FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: Z28QN

Calculation Name: 7KQO-B-Xray89

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 7KQO

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2021-01-18

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:

Apendix: None


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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1755127.426062
FMO2-HF: Nuclear repulsion 1689505.152197
FMO2-HF: Total energy -65622.273865
FMO2-MP2: Total energy -65813.78574


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(B:1:SER )


Summations of interaction energy for fragment #1(B:1:SER )
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.
-2.858-1.157-0.02-0.725-0.9560.001
Interaction energy analysis for fragmet #1(B:1:SER )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.012
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].
3B3VAL 00.0340.0133.823-0.0351.666-0.020-0.725-0.9560.001
4B4ASN 0-0.009-0.0176.367-0.920-0.9200.0000.0000.0000.000
5B5SER 00.0320.0358.354-0.403-0.4030.0000.0000.0000.000
6B6PHE 00.001-0.00810.2170.1060.1060.0000.0000.0000.000
7B7SER 00.011-0.00513.964-0.113-0.1130.0000.0000.0000.000
8B8GLY 00.0250.00616.1860.0370.0370.0000.0000.0000.000
9B9TYR 0-0.074-0.05116.9300.0000.0000.0000.0000.0000.000
10B10LEU 00.0060.01421.098-0.028-0.0280.0000.0000.0000.000
11B11LYS 10.8490.92023.421-0.023-0.0230.0000.0000.0000.000
12B12LEU 0-0.031-0.00424.804-0.010-0.0100.0000.0000.0000.000
13B13THR 00.034-0.00626.449-0.011-0.0110.0000.0000.0000.000
14B14ASP -1-0.851-0.93625.3080.0330.0330.0000.0000.0000.000
15B15ASN 0-0.050-0.02422.512-0.018-0.0180.0000.0000.0000.000
16B16VAL 00.0120.02022.5730.0330.0330.0000.0000.0000.000
17B17TYR 00.0010.00420.697-0.025-0.0250.0000.0000.0000.000
18B18ILE 00.0130.01022.8190.0300.0300.0000.0000.0000.000
19B19LYS 10.8370.89917.678-0.443-0.4430.0000.0000.0000.000
20B20ASN 0-0.048-0.01423.1720.0000.0000.0000.0000.0000.000
21B21ALA 00.027-0.00520.3460.0110.0110.0000.0000.0000.000
22B22ASP -1-0.773-0.86621.3790.4190.4190.0000.0000.0000.000
23B23ILE 00.0420.00619.3520.0530.0530.0000.0000.0000.000
24B24VAL 0-0.005-0.00118.0800.0890.0890.0000.0000.0000.000
25B25GLU -1-0.950-0.97616.7030.5540.5540.0000.0000.0000.000
26B26GLU -1-0.822-0.88015.3970.6640.6640.0000.0000.0000.000
27B27ALA 00.0040.01113.8370.1440.1440.0000.0000.0000.000
28B28LYS 10.9460.97912.081-0.470-0.4700.0000.0000.0000.000
29B29LYS 10.8280.90710.738-0.391-0.3910.0000.0000.0000.000
30B30VAL 0-0.019-0.0069.6350.2940.2940.0000.0000.0000.000
31B31LYS 10.8890.9555.536-2.634-2.6340.0000.0000.0000.000
32B32PRO 00.0160.0228.5240.2290.2290.0000.0000.0000.000
33B33THR 00.0300.01010.8760.2440.2440.0000.0000.0000.000
34B34VAL 0-0.017-0.01811.817-0.048-0.0480.0000.0000.0000.000
35B35VAL 0-0.0080.00615.368-0.004-0.0040.0000.0000.0000.000
36B36VAL 00.0050.00517.246-0.028-0.0280.0000.0000.0000.000
37B37ASN 0-0.001-0.03220.999-0.001-0.0010.0000.0000.0000.000
38B38ALA 0-0.0090.02023.466-0.023-0.0230.0000.0000.0000.000
39B39ALA 00.0360.03626.725-0.010-0.0100.0000.0000.0000.000
40B40ASN 00.003-0.01728.506-0.022-0.0220.0000.0000.0000.000
41B41VAL 00.0550.02231.2480.0110.0110.0000.0000.0000.000
42B42TYR 00.0340.01533.162-0.001-0.0010.0000.0000.0000.000
43B43LEU 0-0.0240.00127.1820.0060.0060.0000.0000.0000.000
44B44LYS 10.8670.93929.744-0.196-0.1960.0000.0000.0000.000
45B45HIS 00.000-0.00226.387-0.011-0.0110.0000.0000.0000.000
46B46GLY 00.0040.00129.1550.0070.0070.0000.0000.0000.000
47B47GLY 00.0250.00130.826-0.007-0.0070.0000.0000.0000.000
48B48GLY 0-0.0010.00829.7010.0090.0090.0000.0000.0000.000
49B49VAL 00.0510.01023.7320.0150.0150.0000.0000.0000.000
50B50ALA 00.0060.01924.8850.0300.0300.0000.0000.0000.000
51B51GLY 0-0.0140.00025.7390.0170.0170.0000.0000.0000.000
52B52ALA 0-0.027-0.01724.1790.0110.0110.0000.0000.0000.000
53B53LEU 00.0190.00119.5000.0350.0350.0000.0000.0000.000
54B54ASN 00.0710.02121.5130.0500.0500.0000.0000.0000.000
55B55LYS 10.9290.97223.542-0.286-0.2860.0000.0000.0000.000
56B56ALA 0-0.0120.00719.1020.0070.0070.0000.0000.0000.000
57B57THR 0-0.028-0.00518.6160.0360.0360.0000.0000.0000.000
58B58ASN 0-0.028-0.02120.465-0.018-0.0180.0000.0000.0000.000
59B59ASN 00.0010.00123.485-0.026-0.0260.0000.0000.0000.000
60B60ALA 00.0330.02621.073-0.023-0.0230.0000.0000.0000.000
61B61MET 00.0070.01620.453-0.027-0.0270.0000.0000.0000.000
62B62GLN 0-0.036-0.03123.173-0.020-0.0200.0000.0000.0000.000
63B63VAL 0-0.0060.00225.926-0.020-0.0200.0000.0000.0000.000
64B64GLU -1-0.719-0.83621.1160.4480.4480.0000.0000.0000.000
65B65SER 0-0.010-0.01425.333-0.014-0.0140.0000.0000.0000.000
66B66ASP -1-0.818-0.89327.2670.2010.2010.0000.0000.0000.000
67B67ASP -1-0.929-0.95227.8820.2060.2060.0000.0000.0000.000
68B68TYR 00.0490.01126.889-0.011-0.0110.0000.0000.0000.000
69B69ILE 0-0.031-0.01629.013-0.017-0.0170.0000.0000.0000.000
70B70ALA 0-0.029-0.00532.329-0.014-0.0140.0000.0000.0000.000
71B71THR 0-0.033-0.00631.066-0.014-0.0140.0000.0000.0000.000
72B72ASN 0-0.093-0.05529.520-0.015-0.0150.0000.0000.0000.000
73B73GLY 0-0.0140.01133.280-0.008-0.0080.0000.0000.0000.000
74B74PRO 0-0.057-0.03433.4460.0120.0120.0000.0000.0000.000
75B75LEU 0-0.009-0.00428.501-0.006-0.0060.0000.0000.0000.000
76B76LYS 10.9790.97933.105-0.133-0.1330.0000.0000.0000.000
77B77VAL 00.0250.00433.4800.0110.0110.0000.0000.0000.000
78B78GLY 00.0030.00632.881-0.010-0.0100.0000.0000.0000.000
79B79GLY 0-0.0180.00130.9920.0000.0000.0000.0000.0000.000
80B80SER 0-0.040-0.05525.7420.0160.0160.0000.0000.0000.000
81B81CYS 0-0.0200.01625.721-0.010-0.0100.0000.0000.0000.000
82B82VAL 00.0020.00419.4190.0240.0240.0000.0000.0000.000
83B83LEU 00.0040.01020.890-0.024-0.0240.0000.0000.0000.000
84B84SER 00.0450.02216.9490.0980.0980.0000.0000.0000.000
85B85GLY 00.0170.02015.057-0.050-0.0500.0000.0000.0000.000
86B86HIS 0-0.032-0.03315.4530.0820.0820.0000.0000.0000.000
87B87ASN 0-0.059-0.04613.3590.1300.1300.0000.0000.0000.000
88B88LEU 0-0.058-0.03313.5380.0650.0650.0000.0000.0000.000
89B89ALA 00.0340.02311.6160.0930.0930.0000.0000.0000.000
90B90LYS 10.9190.98810.352-0.953-0.9530.0000.0000.0000.000
91B91HIS 00.004-0.00612.099-0.110-0.1100.0000.0000.0000.000
92B92CYS 0-0.030-0.01015.8090.0420.0420.0000.0000.0000.000
93B93LEU 0-0.0170.01018.697-0.046-0.0460.0000.0000.0000.000
94B94HIS 00.0390.00021.337-0.028-0.0280.0000.0000.0000.000
95B95VAL 00.0220.00924.454-0.024-0.0240.0000.0000.0000.000
96B96VAL 0-0.0370.00726.9920.0030.0030.0000.0000.0000.000
97B97GLY 00.0320.02130.645-0.012-0.0120.0000.0000.0000.000
98B98PRO 00.0080.01832.3380.0020.0020.0000.0000.0000.000
99B99ASN 0-0.013-0.00535.365-0.002-0.0020.0000.0000.0000.000
100B100VAL 00.0760.03337.201-0.007-0.0070.0000.0000.0000.000
101B101ASN 0-0.032-0.01138.172-0.013-0.0130.0000.0000.0000.000
102B102LYS 10.7910.90036.711-0.161-0.1610.0000.0000.0000.000
103B103GLY 00.0000.00641.819-0.003-0.0030.0000.0000.0000.000
104B104GLU -1-0.795-0.84837.4810.1460.1460.0000.0000.0000.000
105B105ASP -1-0.811-0.91341.0730.0970.0970.0000.0000.0000.000
106B106ILE 00.0350.00537.1760.0070.0070.0000.0000.0000.000
107B107GLN 00.004-0.00338.0570.0060.0060.0000.0000.0000.000
108B108LEU 0-0.029-0.01336.4330.0010.0010.0000.0000.0000.000
109B109LEU 0-0.031-0.01731.9980.0100.0100.0000.0000.0000.000
110B110LYS 10.9070.94132.582-0.094-0.0940.0000.0000.0000.000
111B111SER 00.0210.00932.1460.0040.0040.0000.0000.0000.000
112B112ALA 00.0270.00730.4440.0090.0090.0000.0000.0000.000
113B113TYR 00.027-0.00926.8400.0240.0240.0000.0000.0000.000
114B114GLU -1-0.833-0.87427.2790.1250.1250.0000.0000.0000.000
115B115ASN 0-0.0110.00925.8930.0030.0030.0000.0000.0000.000
116B116PHE 00.032-0.00923.0420.0230.0230.0000.0000.0000.000
117B117ASN 0-0.028-0.01422.2800.0090.0090.0000.0000.0000.000
118B118GLN 0-0.044-0.00722.838-0.018-0.0180.0000.0000.0000.000
119B119HIS 0-0.018-0.01017.9770.0500.0500.0000.0000.0000.000
120B120GLU -1-0.862-0.93015.9070.1060.1060.0000.0000.0000.000
121B121VAL 0-0.012-0.01313.138-0.023-0.0230.0000.0000.0000.000
122B122LEU 0-0.0280.02315.8850.0860.0860.0000.0000.0000.000
123B123LEU 00.0020.01915.346-0.033-0.0330.0000.0000.0000.000
124B124ALA 00.009-0.00517.6500.0120.0120.0000.0000.0000.000
125B125PRO 0-0.0120.00721.268-0.012-0.0120.0000.0000.0000.000
126B126LEU 00.0220.01224.482-0.007-0.0070.0000.0000.0000.000
127B127LEU 00.0050.00926.4640.0000.0000.0000.0000.0000.000
128B128SER 00.015-0.02029.358-0.013-0.0130.0000.0000.0000.000
129B129ALA 00.0100.02430.608-0.013-0.0130.0000.0000.0000.000
130B130GLY 00.0190.00232.4110.0100.0100.0000.0000.0000.000
131B131ILE 0-0.015-0.01732.002-0.011-0.0110.0000.0000.0000.000
132B132PHE 0-0.078-0.02931.288-0.007-0.0070.0000.0000.0000.000
133B133GLY 00.0240.01235.218-0.008-0.0080.0000.0000.0000.000
134B134ALA 00.0100.01835.385-0.009-0.0090.0000.0000.0000.000
135B135ASP -1-0.794-0.90036.4740.1220.1220.0000.0000.0000.000
136B136PRO 0-0.048-0.02432.8730.0030.0030.0000.0000.0000.000
137B137ILE 00.0330.00733.2320.0060.0060.0000.0000.0000.000
138B138HIS 00.0510.02535.090-0.003-0.0030.0000.0000.0000.000
139B139SER 0-0.035-0.03631.2530.0030.0030.0000.0000.0000.000
140B140LEU 0-0.017-0.00728.7840.0070.0070.0000.0000.0000.000
141B141ARG 10.9090.95831.193-0.094-0.0940.0000.0000.0000.000
142B142VAL 00.0300.01732.456-0.003-0.0030.0000.0000.0000.000
143B143CYS 0-0.0140.01126.9830.0070.0070.0000.0000.0000.000
144B144VAL 0-0.031-0.00428.5130.0000.0000.0000.0000.0000.000
145B145ASP -1-0.843-0.91429.9390.0820.0820.0000.0000.0000.000
146B146THR 0-0.125-0.06629.947-0.011-0.0110.0000.0000.0000.000
147B147VAL 0-0.053-0.01423.9810.0000.0000.0000.0000.0000.000
148B148ARG 10.8960.95525.754-0.112-0.1120.0000.0000.0000.000
149B149THR 0-0.0130.01920.292-0.019-0.0190.0000.0000.0000.000
150B150ASN 0-0.043-0.01217.813-0.021-0.0210.0000.0000.0000.000
151B151VAL 00.0310.01018.8820.0540.0540.0000.0000.0000.000
152B152TYR 0-0.016-0.00416.786-0.029-0.0290.0000.0000.0000.000
153B153LEU 00.024-0.00319.8330.0450.0450.0000.0000.0000.000
154B154ALA 0-0.005-0.00120.514-0.007-0.0070.0000.0000.0000.000
155B155VAL 0-0.027-0.01922.581-0.011-0.0110.0000.0000.0000.000
156B156PHE 00.0270.01925.113-0.008-0.0080.0000.0000.0000.000
157B157ASP -1-0.823-0.91126.6300.1590.1590.0000.0000.0000.000
158B158LYS 10.8790.92029.206-0.145-0.1450.0000.0000.0000.000
159B159ASN 0-0.027-0.03630.385-0.018-0.0180.0000.0000.0000.000
160B160LEU 0-0.045-0.01931.134-0.009-0.0090.0000.0000.0000.000
161B161TYR 00.0060.00325.817-0.009-0.0090.0000.0000.0000.000
162B162ASP -1-0.773-0.86730.3220.1240.1240.0000.0000.0000.000
163B163LYS 10.9320.99733.036-0.131-0.1310.0000.0000.0000.000
164B164LEU 0-0.0110.01930.001-0.006-0.0060.0000.0000.0000.000
165B165VAL 00.0280.00829.212-0.006-0.0060.0000.0000.0000.000
166B166SER 0-0.087-0.06232.088-0.010-0.0100.0000.0000.0000.000
167B167SER 0-0.001-0.01535.608-0.006-0.0060.0000.0000.0000.000
168B168PHE 0-0.033-0.00831.340-0.001-0.0010.0000.0000.0000.000
169B169LEU -1-0.917-0.94734.1860.0600.0600.0000.0000.0000.000
170B237HOH 0-0.063-0.04412.4200.0080.0080.0000.0000.0000.000
171B245HOH 0-0.007-0.01932.1210.0000.0000.0000.0000.0000.000
172B270HOH 0-0.038-0.03038.980-0.001-0.0010.0000.0000.0000.000
173B278HOH 00.022-0.00130.1690.0010.0010.0000.0000.0000.000
174B284HOH 0-0.002-0.00834.0850.0010.0010.0000.0000.0000.000
175B288HOH 0-0.028-0.01327.7210.0000.0000.0000.0000.0000.000
176B290HOH 0-0.010-0.01129.135-0.004-0.0040.0000.0000.0000.000
177B298HOH 0-0.027-0.02331.9370.0000.0000.0000.0000.0000.000
178B302HOH 0-0.010-0.03420.172-0.013-0.0130.0000.0000.0000.000
179B304HOH 0-0.064-0.06134.5850.0020.0020.0000.0000.0000.000
180B311HOH 0-0.009-0.01715.469-0.016-0.0160.0000.0000.0000.000
181B317HOH 0-0.064-0.04829.817-0.007-0.0070.0000.0000.0000.000
182B330HOH 0-0.017-0.02028.745-0.004-0.0040.0000.0000.0000.000
183B332HOH 0-0.028-0.02823.6540.0060.0060.0000.0000.0000.000
184B334HOH 0-0.017-0.03113.2460.0400.0400.0000.0000.0000.000
185B339HOH 00.010-0.01428.652-0.003-0.0030.0000.0000.0000.000
186B340HOH 0-0.012-0.01229.254-0.007-0.0070.0000.0000.0000.000
187B343HOH 00.0230.01328.7510.0010.0010.0000.0000.0000.000
188B359HOH 0-0.021-0.01432.2390.0000.0000.0000.0000.0000.000
189B364HOH 00.0330.01729.5090.0050.0050.0000.0000.0000.000
190B374HOH 0-0.019-0.00330.1250.0060.0060.0000.0000.0000.000
191B377HOH 0-0.023-0.01134.857-0.003-0.0030.0000.0000.0000.000
192B382HOH 0-0.046-0.04535.8890.0020.0020.0000.0000.0000.000
193B399HOH 0-0.014-0.01430.505-0.001-0.0010.0000.0000.0000.000
194B419HOH 0-0.013-0.02629.3360.0010.0010.0000.0000.0000.000
195B422HOH 00.0120.00235.0070.0050.0050.0000.0000.0000.000
196B428HOH 0-0.049-0.03229.8810.0030.0030.0000.0000.0000.000