# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:46:57 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 6-(5H-dibenzo[b,f]azepin-5-ylmethyl)pteridine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2nc(CN3c4ccccc4C=Cc5ccccc35)cnc2n1
#
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
 PMD  PMD  6-(5H-dibenzo[b,f]azepin-5-ylmethyl)pteridine-2,4-diamine  ligand  45  28  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PMD
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
 PMD  C2B   C  CR6   0   0.550  -0.2605   0.5885   5.2350
 PMD  C4B   C  CR6   0   0.480  -0.2001  -1.3525   4.0363
 PMD  C4    C  CR66  0   0.008  -0.4705  -0.5850   2.8446
 PMD  C6B   C  CR6   0   0.168  -0.8141  -0.4259   0.6168
 PMD  C7B   C  CR16  0  -0.071  -0.9514   0.9714   0.7786
 PMD  C8    C  CR66  0   0.388  -0.6083   0.8024   3.0163
 PMD  C9B   C  CH2   0  -0.404  -0.9742  -1.0697  -0.7310
 PMD  C0'   C  CR6   0   0.236  -0.7159  -0.4469  -3.0799
 PMD  C1'   C  CR16  0  -0.292  -1.2508  -1.6486  -3.5379
 PMD  C2'   C  CR16  0  -0.269  -1.7681  -1.7522  -4.8211
 PMD  C3'   C  CR16  0  -0.249  -1.7436  -0.6546  -5.6704
 PMD  C4'   C  CR16  0  -0.334  -1.1997   0.5382  -5.2237
 PMD  C5'   C  CR6   0   0.103  -0.6717   0.6634  -3.9365
 PMD  C6'   C  C1    0  -0.272  -0.1095   1.9450  -3.5275
 PMD  C6    C  C1    0  -0.274   0.9042   2.1452  -2.6742
 PMD  C7'   C  CR6   0   0.111   1.6710   1.1259  -1.9680
 PMD  C8'   C  CR16  0  -0.335   3.0171   1.3720  -1.6857
 PMD  C9'   C  CR16  0  -0.249   3.8008   0.4388  -1.0285
 PMD  CA'   C  CR16  0  -0.267   3.2372  -0.7680  -0.6372
 PMD  CB'   C  CR16  0  -0.274   1.9013  -1.0299  -0.9029
 PMD  CC'   C  CR6   0   0.231   1.1071  -0.0903  -1.5554
 PMD  N1'   N  N     0  -0.510  -0.5038   1.3956   4.2115
 PMD  N2'   N  NH2   0  -0.815  -0.1664   1.1432   6.4508
 PMD  N3'   N  N     0  -0.502  -0.1021  -0.7539   5.2019
 PMD  N4'   N  NH2   0  -0.804  -0.0525  -2.6683   3.9420
 PMD  N5'   N  N     0  -0.391  -0.5713  -1.1833   1.6581
 PMD  N8'   N  N     0  -0.392  -0.8547   1.5739   1.9352
 PMD  N0'   N  NT    0  -0.594  -0.2779  -0.3056  -1.7456
 PMD  H7'1  H  HCR6  0   0.273  -1.1427   1.5914  -0.0914
 PMD  H9'1  H  HCH2  0   0.253  -0.6710  -2.1207  -0.6539
 PMD  H9'2  H  HCH2  0   0.291  -2.0342  -1.0736  -0.9992
 PMD  H2'1  H  HCR6  0   0.260  -2.1922  -2.6909  -5.1527
 PMD  H3'1  H  HCR6  0   0.256  -2.1519  -0.7247  -6.6700
 PMD  H4'1  H  HCR6  0   0.255  -1.1861   1.4009  -5.8792
 PMD  H6'1  H  H     0   0.258  -0.5041   2.8139  -4.0429
 PMD  H61   H  H     0   0.258   1.2613   3.1626  -2.5567
 PMD  H8'1  H  HCR6  0   0.255   3.4488   2.3191  -1.9874
 PMD  H9B   H  HCR6  0   0.256   4.8394   0.6541  -0.8155
 PMD  H10'  H  HCR6  0   0.260   3.8322  -1.5070  -0.1166
 PMD  H11'  H  HCR6  0   0.261   1.4764  -1.9714  -0.5802
 PMD  HN21  H  HNH2  0   0.400   0.0841   0.5837   7.2459
 PMD  HN22  H  HNH2  0   0.399  -0.2095   2.1410   6.5567
 PMD  HN41  H  HNH2  0   0.408   0.1484  -3.2218   4.7572
 PMD  HN42  H  HNH2  0   0.414  -0.1214  -3.1253   3.0488
 PMD  H1'1  H  HCR6  0   0.267  -1.2779  -2.5105  -2.8836

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
 PMD  C2B  N1'   aromatic  1.326  0.020  1.326
 PMD  C2B  N2'   single    1.340  0.020  1.340
 PMD  C2B  N3'   aromatic  1.352  0.020  1.352
 PMD  C4B  C4    aromatic  1.443  0.020  1.443
 PMD  C4B  N3'   aromatic  1.314  0.020  1.314
 PMD  C4B  N4'   single    1.327  0.020  1.327
 PMD  C4   C8    aromatic  1.405  0.020  1.405
 PMD  C4   N5'   aromatic  1.333  0.020  1.333
 PMD  C6B  C7B   aromatic  1.413  0.020  1.413
 PMD  C6B  C9B   single    1.502  0.020  1.502
 PMD  C6B  N5'   aromatic  1.310  0.020  1.310
 PMD  C7B  N8'   aromatic  1.308  0.020  1.308
 PMD  C7B  H7'1  single    0.930  0.020  1.080
 PMD  C8   N1'   aromatic  1.338  0.020  1.338
 PMD  C8   N8'   aromatic  1.351  0.020  1.351
 PMD  C9B  N0'   single    1.449  0.020  1.449
 PMD  C9B  H9'1  single    0.970  0.020  1.090
 PMD  C9B  H9'2  single    0.970  0.020  1.090
 PMD  C0'  C1'   aromatic  1.393  0.020  1.393
 PMD  C0'  C5'   aromatic  1.403  0.020  1.403
 PMD  C0'  N0'   single    1.411  0.020  1.411
 PMD  C1'  C2'   aromatic  1.387  0.020  1.387
 PMD  C1'  H1'1  single    0.930  0.020  1.080
 PMD  C2'  C3'   aromatic  1.388  0.020  1.388
 PMD  C2'  H2'1  single    0.930  0.020  1.080
 PMD  C3'  C4'   aromatic  1.385  0.020  1.385
 PMD  C3'  H3'1  single    0.930  0.020  1.080
 PMD  C4'  C5'   aromatic  1.397  0.020  1.397
 PMD  C4'  H4'1  single    0.930  0.020  1.080
 PMD  C5'  C6'   single    1.458  0.020  1.458
 PMD  C6'  C6    double    1.340  0.020  1.340
 PMD  C6'  H6'1  single    0.930  0.020  1.080
 PMD  C6   C7'   single    1.458  0.020  1.458
 PMD  C6   H61   single    0.930  0.020  1.080
 PMD  C7'  C8'   aromatic  1.397  0.020  1.397
 PMD  C7'  CC'   aromatic  1.403  0.020  1.403
 PMD  C8'  C9'   aromatic  1.385  0.020  1.385
 PMD  C8'  H8'1  single    0.930  0.020  1.080
 PMD  C9'  CA'   aromatic  1.388  0.020  1.388
 PMD  C9'  H9B   single    0.930  0.020  1.080
 PMD  CA'  CB'   aromatic  1.387  0.020  1.387
 PMD  CA'  H10'  single    0.930  0.020  1.080
 PMD  CB'  CC'   aromatic  1.393  0.020  1.393
 PMD  CB'  H11'  single    0.930  0.020  1.080
 PMD  CC'  N0'   single    1.414  0.020  1.414
 PMD  N2'  HN21  single    0.860  0.020  1.020
 PMD  N2'  HN22  single    0.860  0.020  1.020
 PMD  N4'  HN41  single    0.860  0.020  1.020
 PMD  N4'  HN42  single    0.860  0.020  1.020

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
 PMD  N3'   C2B  N2'   115.16  3.000
 PMD  N3'   C2B  N1'   127.37  3.000
 PMD  N2'   C2B  N1'   117.47  3.000
 PMD  N4'   C4B  N3'   120.42  3.000
 PMD  N4'   C4B  C4    119.30  3.000
 PMD  N3'   C4B  C4    120.28  3.000
 PMD  N5'   C4   C8    123.01  3.000
 PMD  N5'   C4   C4B   120.71  3.000
 PMD  C8    C4   C4B   116.28  3.000
 PMD  N5'   C6B  C9B   119.01  3.000
 PMD  N5'   C6B  C7B   119.90  3.000
 PMD  C9B   C6B  C7B   121.07  3.000
 PMD  H7'1  C7B  N8'   117.31  3.000
 PMD  H7'1  C7B  C6B   119.35  3.000
 PMD  N8'   C7B  C6B   123.34  3.000
 PMD  N8'   C8   N1'   118.41  3.000
 PMD  N8'   C8   C4    118.96  3.000
 PMD  N1'   C8   C4    122.63  3.000
 PMD  H9'2  C9B  H9'1  106.37  3.000
 PMD  H9'2  C9B  N0'   107.22  3.000
 PMD  H9'1  C9B  N0'   114.96  3.000
 PMD  H9'2  C9B  C6B   108.96  3.000
 PMD  H9'1  C9B  C6B   108.56  3.000
 PMD  N0'   C9B  C6B   110.56  3.000
 PMD  N0'   C0'  C5'   119.22  3.000
 PMD  N0'   C0'  C1'   121.09  3.000
 PMD  C5'   C0'  C1'   119.61  3.000
 PMD  H1'1  C1'  C2'   119.36  3.000
 PMD  H1'1  C1'  C0'   119.86  3.000
 PMD  C2'   C1'  C0'   120.78  3.000
 PMD  H2'1  C2'  C3'   120.35  3.000
 PMD  H2'1  C2'  C1'   119.63  3.000
 PMD  C3'   C2'  C1'   120.02  3.000
 PMD  H3'1  C3'  C4'   120.13  3.000
 PMD  H3'1  C3'  C2'   120.49  3.000
 PMD  C4'   C3'  C2'   119.38  3.000
 PMD  H4'1  C4'  C5'   118.77  3.000
 PMD  H4'1  C4'  C3'   119.71  3.000
 PMD  C5'   C4'  C3'   121.53  3.000
 PMD  C6'   C5'  C4'   118.89  3.000
 PMD  C6'   C5'  C0'   122.44  3.000
 PMD  C4'   C5'  C0'   118.67  3.000
 PMD  H6'1  C6'  C6    117.27  3.000
 PMD  H6'1  C6'  C5'   115.50  3.000
 PMD  C6    C6'  C5'   126.99  3.000
 PMD  H61   C6   C7'   115.48  3.000
 PMD  H61   C6   C6'   117.27  3.000
 PMD  C7'   C6   C6'   127.00  3.000
 PMD  CC'   C7'  C8'   118.73  3.000
 PMD  CC'   C7'  C6    122.49  3.000
 PMD  C8'   C7'  C6    118.78  3.000
 PMD  H8'1  C8'  C9'   119.72  3.000
 PMD  H8'1  C8'  C7'   118.78  3.000
 PMD  C9'   C8'  C7'   121.50  3.000
 PMD  H9B   C9'  CA'   120.48  3.000
 PMD  H9B   C9'  C8'   120.18  3.000
 PMD  CA'   C9'  C8'   119.34  3.000
 PMD  H10'  CA'  CB'   119.52  3.000
 PMD  H10'  CA'  C9'   120.40  3.000
 PMD  CB'   CA'  C9'   120.08  3.000
 PMD  H11'  CB'  CC'   120.18  3.000
 PMD  H11'  CB'  CA'   119.04  3.000
 PMD  CC'   CB'  CA'   120.77  3.000
 PMD  N0'   CC'  CB'   121.25  3.000
 PMD  N0'   CC'  C7'   119.08  3.000
 PMD  CB'   CC'  C7'   119.57  3.000
 PMD  C8    N1'  C2B   115.71  3.000
 PMD  HN22  N2'  HN21  118.74  3.000
 PMD  HN22  N2'  C2B   120.27  3.000
 PMD  HN21  N2'  C2B   120.36  3.000
 PMD  C4B   N3'  C2B   117.73  3.000
 PMD  HN42  N4'  HN41  118.92  3.000
 PMD  HN42  N4'  C4B   120.40  3.000
 PMD  HN41  N4'  C4B   120.67  3.000
 PMD  C6B   N5'  C4    117.52  3.000
 PMD  C8    N8'  C7B   117.27  3.000
 PMD  CC'   N0'  C0'   116.50  3.000
 PMD  CC'   N0'  C9B   117.18  3.000
 PMD  C0'   N0'  C9B   117.40  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
 PMD  CONST_01  C4    C8   N1'  C2B     0.00   0.0  0
 PMD  CONST_02  N8'   C8   N1'  C2B   180.00   0.0  0
 PMD  CONST_03  C4    C4B  N3'  C2B     0.00   0.0  0
 PMD  CONST_04  N1'   C8   C4   C4B     0.00   0.0  0
 PMD  CONST_05  N8'   C8   C4   C4B   180.00   0.0  0
 PMD  CONST_06  C6B   N5'  C4   C4B   180.00   0.0  0
 PMD  CONST_07  N1'   C2B  N3'  C4B     0.00   0.0  0
 PMD  CONST_08  C7B   N8'  C8   C4      0.00   0.0  0
 PMD  CONST_09  C7B   C6B  N5'  C4      0.00   0.0  0
 PMD  CONST_10  C8    N8'  C7B  C6B     0.00   0.0  0
 PMD  CONST_11  C8    C4   N5'  C6B     0.00   0.0  0
 PMD  CONST_12  N1'   C8   N8'  C7B   180.00   0.0  0
 PMD  CONST_13  N3'   C4B  C4   C8      0.00   0.0  0
 PMD  CONST_14  N3'   C2B  N1'  C8      0.00   0.0  0
 PMD  CONST_15  C3'   C2'  C1'  C0'     0.00   0.0  0
 PMD  CONST_16  C3'   C4'  C5'  C0'     0.00   0.0  0
 PMD  CONST_17  C4'   C5'  C0'  C1'     0.00   0.0  0
 PMD  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 PMD  CONST_19  C5'   C0'  C1'  C2'     0.00   0.0  0
 PMD  CONST_20  C5'   C4'  C3'  C2'     0.00   0.0  0
 PMD  CONST_21  CA'   C9'  C8'  C7'     0.00   0.0  0
 PMD  CONST_22  CA'   CB'  CC'  C7'     0.00   0.0  0
 PMD  CONST_23  CB'   CC'  C7'  C8'     0.00   0.0  0
 PMD  CONST_24  CB'   CA'  C9'  C8'     0.00   0.0  0
 PMD  CONST_25  CC'   C7'  C8'  C9'     0.00   0.0  0
 PMD  CONST_26  CC'   CB'  CA'  C9'     0.00   0.0  0
 PMD  CONST_27  N5'   C4   C8   N1'   180.00   0.0  0
 PMD  CONST_28  N5'   C4   C4B  N3'   180.00   0.0  0
 PMD  CONST_29  N8'   C8   C4   N5'     0.00   0.0  0
 PMD  CONST_30  N8'   C7B  C6B  N5'     0.00   0.0  0
 PMD  CONST_31  N4'   C4B  N3'  C2B   180.00   0.0  0
 PMD  CONST_32  N2'   C2B  N3'  C4B   180.00   0.0  0
 PMD  CONST_33  C9B   C6B  N5'  C4    180.00   0.0  0
 PMD  CONST_34  N4'   C4B  C4   C8    180.00   0.0  0
 PMD  CONST_35  N2'   C2B  N1'  C8    180.00   0.0  0
 PMD  CONST_36  N8'   C7B  C6B  C9B   180.00   0.0  0
 PMD  CONST_37  N5'   C4   C4B  N4'     0.00   0.0  0
 PMD  CONST_38  H7'1  C7B  N8'  C8    180.00   0.0  0
 PMD  CONST_39  H2'1  C2'  C1'  C0'   180.00   0.0  0
 PMD  CONST_40  H4'1  C4'  C5'  C0'   180.00   0.0  0
 PMD  CONST_41  H3'1  C3'  C2'  C1'   180.00   0.0  0
 PMD  CONST_42  H1'1  C1'  C2'  C3'   180.00   0.0  0
 PMD  CONST_43  H8'1  C8'  C7'  C6      0.00   0.0  0
 PMD  CONST_44  H9B   C9'  C8'  C7'   180.00   0.0  0
 PMD  CONST_45  H11'  CB'  CC'  C7'   180.00   0.0  0
 PMD  CONST_46  H10'  CA'  C9'  C8'   180.00   0.0  0
 PMD  CONST_47  HN41  N4'  C4B  C4    180.00   0.0  0
 PMD  CONST_48  HN42  N4'  C4B  C4      0.00   0.0  0
 PMD  CONST_49  HN21  N2'  C2B  N1'   180.00   0.0  0
 PMD  CONST_50  HN22  N2'  C2B  N1'     0.00   0.0  0
 PMD  Var_01    C6    C6'  C5'  C0'    32.35  30.0  1
 PMD  Var_02    C7'   CC'  N0'  C0'    68.76  30.0  1
 PMD  Var_03    CC'   N0'  C0'  C1'   114.77  30.0  1
 PMD  Var_04    C7'   C6   C6'  C5'     0.13  30.0  1
 PMD  Var_05    C8'   C7'  C6   C6'   148.06  30.0  1
 PMD  Var_06    C0'   N0'  C9B  C6B  -156.53  30.0  3
 PMD  Var_07    N0'   C9B  C6B  C7B    44.10  30.0  2

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
 PMD  plan-1  C2B   0.020
 PMD  plan-1  C4B   0.020
 PMD  plan-1  C4    0.020
 PMD  plan-1  C6B   0.020
 PMD  plan-1  C7B   0.020
 PMD  plan-1  C8    0.020
 PMD  plan-1  C9B   0.020
 PMD  plan-1  N1'   0.020
 PMD  plan-1  N2'   0.020
 PMD  plan-1  N3'   0.020
 PMD  plan-1  N4'   0.020
 PMD  plan-1  N5'   0.020
 PMD  plan-1  N8'   0.020
 PMD  plan-1  H7'1  0.020
 PMD  plan-2  C0'   0.020
 PMD  plan-2  C1'   0.020
 PMD  plan-2  C2'   0.020
 PMD  plan-2  C3'   0.020
 PMD  plan-2  C4'   0.020
 PMD  plan-2  C5'   0.020
 PMD  plan-2  C6'   0.020
 PMD  plan-2  N0'   0.020
 PMD  plan-2  H2'1  0.020
 PMD  plan-2  H3'1  0.020
 PMD  plan-2  H4'1  0.020
 PMD  plan-2  H1'1  0.020
 PMD  plan-3  C6    0.020
 PMD  plan-3  C7'   0.020
 PMD  plan-3  C8'   0.020
 PMD  plan-3  C9'   0.020
 PMD  plan-3  CA'   0.020
 PMD  plan-3  CB'   0.020
 PMD  plan-3  CC'   0.020
 PMD  plan-3  N0'   0.020
 PMD  plan-3  H8'1  0.020
 PMD  plan-3  H9B   0.020
 PMD  plan-3  H10'  0.020
 PMD  plan-3  H11'  0.020
 PMD  plan-4  C2B   0.020
 PMD  plan-4  N2'   0.020
 PMD  plan-4  HN21  0.020
 PMD  plan-4  HN22  0.020
 PMD  plan-5  C4B   0.020
 PMD  plan-5  N4'   0.020
 PMD  plan-5  HN41  0.020
 PMD  plan-5  HN42  0.020

