Manual

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: 52K9Z

Calculation Name: 2QHT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QHT

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLQ3

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2472022.665011
FMO2-HF: Nuclear repulsion 2391944.598748
FMO2-HF: Total energy -80078.066263
FMO2-MP2: Total energy -80316.256983


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-14.612-19.40320.26-6.613-8.8550.016
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.021
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].
3A3PHE0-0.038-0.0233.870-0.1881.606-0.023-0.989-0.7820.000
4A4LEU00.0080.0176.8990.0430.0430.0000.0000.0000.000
5A5VAL00.001-0.00710.418-0.051-0.0510.0000.0000.0000.000
6A6GLU-1-0.755-0.85113.3950.0510.0510.0000.0000.0000.000
7A7ASP-1-0.802-0.89316.778-0.079-0.0790.0000.0000.0000.000
8A8LEU0-0.022-0.01619.7170.0150.0150.0000.0000.0000.000
9A9GLY00.0160.02122.4310.0070.0070.0000.0000.0000.000
10A10LEU0-0.034-0.01725.280-0.009-0.0090.0000.0000.0000.000
11A11VAL00.0430.01824.8640.0050.0050.0000.0000.0000.000
12A12PRO00.0510.01828.239-0.007-0.0070.0000.0000.0000.000
13A13TYR0-0.029-0.00525.985-0.003-0.0030.0000.0000.0000.000
14A14GLY00.0230.01427.903-0.004-0.0040.0000.0000.0000.000
15A15GLU-1-0.900-0.96428.134-0.031-0.0310.0000.0000.0000.000
16A16ALA00.0460.03024.5110.0000.0000.0000.0000.0000.000
17A17TRP0-0.035-0.02123.480-0.005-0.0050.0000.0000.0000.000
18A18ALA00.010-0.00523.876-0.003-0.0030.0000.0000.0000.000
19A19TYR0-0.055-0.04818.8490.0040.0040.0000.0000.0000.000
20A20GLN00.0500.02419.529-0.011-0.0110.0000.0000.0000.000
21A21LYS10.7730.87919.4810.0910.0910.0000.0000.0000.000
22A22ARG10.8570.94720.9440.0080.0080.0000.0000.0000.000
23A23VAL00.0730.03615.0500.0050.0050.0000.0000.0000.000
24A24HIS0-0.040-0.03215.6460.0210.0210.0000.0000.0000.000
25A25ARG10.9060.93916.2900.0500.0500.0000.0000.0000.000
26A26GLU-1-0.817-0.89215.8190.0200.0200.0000.0000.0000.000
27A27VAL0-0.021-0.00510.5970.0180.0180.0000.0000.0000.000
28A28VAL0-0.040-0.02512.8430.0000.0000.0000.0000.0000.000
29A29ALA0-0.052-0.02015.391-0.009-0.0090.0000.0000.0000.000
30A30GLY0-0.0040.00711.857-0.003-0.0030.0000.0000.0000.000
31A31ASN0-0.094-0.05311.9890.0550.0550.0000.0000.0000.000
32A32ARG10.7790.86411.787-0.019-0.0190.0000.0000.0000.000
33A33PRO00.0270.0196.8770.0230.0230.0000.0000.0000.000
34A34PRO00.0160.0054.930-0.203-0.2030.0000.0000.0000.000
35A35THR00.0250.0188.075-0.018-0.0180.0000.0000.0000.000
36A36LEU0-0.052-0.02311.199-0.043-0.0430.0000.0000.0000.000
37A37LEU00.0130.01813.1260.0310.0310.0000.0000.0000.000
38A38LEU0-0.017-0.01816.437-0.027-0.0270.0000.0000.0000.000
39A39LEU0-0.015-0.00419.0650.0180.0180.0000.0000.0000.000
40A40GLU-1-0.838-0.92022.819-0.062-0.0620.0000.0000.0000.000
41A41HIS0-0.011-0.00325.657-0.007-0.0070.0000.0000.0000.000
42A42PRO00.0590.02529.0330.0010.0010.0000.0000.0000.000
43A43ARG10.7610.85032.1250.0360.0360.0000.0000.0000.000
44A44VAL0-0.031-0.00430.1850.0020.0020.0000.0000.0000.000
45A45ILE00.0180.01932.675-0.005-0.0050.0000.0000.0000.000
46A46THR0-0.007-0.00228.712-0.002-0.0020.0000.0000.0000.000
47A47LEU00.0170.00631.742-0.003-0.0030.0000.0000.0000.000
48A48GLY00.0310.01529.7030.0000.0000.0000.0000.0000.000
49A49ARG10.8230.87424.0940.1400.1400.0000.0000.0000.000
50A50LYS10.8640.92730.6160.0980.0980.0000.0000.0000.000
51A51ALA00.0030.01733.2660.0020.0020.0000.0000.0000.000
52A52THR0-0.046-0.03835.1560.0000.0000.0000.0000.0000.000
53A53GLY00.0340.01538.9520.0000.0000.0000.0000.0000.000
54A54GLU-1-0.849-0.91741.793-0.054-0.0540.0000.0000.0000.000
55A55ASN0-0.066-0.04936.461-0.002-0.0020.0000.0000.0000.000
56A56LEU0-0.022-0.00938.077-0.002-0.0020.0000.0000.0000.000
57A57LEU0-0.0150.01141.2470.0020.0020.0000.0000.0000.000
58A58PHE00.0060.00843.7450.0030.0030.0000.0000.0000.000
59A59PRO00.0460.00544.183-0.002-0.0020.0000.0000.0000.000
60A60GLU-1-0.728-0.85839.730-0.048-0.0480.0000.0000.0000.000
61A61SER0-0.038-0.01442.560-0.001-0.0010.0000.0000.0000.000
62A62TRP00.0810.05142.151-0.001-0.0010.0000.0000.0000.000
63A63TYR00.023-0.01039.7520.0010.0010.0000.0000.0000.000
64A64ARG10.7910.87638.0540.0440.0440.0000.0000.0000.000
65A65GLU-1-0.929-0.95542.101-0.027-0.0270.0000.0000.0000.000
66A66ASN0-0.086-0.04643.9720.0020.0020.0000.0000.0000.000
67A67GLY00.0200.02441.303-0.001-0.0010.0000.0000.0000.000
68A68PHE0-0.033-0.02136.506-0.002-0.0020.0000.0000.0000.000
69A69GLU-1-0.803-0.89833.098-0.045-0.0450.0000.0000.0000.000
70A70LEU0-0.023-0.02535.137-0.003-0.0030.0000.0000.0000.000
71A71TYR0-0.059-0.04731.7260.0030.0030.0000.0000.0000.000
72A72TRP00.011-0.00133.009-0.006-0.0060.0000.0000.0000.000
73A73VAL0-0.023-0.02027.5920.0000.0000.0000.0000.0000.000
74A74GLU-1-0.756-0.88225.472-0.098-0.0980.0000.0000.0000.000
75A75ARG10.7620.89824.5450.0930.0930.0000.0000.0000.000
76A76GLY0-0.013-0.01124.4490.0070.0070.0000.0000.0000.000
77A77GLY00.0320.01626.0840.0010.0010.0000.0000.0000.000
78A78ASP-1-0.787-0.87628.895-0.085-0.0850.0000.0000.0000.000
79A79VAL00.0490.03631.796-0.001-0.0010.0000.0000.0000.000
80A80THR0-0.056-0.03427.844-0.002-0.0020.0000.0000.0000.000
81A81TYR00.022-0.01931.2660.0020.0020.0000.0000.0000.000
82A82HIS10.8040.90125.7620.0910.0910.0000.0000.0000.000
83A83GLY00.0740.04930.0450.0050.0050.0000.0000.0000.000
84A84PRO00.0260.01330.213-0.005-0.0050.0000.0000.0000.000
85A85GLY00.0300.01730.0740.0010.0010.0000.0000.0000.000
86A86GLN0-0.020-0.01226.485-0.008-0.0080.0000.0000.0000.000
87A87LEU00.0220.01620.7680.0020.0020.0000.0000.0000.000
88A88VAL0-0.036-0.01522.501-0.016-0.0160.0000.0000.0000.000
89A89GLY00.0380.01818.6870.0040.0040.0000.0000.0000.000
90A90TYR0-0.077-0.06317.783-0.007-0.0070.0000.0000.0000.000
91A91PRO00.0210.02212.9550.0110.0110.0000.0000.0000.000
92A92ILE0-0.0200.02213.306-0.005-0.0050.0000.0000.0000.000
93A93PHE00.0530.0138.6490.0230.0230.0000.0000.0000.000
94A94PRO00.0350.0227.9150.0170.0170.0000.0000.0000.000
95A95VAL0-0.0010.00110.189-0.093-0.0930.0000.0000.0000.000
96A96GLY00.0420.01912.286-0.011-0.0110.0000.0000.0000.000
97A97ARG10.9280.94014.3890.2840.2840.0000.0000.0000.000
98A98GLU-1-0.841-0.89014.178-0.427-0.4270.0000.0000.0000.000
99A99VAL00.0150.00515.932-0.024-0.0240.0000.0000.0000.000
100A100ARG10.9740.96717.7250.1810.1810.0000.0000.0000.000
101A101ARG10.8330.92010.9130.7170.7170.0000.0000.0000.000
102A102PHE00.0290.00812.021-0.006-0.0060.0000.0000.0000.000
103A103LEU0-0.011-0.00214.767-0.004-0.0040.0000.0000.0000.000
104A104ARG10.9850.99717.7180.3030.3030.0000.0000.0000.000
105A105GLN0-0.012-0.00310.0910.0560.0560.0000.0000.0000.000
106A106ILE0-0.0060.00414.867-0.007-0.0070.0000.0000.0000.000
107A107GLU-1-0.928-0.98816.355-0.215-0.2150.0000.0000.0000.000
108A108GLU-1-0.876-0.94416.792-0.249-0.2490.0000.0000.0000.000
109A109ALA00.0030.01214.7780.0190.0190.0000.0000.0000.000
110A110ILE00.004-0.01716.8330.0390.0390.0000.0000.0000.000
111A111VAL0-0.019-0.00920.2020.0280.0280.0000.0000.0000.000
112A112ARG10.8340.90115.4660.3010.3010.0000.0000.0000.000
113A113VAL0-0.027-0.00618.8100.0230.0230.0000.0000.0000.000
114A114ALA0-0.025-0.01021.1570.0230.0230.0000.0000.0000.000
115A115ALA00.0360.01723.0100.0160.0160.0000.0000.0000.000
116A116GLY00.0250.01922.9870.0140.0140.0000.0000.0000.000
117A117TYR0-0.095-0.07423.8490.0100.0100.0000.0000.0000.000
118A118GLY0-0.0010.00427.1420.0090.0090.0000.0000.0000.000
119A119ILE0-0.056-0.02427.9270.0020.0020.0000.0000.0000.000
120A120SER00.0170.00827.360-0.012-0.0120.0000.0000.0000.000
121A121ALA0-0.008-0.00525.7680.0050.0050.0000.0000.0000.000
122A122TYR0-0.042-0.03425.703-0.008-0.0080.0000.0000.0000.000
123A123PRO00.0750.03122.9300.0080.0080.0000.0000.0000.000
124A124THR0-0.0220.00725.5850.0120.0120.0000.0000.0000.000
125A125PRO00.013-0.02127.787-0.009-0.0090.0000.0000.0000.000
126A126GLY0-0.020-0.00529.840-0.002-0.0020.0000.0000.0000.000
127A127TYR0-0.0250.00829.8430.0060.0060.0000.0000.0000.000
128A128ALA00.0160.01826.552-0.007-0.0070.0000.0000.0000.000
129A129GLY0-0.011-0.00925.1090.0110.0110.0000.0000.0000.000
130A130VAL00.0100.01622.358-0.008-0.0080.0000.0000.0000.000
131A131TRP0-0.037-0.01825.6850.0160.0160.0000.0000.0000.000
132A132VAL00.0540.01428.780-0.006-0.0060.0000.0000.0000.000
133A133GLY00.0380.02531.4060.0060.0060.0000.0000.0000.000
134A134GLU-1-0.820-0.88933.983-0.065-0.0650.0000.0000.0000.000
135A135ASP-1-0.807-0.90633.723-0.067-0.0670.0000.0000.0000.000
136A136LYS10.8520.91528.4210.1060.1060.0000.0000.0000.000
137A137LEU00.0040.01126.7490.0060.0060.0000.0000.0000.000
138A138CYS0-0.031-0.00622.222-0.001-0.0010.0000.0000.0000.000
139A139ALA0-0.0060.01325.932-0.001-0.0010.0000.0000.0000.000
140A140ILE00.035-0.00320.457-0.006-0.0060.0000.0000.0000.000
141A141GLY0-0.014-0.00822.4220.0100.0100.0000.0000.0000.000
142A142VAL00.0080.01818.5040.0050.0050.0000.0000.0000.000
143A143ALA00.000-0.00720.2670.0150.0150.0000.0000.0000.000
144A144VAL00.004-0.00116.842-0.017-0.0170.0000.0000.0000.000
145A145LYS10.8120.89818.5110.1080.1080.0000.0000.0000.000
146A146GLU-1-0.757-0.86218.109-0.108-0.1080.0000.0000.0000.000
147A147GLY00.0080.02015.907-0.004-0.0040.0000.0000.0000.000
148A148VAL0-0.0090.00312.824-0.047-0.0470.0000.0000.0000.000
149A149SER0-0.040-0.04014.0160.0140.0140.0000.0000.0000.000
150A150PHE00.030-0.00715.8730.0230.0230.0000.0000.0000.000
151A151HIS0-0.0110.00218.272-0.009-0.0090.0000.0000.0000.000
152A152GLY0-0.008-0.01118.503-0.018-0.0180.0000.0000.0000.000
153A153PHE0-0.029-0.01116.2440.0030.0030.0000.0000.0000.000
154A154ALA00.0260.00821.2890.0100.0100.0000.0000.0000.000
155A155LEU00.0530.02722.3130.0040.0040.0000.0000.0000.000
156A156ASN00.0070.01324.6890.0100.0100.0000.0000.0000.000
157A157VAL00.0100.01025.532-0.001-0.0010.0000.0000.0000.000
158A158ASN0-0.003-0.01628.3630.0060.0060.0000.0000.0000.000
159A159THR0-0.016-0.01130.0960.0040.0040.0000.0000.0000.000
160A160ASP-1-0.783-0.88332.501-0.041-0.0410.0000.0000.0000.000
161A161LEU0-0.072-0.04632.885-0.002-0.0020.0000.0000.0000.000
162A162ASN0-0.006-0.00636.047-0.001-0.0010.0000.0000.0000.000
163A163ASP-1-0.713-0.78636.393-0.045-0.0450.0000.0000.0000.000
164A164PHE0-0.057-0.04030.724-0.003-0.0030.0000.0000.0000.000
165A165THR0-0.048-0.03336.847-0.001-0.0010.0000.0000.0000.000
166A166VAL00.0060.01939.7300.0020.0020.0000.0000.0000.000
167A167ILE0-0.039-0.00234.5070.0000.0000.0000.0000.0000.000
168A168VAL00.0160.00838.691-0.001-0.0010.0000.0000.0000.000
169A169PRO00.0090.02434.208-0.001-0.0010.0000.0000.0000.000
170A170CYS00.0410.01736.1770.0030.0030.0000.0000.0000.000
171A171GLY0-0.030-0.02335.373-0.004-0.0040.0000.0000.0000.000
172A172LEU0-0.014-0.00534.0490.0040.0040.0000.0000.0000.000
173A173LYS10.8150.89233.5850.0680.0680.0000.0000.0000.000
174A174GLY00.0340.02333.9780.0030.0030.0000.0000.0000.000
175A175LYS10.8180.87835.6970.0580.0580.0000.0000.0000.000
176A176GLY00.0510.04236.5110.0040.0040.0000.0000.0000.000
177A177VAL0-0.0230.00533.238-0.007-0.0070.0000.0000.0000.000
178A178THR00.0090.00331.5000.0080.0080.0000.0000.0000.000
179A179SER00.0630.02030.464-0.006-0.0060.0000.0000.0000.000
180A180LEU00.009-0.00125.5550.0020.0020.0000.0000.0000.000
181A181GLU-1-0.804-0.88330.243-0.041-0.0410.0000.0000.0000.000
182A182LYS10.7820.88433.4940.0660.0660.0000.0000.0000.000
183A183LEU0-0.056-0.02830.7720.0020.0020.0000.0000.0000.000
184A184LEU0-0.040-0.01429.9080.0020.0020.0000.0000.0000.000
185A185GLY0-0.0030.01034.6100.0040.0040.0000.0000.0000.000
186A186ARG10.9250.96831.3810.0430.0430.0000.0000.0000.000
187A187LYS10.8430.90833.4660.0380.0380.0000.0000.0000.000
188A188VAL0-0.011-0.00927.7350.0040.0040.0000.0000.0000.000
189A189PRO00.0300.01527.473-0.003-0.0030.0000.0000.0000.000
190A190MET00.0090.01725.204-0.011-0.0110.0000.0000.0000.000
191A191GLU-1-0.909-0.95023.419-0.020-0.0200.0000.0000.0000.000
192A192GLU-1-0.787-0.86522.328-0.068-0.0680.0000.0000.0000.000
193A193ALA00.0280.01222.225-0.014-0.0140.0000.0000.0000.000
194A194LYS10.8270.89319.9210.0440.0440.0000.0000.0000.000
195A195ALA00.0150.01418.135-0.031-0.0310.0000.0000.0000.000
196A196ARG10.7830.87617.2490.0520.0520.0000.0000.0000.000
197A197VAL00.0070.00116.359-0.038-0.0380.0000.0000.0000.000
198A198VAL0-0.0020.00112.731-0.071-0.0710.0000.0000.0000.000
199A199ALA00.0140.00612.649-0.107-0.1070.0000.0000.0000.000
200A200ALA0-0.0040.00612.974-0.069-0.0690.0000.0000.0000.000
201A201PHE00.007-0.01810.987-0.043-0.0430.0000.0000.0000.000
202A202ALA0-0.013-0.0058.570-0.188-0.1880.0000.0000.0000.000
203A203GLU-1-0.832-0.8918.319-0.605-0.6050.0000.0000.0000.000
204A204VAL0-0.049-0.02010.275-0.097-0.0970.0000.0000.0000.000
205A205PHE0-0.052-0.0397.1760.0830.0830.0000.0000.0000.000
206A206GLY00.0040.0276.351-0.364-0.3640.0000.0000.0000.000
207A207LEU0-0.108-0.0432.255-2.719-2.0021.408-0.415-1.709-0.006
208A208ARG10.8580.8602.356-11.391-18.69318.875-5.209-6.3640.022
209A209PRO00.0010.0105.956-0.094-0.0940.0000.0000.0000.000
210A210VAL00.0110.0117.8600.1600.1600.0000.0000.0000.000