FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: VZG21

Calculation Name: 1EJB-A-Xray549

Preferred Name:

Target Type:

Ligand Name: 5-(6-d-ribitylamino-2,4-dihydroxypyrimidin-5-yl)-1-pentyl-phosphonic acid

Ligand 3-letter code: INJ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EJB

Chain ID: A

ChEMBL ID:

UniProt ID: P50861

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 168
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1655681.748986
FMO2-HF: Nuclear repulsion 1590501.398158
FMO2-HF: Total energy -65180.350828
FMO2-MP2: Total energy -65368.299241


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-41.368-40.067-0.013-0.507-0.7810
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.918
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A3LYS10.9610.9823.84838.92740.228-0.013-0.507-0.7810.000
4A4GLY00.0450.0256.1420.7590.7590.0000.0000.0000.000
5A5LEU00.0320.0039.487-1.256-1.2560.0000.0000.0000.000
6A6GLY0-0.0240.00511.3751.5221.5220.0000.0000.0000.000
7A7LYS10.9100.95213.31419.20319.2030.0000.0000.0000.000
8A8PRO0-0.007-0.00715.9430.5010.5010.0000.0000.0000.000
9A9ASP-1-0.877-0.94019.030-14.851-14.8510.0000.0000.0000.000
10A10GLN0-0.0030.00617.384-0.434-0.4340.0000.0000.0000.000
11A11VAL0-0.030-0.01719.489-0.550-0.5500.0000.0000.0000.000
12A12TYR00.0450.02221.6020.9830.9830.0000.0000.0000.000
13A13ASP-1-0.825-0.87823.082-12.533-12.5330.0000.0000.0000.000
14A14GLY00.0650.01124.0080.4900.4900.0000.0000.0000.000
15A15SER0-0.053-0.05425.3170.4530.4530.0000.0000.0000.000
16A16LYS10.8160.89826.88911.21511.2150.0000.0000.0000.000
17A17ILE0-0.0080.02725.9340.3400.3400.0000.0000.0000.000
18A18ARG10.7720.87928.7519.7339.7330.0000.0000.0000.000
19A19VAL00.0210.01725.0280.2360.2360.0000.0000.0000.000
20A20GLY0-0.016-0.00527.501-0.046-0.0460.0000.0000.0000.000
21A21ILE00.004-0.00322.005-0.227-0.2270.0000.0000.0000.000
22A22ILE0-0.036-0.01026.2890.2080.2080.0000.0000.0000.000
23A23HIS0-0.012-0.01525.414-0.178-0.1780.0000.0000.0000.000
24A24ALA00.0050.01127.3890.3770.3770.0000.0000.0000.000
25A25ARG10.9060.93527.2019.5959.5950.0000.0000.0000.000
26A26TRP00.0040.00228.300-0.124-0.1240.0000.0000.0000.000
27A27ASN0-0.026-0.03024.783-0.240-0.2400.0000.0000.0000.000
28A28ARG10.8690.92623.62912.36112.3610.0000.0000.0000.000
29A29VAL00.0450.01818.746-0.303-0.3030.0000.0000.0000.000
30A30ILE00.0280.01619.042-0.825-0.8250.0000.0000.0000.000
31A31ILE0-0.0240.00419.463-0.550-0.5500.0000.0000.0000.000
32A32ASP-1-0.799-0.89919.692-14.570-14.5700.0000.0000.0000.000
33A33ALA0-0.0220.00115.140-0.616-0.6160.0000.0000.0000.000
34A34LEU0-0.0040.01615.986-0.838-0.8380.0000.0000.0000.000
35A35VAL0-0.017-0.01518.228-0.067-0.0670.0000.0000.0000.000
36A36LYS10.9430.97815.06718.55518.5550.0000.0000.0000.000
37A37GLY00.0940.04914.121-0.360-0.3600.0000.0000.0000.000
38A38ALA0-0.013-0.00115.040-0.097-0.0970.0000.0000.0000.000
39A39ILE0-0.003-0.01518.2300.3080.3080.0000.0000.0000.000
40A40GLU-1-0.926-0.96412.476-24.667-24.6670.0000.0000.0000.000
41A41ARG10.8420.91314.35119.21319.2130.0000.0000.0000.000
42A42MET00.0110.03116.0050.6990.6990.0000.0000.0000.000
43A43ALA00.0510.03617.1860.4900.4900.0000.0000.0000.000
44A44SER0-0.128-0.07714.730-0.099-0.0990.0000.0000.0000.000
45A45LEU0-0.049-0.02416.616-0.072-0.0720.0000.0000.0000.000
46A46GLY00.0220.01519.9870.8560.8560.0000.0000.0000.000
47A47VAL0-0.049-0.01621.9190.7210.7210.0000.0000.0000.000
48A48GLU-1-0.905-0.95122.686-13.258-13.2580.0000.0000.0000.000
49A49GLU-1-0.918-0.96022.201-13.748-13.7480.0000.0000.0000.000
50A50ASN0-0.034-0.02624.158-0.060-0.0600.0000.0000.0000.000
51A51ASN0-0.024-0.01726.9120.9270.9270.0000.0000.0000.000
52A52ILE00.0500.03021.5890.0360.0360.0000.0000.0000.000
53A53ILE0-0.039-0.01425.7590.0750.0750.0000.0000.0000.000
54A54ILE00.0270.00623.681-0.094-0.0940.0000.0000.0000.000
55A55GLU-1-0.802-0.87027.560-9.300-9.3000.0000.0000.0000.000
56A56THR0-0.047-0.02428.230-0.306-0.3060.0000.0000.0000.000
57A57VAL0-0.016-0.00830.5520.4550.4550.0000.0000.0000.000
58A58PRO0-0.007-0.01531.474-0.292-0.2920.0000.0000.0000.000
59A59GLY00.0340.01131.720-0.364-0.3640.0000.0000.0000.000
60A60SER00.033-0.01129.709-0.036-0.0360.0000.0000.0000.000
61A61TYR00.0140.02831.8140.0630.0630.0000.0000.0000.000
62A62GLU-1-0.831-0.92935.012-8.739-8.7390.0000.0000.0000.000
63A63LEU0-0.0190.01429.2820.1310.1310.0000.0000.0000.000
64A64PRO00.0270.03133.387-0.011-0.0110.0000.0000.0000.000
65A65TRP00.0490.01035.9850.0860.0860.0000.0000.0000.000
66A66GLY00.0140.01035.2770.1120.1120.0000.0000.0000.000
67A67THR00.021-0.01732.765-0.112-0.1120.0000.0000.0000.000
68A68LYS10.8490.92634.6027.6657.6650.0000.0000.0000.000
69A69ARG10.8260.89338.2447.7377.7370.0000.0000.0000.000
70A70PHE0-0.0070.01330.1290.1530.1530.0000.0000.0000.000
71A71VAL00.0690.03134.9460.0180.0180.0000.0000.0000.000
72A72ASP-1-0.790-0.86836.889-7.571-7.5710.0000.0000.0000.000
73A73ARG10.7790.87733.8599.3849.3840.0000.0000.0000.000
74A74GLN00.0280.00133.6900.1200.1200.0000.0000.0000.000
75A75ALA00.0270.01137.0640.0240.0240.0000.0000.0000.000
76A76LYS10.9130.95939.8207.1427.1420.0000.0000.0000.000
77A77LEU0-0.025-0.01537.0090.1610.1610.0000.0000.0000.000
78A78GLY0-0.0100.01339.788-0.037-0.0370.0000.0000.0000.000
79A79LYS10.8680.93534.6358.8318.8310.0000.0000.0000.000
80A80PRO00.0630.02935.008-0.222-0.2220.0000.0000.0000.000
81A81LEU0-0.027-0.00630.792-0.195-0.1950.0000.0000.0000.000
82A82ASP-1-0.771-0.88031.037-9.593-9.5930.0000.0000.0000.000
83A83VAL0-0.013-0.00127.6580.0420.0420.0000.0000.0000.000
84A84VAL0-0.026-0.01328.879-0.105-0.1050.0000.0000.0000.000
85A85ILE00.0170.01122.7460.0200.0200.0000.0000.0000.000
86A86PRO0-0.024-0.00426.660-0.122-0.1220.0000.0000.0000.000
87A87ILE0-0.0020.00421.608-0.198-0.1980.0000.0000.0000.000
88A88GLY00.011-0.01725.5870.4390.4390.0000.0000.0000.000
89A89VAL0-0.0080.00522.533-0.278-0.2780.0000.0000.0000.000
90A90LEU0-0.0240.00525.7340.3640.3640.0000.0000.0000.000
91A91ILE00.0370.00924.970-0.339-0.3390.0000.0000.0000.000
92A92LYS10.7770.87228.6759.2799.2790.0000.0000.0000.000
93A93GLY00.0410.02831.710-0.107-0.1070.0000.0000.0000.000
94A94SER0-0.006-0.02534.2850.0280.0280.0000.0000.0000.000
95A95THR00.0110.00937.6460.1560.1560.0000.0000.0000.000
96A96MET00.0220.01837.618-0.235-0.2350.0000.0000.0000.000
97A97HIS00.0230.01137.4070.0330.0330.0000.0000.0000.000
98A98PHE00.0030.01929.431-0.025-0.0250.0000.0000.0000.000
99A99GLU-1-0.743-0.84834.284-9.041-9.0410.0000.0000.0000.000
100A100TYR00.0330.01336.064-0.014-0.0140.0000.0000.0000.000
101A101ILE00.0070.02833.7350.0320.0320.0000.0000.0000.000
102A102SER0-0.010-0.01132.217-0.233-0.2330.0000.0000.0000.000
103A103ASP-1-0.876-0.91833.544-8.476-8.4760.0000.0000.0000.000
104A104SER0-0.023-0.03036.295-0.028-0.0280.0000.0000.0000.000
105A105THR0-0.030-0.04232.4310.0650.0650.0000.0000.0000.000
106A106THR0-0.012-0.02232.371-0.220-0.2200.0000.0000.0000.000
107A107HIS0-0.041-0.02533.8020.0060.0060.0000.0000.0000.000
108A108ALA0-0.032-0.00837.0140.1090.1090.0000.0000.0000.000
109A109LEU0-0.022-0.02230.6490.0770.0770.0000.0000.0000.000
110A110MET00.0040.01732.846-0.036-0.0360.0000.0000.0000.000
111A111ASN00.023-0.00435.2630.0140.0140.0000.0000.0000.000
112A112LEU0-0.046-0.01534.9880.1880.1880.0000.0000.0000.000
113A113GLN00.0270.00933.215-0.104-0.1040.0000.0000.0000.000
114A114GLU-1-0.833-0.89636.910-7.270-7.2700.0000.0000.0000.000
115A115LYS10.7690.86240.1797.4397.4390.0000.0000.0000.000
116A116VAL0-0.071-0.03435.4360.1000.1000.0000.0000.0000.000
117A117ASP-1-0.851-0.89838.234-7.969-7.9690.0000.0000.0000.000
118A118MET0-0.0080.00733.928-0.193-0.1930.0000.0000.0000.000
119A119PRO00.0090.00830.5880.0500.0500.0000.0000.0000.000
120A120VAL0-0.026-0.02530.746-0.149-0.1490.0000.0000.0000.000
121A121ILE0-0.030-0.01024.212-0.017-0.0170.0000.0000.0000.000
122A122PHE00.017-0.01326.4940.0530.0530.0000.0000.0000.000
123A123GLY00.0530.02723.969-0.414-0.4140.0000.0000.0000.000
124A124LEU0-0.036-0.01824.753-0.055-0.0550.0000.0000.0000.000
125A125LEU0-0.0190.00520.033-0.149-0.1490.0000.0000.0000.000
126A126THR00.012-0.00324.5800.3310.3310.0000.0000.0000.000
127A127CYS0-0.049-0.00223.733-0.213-0.2130.0000.0000.0000.000
128A128MET00.0320.00226.3520.3950.3950.0000.0000.0000.000
129A129THR0-0.012-0.01424.9620.0730.0730.0000.0000.0000.000
130A130GLU-1-0.873-0.94622.276-13.541-13.5410.0000.0000.0000.000
131A131GLU-1-0.848-0.92318.335-17.225-17.2250.0000.0000.0000.000
132A132GLN0-0.038-0.02519.415-0.570-0.5700.0000.0000.0000.000
133A133ALA00.0610.01720.145-0.430-0.4300.0000.0000.0000.000
134A134LEU00.0230.00717.205-0.522-0.5220.0000.0000.0000.000
135A135ALA00.0250.01715.171-1.099-1.0990.0000.0000.0000.000
136A136ARG10.8780.93614.96914.22314.2230.0000.0000.0000.000
137A137ALA00.0230.02116.0050.0360.0360.0000.0000.0000.000
138A138GLY0-0.029-0.00711.837-1.015-1.0150.0000.0000.0000.000
139A139ILE0-0.072-0.04811.057-2.610-2.6100.0000.0000.0000.000
140A140ASP-1-0.735-0.83513.462-21.372-21.3720.0000.0000.0000.000
141A141GLU-1-0.930-0.96612.797-23.048-23.0480.0000.0000.0000.000
142A142ALA0-0.049-0.03612.260-1.815-1.8150.0000.0000.0000.000
143A143HIS10.7960.9098.87727.36327.3630.0000.0000.0000.000
144A144SER0-0.034-0.03910.621-0.901-0.9010.0000.0000.0000.000
145A145MET0-0.079-0.03713.0481.5301.5300.0000.0000.0000.000
146A146HIS0-0.033-0.02611.291-3.074-3.0740.0000.0000.0000.000
147A147ASN00.0480.01011.8573.2723.2720.0000.0000.0000.000
148A148HIS0-0.026-0.03113.7311.0091.0090.0000.0000.0000.000
149A149GLY00.0400.02416.8410.8290.8290.0000.0000.0000.000
150A150GLU-1-0.926-0.96411.102-26.920-26.9200.0000.0000.0000.000
151A151ASP-1-0.855-0.92115.851-18.146-18.1460.0000.0000.0000.000
152A152TRP0-0.0010.00218.3180.7050.7050.0000.0000.0000.000
153A153GLY00.0530.02319.3260.7440.7440.0000.0000.0000.000
154A154ALA0-0.028-0.02318.2120.5390.5390.0000.0000.0000.000
155A155ALA00.0040.00120.2690.6390.6390.0000.0000.0000.000
156A156ALA0-0.003-0.00423.2690.6830.6830.0000.0000.0000.000
157A157VAL00.0280.01522.2540.5670.5670.0000.0000.0000.000
158A158GLU-1-0.863-0.90524.176-11.827-11.8270.0000.0000.0000.000
159A159MET0-0.030-0.02025.8270.5200.5200.0000.0000.0000.000
160A160ALA00.006-0.00528.2410.4680.4680.0000.0000.0000.000
161A161VAL0-0.015-0.01226.9260.3780.3780.0000.0000.0000.000
162A162LYS10.7720.87927.33311.56011.5600.0000.0000.0000.000
163A163PHE0-0.033-0.03930.6830.2900.2900.0000.0000.0000.000
164A164GLY00.0550.04132.7240.1720.1720.0000.0000.0000.000
165A165LYS10.8060.89333.8818.0338.0330.0000.0000.0000.000
166A166ASN0-0.088-0.05635.5980.4750.4750.0000.0000.0000.000
167A167ALA0-0.0240.00233.939-0.031-0.0310.0000.0000.0000.000
168A168PHE-1-0.990-0.97735.621-7.984-7.9840.0000.0000.0000.000