Manual

About

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: VQLK1

Calculation Name: 3K6Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K6Y

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHR9

Base Structure: X-ray

Registration Date: 2023-09-23

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405274.04762
FMO2-HF: Nuclear repulsion 2324997.342475
FMO2-HF: Total energy -80276.705145
FMO2-MP2: Total energy -80514.530773


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:171:ALA)


Summations of interaction energy for fragment #1(A:171: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.
-1.863-0.4120.004-0.711-0.7440.001
Interaction energy analysis for fragmet #1(A:171:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.036
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].
3A173LEU0-0.033-0.0203.758-1.858-0.4070.004-0.711-0.7440.001
4A174GLU-1-0.873-0.9415.971-0.065-0.0650.0000.0000.0000.000
5A175PRO0-0.069-0.0219.1040.1420.1420.0000.0000.0000.000
6A176PHE00.0260.00312.0300.0240.0240.0000.0000.0000.000
7A177SER0-0.035-0.02015.1370.0000.0000.0000.0000.0000.000
8A178ARG10.8580.90417.3330.1500.1500.0000.0000.0000.000
9A179THR00.0210.00820.839-0.018-0.0180.0000.0000.0000.000
10A180PRO0-0.028-0.01223.1420.0060.0060.0000.0000.0000.000
11A181VAL00.0390.02825.9270.0070.0070.0000.0000.0000.000
12A182ILE00.0050.00829.395-0.004-0.0040.0000.0000.0000.000
13A183PRO0-0.014-0.00929.8580.0040.0040.0000.0000.0000.000
14A184VAL0-0.0180.00932.8900.0040.0040.0000.0000.0000.000
15A185ALA00.0130.00736.707-0.003-0.0030.0000.0000.0000.000
16A186SER00.0610.01839.8200.0000.0000.0000.0000.0000.000
17A187PRO00.0300.03241.1350.0020.0020.0000.0000.0000.000
18A188ASP-1-0.826-0.90644.112-0.033-0.0330.0000.0000.0000.000
19A189PRO0-0.025-0.01647.5720.0010.0010.0000.0000.0000.000
20A190ALA0-0.010-0.01849.5200.0010.0010.0000.0000.0000.000
21A191LEU0-0.024-0.01247.6360.0020.0020.0000.0000.0000.000
22A192VAL0-0.014-0.00151.0420.0010.0010.0000.0000.0000.000
23A193ASN0-0.032-0.01153.2050.0020.0020.0000.0000.0000.000
24A194ASN00.0030.01353.3050.0020.0020.0000.0000.0000.000
25A195PRO00.015-0.01056.0930.0000.0000.0000.0000.0000.000
26A196VAL00.0010.01553.3390.0010.0010.0000.0000.0000.000
27A197VAL00.0250.03053.2440.0010.0010.0000.0000.0000.000
28A198ALA00.0430.01655.7360.0010.0010.0000.0000.0000.000
29A199ALA0-0.064-0.02958.7920.0010.0010.0000.0000.0000.000
30A200THR0-0.028-0.03253.6120.0010.0010.0000.0000.0000.000
31A201GLU-1-0.925-0.95956.610-0.018-0.0180.0000.0000.0000.000
32A202PRO0-0.046-0.02157.5850.0000.0000.0000.0000.0000.000
33A203SER0-0.028-0.03457.3900.0010.0010.0000.0000.0000.000
34A204VAL0-0.035-0.01352.3580.0000.0000.0000.0000.0000.000
35A205VAL0-0.0050.02054.6060.0000.0000.0000.0000.0000.000
36A206LYS10.8520.92154.0020.0200.0200.0000.0000.0000.000
37A207ILE0-0.047-0.03451.5140.0020.0020.0000.0000.0000.000
38A208ARG10.8880.93353.0970.0160.0160.0000.0000.0000.000
39A209SER00.011-0.02551.0770.0020.0020.0000.0000.0000.000
40A210LEU0-0.0220.00752.573-0.001-0.0010.0000.0000.0000.000
41A211ALA00.0730.02249.8930.0010.0010.0000.0000.0000.000
42A212PRO00.0300.02451.148-0.001-0.0010.0000.0000.0000.000
43A213ARG10.8110.90248.8220.0090.0090.0000.0000.0000.000
44A214CYS0-0.026-0.00744.6200.0000.0000.0000.0000.0000.000
45A215GLN0-0.031-0.01747.822-0.002-0.0020.0000.0000.0000.000
46A216LYS10.9310.98143.2700.0240.0240.0000.0000.0000.000
47A217VAL0-0.024-0.01450.2810.0020.0020.0000.0000.0000.000
48A218LEU0-0.0210.00746.515-0.002-0.0020.0000.0000.0000.000
49A219GLU-1-0.779-0.88749.348-0.019-0.0190.0000.0000.0000.000
50A220GLY0-0.0060.00948.756-0.002-0.0020.0000.0000.0000.000
51A221THR0-0.0040.00948.9710.0010.0010.0000.0000.0000.000
52A222GLY00.0380.02849.7260.0000.0000.0000.0000.0000.000
53A223PHE00.0160.00748.3000.0000.0000.0000.0000.0000.000
54A224VAL0-0.0020.01653.4400.0010.0010.0000.0000.0000.000
55A225ILE0-0.029-0.01251.6290.0000.0000.0000.0000.0000.000
56A226SER0-0.016-0.02754.9930.0010.0010.0000.0000.0000.000
57A227PRO00.0560.02058.441-0.001-0.0010.0000.0000.0000.000
58A228ASP-1-0.803-0.87761.057-0.006-0.0060.0000.0000.0000.000
59A229ARG10.7890.88956.1640.0050.0050.0000.0000.0000.000
60A230VAL00.0480.02853.4060.0000.0000.0000.0000.0000.000
61A231MET0-0.0320.01148.0110.0010.0010.0000.0000.0000.000
62A232THR00.0530.00048.413-0.001-0.0010.0000.0000.0000.000
63A233ASN00.001-0.01042.573-0.001-0.0010.0000.0000.0000.000
64A234ALA0-0.0010.01843.0200.0000.0000.0000.0000.0000.000
65A235HIS10.8230.85641.1770.0270.0270.0000.0000.0000.000
66A236VAL0-0.0180.01143.859-0.001-0.0010.0000.0000.0000.000
67A237VAL0-0.0040.00547.3000.0010.0010.0000.0000.0000.000
68A238ALA00.0250.03544.5820.0010.0010.0000.0000.0000.000
69A239GLY0-0.020-0.02246.589-0.001-0.0010.0000.0000.0000.000
70A240SER0-0.066-0.06148.2640.0010.0010.0000.0000.0000.000
71A241ASN0-0.050-0.04351.6750.0000.0000.0000.0000.0000.000
72A242ASN0-0.008-0.00355.1550.0000.0000.0000.0000.0000.000
73A243VAL00.0320.01553.283-0.001-0.0010.0000.0000.0000.000
74A244THR0-0.029-0.00156.0520.0010.0010.0000.0000.0000.000
75A245VAL00.0090.00256.048-0.001-0.0010.0000.0000.0000.000
76A246TYR0-0.023-0.02357.8970.0010.0010.0000.0000.0000.000
77A247ALA00.0470.02158.918-0.001-0.0010.0000.0000.0000.000
78A248GLY00.0350.02161.4290.0010.0010.0000.0000.0000.000
79A249ASP-1-0.908-0.95162.182-0.016-0.0160.0000.0000.0000.000
80A250LYS10.8040.91563.4740.0100.0100.0000.0000.0000.000
81A251PRO00.001-0.00562.4910.0000.0000.0000.0000.0000.000
82A252PHE0-0.017-0.01361.4640.0010.0010.0000.0000.0000.000
83A253GLU-1-0.900-0.94060.935-0.008-0.0080.0000.0000.0000.000
84A254ALA00.006-0.00357.1580.0000.0000.0000.0000.0000.000
85A255THR0-0.050-0.01657.6270.0000.0000.0000.0000.0000.000
86A256VAL00.0270.01250.9660.0000.0000.0000.0000.0000.000
87A257VAL00.0100.01054.0800.0010.0010.0000.0000.0000.000
88A258SER0-0.025-0.02448.5760.0020.0020.0000.0000.0000.000
89A259TYR00.009-0.01744.556-0.002-0.0020.0000.0000.0000.000
90A260ASP-1-0.773-0.83541.721-0.002-0.0020.0000.0000.0000.000
91A261PRO00.0220.00240.515-0.002-0.0020.0000.0000.0000.000
92A262SER0-0.007-0.02937.735-0.002-0.0020.0000.0000.0000.000
93A263VAL00.020-0.01037.538-0.002-0.0020.0000.0000.0000.000
94A264ASP-1-0.749-0.85239.312-0.025-0.0250.0000.0000.0000.000
95A265VAL0-0.013-0.00341.201-0.002-0.0020.0000.0000.0000.000
96A266ALA0-0.018-0.01544.7260.0020.0020.0000.0000.0000.000
97A267ILE0-0.007-0.00448.256-0.001-0.0010.0000.0000.0000.000
98A268LEU0-0.0020.00351.6560.0010.0010.0000.0000.0000.000
99A269ALA00.0070.00554.8990.0000.0000.0000.0000.0000.000
100A270VAL0-0.012-0.02757.6950.0000.0000.0000.0000.0000.000
101A271PRO0-0.018-0.01460.4780.0000.0000.0000.0000.0000.000
102A272HIS0-0.037-0.02464.236-0.001-0.0010.0000.0000.0000.000
103A273LEU00.0050.00959.2700.0000.0000.0000.0000.0000.000
104A274PRO0-0.040-0.02663.8450.0000.0000.0000.0000.0000.000
105A275PRO0-0.0210.00860.9080.0000.0000.0000.0000.0000.000
106A276PRO00.0390.02361.2740.0010.0010.0000.0000.0000.000
107A277PRO0-0.039-0.00657.511-0.001-0.0010.0000.0000.0000.000
108A278LEU00.0250.02153.2150.0000.0000.0000.0000.0000.000
109A279VAL0-0.030-0.02153.5620.0010.0010.0000.0000.0000.000
110A280PHE00.008-0.01047.667-0.001-0.0010.0000.0000.0000.000
111A281ALA00.0040.00747.1570.0010.0010.0000.0000.0000.000
112A282ALA0-0.032-0.01847.7600.0000.0000.0000.0000.0000.000
113A283GLU-1-0.930-0.96145.712-0.006-0.0060.0000.0000.0000.000
114A284PRO0-0.051-0.00640.708-0.002-0.0020.0000.0000.0000.000
115A285ALA00.0070.00142.3430.0000.0000.0000.0000.0000.000
116A286LYS10.9480.95539.5850.0180.0180.0000.0000.0000.000
117A287THR0-0.006-0.02635.3270.0010.0010.0000.0000.0000.000
118A288GLY0-0.022-0.00838.0920.0010.0010.0000.0000.0000.000
119A289ALA0-0.032-0.00240.3770.0000.0000.0000.0000.0000.000
120A290ASP-1-0.771-0.86743.199-0.036-0.0360.0000.0000.0000.000
121A291VAL0-0.050-0.02843.0710.0020.0020.0000.0000.0000.000
122A292VAL00.0100.00046.308-0.002-0.0020.0000.0000.0000.000
123A293VAL00.0060.01643.4170.0020.0020.0000.0000.0000.000
124A294LEU0-0.021-0.00546.7450.0000.0000.0000.0000.0000.000
125A295GLY00.0290.00449.0440.0010.0010.0000.0000.0000.000
126A296TYR0-0.025-0.03550.0340.0010.0010.0000.0000.0000.000
127A297PRO00.0300.02948.2510.0000.0000.0000.0000.0000.000
128A298GLY00.0100.00448.4350.0010.0010.0000.0000.0000.000
129A299GLY0-0.042-0.01149.9660.0010.0010.0000.0000.0000.000
130A300GLY0-0.028-0.00652.7770.0010.0010.0000.0000.0000.000
131A301ASN0-0.004-0.02354.8260.0010.0010.0000.0000.0000.000
132A302PHE00.0540.02753.736-0.001-0.0010.0000.0000.0000.000
133A303THR0-0.024-0.01450.2850.0000.0000.0000.0000.0000.000
134A304ALA00.0030.00450.7600.0000.0000.0000.0000.0000.000
135A305THR00.0330.01844.6790.0000.0000.0000.0000.0000.000
136A306PRO0-0.025-0.01546.1390.0000.0000.0000.0000.0000.000
137A307ALA00.0180.00342.455-0.002-0.0020.0000.0000.0000.000
138A308ARG10.7040.81940.2310.0420.0420.0000.0000.0000.000
139A309ILE0-0.0140.00638.164-0.003-0.0030.0000.0000.0000.000
140A310ARG10.8360.91932.5260.0700.0700.0000.0000.0000.000
141A311GLU-1-0.893-0.96129.939-0.059-0.0590.0000.0000.0000.000
142A312ALA0-0.012-0.00334.3100.0010.0010.0000.0000.0000.000
143A313ILE0-0.0010.00829.6140.0010.0010.0000.0000.0000.000
144A314ARG10.8160.88530.4370.0080.0080.0000.0000.0000.000
145A315LEU0-0.0060.01228.934-0.003-0.0030.0000.0000.0000.000
146A316SER00.0280.01126.7150.0070.0070.0000.0000.0000.000
147A317GLY0-0.0130.00228.247-0.009-0.0090.0000.0000.0000.000
148A318PRO00.0250.02529.3100.0060.0060.0000.0000.0000.000
149A319ASH0-0.018-0.04931.719-0.002-0.0020.0000.0000.0000.000
150A320ILE0-0.044-0.02635.314-0.003-0.0030.0000.0000.0000.000
151A321TYR0-0.068-0.03537.328-0.001-0.0010.0000.0000.0000.000
152A322GLY0-0.0250.00233.274-0.001-0.0010.0000.0000.0000.000
153A323ASP-1-0.854-0.89433.329-0.005-0.0050.0000.0000.0000.000
154A324PRO0-0.048-0.03830.974-0.001-0.0010.0000.0000.0000.000
155A325GLU-1-0.923-0.94129.8870.0200.0200.0000.0000.0000.000
156A326PRO0-0.068-0.02327.534-0.004-0.0040.0000.0000.0000.000
157A327VAL0-0.016-0.01130.6470.0050.0050.0000.0000.0000.000
158A328THR0-0.014-0.03029.147-0.003-0.0030.0000.0000.0000.000
159A329ARG10.8690.94931.8820.0250.0250.0000.0000.0000.000
160A330ASP-1-0.856-0.92433.905-0.013-0.0130.0000.0000.0000.000
161A331VAL0-0.050-0.03633.6510.0000.0000.0000.0000.0000.000
162A332TYR00.0220.01335.312-0.001-0.0010.0000.0000.0000.000
163A333THR00.0020.00831.841-0.001-0.0010.0000.0000.0000.000
164A334ILE00.002-0.00935.3200.0020.0020.0000.0000.0000.000
165A335ARG10.7180.82836.9840.0590.0590.0000.0000.0000.000
166A336ALA00.044-0.00938.0760.0040.0040.0000.0000.0000.000
167A337ASP-1-0.914-0.93539.443-0.053-0.0530.0000.0000.0000.000
168A338VAL0-0.063-0.02940.1330.0030.0030.0000.0000.0000.000
169A339GLU-1-0.877-0.93941.342-0.039-0.0390.0000.0000.0000.000
170A340GLN0-0.060-0.04640.7380.0030.0030.0000.0000.0000.000
171A341GLY00.0170.00344.5490.0010.0010.0000.0000.0000.000
172A342ASP-1-0.772-0.88844.533-0.031-0.0310.0000.0000.0000.000
173A343SER0-0.061-0.01943.2950.0010.0010.0000.0000.0000.000
174A344GLY00.0060.00444.8400.0010.0010.0000.0000.0000.000
175A345GLY00.0420.01846.6960.0020.0020.0000.0000.0000.000
176A346PRO0-0.045-0.00746.581-0.001-0.0010.0000.0000.0000.000
177A347LEU00.0080.00042.247-0.002-0.0020.0000.0000.0000.000
178A348ILE0-0.018-0.02046.2340.0020.0020.0000.0000.0000.000
179A349ASP-1-0.738-0.87047.857-0.020-0.0200.0000.0000.0000.000
180A350LEU0-0.018-0.02649.0000.0000.0000.0000.0000.0000.000
181A351ASN0-0.114-0.06551.4880.0010.0010.0000.0000.0000.000
182A352GLY00.0290.01952.7970.0010.0010.0000.0000.0000.000
183A353GLN0-0.063-0.02651.0830.0010.0010.0000.0000.0000.000
184A354VAL0-0.005-0.00847.654-0.002-0.0020.0000.0000.0000.000
185A355LEU00.0120.00444.1640.0010.0010.0000.0000.0000.000
186A356GLY00.022-0.00743.3340.0010.0010.0000.0000.0000.000
187A357VAL0-0.031-0.00143.3590.0000.0000.0000.0000.0000.000
188A358VAL00.0360.01641.995-0.001-0.0010.0000.0000.0000.000
189A359PHE0-0.053-0.02535.3850.0010.0010.0000.0000.0000.000
190A360GLY00.012-0.00137.6130.0000.0000.0000.0000.0000.000
191A361ALA00.0280.02136.3050.0010.0010.0000.0000.0000.000
192A362ALA0-0.050-0.01130.8380.0000.0000.0000.0000.0000.000
193A363ILE0-0.019-0.01429.8020.0020.0020.0000.0000.0000.000
194A364ASP-1-0.831-0.89126.228-0.113-0.1130.0000.0000.0000.000
195A365ASP-1-0.877-0.93029.376-0.088-0.0880.0000.0000.0000.000
196A366ALA00.006-0.01530.9010.0060.0060.0000.0000.0000.000
197A367GLU-1-0.735-0.81134.260-0.057-0.0570.0000.0000.0000.000
198A368THR0-0.043-0.04732.5000.0020.0020.0000.0000.0000.000
199A369GLY00.0310.02235.1390.0000.0000.0000.0000.0000.000
200A370PHE0-0.020-0.02830.964-0.002-0.0020.0000.0000.0000.000
201A371VAL00.007-0.00337.1480.0020.0020.0000.0000.0000.000
202A372LEU0-0.0090.01238.0550.0000.0000.0000.0000.0000.000
203A373THR00.010-0.00238.5240.0020.0020.0000.0000.0000.000
204A374ALA00.0390.00741.1450.0020.0020.0000.0000.0000.000
205A375GLY0-0.008-0.00142.2690.0020.0020.0000.0000.0000.000
206A376GLU-1-0.783-0.87937.647-0.005-0.0050.0000.0000.0000.000
207A377VAL0-0.014-0.01540.9540.0010.0010.0000.0000.0000.000
208A378ALA00.0230.01544.1190.0010.0010.0000.0000.0000.000
209A379GLY0-0.0060.00344.6950.0010.0010.0000.0000.0000.000
210A380GLN0-0.041-0.04343.8180.0010.0010.0000.0000.0000.000
211A381LEU00.0110.00747.6620.0000.0000.0000.0000.0000.000
212A382ALA0-0.0140.00449.4780.0000.0000.0000.0000.0000.000
213A383LYS10.8600.93249.6340.0020.0020.0000.0000.0000.000
214A384ILE00.0220.01352.5430.0000.0000.0000.0000.0000.000
215A385GLY0-0.0020.00354.5920.0000.0000.0000.0000.0000.000
216A386ALA0-0.0260.00055.0990.0000.0000.0000.0000.0000.000
217A387THR00.006-0.01157.051-0.001-0.0010.0000.0000.0000.000
218A388GLN0-0.035-0.00957.8460.0000.0000.0000.0000.0000.000
219A389PRO00.0420.01956.4320.0000.0000.0000.0000.0000.000
220A390VAL0-0.038-0.01450.9140.0010.0010.0000.0000.0000.000
221A391GLY00.0050.00451.086-0.001-0.0010.0000.0000.0000.000
222A392THR0-0.0070.00048.7380.0010.0010.0000.0000.0000.000
223A393GLY00.0360.01945.653-0.001-0.0010.0000.0000.0000.000
224A394ALA00.0160.01642.8690.0000.0000.0000.0000.0000.000
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