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: QNNVY

Calculation Name: 3Q9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q9S

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRR8

Base Structure: X-ray

Registration Date: 2023-09-27

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2428102.859318
FMO2-HF: Nuclear repulsion 2345745.38019
FMO2-HF: Total energy -82357.479128
FMO2-MP2: Total energy -82600.672417


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:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
94.3999.7170.997-2.455-3.8680.01
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.977 / q_NPA : -0.999
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].
3A5ARG10.8370.9023.797-29.164-27.274-0.019-0.863-1.0080.004
4A6ILE0-0.013-0.0095.991-3.522-3.5220.0000.0000.0000.000
5A7LEU0-0.0230.0009.0100.3570.3570.0000.0000.0000.000
6A8VAL00.003-0.00912.271-1.055-1.0550.0000.0000.0000.000
7A9ILE0-0.028-0.02014.616-0.394-0.3940.0000.0000.0000.000
8A10GLH0-0.040-0.06518.223-0.667-0.6670.0000.0000.0000.000
9A11ASP-1-0.863-0.93220.34912.28112.2810.0000.0000.0000.000
10A12ASP-1-0.877-0.92023.39512.22512.2250.0000.0000.0000.000
11A13HIS00.025-0.02421.3271.0021.0020.0000.0000.0000.000
12A14ASP-1-0.910-0.93620.78513.42513.4250.0000.0000.0000.000
13A15ILE0-0.034-0.02619.8380.6670.6670.0000.0000.0000.000
14A16ALA0-0.023-0.00617.5140.8540.8540.0000.0000.0000.000
15A17ASN0-0.032-0.02616.0632.1312.1310.0000.0000.0000.000
16A18VAL00.0120.01516.0201.0571.0570.0000.0000.0000.000
17A19LEU00.0120.00814.7180.8620.8620.0000.0000.0000.000
18A20ARG10.8930.94811.165-22.235-22.2350.0000.0000.0000.000
19A21MET0-0.0350.00311.3232.1482.1480.0000.0000.0000.000
20A22ASP-1-0.829-0.91312.11720.00820.0080.0000.0000.0000.000
21A23LEU0-0.063-0.0419.2790.9310.9310.0000.0000.0000.000
22A24THR0-0.032-0.0466.7823.3353.3350.0000.0000.0000.000
23A25ASP-1-0.948-0.9567.66729.25429.2540.0000.0000.0000.000
24A26ALA0-0.114-0.0538.627-0.441-0.4410.0000.0000.0000.000
25A27GLY0-0.048-0.0264.6910.1600.289-0.001-0.008-0.1200.000
26A28TYR0-0.069-0.0273.2594.0625.2700.074-0.511-0.770-0.004
27A29VAL00.0360.0202.476-3.556-1.4400.944-1.069-1.9910.010
28A30VAL00.007-0.0014.822-5.603-5.619-0.001-0.0040.0210.000
29A31ASP-1-0.789-0.8708.50521.45721.4570.0000.0000.0000.000
30A32HIS0-0.090-0.05311.467-0.312-0.3120.0000.0000.0000.000
31A33ALA0-0.020-0.00915.023-0.306-0.3060.0000.0000.0000.000
32A34ASP-1-0.826-0.89718.21513.32513.3250.0000.0000.0000.000
33A35SER00.0430.01321.434-0.756-0.7560.0000.0000.0000.000
34A36ALA00.0660.02422.0760.4650.4650.0000.0000.0000.000
35A37MET0-0.046-0.02923.1250.1200.1200.0000.0000.0000.000
36A38ASN00.003-0.01720.5910.0090.0090.0000.0000.0000.000
37A39GLY00.0600.03118.6690.6530.6530.0000.0000.0000.000
38A40LEU0-0.049-0.03118.8610.4320.4320.0000.0000.0000.000
39A41ILE0-0.035-0.01920.4570.0990.0990.0000.0000.0000.000
40A42LYS10.9040.93014.902-18.916-18.9160.0000.0000.0000.000
41A43ALA0-0.022-0.00815.8200.8530.8530.0000.0000.0000.000
42A44ARG10.8340.91916.585-12.548-12.5480.0000.0000.0000.000
43A45GLU-1-0.965-0.97417.02014.14914.1490.0000.0000.0000.000
44A46ASP-1-0.868-0.94412.16722.19322.1930.0000.0000.0000.000
45A47HIS0-0.055-0.00811.2901.9271.9270.0000.0000.0000.000
46A48PRO0-0.0140.0009.8581.9631.9630.0000.0000.0000.000
47A49ASP-1-0.812-0.9006.37429.34829.3480.0000.0000.0000.000
48A50LEU0-0.059-0.0409.666-1.719-1.7190.0000.0000.0000.000
49A51ILE0-0.019-0.00211.8080.6520.6520.0000.0000.0000.000
50A52LEU00.0010.00513.287-0.789-0.7890.0000.0000.0000.000
51A53LEU0-0.0020.00015.942-0.075-0.0750.0000.0000.0000.000
52A54ASP-1-0.770-0.83319.49012.62412.6240.0000.0000.0000.000
53A55LEU0-0.046-0.01721.920-0.242-0.2420.0000.0000.0000.000
54A56GLY00.0770.03925.562-0.037-0.0370.0000.0000.0000.000
55A57LEU0-0.074-0.02227.294-0.271-0.2710.0000.0000.0000.000
56A58PRO00.0360.02230.096-0.090-0.0900.0000.0000.0000.000
57A59ASP-1-0.739-0.87131.2679.7459.7450.0000.0000.0000.000
58A60PHE0-0.078-0.01332.2770.0870.0870.0000.0000.0000.000
59A61ASP-1-0.818-0.92030.6929.2959.2950.0000.0000.0000.000
60A62GLY00.001-0.00127.8970.3040.3040.0000.0000.0000.000
61A63GLY00.007-0.01027.3500.3800.3800.0000.0000.0000.000
62A64ASP-1-0.758-0.83828.55110.23010.2300.0000.0000.0000.000
63A65VAL00.0140.00323.5160.2890.2890.0000.0000.0000.000
64A66VAL00.0160.01323.6860.4410.4410.0000.0000.0000.000
65A67GLN00.0270.00924.2960.1770.1770.0000.0000.0000.000
66A68ARG10.7070.80525.504-9.972-9.9720.0000.0000.0000.000
67A69LEU00.0260.01619.1000.1450.1450.0000.0000.0000.000
68A70ARG10.7990.90119.275-13.227-13.2270.0000.0000.0000.000
69A71LYS10.8060.89222.996-11.488-11.4880.0000.0000.0000.000
70A72ASN0-0.075-0.03423.5170.2340.2340.0000.0000.0000.000
71A73SER00.0640.05018.5920.3960.3960.0000.0000.0000.000
72A74ALA00.0410.00816.976-0.367-0.3670.0000.0000.0000.000
73A75LEU00.0070.01013.1910.2420.2420.0000.0000.0000.000
74A76PRO00.0110.01313.326-1.176-1.1760.0000.0000.0000.000
75A77ILE0-0.033-0.01815.5100.5800.5800.0000.0000.0000.000
76A78ILE0-0.011-0.00914.981-0.631-0.6310.0000.0000.0000.000
77A79VAL0-0.014-0.00718.4580.1930.1930.0000.0000.0000.000
78A80LEU0-0.027-0.01218.553-0.311-0.3110.0000.0000.0000.000
79A81THR00.014-0.02322.411-0.414-0.4140.0000.0000.0000.000
80A82ALA00.0390.03126.1980.1230.1230.0000.0000.0000.000
81A83ARG10.7620.85528.947-9.832-9.8320.0000.0000.0000.000
82A84ASP-1-0.796-0.88930.46910.06010.0600.0000.0000.0000.000
83A85THR0-0.047-0.04931.565-0.190-0.1900.0000.0000.0000.000
84A86VAL00.0240.01032.0210.2960.2960.0000.0000.0000.000
85A87GLU-1-0.831-0.91732.8698.4058.4050.0000.0000.0000.000
86A88GLU-1-0.733-0.82429.16510.06510.0650.0000.0000.0000.000
87A89LYS10.8430.92127.919-9.706-9.7060.0000.0000.0000.000
88A90VAL0-0.006-0.01428.5600.2080.2080.0000.0000.0000.000
89A91ARG10.7740.87130.188-9.666-9.6660.0000.0000.0000.000
90A92LEU00.0160.00225.3860.1070.1070.0000.0000.0000.000
91A93LEU0-0.0160.00824.0780.2260.2260.0000.0000.0000.000
92A94GLY0-0.030-0.01526.5720.0300.0300.0000.0000.0000.000
93A95LEU0-0.078-0.03027.913-0.117-0.1170.0000.0000.0000.000
94A96GLY00.0060.01125.0210.1270.1270.0000.0000.0000.000
95A97ALA00.0160.02521.8670.5830.5830.0000.0000.0000.000
96A98ASP-1-0.771-0.87918.57613.90113.9010.0000.0000.0000.000
97A99ASP-1-0.775-0.87919.14913.40813.4080.0000.0000.0000.000
98A100TYR0-0.041-0.02621.0520.1480.1480.0000.0000.0000.000
99A101LEU0-0.016-0.01718.9480.1300.1300.0000.0000.0000.000
100A102ILE0-0.029-0.01122.400-0.087-0.0870.0000.0000.0000.000
101A103LYS10.8470.93423.187-12.006-12.0060.0000.0000.0000.000
102A104PRO0-0.018-0.04625.717-0.414-0.4140.0000.0000.0000.000
103A105PHE00.0380.00718.912-0.210-0.2100.0000.0000.0000.000
104A106HIS0-0.0060.00120.5860.3490.3490.0000.0000.0000.000
105A107PRO00.0730.02617.2010.1030.1030.0000.0000.0000.000
106A108ASP-1-0.854-0.94316.89817.31117.3110.0000.0000.0000.000
107A109GLU-1-0.933-0.96417.63612.82612.8260.0000.0000.0000.000
108A110LEU0-0.017-0.00714.718-0.010-0.0100.0000.0000.0000.000
109A111LEU00.0340.01511.4720.7070.7070.0000.0000.0000.000
110A112ALA0-0.035-0.00613.2620.6440.6440.0000.0000.0000.000
111A113ARG10.8240.88515.470-14.199-14.1990.0000.0000.0000.000
112A114VAL00.0490.02310.208-0.142-0.1420.0000.0000.0000.000
113A115LYS10.9770.98810.429-20.221-20.2210.0000.0000.0000.000
114A116VAL0-0.072-0.03012.021-0.085-0.0850.0000.0000.0000.000
115A117GLN0-0.035-0.02013.227-0.466-0.4660.0000.0000.0000.000
116A118LEU00.0030.0227.288-0.224-0.2240.0000.0000.0000.000
117A119ARG10.7980.9249.413-14.174-14.1740.0000.0000.0000.000
118A120GLN00.0350.0009.038-1.672-1.6720.0000.0000.0000.000
119A121ARG10.8270.91711.930-16.823-16.8230.0000.0000.0000.000
120A122THR0-0.009-0.02514.985-0.487-0.4870.0000.0000.0000.000
121A123SER0-0.034-0.00718.393-0.082-0.0820.0000.0000.0000.000
122A124GLU-1-0.815-0.87819.90814.22114.2210.0000.0000.0000.000
123A125SER0-0.009-0.02621.6900.0020.0020.0000.0000.0000.000
124A126LEU0-0.0300.00123.192-0.403-0.4030.0000.0000.0000.000
125A127SER0-0.015-0.02526.1380.0840.0840.0000.0000.0000.000
126A128MET0-0.017-0.00529.205-0.257-0.2570.0000.0000.0000.000
127A129GLY00.0160.02032.524-0.089-0.0890.0000.0000.0000.000
128A130ASP-1-0.905-0.96332.2488.6458.6450.0000.0000.0000.000
129A131LEU0-0.0020.01328.5400.1800.1800.0000.0000.0000.000
130A132THR0-0.036-0.02625.7320.1210.1210.0000.0000.0000.000
131A133LEU00.0320.00423.2880.2030.2030.0000.0000.0000.000
132A134ASP-1-0.759-0.87917.73014.68214.6820.0000.0000.0000.000
133A135PRO0-0.050-0.03518.7170.4770.4770.0000.0000.0000.000
134A136GLN0-0.031-0.03913.5180.8390.8390.0000.0000.0000.000
135A137LYS10.8870.95313.747-14.105-14.1050.0000.0000.0000.000
136A138ARG10.7990.90414.995-15.084-15.0840.0000.0000.0000.000
137A139LEU00.0290.03017.328-0.226-0.2260.0000.0000.0000.000
138A140VAL0-0.002-0.01319.633-0.230-0.2300.0000.0000.0000.000
139A141THR0-0.041-0.00523.419-0.103-0.1030.0000.0000.0000.000
140A142TYR0-0.010-0.04326.297-0.109-0.1090.0000.0000.0000.000
141A143LYS10.8640.94730.020-8.021-8.0210.0000.0000.0000.000
142A144GLY0-0.065-0.02730.153-0.135-0.1350.0000.0000.0000.000
143A145GLU-1-0.945-0.95828.8229.9209.9200.0000.0000.0000.000
144A146GLU-1-0.917-0.95821.89012.36312.3630.0000.0000.0000.000
145A147LEU00.006-0.00624.604-0.226-0.2260.0000.0000.0000.000
146A148ARG10.8920.94221.718-10.902-10.9020.0000.0000.0000.000
147A149LEU0-0.040-0.01622.571-0.401-0.4010.0000.0000.0000.000
148A150SER00.0300.01621.3420.6220.6220.0000.0000.0000.000
149A151PRO00.0600.01517.635-0.344-0.3440.0000.0000.0000.000
150A152LYS10.8840.93319.409-13.779-13.7790.0000.0000.0000.000
151A153GLU-1-0.810-0.87623.08810.53810.5380.0000.0000.0000.000
152A154PHE0-0.0020.00120.816-0.258-0.2580.0000.0000.0000.000
153A155ASP-1-0.809-0.90320.29113.36913.3690.0000.0000.0000.000
154A156ILE0-0.021-0.01023.361-0.383-0.3830.0000.0000.0000.000
155A157LEU00.0070.00426.431-0.349-0.3490.0000.0000.0000.000
156A158ALA00.029-0.00124.245-0.257-0.2570.0000.0000.0000.000
157A159LEU0-0.072-0.02126.280-0.186-0.1860.0000.0000.0000.000
158A160LEU0-0.017-0.02328.147-0.307-0.3070.0000.0000.0000.000
159A161ILE00.0080.00628.477-0.259-0.2590.0000.0000.0000.000
160A162ARG10.9350.97222.719-11.617-11.6170.0000.0000.0000.000
161A163GLN0-0.038-0.00930.207-0.379-0.3790.0000.0000.0000.000
162A164PRO00.0620.03833.611-0.149-0.1490.0000.0000.0000.000
163A165GLY0-0.028-0.00735.689-0.132-0.1320.0000.0000.0000.000
164A166ARG10.8070.89833.559-8.699-8.6990.0000.0000.0000.000
165A167VAL00.0000.00036.7880.1040.1040.0000.0000.0000.000
166A168TYR0-0.014-0.00831.378-0.068-0.0680.0000.0000.0000.000
167A169SER0-0.017-0.04135.886-0.055-0.0550.0000.0000.0000.000
168A170ARG10.8950.91334.956-7.553-7.5530.0000.0000.0000.000
169A171GLN0-0.029-0.02833.6550.2350.2350.0000.0000.0000.000
170A172GLU-1-0.733-0.82332.8508.3918.3910.0000.0000.0000.000
171A173ILE0-0.015-0.00329.6370.3110.3110.0000.0000.0000.000
172A174GLY0-0.002-0.00828.8860.3690.3690.0000.0000.0000.000
173A175GLN0-0.002-0.00228.0520.2640.2640.0000.0000.0000.000
174A176GLU-1-0.939-0.96625.79411.12011.1200.0000.0000.0000.000
175A177ILE0-0.034-0.01624.1920.4950.4950.0000.0000.0000.000
176A178TRP00.008-0.01223.3340.3440.3440.0000.0000.0000.000
177A179GLN0-0.023-0.00720.7860.8040.8040.0000.0000.0000.000
178A180GLY00.0250.01724.9090.1870.1870.0000.0000.0000.000
179A181ARG10.7940.90122.153-12.711-12.7110.0000.0000.0000.000
180A182LEU00.0090.01926.152-0.086-0.0860.0000.0000.0000.000
181A183PRO0-0.0030.00628.841-0.221-0.2210.0000.0000.0000.000
182A184GLU-1-0.856-0.93032.3118.3198.3190.0000.0000.0000.000
183A185GLY0-0.015-0.01034.990-0.104-0.1040.0000.0000.0000.000
184A186SER0-0.0220.00733.338-0.105-0.1050.0000.0000.0000.000
185A187ASN00.029-0.00435.548-0.129-0.1290.0000.0000.0000.000
186A188VAL00.0360.02728.806-0.029-0.0290.0000.0000.0000.000
187A189VAL00.0420.02230.8520.1460.1460.0000.0000.0000.000
188A190ASP-1-0.835-0.90232.1238.0608.0600.0000.0000.0000.000
189A191VAL00.0100.00031.432-0.075-0.0750.0000.0000.0000.000
190A192HIS00.0020.00926.5620.3560.3560.0000.0000.0000.000
191A193MET00.000-0.00230.5270.1070.1070.0000.0000.0000.000
192A194ALA0-0.087-0.04933.033-0.146-0.1460.0000.0000.0000.000
193A195ASN0-0.012-0.01629.953-0.106-0.1060.0000.0000.0000.000
194A196LEU00.0190.01928.2310.0320.0320.0000.0000.0000.000
195A197ARG10.9300.95431.204-8.113-8.1130.0000.0000.0000.000
196A198ALA0-0.017-0.00233.461-0.127-0.1270.0000.0000.0000.000
197A199LYS10.8170.89626.032-10.862-10.8620.0000.0000.0000.000
198A200LEU0-0.0080.00928.9840.0890.0890.0000.0000.0000.000
199A201ARG10.9220.95432.957-7.531-7.5310.0000.0000.0000.000
200A202ASP-1-0.760-0.80836.6787.8797.8790.0000.0000.0000.000
201A203LEU0-0.040-0.03238.871-0.133-0.1330.0000.0000.0000.000
202A204ASP-1-0.897-0.94541.6416.3946.3940.0000.0000.0000.000
203A205GLY0-0.037-0.01144.9140.0110.0110.0000.0000.0000.000
204A206TYR0-0.040-0.04440.2980.0750.0750.0000.0000.0000.000
205A207GLY00.015-0.00345.788-0.173-0.1730.0000.0000.0000.000
206A208LEU0-0.032-0.02745.8310.1340.1340.0000.0000.0000.000
207A209LEU0-0.025-0.03545.6480.1030.1030.0000.0000.0000.000
208A210ARG10.9230.97539.702-7.119-7.1190.0000.0000.0000.000
209A211THR00.0550.03942.6200.0890.0890.0000.0000.0000.000
210A212VAL00.0160.02837.0650.1150.1150.0000.0000.0000.000