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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 43QJN

Calculation Name: 7TX4-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7TX4

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2022-12-13

Reference: T. Ohyama, K. Kamisaka, C. Watanabe, T. Honma et. al., FMO-based interaction energy analysis of SARS-Cov-2 related protein and ligand complexes, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHLSideSolv
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water Waters within average of the temperature factors of receptor.
Procedure Auto-FMO protocol ver. 1.20200406
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 16 beta / 20190613
Total energy (hartree)
FMO2-HF: Electronic energy -1659699.777522
FMO2-HF: Nuclear repulsion 1596412.217322
FMO2-HF: Total energy -63287.560199
FMO2-MP2: Total energy -63473.559998


3D Structure
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:3:VAL)


Summations of interaction energy for fragment #1(A:3:VAL)
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.
-7.354-1.961.168-2.578-3.983-0.007
Interaction energy analysis for fragmet #1(A:3:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.015
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].
3A5SER00.0450.0342.355-1.9530.8060.988-1.456-2.2910.004
4A6PHE00.0220.0183.7160.3100.4970.012-0.007-0.1920.000
5A7SER00.002-0.0077.4540.1130.1130.0000.0000.0000.000
6A8GLY00.0370.0109.8920.0130.0130.0000.0000.0000.000
7A9TYR0-0.091-0.06610.819-0.003-0.0030.0000.0000.0000.000
8A10LEU00.0140.01614.3730.0160.0160.0000.0000.0000.000
9A11LYS10.8390.92116.0040.3510.3510.0000.0000.0000.000
10A12LEU00.0000.00218.2920.0340.0340.0000.0000.0000.000
11A13THR00.0420.01319.8960.0180.0180.0000.0000.0000.000
12A14ASP-1-0.875-0.94118.962-0.333-0.3330.0000.0000.0000.000
13A15ASN0-0.044-0.02316.545-0.019-0.0190.0000.0000.0000.000
14A16VAL00.0310.02916.334-0.059-0.0590.0000.0000.0000.000
15A17TYR0-0.003-0.00313.9680.0400.0400.0000.0000.0000.000
16A18ILE00.0110.00616.281-0.016-0.0160.0000.0000.0000.000
17A19LYS10.8350.90012.1090.3980.3980.0000.0000.0000.000
18A20ASN00.0170.01416.8440.0100.0100.0000.0000.0000.000
19A21ALA0-0.007-0.01815.3050.0110.0110.0000.0000.0000.000
20A22ASP-1-0.772-0.88817.026-0.203-0.2030.0000.0000.0000.000
21A23ILE00.0140.01113.866-0.022-0.0220.0000.0000.0000.000
22A24VAL00.0120.00713.366-0.050-0.0500.0000.0000.0000.000
23A25GLU-1-0.992-1.00613.109-0.125-0.1250.0000.0000.0000.000
24A26GLU-1-0.788-0.86611.012-0.512-0.5120.0000.0000.0000.000
25A27ALA00.0100.0029.085-0.126-0.1260.0000.0000.0000.000
26A28LYS10.9330.9708.2700.0470.0470.0000.0000.0000.000
27A29LYS10.8530.9306.3260.4950.4950.0000.0000.0000.000
28A30VAL0-0.099-0.0495.2470.2040.2040.0000.0000.0000.000
29A31LYS10.9030.9673.522-2.214-1.3400.028-0.312-0.590-0.002
30A32PRO00.0170.0142.878-3.867-2.4720.141-0.787-0.748-0.009
31A33THR00.002-0.0133.7940.5750.754-0.001-0.016-0.1620.000
32A34VAL00.0160.0035.7900.4340.4340.0000.0000.0000.000
33A35VAL0-0.0150.0089.400-0.140-0.1400.0000.0000.0000.000
34A36VAL00.0170.00911.3740.0870.0870.0000.0000.0000.000
35A37ASN0-0.004-0.02715.0180.0080.0080.0000.0000.0000.000
36A38ALA0-0.0130.01317.9300.0010.0010.0000.0000.0000.000
37A39ALA00.0250.02221.3710.0200.0200.0000.0000.0000.000
38A40ASN00.006-0.00723.2420.0040.0040.0000.0000.0000.000
39A41VAL00.0380.01226.161-0.001-0.0010.0000.0000.0000.000
40A42TYR00.0160.00528.3790.0040.0040.0000.0000.0000.000
41A43LEU0-0.0200.00522.4380.0050.0050.0000.0000.0000.000
42A44LYS10.8600.93925.4110.0470.0470.0000.0000.0000.000
43A45HIS0-0.002-0.01422.094-0.018-0.0180.0000.0000.0000.000
44A46GLY00.0180.01124.8730.0050.0050.0000.0000.0000.000
45A47GLY00.0270.00226.7590.0070.0070.0000.0000.0000.000
46A48GLY0-0.017-0.00525.067-0.008-0.0080.0000.0000.0000.000
47A49VAL00.0520.01818.6950.0050.0050.0000.0000.0000.000
48A50ALA00.0270.02420.186-0.002-0.0020.0000.0000.0000.000
49A51GLY0-0.019-0.00321.2730.0080.0080.0000.0000.0000.000
50A52ALA0-0.017-0.01320.3640.0130.0130.0000.0000.0000.000
51A53LEU00.0200.00314.7410.0080.0080.0000.0000.0000.000
52A54ASN00.0590.01817.7930.0220.0220.0000.0000.0000.000
53A55LYS10.9530.98520.2080.0530.0530.0000.0000.0000.000
54A56ALA0-0.022-0.00816.4250.0180.0180.0000.0000.0000.000
55A57THR0-0.021-0.00715.4800.0200.0200.0000.0000.0000.000
56A58ASN0-0.056-0.03317.9010.0120.0120.0000.0000.0000.000
57A59ASN00.0090.00721.4800.0010.0010.0000.0000.0000.000
58A60ALA00.0270.02518.748-0.001-0.0010.0000.0000.0000.000
59A61MET00.0070.01816.156-0.004-0.0040.0000.0000.0000.000
60A62GLN0-0.026-0.02319.859-0.012-0.0120.0000.0000.0000.000
61A63VAL0-0.0080.00423.5250.0000.0000.0000.0000.0000.000
62A64GLU-1-0.721-0.83918.196-0.038-0.0380.0000.0000.0000.000
63A65SER0-0.002-0.01521.682-0.012-0.0120.0000.0000.0000.000
64A66ASP-1-0.831-0.89823.574-0.036-0.0360.0000.0000.0000.000
65A67ASP-1-0.922-0.94725.2960.0020.0020.0000.0000.0000.000
66A68TYR00.017-0.00823.294-0.004-0.0040.0000.0000.0000.000
67A69ILE0-0.011-0.00825.563-0.002-0.0020.0000.0000.0000.000
68A70ALA0-0.054-0.01928.3390.0000.0000.0000.0000.0000.000
69A71THR0-0.039-0.00928.0770.0040.0040.0000.0000.0000.000
70A72ASN0-0.081-0.04926.1570.0010.0010.0000.0000.0000.000
71A73GLY00.0030.02229.351-0.004-0.0040.0000.0000.0000.000
72A74PRO0-0.035-0.01828.898-0.005-0.0050.0000.0000.0000.000
73A75LEU0-0.0070.00523.463-0.002-0.0020.0000.0000.0000.000
74A76LYS10.8920.93928.0450.1220.1220.0000.0000.0000.000
75A77VAL00.0700.02127.911-0.011-0.0110.0000.0000.0000.000
76A78GLY00.0040.00326.6660.0050.0050.0000.0000.0000.000
77A79GLY0-0.034-0.00825.106-0.010-0.0100.0000.0000.0000.000
78A80SER0-0.037-0.04120.014-0.013-0.0130.0000.0000.0000.000
79A81CYS00.0000.01920.5060.0150.0150.0000.0000.0000.000
80A82VAL0-0.004-0.00114.494-0.029-0.0290.0000.0000.0000.000
81A83LEU00.0050.01316.4600.0320.0320.0000.0000.0000.000
82A84SER00.0240.01314.057-0.030-0.0300.0000.0000.0000.000
83A85GLY0-0.0090.00611.127-0.038-0.0380.0000.0000.0000.000
84A86HIS0-0.034-0.03412.1750.0160.0160.0000.0000.0000.000
85A87ASN0-0.041-0.03711.2910.0310.0310.0000.0000.0000.000
86A88LEU0-0.054-0.02610.5550.0010.0010.0000.0000.0000.000
87A89ALA00.005-0.0027.029-0.206-0.2060.0000.0000.0000.000
88A90LYS10.8690.9496.6120.2290.2290.0000.0000.0000.000
89A91HIS00.0390.0178.3940.1200.1200.0000.0000.0000.000
90A92CYS0-0.0100.00010.926-0.129-0.1290.0000.0000.0000.000
91A93LEU0-0.0220.00813.7150.0490.0490.0000.0000.0000.000
92A94HIS00.0340.00015.884-0.023-0.0230.0000.0000.0000.000
93A95VAL00.0310.01218.6790.0140.0140.0000.0000.0000.000
94A96VAL0-0.0350.01921.3160.0030.0030.0000.0000.0000.000
95A97GLY00.0320.01724.992-0.001-0.0010.0000.0000.0000.000
96A98PRO0-0.0100.00726.3920.0100.0100.0000.0000.0000.000
97A99ASN0-0.027-0.01629.893-0.003-0.0030.0000.0000.0000.000
98A100VAL00.0780.03331.8750.0070.0070.0000.0000.0000.000
99A101ASN0-0.025-0.00733.6080.0080.0080.0000.0000.0000.000
100A102LYS10.8560.93035.2970.0740.0740.0000.0000.0000.000
101A103GLY00.0240.02337.1520.0030.0030.0000.0000.0000.000
102A104GLU-1-0.848-0.89631.946-0.097-0.0970.0000.0000.0000.000
103A105ASP-1-0.842-0.92835.182-0.096-0.0960.0000.0000.0000.000
104A106ILE00.0430.01131.108-0.007-0.0070.0000.0000.0000.000
105A107GLN00.010-0.00531.588-0.014-0.0140.0000.0000.0000.000
106A108LEU0-0.034-0.01930.115-0.007-0.0070.0000.0000.0000.000
107A109LEU0-0.015-0.00825.747-0.009-0.0090.0000.0000.0000.000
108A110LYS10.8850.94125.9790.1390.1390.0000.0000.0000.000
109A111SER0-0.009-0.01525.553-0.008-0.0080.0000.0000.0000.000
110A112ALA0-0.0020.00424.059-0.010-0.0100.0000.0000.0000.000
111A113TYR00.0620.01420.458-0.027-0.0270.0000.0000.0000.000
112A114GLU-1-0.844-0.90720.618-0.195-0.1950.0000.0000.0000.000
113A115ASN0-0.064-0.03119.6900.0000.0000.0000.0000.0000.000
114A116PHE00.036-0.00816.519-0.020-0.0200.0000.0000.0000.000
115A117ASN0-0.026-0.00815.786-0.067-0.0670.0000.0000.0000.000
116A118GLN0-0.044-0.00216.7880.0120.0120.0000.0000.0000.000
117A119HIS0-0.020-0.01811.541-0.048-0.0480.0000.0000.0000.000
118A120GLU-1-0.878-0.94010.069-0.620-0.6200.0000.0000.0000.000
119A121VAL0-0.021-0.0217.420-0.047-0.0470.0000.0000.0000.000
120A122LEU0-0.055-0.0089.181-0.034-0.0340.0000.0000.0000.000
121A123LEU0-0.0240.0059.627-0.012-0.0120.0000.0000.0000.000
122A124ALA00.007-0.01011.3570.0710.0710.0000.0000.0000.000
123A125PRO0-0.017-0.00314.9970.0030.0030.0000.0000.0000.000
124A126LEU00.0170.00318.368-0.005-0.0050.0000.0000.0000.000
125A127LEU0-0.026-0.00520.2110.0190.0190.0000.0000.0000.000
126A128SER00.022-0.01823.2920.0040.0040.0000.0000.0000.000
127A129ALA00.0330.03425.0780.0130.0130.0000.0000.0000.000
128A130GLY00.007-0.00626.9860.0020.0020.0000.0000.0000.000
129A131ILE00.004-0.01328.0970.0070.0070.0000.0000.0000.000
130A132PHE0-0.076-0.02625.6660.0070.0070.0000.0000.0000.000
131A133GLY00.0300.00730.1300.0030.0030.0000.0000.0000.000
132A134ALA0-0.0080.01029.2440.0050.0050.0000.0000.0000.000
133A135ASP-1-0.815-0.91230.340-0.135-0.1350.0000.0000.0000.000
134A136PRO00.000-0.00426.940-0.009-0.0090.0000.0000.0000.000
135A137ILE00.012-0.00926.890-0.016-0.0160.0000.0000.0000.000
136A138HIS00.0090.00928.486-0.009-0.0090.0000.0000.0000.000
137A139SER0-0.031-0.03225.264-0.014-0.0140.0000.0000.0000.000
138A140LEU0-0.017-0.00322.203-0.015-0.0150.0000.0000.0000.000
139A141ARG10.8970.95824.7500.1480.1480.0000.0000.0000.000
140A142VAL00.0530.02825.992-0.004-0.0040.0000.0000.0000.000
141A143CYS0-0.051-0.01020.515-0.020-0.0200.0000.0000.0000.000
142A144VAL0-0.008-0.01222.340-0.018-0.0180.0000.0000.0000.000
143A145ASP-1-0.923-0.94723.546-0.180-0.1800.0000.0000.0000.000
144A146THR0-0.114-0.05823.3450.0120.0120.0000.0000.0000.000
145A147VAL0-0.077-0.04417.5050.0000.0000.0000.0000.0000.000
146A148ARG10.9480.97119.4500.2410.2410.0000.0000.0000.000
147A149THR0-0.0280.00814.0250.0070.0070.0000.0000.0000.000
148A150ASN0-0.032-0.00811.6090.0770.0770.0000.0000.0000.000
149A151VAL00.0160.00012.326-0.114-0.1140.0000.0000.0000.000
150A152TYR0-0.023-0.01110.565-0.008-0.0080.0000.0000.0000.000
151A153LEU00.0370.00913.523-0.007-0.0070.0000.0000.0000.000
152A154ALA0-0.005-0.00114.7110.0100.0100.0000.0000.0000.000
153A155VAL0-0.0090.00416.7390.0260.0260.0000.0000.0000.000
154A156PHE00.0100.00220.2230.0060.0060.0000.0000.0000.000
155A157ASP-1-0.804-0.89521.381-0.113-0.1130.0000.0000.0000.000
156A158LYS10.8980.92824.3000.1310.1310.0000.0000.0000.000
157A159ASN0-0.070-0.04925.5880.0020.0020.0000.0000.0000.000
158A160LEU0-0.003-0.00125.509-0.001-0.0010.0000.0000.0000.000
159A161TYR0-0.011-0.00719.4450.0020.0020.0000.0000.0000.000
160A162ASP-1-0.777-0.87324.545-0.147-0.1470.0000.0000.0000.000
161A163LYS10.9120.97927.0120.1230.1230.0000.0000.0000.000
162A164LEU0-0.0070.00523.8750.0020.0020.0000.0000.0000.000
163A165VAL00.0280.00822.728-0.003-0.0030.0000.0000.0000.000
164A166SER0-0.028-0.02425.4440.0030.0030.0000.0000.0000.000
165A167SER0-0.067-0.04528.7830.0110.0110.0000.0000.0000.000
166A168PHE0-0.078-0.05325.6550.0020.0020.0000.0000.0000.000
167A169LEU-1-0.924-0.93423.135-0.148-0.1480.0000.0000.0000.000
168A227HOH0-0.016-0.01923.469-0.001-0.0010.0000.0000.0000.000
169A228HOH00.009-0.01124.468-0.005-0.0050.0000.0000.0000.000
170A229HOH0-0.008-0.03216.289-0.011-0.0110.0000.0000.0000.000
171A232HOH00.0340.02117.747-0.015-0.0150.0000.0000.0000.000
172A238HOH0-0.042-0.04129.2050.0020.0020.0000.0000.0000.000
173A248HOH0-0.002-0.00627.406-0.004-0.0040.0000.0000.0000.000
174A249HOH0-0.008-0.01619.6990.0030.0030.0000.0000.0000.000
175A250HOH0-0.017-0.02623.933-0.003-0.0030.0000.0000.0000.000
176A259HOH0-0.004-0.00823.311-0.003-0.0030.0000.0000.0000.000
177A286HOH0-0.005-0.01829.7830.0000.0000.0000.0000.0000.000