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: K9463

Calculation Name: 3QKA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKA

Chain ID: A

ChEMBL ID:

UniProt ID: B2HSK3

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2608863.628131
FMO2-HF: Nuclear repulsion 2522412.560578
FMO2-HF: Total energy -86451.067553
FMO2-MP2: Total energy -86700.180435


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:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
-19.642-11.8980.466-3.739-4.4730.032
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.886 / q_NPA : -0.956
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].
3A5VAL0-0.021-0.0172.632-25.507-19.9110.335-2.992-2.9390.033
4A6GLN00.0010.0183.2316.8598.1000.121-0.505-0.858-0.001
5A7VAL00.020-0.0024.925-5.123-5.017-0.001-0.004-0.1010.000
6A8GLU-1-0.843-0.8948.05324.97124.9710.0000.0000.0000.000
7A9ARG10.8280.89810.742-20.775-20.7750.0000.0000.0000.000
8A10ASN00.0130.00814.187-0.655-0.6550.0000.0000.0000.000
9A11GLY00.0260.01017.499-0.687-0.6870.0000.0000.0000.000
10A12PRO00.0060.01118.9980.7220.7220.0000.0000.0000.000
11A13VAL00.0330.02417.3140.0930.0930.0000.0000.0000.000
12A14THR0-0.025-0.01412.8560.9290.9290.0000.0000.0000.000
13A15THR0-0.029-0.05312.024-0.848-0.8480.0000.0000.0000.000
14A16VAL0-0.026-0.0118.9972.4812.4810.0000.0000.0000.000
15A17ILE00.019-0.0057.706-2.417-2.4170.0000.0000.0000.000
16A18ILE0-0.017-0.0127.2265.3575.3570.0000.0000.0000.000
17A19ASN0-0.032-0.0263.031-9.139-8.5030.012-0.227-0.4220.000
18A20ARG10.8010.8715.632-25.377-25.3770.0000.0000.0000.000
19A21PRO00.0840.0537.500-2.854-2.8540.0000.0000.0000.000
20A22GLN00.0240.0117.034-2.636-2.6360.0000.0000.0000.000
21A23ALA0-0.040-0.02511.461-1.518-1.5180.0000.0000.0000.000
22A24ARG10.9210.95613.246-16.522-16.5220.0000.0000.0000.000
23A25ASN0-0.005-0.01810.4750.9580.9580.0000.0000.0000.000
24A26ALA00.0280.01712.327-0.073-0.0730.0000.0000.0000.000
25A27VAL0-0.0120.00010.8082.3562.3560.0000.0000.0000.000
26A28ASN00.0460.0379.6750.2120.2120.0000.0000.0000.000
27A29GLY00.0490.02011.3731.1051.1050.0000.0000.0000.000
28A30PRO00.013-0.0017.9400.7420.7420.0000.0000.0000.000
29A31THR00.001-0.0156.6734.8264.8260.0000.0000.0000.000
30A32ALA00.0160.0097.7521.1051.1050.0000.0000.0000.000
31A33ALA0-0.021-0.0088.821-1.033-1.0330.0000.0000.0000.000
32A34ALA00.0480.0264.547-1.541-1.376-0.001-0.011-0.1530.000
33A35LEU00.0060.0046.571-1.146-1.1460.0000.0000.0000.000
34A36TYR0-0.023-0.0139.158-2.556-2.5560.0000.0000.0000.000
35A37SER0-0.028-0.0268.229-2.467-2.4670.0000.0000.0000.000
36A38ALA00.0300.0317.871-1.577-1.5770.0000.0000.0000.000
37A39PHE00.038-0.0059.735-2.234-2.2340.0000.0000.0000.000
38A40ALA0-0.019-0.00713.022-1.838-1.8380.0000.0000.0000.000
39A41GLU-1-0.982-1.00210.04129.92429.9240.0000.0000.0000.000
40A42PHE0-0.0030.00313.579-1.158-1.1580.0000.0000.0000.000
41A43ASP-1-0.788-0.89415.24114.37414.3740.0000.0000.0000.000
42A44ARG10.9140.96813.872-21.570-21.5700.0000.0000.0000.000
43A45ASP-1-0.784-0.84016.13717.56717.5670.0000.0000.0000.000
44A46GLU-1-0.903-0.94718.26513.10113.1010.0000.0000.0000.000
45A47SER0-0.108-0.06518.949-0.419-0.4190.0000.0000.0000.000
46A48ALA0-0.076-0.04017.1730.0720.0720.0000.0000.0000.000
47A49SER0-0.031-0.03019.264-0.649-0.6490.0000.0000.0000.000
48A50VAL0-0.021-0.01120.554-0.360-0.3600.0000.0000.0000.000
49A51ALA00.0040.01315.5270.7110.7110.0000.0000.0000.000
50A52VAL00.0180.00415.643-1.186-1.1860.0000.0000.0000.000
51A53LEU0-0.0070.01512.3181.6561.6560.0000.0000.0000.000
52A54CYS0-0.038-0.00612.559-1.506-1.5060.0000.0000.0000.000
53A55GLY00.0480.03411.5582.1752.1750.0000.0000.0000.000
54A56ASN00.004-0.0137.235-3.538-3.5380.0000.0000.0000.000
55A57GLY0-0.021-0.01011.080-0.199-0.1990.0000.0000.0000.000
56A58GLY00.0020.00813.293-0.893-0.8930.0000.0000.0000.000
57A59THR0-0.012-0.01614.767-1.406-1.4060.0000.0000.0000.000
58A60PHE0-0.0250.01414.7041.4241.4240.0000.0000.0000.000
59A61CYS0-0.0290.00814.0911.2371.2370.0000.0000.0000.000
60A62ALA00.0140.00515.996-1.242-1.2420.0000.0000.0000.000
61A63GLY0-0.003-0.01416.894-1.017-1.0170.0000.0000.0000.000
62A64ALA00.0730.02815.9131.2981.2980.0000.0000.0000.000
63A65ASP-1-0.859-0.90913.87519.91619.9160.0000.0000.0000.000
64A66LEU00.007-0.01316.135-0.321-0.3210.0000.0000.0000.000
65A67LYS10.8860.94517.426-15.078-15.0780.0000.0000.0000.000
66A68ALA00.0540.04714.748-0.035-0.0350.0000.0000.0000.000
67A69PHE0-0.0080.00616.758-0.157-0.1570.0000.0000.0000.000
68A70GLY0-0.0060.00119.921-0.346-0.3460.0000.0000.0000.000
69A71THR0-0.045-0.03016.5710.0490.0490.0000.0000.0000.000
70A72ALA00.0200.00715.606-0.027-0.0270.0000.0000.0000.000
71A73GLU-1-0.906-0.96211.75322.84422.8440.0000.0000.0000.000
72A74ALA0-0.024-0.00113.6960.9080.9080.0000.0000.0000.000
73A75ASN0-0.052-0.05914.5610.4470.4470.0000.0000.0000.000
74A76ALA00.0230.02315.873-1.033-1.0330.0000.0000.0000.000
75A77VAL00.006-0.00317.800-0.104-0.1040.0000.0000.0000.000
76A78HIS00.0560.03619.593-1.164-1.1640.0000.0000.0000.000
77A79ARG10.9720.98622.882-10.770-10.7700.0000.0000.0000.000
78A80THR0-0.017-0.01223.843-0.114-0.1140.0000.0000.0000.000
79A81GLY00.0450.02520.0990.3490.3490.0000.0000.0000.000
80A82PRO00.0370.01315.427-0.774-0.7740.0000.0000.0000.000
81A83GLY0-0.0110.01017.651-0.668-0.6680.0000.0000.0000.000
82A84PRO00.0190.01016.4571.1781.1780.0000.0000.0000.000
83A85MET0-0.062-0.01714.6531.2881.2880.0000.0000.0000.000
84A86GLY00.0470.01812.7481.7601.7600.0000.0000.0000.000
85A87PRO0-0.010-0.01312.746-0.914-0.9140.0000.0000.0000.000
86A88SER0-0.037-0.03515.373-1.031-1.0310.0000.0000.0000.000
87A89ARG10.8240.89018.565-15.725-15.7250.0000.0000.0000.000
88A90MET0-0.0460.00915.679-0.180-0.1800.0000.0000.0000.000
89A91MET0-0.0190.00120.042-0.327-0.3270.0000.0000.0000.000
90A92LEU0-0.0080.00716.964-0.024-0.0240.0000.0000.0000.000
91A93SER0-0.008-0.01721.204-0.880-0.8800.0000.0000.0000.000
92A94LYS10.8030.90719.250-16.630-16.6300.0000.0000.0000.000
93A95PRO0-0.012-0.00821.2870.3930.3930.0000.0000.0000.000
94A96VAL00.009-0.00116.7610.7290.7290.0000.0000.0000.000
95A97ILE0-0.029-0.00519.396-0.794-0.7940.0000.0000.0000.000
96A98ALA00.006-0.01018.3480.9740.9740.0000.0000.0000.000
97A99ALA00.0060.00517.019-0.977-0.9770.0000.0000.0000.000
98A100VAL0-0.040-0.03917.6440.8970.8970.0000.0000.0000.000
99A101SER00.0760.04517.030-0.648-0.6480.0000.0000.0000.000
100A102GLY00.0470.02019.2820.5190.5190.0000.0000.0000.000
101A103TYR0-0.006-0.00219.669-0.590-0.5900.0000.0000.0000.000
102A104ALA00.0270.02519.2061.0481.0480.0000.0000.0000.000
103A105VAL0-0.010-0.01320.457-0.820-0.8200.0000.0000.0000.000
104A106ALA0-0.047-0.02320.6180.7350.7350.0000.0000.0000.000
105A107GLY00.0780.02618.898-0.064-0.0640.0000.0000.0000.000
106A108GLY00.032-0.00117.4170.5550.5550.0000.0000.0000.000
107A109LEU0-0.025-0.00518.3750.0030.0030.0000.0000.0000.000
108A110GLU-1-0.800-0.92420.50713.56813.5680.0000.0000.0000.000
109A111LEU00.0060.00414.147-0.162-0.1620.0000.0000.0000.000
110A112ALA00.0280.01718.310-0.022-0.0220.0000.0000.0000.000
111A113LEU0-0.065-0.03120.450-0.506-0.5060.0000.0000.0000.000
112A114TRP0-0.061-0.03915.741-0.251-0.2510.0000.0000.0000.000
113A115CYS0-0.0270.01218.4870.3400.3400.0000.0000.0000.000
114A116ASP-1-0.715-0.82720.86712.98612.9860.0000.0000.0000.000
115A117LEU0-0.046-0.02123.137-0.752-0.7520.0000.0000.0000.000
116A118ARG10.7800.89122.727-11.997-11.9970.0000.0000.0000.000
117A119VAL0-0.0050.00122.184-0.759-0.7590.0000.0000.0000.000
118A120ALA00.006-0.00622.3720.6360.6360.0000.0000.0000.000
119A121GLU-1-0.787-0.89220.79213.90713.9070.0000.0000.0000.000
120A122GLN0-0.043-0.01724.684-0.219-0.2190.0000.0000.0000.000
121A123ASP-1-0.828-0.91225.75010.53010.5300.0000.0000.0000.000
122A124ALA0-0.082-0.02623.3410.2210.2210.0000.0000.0000.000
123A125VAL0-0.049-0.03423.852-0.589-0.5890.0000.0000.0000.000
124A126PHE00.0270.01423.4360.7480.7480.0000.0000.0000.000
125A127GLY00.0790.02425.066-0.556-0.5560.0000.0000.0000.000
126A128VAL00.0290.02125.1170.6750.6750.0000.0000.0000.000
127A129PHE00.037-0.00124.444-0.275-0.2750.0000.0000.0000.000
128A130CYS0-0.026-0.00223.982-0.223-0.2230.0000.0000.0000.000
129A131ARG10.8740.94625.913-10.356-10.3560.0000.0000.0000.000
130A132ARG10.9680.97528.170-11.017-11.0170.0000.0000.0000.000
131A133TRP0-0.071-0.04321.653-0.208-0.2080.0000.0000.0000.000
132A134GLY00.0270.03927.7560.0260.0260.0000.0000.0000.000
133A135VAL0-0.030-0.01223.0310.0430.0430.0000.0000.0000.000
134A136PRO0-0.011-0.00626.481-0.023-0.0230.0000.0000.0000.000
135A137LEU0-0.017-0.01024.6910.4410.4410.0000.0000.0000.000
136A138ILE0-0.033-0.01722.207-0.486-0.4860.0000.0000.0000.000
137A139ASP-1-0.763-0.84718.71417.27217.2720.0000.0000.0000.000
138A140GLY00.0480.01221.7080.2320.2320.0000.0000.0000.000
139A141GLY00.0060.00924.450-0.423-0.4230.0000.0000.0000.000
140A142THR0-0.029-0.03025.866-0.245-0.2450.0000.0000.0000.000
141A143VAL0-0.027-0.00527.668-0.427-0.4270.0000.0000.0000.000
142A144ARG10.8690.92621.836-14.232-14.2320.0000.0000.0000.000
143A145LEU00.0360.03127.992-0.236-0.2360.0000.0000.0000.000
144A146PRO0-0.016-0.02729.468-0.246-0.2460.0000.0000.0000.000
145A147ARG10.8880.96830.424-10.419-10.4190.0000.0000.0000.000
146A148LEU0-0.032-0.00326.396-0.180-0.1800.0000.0000.0000.000
147A149ILE00.0090.00930.855-0.150-0.1500.0000.0000.0000.000
148A150GLY00.0320.02933.535-0.332-0.3320.0000.0000.0000.000
149A151HIS00.036-0.01735.5190.2710.2710.0000.0000.0000.000
150A152SER0-0.035-0.00937.0330.1010.1010.0000.0000.0000.000
151A153ARG11.0431.01635.305-8.478-8.4780.0000.0000.0000.000
152A154ALA00.0380.03732.5920.1780.1780.0000.0000.0000.000
153A155MET00.001-0.00133.2680.2410.2410.0000.0000.0000.000
154A156ASP-1-0.819-0.87035.6448.8668.8660.0000.0000.0000.000
155A157MET00.0260.03428.4140.0960.0960.0000.0000.0000.000
156A158ILE0-0.013-0.01130.1350.2500.2500.0000.0000.0000.000
157A159LEU0-0.019-0.00631.9830.1350.1350.0000.0000.0000.000
158A160THR0-0.020-0.02734.5550.1150.1150.0000.0000.0000.000
159A161GLY0-0.030-0.01130.3620.0450.0450.0000.0000.0000.000
160A162ARG10.6690.78530.239-8.830-8.8300.0000.0000.0000.000
161A163ALA0-0.038-0.02429.1060.2890.2890.0000.0000.0000.000
162A164VAL0-0.010-0.00929.128-0.367-0.3670.0000.0000.0000.000
163A165GLN00.0170.01528.7800.5290.5290.0000.0000.0000.000
164A166ALA00.0710.02527.802-0.150-0.1500.0000.0000.0000.000
165A167ASP-1-0.860-0.92429.3719.2779.2770.0000.0000.0000.000
166A168GLU-1-0.789-0.86733.0429.0169.0160.0000.0000.0000.000
167A169ALA0-0.005-0.01829.015-0.077-0.0770.0000.0000.0000.000
168A170LEU0-0.0020.00330.8550.0230.0230.0000.0000.0000.000
169A171ALA0-0.034-0.00432.228-0.172-0.1720.0000.0000.0000.000
170A172ILE0-0.109-0.06632.024-0.249-0.2490.0000.0000.0000.000
171A173GLY00.0120.01232.668-0.017-0.0170.0000.0000.0000.000
172A174LEU0-0.035-0.01026.7170.2750.2750.0000.0000.0000.000
173A175ALA0-0.021-0.01327.1740.5800.5800.0000.0000.0000.000
174A176ASN00.0310.00627.381-0.028-0.0280.0000.0000.0000.000
175A177ARG10.9330.95926.771-10.871-10.8710.0000.0000.0000.000
176A178VAL00.0280.02527.1780.3810.3810.0000.0000.0000.000
177A179VAL0-0.019-0.00324.199-0.288-0.2880.0000.0000.0000.000
178A180PRO00.0310.00926.7670.1010.1010.0000.0000.0000.000
179A181ASN0-0.008-0.03924.0640.5280.5280.0000.0000.0000.000
180A182GLY0-0.038-0.01820.571-0.260-0.2600.0000.0000.0000.000
181A183GLN00.0090.00720.5760.3150.3150.0000.0000.0000.000
182A184ALA00.0070.01120.120-0.087-0.0870.0000.0000.0000.000
183A185ARG10.7590.83611.814-20.997-20.9970.0000.0000.0000.000
184A186GLN00.0400.01918.1010.5500.5500.0000.0000.0000.000
185A187ALA00.0720.03420.448-0.232-0.2320.0000.0000.0000.000
186A188ALA0-0.035-0.01519.338-0.348-0.3480.0000.0000.0000.000
187A189GLU-1-0.765-0.85215.57518.45818.4580.0000.0000.0000.000
188A190GLU-1-0.951-0.96820.03311.86411.8640.0000.0000.0000.000
189A191LEU0-0.062-0.03023.700-0.461-0.4610.0000.0000.0000.000
190A192ALA00.022-0.00820.757-0.325-0.3250.0000.0000.0000.000
191A193ALA00.0170.00322.662-0.129-0.1290.0000.0000.0000.000
192A194GLN0-0.039-0.01924.066-0.553-0.5530.0000.0000.0000.000
193A195LEU0-0.022-0.01224.797-0.349-0.3490.0000.0000.0000.000
194A196ALA0-0.013-0.01423.531-0.235-0.2350.0000.0000.0000.000
195A197ALA0-0.030-0.00125.675-0.145-0.1450.0000.0000.0000.000
196A198LEU0-0.0320.00428.875-0.463-0.4630.0000.0000.0000.000
197A199PRO00.020-0.00830.2450.2940.2940.0000.0000.0000.000
198A200GLN00.0410.02226.1760.3910.3910.0000.0000.0000.000
199A201GLN00.0240.00229.3930.3650.3650.0000.0000.0000.000
200A202CYS00.000-0.00731.201-0.048-0.0480.0000.0000.0000.000
201A203LEU00.0290.03927.1560.0020.0020.0000.0000.0000.000
202A204ARG10.9300.94724.500-12.604-12.6040.0000.0000.0000.000
203A205SER0-0.020-0.00528.6350.0890.0890.0000.0000.0000.000
204A206ASP-1-0.876-0.93331.7329.2649.2640.0000.0000.0000.000
205A207ARG10.7580.85222.529-13.369-13.3690.0000.0000.0000.000
206A208LEU0-0.019-0.02326.0160.0900.0900.0000.0000.0000.000
207A209SER00.0270.02529.477-0.072-0.0720.0000.0000.0000.000
208A210ALA00.0260.00931.402-0.139-0.1390.0000.0000.0000.000
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