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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4NZ7N

Calculation Name: 7KR1-A-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7KR1

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2020-12-21

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 176
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1670020.487788
FMO2-HF: Nuclear repulsion 1606413.073796
FMO2-HF: Total energy -63607.413992
FMO2-MP2: Total energy -63794.449865


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.
-11.514-3.811.704-4.001-5.408-0.022
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 : 0.015 / q_NPA : 0.001
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].
3A5SER 0-0.0130.0022.501-4.076-0.5930.802-1.947-2.338-0.008
4A6PHE 00.0270.0174.3820.9931.179-0.001-0.027-0.1590.000
5A7SER 00.015-0.0028.0490.1330.1330.0000.0000.0000.000
6A8GLY 00.013-0.00110.5800.1020.1020.0000.0000.0000.000
7A9TYR 0-0.078-0.05011.0300.0420.0420.0000.0000.0000.000
8A10LEU 00.0130.01615.092-0.013-0.0130.0000.0000.0000.000
9A11LYS 10.8460.91217.2190.4800.4800.0000.0000.0000.000
10A12LEU 0-0.0220.00519.3380.0390.0390.0000.0000.0000.000
11A13THR 00.0480.02220.1210.0190.0190.0000.0000.0000.000
12A14ASP -1-0.848-0.93519.356-0.437-0.4370.0000.0000.0000.000
13A15ASN 0-0.069-0.04115.888-0.040-0.0400.0000.0000.0000.000
14A16VAL 00.0180.02115.586-0.039-0.0390.0000.0000.0000.000
15A17TYR 00.0120.00314.0950.0110.0110.0000.0000.0000.000
16A18ILE 00.0200.01316.5870.0100.0100.0000.0000.0000.000
17A19LYS 10.8150.89212.2190.5030.5030.0000.0000.0000.000
18A20ASN 00.0130.01717.3350.0320.0320.0000.0000.0000.000
19A21ALA 0-0.026-0.03215.6140.0050.0050.0000.0000.0000.000
20A22ASP -1-0.788-0.90417.119-0.037-0.0370.0000.0000.0000.000
21A23ILE 00.0230.01713.875-0.010-0.0100.0000.0000.0000.000
22A24VAL 00.0080.00413.013-0.004-0.0040.0000.0000.0000.000
23A25GLU -1-0.830-0.91412.7810.1920.1920.0000.0000.0000.000
24A26GLU -1-0.845-0.88810.970-0.455-0.4550.0000.0000.0000.000
25A27ALA 00.0340.0198.712-0.078-0.0780.0000.0000.0000.000
26A28LYS 10.8440.9087.732-0.075-0.0750.0000.0000.0000.000
27A29LYS 10.8440.9278.1430.4630.4630.0000.0000.0000.000
28A30VAL 0-0.043-0.0205.3020.3060.3060.0000.0000.0000.000
29A31LYS 10.8980.9572.454-5.767-4.3040.599-0.756-1.307-0.002
30A32PRO 00.0170.0093.031-3.019-0.8380.300-1.216-1.265-0.012
31A33THR 00.0260.0053.632-0.0310.3290.005-0.054-0.3110.000
32A34VAL 0-0.004-0.0035.0730.1990.230-0.001-0.001-0.0280.000
33A35VAL 00.0070.0148.688-0.125-0.1250.0000.0000.0000.000
34A36VAL 00.0060.00411.0160.0570.0570.0000.0000.0000.000
35A37ASN 0-0.027-0.04214.6200.0000.0000.0000.0000.0000.000
36A38ALA 0-0.0130.00617.583-0.008-0.0080.0000.0000.0000.000
37A39ALA 00.0080.01521.0830.0160.0160.0000.0000.0000.000
38A40ASN 00.010-0.00722.824-0.006-0.0060.0000.0000.0000.000
39A41VAL 00.0430.01425.7270.0040.0040.0000.0000.0000.000
40A42TYR 00.000-0.00127.8340.0020.0020.0000.0000.0000.000
41A43LEU 00.0020.01521.9280.0080.0080.0000.0000.0000.000
42A44LYS 10.8370.92724.890-0.029-0.0290.0000.0000.0000.000
43A45HIS 00.025-0.00521.486-0.023-0.0230.0000.0000.0000.000
44A46GLY 00.0060.00624.3160.0100.0100.0000.0000.0000.000
45A47GLY 00.023-0.00326.2390.0040.0040.0000.0000.0000.000
46A48GLY 0-0.0030.00724.815-0.005-0.0050.0000.0000.0000.000
47A49VAL 00.0490.01218.5650.0120.0120.0000.0000.0000.000
48A50ALA 00.0540.04619.9600.0130.0130.0000.0000.0000.000
49A51GLY 0-0.027-0.00720.9380.0190.0190.0000.0000.0000.000
50A52ALA 0-0.006-0.01119.8480.0200.0200.0000.0000.0000.000
51A53LEU 00.0260.00614.4660.0270.0270.0000.0000.0000.000
52A54ASN 00.0530.01517.4740.0500.0500.0000.0000.0000.000
53A55LYS 10.9320.96119.832-0.061-0.0610.0000.0000.0000.000
54A56ALA 00.0000.02015.8510.0200.0200.0000.0000.0000.000
55A57THR 0-0.0160.00915.1950.0450.0450.0000.0000.0000.000
56A58ASN 0-0.061-0.04217.5720.0260.0260.0000.0000.0000.000
57A59ASN 0-0.011-0.00721.089-0.009-0.0090.0000.0000.0000.000
58A60ALA 00.0240.02418.242-0.014-0.0140.0000.0000.0000.000
59A61MET 00.0170.02115.610-0.020-0.0200.0000.0000.0000.000
60A62GLN 0-0.029-0.02619.231-0.023-0.0230.0000.0000.0000.000
61A63VAL 0-0.0040.00222.918-0.010-0.0100.0000.0000.0000.000
62A64GLU -1-0.726-0.84117.4330.1280.1280.0000.0000.0000.000
63A65SER 0-0.007-0.01521.000-0.018-0.0180.0000.0000.0000.000
64A66ASP -1-0.833-0.90122.8340.0430.0430.0000.0000.0000.000
65A67ASP -1-0.926-0.95124.2540.0730.0730.0000.0000.0000.000
66A68TYR 00.0330.01022.430-0.009-0.0090.0000.0000.0000.000
67A69ILE 0-0.057-0.03024.845-0.009-0.0090.0000.0000.0000.000
68A70ALA 0-0.032-0.01027.652-0.006-0.0060.0000.0000.0000.000
69A71THR 0-0.066-0.02426.757-0.003-0.0030.0000.0000.0000.000
70A72ASN 0-0.047-0.02726.829-0.008-0.0080.0000.0000.0000.000
71A73GLY 00.0150.01728.893-0.006-0.0060.0000.0000.0000.000
72A74PRO 0-0.062-0.02928.7550.0000.0000.0000.0000.0000.000
73A75LEU 00.0440.01722.853-0.003-0.0030.0000.0000.0000.000
74A76LYS 10.9430.96127.5690.0410.0410.0000.0000.0000.000
75A77VAL 00.0260.01027.421-0.005-0.0050.0000.0000.0000.000
76A78GLY 0-0.0010.00526.2950.0000.0000.0000.0000.0000.000
77A79GLY 0-0.027-0.00724.760-0.009-0.0090.0000.0000.0000.000
78A80SER 0-0.050-0.05419.567-0.004-0.0040.0000.0000.0000.000
79A81CYS 0-0.0110.01519.8290.0090.0090.0000.0000.0000.000
80A82VAL 0-0.0060.00013.821-0.012-0.0120.0000.0000.0000.000
81A83LEU 00.0010.01215.6900.0150.0150.0000.0000.0000.000
82A84SER 00.0350.01613.2430.0060.0060.0000.0000.0000.000
83A85GLY 0-0.0140.00510.568-0.046-0.0460.0000.0000.0000.000
84A86HIS 0-0.042-0.04211.6090.0600.0600.0000.0000.0000.000
85A87ASN 0-0.030-0.02910.7460.0430.0430.0000.0000.0000.000
86A88LEU 0-0.043-0.02110.0660.1110.1110.0000.0000.0000.000
87A89ALA 00.0180.0066.694-0.081-0.0810.0000.0000.0000.000
88A90LYS 10.8710.9575.860-0.061-0.0610.0000.0000.0000.000
89A91HIS 00.0180.0047.6370.0630.0630.0000.0000.0000.000
90A92CYS 00.000-0.00110.254-0.051-0.0510.0000.0000.0000.000
91A93LEU 0-0.0250.00413.0080.0150.0150.0000.0000.0000.000
92A94HIS 00.0240.00015.200-0.031-0.0310.0000.0000.0000.000
93A95VAL 00.0450.01718.1540.0010.0010.0000.0000.0000.000
94A96VAL 0-0.0400.00920.7840.0040.0040.0000.0000.0000.000
95A97GLY 00.0440.02724.495-0.006-0.0060.0000.0000.0000.000
96A98PRO 0-0.0030.00826.0500.0110.0110.0000.0000.0000.000
97A99ASN 0-0.017-0.00629.631-0.004-0.0040.0000.0000.0000.000
98A100VAL 00.0400.01431.6890.0040.0040.0000.0000.0000.000
99A101ASN 0-0.031-0.01233.6900.0030.0030.0000.0000.0000.000
100A102LYS 10.8040.90832.4280.0330.0330.0000.0000.0000.000
101A103GLY 00.0140.01636.9840.0020.0020.0000.0000.0000.000
102A104GLU -1-0.778-0.84531.711-0.048-0.0480.0000.0000.0000.000
103A105ASP -1-0.812-0.92134.675-0.072-0.0720.0000.0000.0000.000
104A106ILE 00.0520.02030.871-0.005-0.0050.0000.0000.0000.000
105A107GLN 00.0090.00431.135-0.013-0.0130.0000.0000.0000.000
106A108LEU 0-0.053-0.02929.726-0.007-0.0070.0000.0000.0000.000
107A109LEU 0-0.033-0.02125.430-0.003-0.0030.0000.0000.0000.000
108A110LYS 10.9170.94625.5230.1220.1220.0000.0000.0000.000
109A111SER 00.000-0.01225.043-0.007-0.0070.0000.0000.0000.000
110A112ALA 00.0030.00523.581-0.004-0.0040.0000.0000.0000.000
111A113TYR 00.032-0.00619.925-0.013-0.0130.0000.0000.0000.000
112A114GLU -1-0.743-0.83520.254-0.190-0.1900.0000.0000.0000.000
113A115ASN 0-0.066-0.02019.241-0.001-0.0010.0000.0000.0000.000
114A116PHE 00.019-0.01016.014-0.005-0.0050.0000.0000.0000.000
115A117ASN 0-0.008-0.00215.268-0.064-0.0640.0000.0000.0000.000
116A118GLN 0-0.068-0.02316.3090.0090.0090.0000.0000.0000.000
117A119HIS 0-0.007-0.00611.1550.0010.0010.0000.0000.0000.000
118A120GLU -1-0.904-0.9449.308-0.639-0.6390.0000.0000.0000.000
119A121VAL 00.001-0.0176.887-0.073-0.0730.0000.0000.0000.000
120A122LEU 0-0.051-0.0078.7210.0670.0670.0000.0000.0000.000
121A123LEU 0-0.0300.0079.577-0.056-0.0560.0000.0000.0000.000
122A124ALA 00.013-0.00611.3020.1020.1020.0000.0000.0000.000
123A125PRO 0-0.023-0.00614.928-0.014-0.0140.0000.0000.0000.000
124A126LEU 00.0210.00318.398-0.008-0.0080.0000.0000.0000.000
125A127LEU 0-0.033-0.00719.8920.0240.0240.0000.0000.0000.000
126A128SER 00.023-0.01523.126-0.003-0.0030.0000.0000.0000.000
127A129ALA 00.0440.03925.3960.0070.0070.0000.0000.0000.000
128A130GLY 00.009-0.00527.2190.0080.0080.0000.0000.0000.000
129A131ILE 0-0.001-0.01628.4800.0020.0020.0000.0000.0000.000
130A132PHE 0-0.073-0.03025.8240.0050.0050.0000.0000.0000.000
131A133GLY 00.0240.01230.1600.0000.0000.0000.0000.0000.000
132A134ALA 00.0010.01329.3260.0010.0010.0000.0000.0000.000
133A135ASP -1-0.803-0.91430.463-0.113-0.1130.0000.0000.0000.000
134A136PRO 0-0.015-0.00926.938-0.008-0.0080.0000.0000.0000.000
135A137ILE 00.0230.00326.734-0.016-0.0160.0000.0000.0000.000
136A138HIS 00.0220.01028.129-0.012-0.0120.0000.0000.0000.000
137A139SER 0-0.021-0.02925.084-0.012-0.0120.0000.0000.0000.000
138A140LEU 0-0.002-0.00122.007-0.012-0.0120.0000.0000.0000.000
139A141ARG 10.9030.94324.2320.1430.1430.0000.0000.0000.000
140A142VAL 00.0160.01325.438-0.005-0.0050.0000.0000.0000.000
141A143CYS 0-0.066-0.01919.929-0.018-0.0180.0000.0000.0000.000
142A144VAL 0-0.020-0.02621.516-0.015-0.0150.0000.0000.0000.000
143A145ASP -1-0.965-0.96022.778-0.167-0.1670.0000.0000.0000.000
144A146THR 0-0.049-0.01422.4360.0100.0100.0000.0000.0000.000
145A147VAL 0-0.082-0.04516.8420.0010.0010.0000.0000.0000.000
146A148ARG 10.8870.93418.8840.2040.2040.0000.0000.0000.000
147A149THR 0-0.0300.00513.338-0.014-0.0140.0000.0000.0000.000
148A150ASN 0-0.025-0.00510.8500.0350.0350.0000.0000.0000.000
149A151VAL 00.0270.00811.724-0.052-0.0520.0000.0000.0000.000
150A152TYR 0-0.013-0.00810.120-0.051-0.0510.0000.0000.0000.000
151A153LEU 00.012-0.00213.2290.0360.0360.0000.0000.0000.000
152A154ALA 00.0010.00414.578-0.016-0.0160.0000.0000.0000.000
153A155VAL 0-0.0050.00216.6050.0410.0410.0000.0000.0000.000
154A156PHE 0-0.004-0.00120.299-0.001-0.0010.0000.0000.0000.000
155A157ASP -1-0.810-0.90221.547-0.090-0.0900.0000.0000.0000.000
156A158LYS 10.9070.93124.7010.1360.1360.0000.0000.0000.000
157A159ASN 0-0.066-0.04525.840-0.006-0.0060.0000.0000.0000.000
158A160LEU 0-0.029-0.01525.460-0.003-0.0030.0000.0000.0000.000
159A161TYR 00.0000.00219.945-0.004-0.0040.0000.0000.0000.000
160A162ASP -1-0.779-0.87424.904-0.161-0.1610.0000.0000.0000.000
161A163LYS 10.9510.98427.5650.0990.0990.0000.0000.0000.000
162A164LEU 0-0.028-0.00723.8040.0000.0000.0000.0000.0000.000
163A165VAL 00.002-0.01023.498-0.008-0.0080.0000.0000.0000.000
164A166SER 0-0.040-0.03326.209-0.001-0.0010.0000.0000.0000.000
165A167SER 0-0.007-0.01629.4540.0050.0050.0000.0000.0000.000
166A168PHE 0-0.090-0.05724.7720.0020.0020.0000.0000.0000.000
167A169LEU 0-0.054-0.03724.250-0.009-0.0090.0000.0000.0000.000
168A170GLU -2-1.853-1.85428.717-0.278-0.2780.0000.0000.0000.000
169A223HOH 0-0.007-0.03115.664-0.014-0.0140.0000.0000.0000.000
170A228HOH 0-0.014-0.01923.062-0.004-0.0040.0000.0000.0000.000
171A231HOH 0-0.064-0.05728.8780.0030.0030.0000.0000.0000.000
172A233HOH 00.005-0.01124.248-0.006-0.0060.0000.0000.0000.000
173A241HOH 00.0240.01218.4830.0040.0040.0000.0000.0000.000
174A244HOH 0-0.022-0.02623.390-0.004-0.0040.0000.0000.0000.000
175A247HOH 0-0.009-0.01719.6530.0000.0000.0000.0000.0000.000
176A268HOH 0-0.054-0.05030.5630.0030.0030.0000.0000.0000.000