FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9M492

Calculation Name: 5KW6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KW6

Chain ID: B

ChEMBL ID:

UniProt ID: Q9UHX1

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079457.003754
FMO2-HF: Nuclear repulsion 2002856.410806
FMO2-HF: Total energy -76600.592948
FMO2-MP2: Total energy -76822.281695


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:113:MET)


Summations of interaction energy for fragment #1(B:113:MET)
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.
-0.9740.5430.009-0.675-0.8510.002
Interaction energy analysis for fragmet #1(B:113:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.011
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].
3B115ARG10.8770.9263.357-0.7630.7540.009-0.675-0.8510.002
4B116GLY00.0680.0476.308-0.007-0.0070.0000.0000.0000.000
5B117SER00.014-0.0107.8000.3760.3760.0000.0000.0000.000
6B118ALA00.0720.0219.285-0.237-0.2370.0000.0000.0000.000
7B119ALA00.0270.01712.000-0.168-0.1680.0000.0000.0000.000
8B120GLN00.0330.02510.5200.1350.1350.0000.0000.0000.000
9B121ARG10.7330.8329.097-1.255-1.2550.0000.0000.0000.000
10B122GLN00.0700.03513.649-0.077-0.0770.0000.0000.0000.000
11B123GLY0-0.005-0.00216.595-0.075-0.0750.0000.0000.0000.000
12B124ALA0-0.005-0.00915.841-0.063-0.0630.0000.0000.0000.000
13B125LEU00.0440.01116.909-0.056-0.0560.0000.0000.0000.000
14B126ALA0-0.0200.00619.460-0.045-0.0450.0000.0000.0000.000
15B127ILE0-0.031-0.01920.114-0.035-0.0350.0000.0000.0000.000
16B128MET0-0.023-0.01018.704-0.013-0.0130.0000.0000.0000.000
17B129SER0-0.027-0.00922.782-0.020-0.0200.0000.0000.0000.000
18B130ARG10.8090.88625.251-0.195-0.1950.0000.0000.0000.000
19B131VAL00.0030.00727.590-0.004-0.0040.0000.0000.0000.000
20B132TYR0-0.031-0.00730.356-0.001-0.0010.0000.0000.0000.000
21B133VAL00.0450.01132.869-0.005-0.0050.0000.0000.0000.000
22B134GLY00.0580.01736.4790.0010.0010.0000.0000.0000.000
23B135SER0-0.060-0.02639.261-0.005-0.0050.0000.0000.0000.000
24B136ILE00.0440.04039.684-0.004-0.0040.0000.0000.0000.000
25B137TYR00.010-0.00543.813-0.002-0.0020.0000.0000.0000.000
26B138TYR00.025-0.00447.2430.0030.0030.0000.0000.0000.000
27B139GLU-1-0.896-0.95148.8130.0540.0540.0000.0000.0000.000
28B140LEU0-0.087-0.02145.9170.0010.0010.0000.0000.0000.000
29B141GLY00.0920.04845.1500.0010.0010.0000.0000.0000.000
30B142GLU-1-0.857-0.96140.8190.0890.0890.0000.0000.0000.000
31B143ASP-1-0.854-0.91641.6710.0770.0770.0000.0000.0000.000
32B144THR0-0.023-0.02243.850-0.001-0.0010.0000.0000.0000.000
33B145ILE0-0.024-0.01338.324-0.001-0.0010.0000.0000.0000.000
34B146ARG10.9130.94739.083-0.087-0.0870.0000.0000.0000.000
35B147GLN0-0.023-0.00940.1610.0050.0050.0000.0000.0000.000
36B148ALA0-0.029-0.01341.159-0.001-0.0010.0000.0000.0000.000
37B149PHE00.0240.00234.961-0.002-0.0020.0000.0000.0000.000
38B150ALA00.0550.03936.1610.0060.0060.0000.0000.0000.000
39B151PRO0-0.0140.00636.9810.0040.0040.0000.0000.0000.000
40B152PHE00.0080.01332.763-0.001-0.0010.0000.0000.0000.000
41B153GLY00.0460.02432.3760.0100.0100.0000.0000.0000.000
42B154PRO0-0.0200.00732.424-0.006-0.0060.0000.0000.0000.000
43B155ILE0-0.025-0.02232.7070.0090.0090.0000.0000.0000.000
44B156LYS10.8180.90627.019-0.237-0.2370.0000.0000.0000.000
45B157SER0-0.036-0.05031.167-0.002-0.0020.0000.0000.0000.000
46B158ILE00.001-0.01933.781-0.003-0.0030.0000.0000.0000.000
47B159ASP-1-0.815-0.86832.2750.1570.1570.0000.0000.0000.000
48B160MET0-0.013-0.01335.681-0.004-0.0040.0000.0000.0000.000
49B161SER0-0.068-0.03738.9790.0000.0000.0000.0000.0000.000
50B162TRP00.036-0.00139.969-0.002-0.0020.0000.0000.0000.000
51B163ASP-1-0.850-0.91843.0840.0620.0620.0000.0000.0000.000
52B164SER00.0130.00545.8990.0000.0000.0000.0000.0000.000
53B165VAL0-0.061-0.02248.135-0.002-0.0020.0000.0000.0000.000
54B166THR0-0.049-0.05649.443-0.003-0.0030.0000.0000.0000.000
55B167MET0-0.075-0.02149.4240.0000.0000.0000.0000.0000.000
56B168LYN00.0630.04247.7680.0000.0000.0000.0000.0000.000
57B169HIS0-0.0010.00943.0430.0030.0030.0000.0000.0000.000
58B170LYS10.8930.94742.098-0.070-0.0700.0000.0000.0000.000
59B171GLY00.0120.01343.076-0.002-0.0020.0000.0000.0000.000
60B172PHE0-0.081-0.05236.132-0.002-0.0020.0000.0000.0000.000
61B173ALA00.0470.04437.1920.0010.0010.0000.0000.0000.000
62B174PHE0-0.024-0.00830.937-0.002-0.0020.0000.0000.0000.000
63B175VAL00.0180.01732.574-0.001-0.0010.0000.0000.0000.000
64B176GLU-1-0.820-0.86827.7000.2270.2270.0000.0000.0000.000
65B177TYR0-0.015-0.01828.614-0.009-0.0090.0000.0000.0000.000
66B178GLU-1-0.789-0.86427.7160.2110.2110.0000.0000.0000.000
67B179VAL0-0.015-0.00124.4260.0260.0260.0000.0000.0000.000
68B180PRO00.017-0.00121.001-0.021-0.0210.0000.0000.0000.000
69B181GLU-1-0.752-0.86122.5460.2090.2090.0000.0000.0000.000
70B182ALA00.0060.02426.249-0.017-0.0170.0000.0000.0000.000
71B183ALA00.0240.01326.788-0.014-0.0140.0000.0000.0000.000
72B184GLN0-0.054-0.03126.031-0.004-0.0040.0000.0000.0000.000
73B185LEU00.0280.00528.119-0.013-0.0130.0000.0000.0000.000
74B186ALA00.0190.01331.431-0.010-0.0100.0000.0000.0000.000
75B187LEU0-0.084-0.04628.475-0.009-0.0090.0000.0000.0000.000
76B188GLU-1-0.910-0.94429.6230.0610.0610.0000.0000.0000.000
77B189GLN0-0.026-0.00833.381-0.008-0.0080.0000.0000.0000.000
78B190MET0-0.0030.01636.076-0.004-0.0040.0000.0000.0000.000
79B191ASN00.0180.00035.7490.0000.0000.0000.0000.0000.000
80B192SER0-0.043-0.03137.809-0.005-0.0050.0000.0000.0000.000
81B193VAL00.0330.03940.806-0.004-0.0040.0000.0000.0000.000
82B194MET0-0.030-0.00842.9770.0010.0010.0000.0000.0000.000
83B195LEU00.0100.00342.7880.0010.0010.0000.0000.0000.000
84B196GLY00.0210.00346.4230.0000.0000.0000.0000.0000.000
85B197GLY00.0040.00449.637-0.001-0.0010.0000.0000.0000.000
86B198ARG10.8890.93746.213-0.049-0.0490.0000.0000.0000.000
87B199ASN00.0030.01744.0160.0030.0030.0000.0000.0000.000
88B200ILE00.0120.01739.724-0.001-0.0010.0000.0000.0000.000
89B201LYS10.8110.89137.782-0.047-0.0470.0000.0000.0000.000
90B202VAL00.0320.01733.0090.0050.0050.0000.0000.0000.000
91B203GLY00.0120.00631.443-0.008-0.0080.0000.0000.0000.000
92B204ARG10.9470.97124.561-0.090-0.0900.0000.0000.0000.000
93B205PRO00.000-0.00325.912-0.012-0.0120.0000.0000.0000.000
94B206SER00.0300.01726.3740.0050.0050.0000.0000.0000.000
95B207ASN0-0.029-0.00825.972-0.012-0.0120.0000.0000.0000.000
96B208ILE00.0560.02721.4250.0230.0230.0000.0000.0000.000
97B209GLY00.0240.00520.3750.0160.0160.0000.0000.0000.000
98B210GLN0-0.030-0.02414.1550.1070.1070.0000.0000.0000.000
99B211ALA00.0360.02215.7160.0240.0240.0000.0000.0000.000
100B212GLN0-0.031-0.01716.3570.0360.0360.0000.0000.0000.000
101B213PRO00.0430.01713.0050.0010.0010.0000.0000.0000.000
102B214ILE0-0.056-0.03310.6350.0370.0370.0000.0000.0000.000
103B215ILE00.017-0.00213.4840.0370.0370.0000.0000.0000.000
104B216ASP-1-0.850-0.91415.4120.0510.0510.0000.0000.0000.000
105B217GLN0-0.084-0.0499.145-0.187-0.1870.0000.0000.0000.000
106B218LEU0-0.042-0.02312.8950.0180.0180.0000.0000.0000.000
107B219ALA00.0450.01714.873-0.014-0.0140.0000.0000.0000.000
108B220GLU-1-0.861-0.89413.346-0.165-0.1650.0000.0000.0000.000
109B221GLU-1-0.759-0.84410.0430.8070.8070.0000.0000.0000.000
110B222ALA0-0.0060.00214.1580.0020.0020.0000.0000.0000.000
111B223ARG10.7900.85417.0980.0810.0810.0000.0000.0000.000
112B224ALA0-0.042-0.00115.038-0.031-0.0310.0000.0000.0000.000
113B225PHE0-0.035-0.01814.8700.0130.0130.0000.0000.0000.000
114B226ASN0-0.064-0.02519.901-0.018-0.0180.0000.0000.0000.000
115B227ARG10.8800.93920.922-0.254-0.2540.0000.0000.0000.000
116B228ILE0-0.008-0.00623.881-0.007-0.0070.0000.0000.0000.000
117B229TYR0-0.032-0.03926.8750.0180.0180.0000.0000.0000.000
118B230VAL00.0260.01128.540-0.014-0.0140.0000.0000.0000.000
119B231ALA00.0130.00332.2620.0100.0100.0000.0000.0000.000
120B232SER0-0.010-0.01834.379-0.010-0.0100.0000.0000.0000.000
121B233VAL0-0.0160.00334.880-0.006-0.0060.0000.0000.0000.000
122B234HIS00.0790.03338.0050.0070.0070.0000.0000.0000.000
123B235GLN0-0.111-0.07540.6800.0070.0070.0000.0000.0000.000
124B236ASP-1-0.841-0.93041.5550.0780.0780.0000.0000.0000.000
125B237LEU0-0.062-0.00239.748-0.001-0.0010.0000.0000.0000.000
126B238SER0-0.006-0.03838.4480.0090.0090.0000.0000.0000.000
127B239ASP-1-0.795-0.89932.7070.1300.1300.0000.0000.0000.000
128B240ASP-1-0.876-0.91035.1520.0900.0900.0000.0000.0000.000
129B241ASP-1-0.842-0.91237.3970.0680.0680.0000.0000.0000.000
130B242ILE0-0.021-0.00933.768-0.004-0.0040.0000.0000.0000.000
131B243LYS10.8460.92231.756-0.078-0.0780.0000.0000.0000.000
132B244SER0-0.029-0.00934.930-0.006-0.0060.0000.0000.0000.000
133B245VAL0-0.005-0.00838.341-0.005-0.0050.0000.0000.0000.000
134B246PHE00.0350.01633.287-0.004-0.0040.0000.0000.0000.000
135B247GLU-1-0.886-0.96234.2820.0570.0570.0000.0000.0000.000
136B248ALA00.0010.01435.215-0.006-0.0060.0000.0000.0000.000
137B249PHE00.0130.01234.214-0.005-0.0050.0000.0000.0000.000
138B250GLY0-0.017-0.00433.279-0.006-0.0060.0000.0000.0000.000
139B251LYS10.8640.90831.202-0.021-0.0210.0000.0000.0000.000
140B252ILE00.0150.02829.3440.0000.0000.0000.0000.0000.000
141B253LYS10.7960.89221.132-0.124-0.1240.0000.0000.0000.000
142B254SER00.0130.00025.7510.0050.0050.0000.0000.0000.000
143B255ALA00.005-0.00128.005-0.001-0.0010.0000.0000.0000.000
144B256THR0-0.026-0.00927.0810.0040.0040.0000.0000.0000.000
145B257LEU00.0180.00329.2870.0090.0090.0000.0000.0000.000
146B258ALA0-0.026-0.00429.1180.0090.0090.0000.0000.0000.000
147B259ARG10.8460.89130.513-0.144-0.1440.0000.0000.0000.000
148B260ASP-1-0.781-0.87031.6790.1710.1710.0000.0000.0000.000
149B261PRO0-0.050-0.03230.297-0.005-0.0050.0000.0000.0000.000
150B262THR0-0.063-0.02532.9190.0000.0000.0000.0000.0000.000
151B263THR0-0.025-0.02836.564-0.009-0.0090.0000.0000.0000.000
152B264GLY0-0.0070.01235.481-0.007-0.0070.0000.0000.0000.000
153B265LYS10.8810.94536.313-0.108-0.1080.0000.0000.0000.000
154B266HIS0-0.0140.00334.8490.0160.0160.0000.0000.0000.000
155B267LYS10.8370.88629.815-0.204-0.2040.0000.0000.0000.000
156B268GLY00.0520.03735.4260.0000.0000.0000.0000.0000.000
157B269TYR0-0.092-0.08728.2710.0000.0000.0000.0000.0000.000
158B270GLY00.0320.01629.7260.0060.0060.0000.0000.0000.000
159B271PHE0-0.063-0.01524.6140.0020.0020.0000.0000.0000.000
160B272ILE00.0350.02327.227-0.002-0.0020.0000.0000.0000.000
161B273GLU-1-0.814-0.90121.1180.1880.1880.0000.0000.0000.000
162B274TYR00.029-0.00325.719-0.004-0.0040.0000.0000.0000.000
163B275GLU-1-0.800-0.89025.3830.0320.0320.0000.0000.0000.000
164B276LYS10.8280.89525.876-0.019-0.0190.0000.0000.0000.000
165B277ALA00.0720.04124.7880.0080.0080.0000.0000.0000.000
166B278GLN0-0.073-0.03526.5540.0000.0000.0000.0000.0000.000
167B279SER00.0530.01530.1730.0020.0020.0000.0000.0000.000
168B280SER0-0.071-0.04327.1860.0070.0070.0000.0000.0000.000
169B281GLN0-0.034-0.01129.3540.0030.0030.0000.0000.0000.000
170B282ASP-1-0.797-0.89830.8300.0110.0110.0000.0000.0000.000
171B283ALA00.0120.02632.0640.0010.0010.0000.0000.0000.000
172B284VAL0-0.031-0.02629.5530.0030.0030.0000.0000.0000.000
173B285SER0-0.061-0.03832.947-0.001-0.0010.0000.0000.0000.000
174B286SER0-0.041-0.01935.815-0.005-0.0050.0000.0000.0000.000
175B287MET0-0.020-0.00135.603-0.001-0.0010.0000.0000.0000.000
176B288ASN00.0140.01835.0990.0110.0110.0000.0000.0000.000
177B289LEU0-0.046-0.03436.991-0.005-0.0050.0000.0000.0000.000
178B290PHE00.0200.02539.854-0.004-0.0040.0000.0000.0000.000
179B291ASP-1-0.829-0.91041.5340.0560.0560.0000.0000.0000.000
180B292LEU0-0.012-0.01539.632-0.002-0.0020.0000.0000.0000.000
181B293GLY00.0120.00043.1250.0040.0040.0000.0000.0000.000
182B294GLY0-0.038-0.00745.8320.0010.0010.0000.0000.0000.000
183B295GLN0-0.060-0.04042.2370.0050.0050.0000.0000.0000.000
184B296TYR0-0.056-0.03142.082-0.001-0.0010.0000.0000.0000.000
185B297LEU00.0130.01137.1240.0050.0050.0000.0000.0000.000
186B298ARG10.8520.93934.774-0.075-0.0750.0000.0000.0000.000
187B299VAL00.008-0.00432.1390.0090.0090.0000.0000.0000.000
188B300GLY00.0530.02929.691-0.009-0.0090.0000.0000.0000.000
189B301LYS10.9410.96523.454-0.030-0.0300.0000.0000.0000.000
190B302ALA0-0.039-0.01621.8970.0050.0050.0000.0000.0000.000
191B303VAL0-0.037-0.02621.113-0.021-0.0210.0000.0000.0000.000
192B304THR0-0.023-0.02717.8740.0300.0300.0000.0000.0000.000
193B305PRO00.0070.01213.972-0.041-0.0410.0000.0000.0000.000
194B306PRO00.0070.00116.8450.0260.0260.0000.0000.0000.000
195B307MET0-0.025-0.01715.8970.0030.0030.0000.0000.0000.000
196B308PRO00.0220.02414.1910.1270.1270.0000.0000.0000.000
197B309LEU0-0.024-0.01013.0650.1330.1330.0000.0000.0000.000
198B310LEU0-0.0150.0109.4450.1250.1250.0000.0000.0000.000