10.1011   0.7444  -1.2996
 BDM  HN1   H   HNR6   0   0.452    6.6293  -4.6247  -1.0475
 BDM  HN21  H   HNH2   0   0.431    7.1947  -5.7980   0.8926
 BDM  HN22  H   HNH2   0   0.428    6.0976  -5.8142   2.2240
 BDM  HN41  H   HNH2   0   0.420    2.1381  -3.7004   2.0783
 BDM  HN42  H   HNH2   0   0.430    1.5971  -2.7926   0.7219
 BDM  H6    H   HCR6   0   0.334    5.1924  -3.3426  -2.3333
 BDM  H71   H   HCH2   0   0.287    1.7527  -2.9680  -1.6873
 BDM  H72   H   HCH2   0   0.300    3.0696  -2.3005  -2.6133
 BDM  H9    H   HCR6   0   0.292    0.3167  -1.2583  -1.1578
 BDM  H13   H   HCR6   0   0.275    4.5145  -0.6258  -0.7301
 BDM  H141  H   HCH3   0   0.267    6.1761   2.2379   0.6432
 BDM  H142  H   HCH3   0   0.234    5.7559   0.5301   0.8661
 BDM  H143  H   HCH3   0   0.235    5.8923   1.2118  -0.7728
 BDM  H151  H   HCH2   0   0.227   -1.4414   0.0358  -1.5245
 BDM  H152  H   HCH2   0   0.225   -1.4759  -0.5410   0.1482
 BDM  H161  H   HCH2   0   0.233   -2.7218   1.5501   0.7937
 BDM  H162  H   HCH2   0   0.226   -2.7320   2.0438  -0.8962
 BDM  H171  H   HCH2   0   0.209   -3.9193  -0.1305  -1.4625
 BDM  H172  H   HCH2   0   0.209   -4.0161  -0.4840   0.2508
 BDM  H18   H   HCH1   0   0.182   -5.2431   1.9296  -1.1422
 BDM  H191  H   HCH2   0   0.195   -6.3025  -0.2626  -1.6663
 BDM  H192  H   HCH2   0   0.195   -6.5216  -0.5694   0.0398
 BDM  H201  H   HCH2   0   0.222   -8.0134   1.4305   0.2185
 BDM  H202  H   HCH2   0   0.209   -7.7405   1.8036  -1.4571

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
 BDM  N1   C2    aromatic  1.353  0.020  1.353
 BDM  N1   C6    aromatic  1.355  0.020  1.355
 BDM  N1   HN1   single    0.860  0.020  1.020
 BDM  C2   N2    single    1.324  0.020  1.324
 BDM  C2   N3    aromatic  1.317  0.020  1.317
 BDM  N2   HN21  single    0.860  0.020  1.020
 BDM  N2   HN22  single    0.860  0.020  1.020
 BDM  N3   C4    aromatic  1.331  0.020  1.331
 BDM  C4   N4    single    1.322  0.020  1.322
 BDM  C4   C5    aromatic  1.438  0.020  1.438
 BDM  N4   HN41  single    0.860  0.020  1.020
 BDM  N4   HN42  single    0.860  0.020  1.020
 BDM  C5   C6    aromatic  1.350  0.020  1.350
 BDM  C5   C7    single    1.498  0.020  1.498
 BDM  C6   H6    single    0.930  0.020  1.080
 BDM  C7   C8    single    1.512  0.020  1.512
 BDM  C7   H71   single    0.970  0.020  1.090
 BDM  C7   H72   single    0.970  0.020  1.090
 BDM  C8   C9    aromatic  1.387  0.020  1.387
 BDM  C8   C13   aromatic  1.388  0.020  1.388
 BDM  C9   C10   aromatic  1.397  0.020  1.397
 BDM  C9   H9    single    0.930  0.020  1.080
 BDM  C10  O10   single    1.335  0.020  1.335
 BDM  C10  C11   aromatic  1.395  0.020  1.395
 BDM  O10  C15   single    1.425  0.020  1.425
 BDM  C11  BR11  single    1.877  0.020  1.877
 BDM  C11  C12   aromatic  1.398  0.020  1.398
 BDM  C12  O12   single    1.337  0.020  1.337
 BDM  C12  C13   aromatic  1.393  0.020  1.393
 BDM  O12  C14   single    1.417  0.020  1.417
 BDM  C13  H13   single    0.930  0.020  1.080
 BDM  C14  H141  single    0.970  0.020  1.090
 BDM  C14  H142  single    0.970  0.020  1.090
 BDM  C14  H143  single    0.970  0.020  1.090
 BDM  C15  C16   single    1.513  0.020  1.513
 BDM  C15  H151  single    0.970  0.020  1.090
 BDM  C15  H152  single    0.970  0.020  1.090
 BDM  C16  C17   single    1.525  0.020  1.525
 BDM  C16  H161  single    0.970  0.020  1.090
 BDM  C16  H162  single    0.970  0.020  1.090
 BDM  C17  C18   single    1.528  0.020  1.528
 BDM  C17  H171  single    0.970  0.020  1.090
 BDM  C17  H172  single    0.970  0.020  1.090
 BDM  C18  C19   single    1.530  0.020  1.530
 BDM  C18  C21   single    1.540  0.020  1.540
 BDM  C18  H18   single    0.970  0.020  1.090
 BDM  C19  C20   single    1.520  0.020  1.520
 BDM  C19  H191  single    0.970  0.020  1.090
 BDM  C19  H192  single    0.970  0.020  1.090
 BDM  C20  C22   single    1.539  0.020  1.539
 BDM  C20  H201  single    0.970  0.020  1.090
 BDM  C20  H202  single    0.970  0.020  1.090
 BDM  C21  OXV   deloc     1.248  0.020  1.248
 BDM  C21  OXW   deloc     1.250  0.020  1.250
 BDM  C22  OX5   deloc     1.247  0.020  1.247
 BDM  C22  OX6   deloc     1.250  0.020  1.250

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
 BDM  HN1   N1   C6    119.05  3.000
 BDM  HN1   N1   C2    120.51  3.000
 BDM  C6    N1   C2    120.44  3.000
 BDM  N3    C2   N2    119.93  3.000
 BDM  N3    C2   N1    121.31  3.000
 BDM  N2    C2   N1    118.77  3.000
 BDM  HN22  N2   HN21  118.10  3.000
 BDM  HN22  N2   C2    119.25  3.000
 BDM  HN21  N2   C2    122.60  3.000
 BDM  C4    N3   C2    119.45  3.000
 BDM  C5    C4   N4    120.80  3.000
 BDM  C5    C4   N3    122.09  3.000
 BDM  N4    C4   N3    117.11  3.000
 BDM  HN42  N4   HN41  117.31  3.000
 BDM  HN42  N4   C4    122.79  3.000
 BDM  HN41  N4   C4    119.80  3.000
 BDM  C7    C5   C6    122.25  3.000
 BDM  C7    C5   C4    122.40  3.000
 BDM  C6    C5   C4    115.35  3.000
 BDM  H6    C6   C5    122.97  3.000
 BDM  H6    C6   N1    115.67  3.000
 BDM  C5    C6   N1    121.36  3.000
 BDM  H72   C7   H71   105.71  3.000
 BDM  H72   C7   C8    109.11  3.000
 BDM  H71   C7   C8    109.55  3.000
 BDM  H72   C7   C5    108.59  3.000
 BDM  H71   C7   C5    110.05  3.000
 BDM  C8    C7   C5    113.52  3.000
 BDM  C13   C8   C9    120.66  3.000
 BDM  C13   C8   C7    119.86  3.000
 BDM  C9    C8   C7    119.47  3.000
 BDM  H9    C9   C10   120.59  3.000
 BDM  H9    C9   C8    119.24  3.000
 BDM  C10   C9   C8    120.17  3.000
 BDM  C11   C10  O10   117.03  3.000
 BDM  C11   C10  C9    118.96  3.000
 BDM  O10   C10  C9    124.01  3.000
 BDM  C15   O10  C10   119.16  3.000
 BDM  C12   C11  BR11  119.52  3.000
 BDM  C12   C11  C10   120.99  3.000
 BDM  BR11  C11  C10   119.49  3.000
 BDM  C13   C12  O12   124.13  3.000
 BDM  C13   C12  C11   119.26  3.000
 BDM  O12   C12  C11   116.61  3.000
 BDM  C14   O12  C12   118.91  3.000
 BDM  H13   C13  C12   120.58  3.000
 BDM  H13   C13  C8    119.47  3.000
 BDM  C12   C13  C8    119.95  3.000
 BDM  H143  C14  H142  109.14  3.000
 BDM  H143  C14  H141  108.79  3.000
 BDM  H142  C14  H141  108.89  3.000
 BDM  H143  C14  O12   111.94  3.000
 BDM  H142  C14  O12   111.78  3.000
 BDM  H141  C14  O12   106.19  3.000
 BDM  H152  C15  H151  107.73  3.000
 BDM  H152  C15  C16   110.70  3.000
 BDM  H151  C15  C16   110.13  3.000
 BDM  H152  C15  O10   109.67  3.000
 BDM  H151  C15  O10   110.14  3.000
 BDM  C16   C15  O10   108.47  3.000
 BDM  H162  C16  H161  107.22  3.000
 BDM  H162  C16  C17   109.89  3.000
 BDM  H161  C16  C17   110.12  3.000
 BDM  H162  C16  C15   109.32  3.000
 BDM  H161  C16  C15   109.36  3.000
 BDM  C17   C16  C15   110.85  3.000
 BDM  H172  C17  H171  106.22  3.000
 BDM  H172  C17  C18   109.14  3.000
 BDM  H171  C17  C18   108.71  3.000
 BDM  H172  C17  C16   109.44  3.000
 BDM  H171  C17  C16   109.22  3.000
 BDM  C18   C17  C16   113.82  3.000
 BDM  H18   C18  C21   108.39  3.000
 BDM  H18   C18  C19   108.42  3.000
 BDM  C21   C18  C19   111.03  3.000
 BDM  H18   C18  C17   107.99  3.000
 BDM  C21   C18  C17   110.70  3.000
 BDM  C19   C18  C17   110.20  3.000
 BDM  H192  C19  H191  106.01  3.000
 BDM  H192  C19  C20   109.92  3.000
 BDM  H191  C19  C20   109.23  3.000
 BDM  H192  C19  C18   108.84  3.000
 BDM  H191  C19  C18   108.80  3.000
 BDM  C20   C19  C18   113.74  3.000
 BDM  H202  C20  H201  104.90  3.000
 BDM  H202  C20  C22   108.29  3.000
 BDM  H201  C20  C22   107.34  3.000
 BDM  H202  C20  C19   109.77  3.000
 BDM  H201  C20  C19   110.00  3.000
 BDM  C22   C20  C19   115.95  3.000
 BDM  OXW   C21  OXV   125.92  3.000
 BDM  OXW   C21  C18   116.21  3.000
 BDM  OXV   C21  C18   117.86  3.000
 BDM  OX6   C22  OX5   125.99  3.000
 BDM  OX6   C22  C20   115.94  3.000
 BDM  OX5   C22  C20   118.06  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
 BDM  CONST_01  C4    N3   C2   N1       0.00   0.0  0
 BDM  CONST_02  C4    C5   C6   N1       0.00   0.0  0
 BDM  CONST_03  C5    C6   N1   C2       0.00   0.0  0
 BDM  CONST_04  C5    C4   N3   C2       0.00   0.0  0
 BDM  CONST_05  C6    N1   C2   N3       0.00   0.0  0
 BDM  CONST_06  C6    C5   C4   N3       0.00   0.0  0
 BDM  CONST_07  C11   C10  C9   C8       0.00   0.0  0
 BDM  CONST_08  C11   C12  C13  C8       0.00   0.0  0
 BDM  CONST_09  C12   C13  C8   C9       0.00   0.0  0
 BDM  CONST_10  C12   C11  C10  C9       0.00   0.0  0
 BDM  CONST_11  C13   C8   C9   C10      0.00   0.0  0
 BDM  CONST_12  C13   C12  C11  C10      0.00   0.0  0
 BDM  CONST_13  C7    C5   C6   N1     180.00   0.0  0
 BDM  CONST_14  N4    C4   N3   C2     180.00   0.0  0
 BDM  CONST_15  C6    N1   C2   N2     180.00   0.0  0
 BDM  CONST_16  C4    N3   C2   N2     180.00   0.0  0
 BDM  CONST_17  C7    C5   C4   N3     180.00   0.0  0
 BDM  CONST_18  C6    C5   C4   N4     180.00   0.0  0
 BDM  CONST_19  C10   C9   C8   C7     180.00   0.0  0
 BDM  CONST_20  C12   C13  C8   C7     180.00   0.0  0
 BDM  CONST_21  O10   C10  C9   C8     180.00   0.0  0
 BDM  CONST_22  O12   C12  C13  C8     180.00   0.0  0
 BDM  CONST_23  BR11  C11  C10  C9     180.00   0.0  0
 BDM  CONST_24  O12   C12  C11  C10    180.00   0.0  0
 BDM  CONST_25  C12   C11  C10  O10    180.00   0.0  0
 BDM  CONST_26  C13   C12  C11  BR11   180.00   0.0  0
 BDM  CONST_27  H6    C6   N1   C2     180.00   0.0  0
 BDM  CONST_28  HN1   N1   C2   N3     180.00   0.0  0
 BDM  CONST_29  H13   C13  C8   C9     180.00   0.0  0
 BDM  CONST_30  H9    C9   C10  C11    180.00   0.0  0
 BDM  CONST_31  HN21  N2   C2   N1       0.00   0.0  0
 BDM  CONST_32  HN22  N2   C2   N1     180.00   0.0  0
 BDM  CONST_33  HN41  N4   C4   N3       0.00   0.0  0
 BDM  CONST_34  HN42  N4   C4   N3     180.00   0.0  0
 BDM  Var_01    C8    C7   C5   C4      64.56  30.0  2
 BDM  Var_02    C9    C8   C7   C5    -133.22  30.0  2
 BDM  Var_03    C16   C15  O10  C10   -179.17  30.0  3
 BDM  Var_04    H141  C14  O12  C12   -178.79  30.0  3
 BDM  Var_05    C17   C16  C15  O10   -176.88  30.0  3
 BDM  Var_06    C18   C17  C16  C15   -173.84  30.0  3
 BDM  Var_07    C22   C20  C19  C18    177.47  30.0  3
 BDM  Var_08    OX5   C22  C20  C19      7.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BDM  chir_01  C18  C17  C19  C21  negativ

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
 BDM  plan-1  N1    0.020
 BDM  plan-1  C2    0.020
 BDM  plan-1  N2    0.020
 BDM  plan-1  N3    0.020
 BDM  plan-1  C4    0.020
 BDM  plan-1  N4    0.020
 BDM  plan-1  C5    0.020
 BDM  plan-1  C6    0.020
 BDM  plan-1  C7    0.020
 BDM  plan-1  HN1   0.020
 BDM  plan-1  H6    0.020
 BDM  plan-2  C7    0.020
 BDM  plan-2  C8    0.020
 BDM  plan-2  C9    0.020
 BDM  plan-2  C10   0.020
 BDM  plan-2  O10   0.020
 BDM  plan-2  C11   0.020
 BDM  plan-2  BR11  0.020
 BDM  plan-2  C12   0.020
 BDM  plan-2  O12   0.020
 BDM  plan-2  C13   0.020
 BDM  plan-2  H9    0.020
 BDM  plan-2  H13   0.020
 BDM  plan-3  C2    0.020
 BDM  plan-3  N2    0.020
 BDM  plan-3  HN21  0.020
 BDM  plan-3  HN22  0.020
 BDM  plan-4  C4    0.020
 BDM  plan-4  N4    0.020
 BDM  plan-4  HN41  0.020
 BDM  plan-4  HN42  0.020
 BDM  plan-5  C18   0.020
 BDM  plan-5  C21   0.020
 BDM  plan-5  OXV   0.020
 BDM  plan-5  OXW   0.020
 BDM  plan-6  C20   0.020
 BDM  plan-6  C22   0.020
 BDM  plan-6  OX5   0.020
 BDM  plan-6  OX6   0.020

