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: YZY42

Calculation Name: 3MQ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MQ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q10589

Base Structure: X-ray

Registration Date: 2023-06-21

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 454
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7025833.931411
FMO2-HF: Nuclear repulsion 6852226.388696
FMO2-HF: Total energy -173607.542716
FMO2-MP2: Total energy -174119.817548


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:4:GLU)


Summations of interaction energy for fragment #1(A:4: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.
89.75195.7351.517-3.443-4.057-0.003
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.980 / 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].
3A6LYS10.8780.9363.392-39.669-36.669-0.001-1.522-1.4770.003
4A7LEU00.0110.0194.5674.2764.4420.000-0.021-0.1440.000
5A8VAL0-0.028-0.0086.216-2.592-2.5920.0000.0000.0000.000
6A9ILE00.0130.0048.698-0.273-0.2730.0000.0000.0000.000
7A10TRP0-0.026-0.02712.176-1.063-1.0630.0000.0000.0000.000
8A11ILE00.0190.01514.944-0.404-0.4040.0000.0000.0000.000
9A12ASN00.021-0.00818.5900.2280.2280.0000.0000.0000.000
10A13GLY00.011-0.00921.7070.0500.0500.0000.0000.0000.000
11A14ASP-1-0.855-0.89723.66310.44110.4410.0000.0000.0000.000
12A15LYS10.9170.94622.827-10.984-10.9840.0000.0000.0000.000
13A16GLY00.0710.04924.3320.0300.0300.0000.0000.0000.000
14A17TYR00.009-0.00819.4410.4580.4580.0000.0000.0000.000
15A18ASN0-0.020-0.01419.7640.9530.9530.0000.0000.0000.000
16A19GLY00.0440.00621.3920.2410.2410.0000.0000.0000.000
17A20LEU0-0.010-0.00317.0730.1510.1510.0000.0000.0000.000
18A21ALA00.006-0.00817.0290.6780.6780.0000.0000.0000.000
19A22GLU-1-0.871-0.90517.88513.12113.1210.0000.0000.0000.000
20A23VAL00.0060.00718.0810.1290.1290.0000.0000.0000.000
21A24GLY00.009-0.00315.2010.4790.4790.0000.0000.0000.000
22A25LYS10.8400.89515.220-12.567-12.5670.0000.0000.0000.000
23A26LYS10.7500.86317.469-13.187-13.1870.0000.0000.0000.000
24A27PHE00.0580.02510.460-0.187-0.1870.0000.0000.0000.000
25A28GLU-1-0.809-0.88613.41419.72219.7220.0000.0000.0000.000
26A29LYS10.8560.93114.526-12.487-12.4870.0000.0000.0000.000
27A30ASP-1-0.800-0.86917.30813.73113.7310.0000.0000.0000.000
28A31THR0-0.0060.00312.6770.3490.3490.0000.0000.0000.000
29A32GLY0-0.0120.00512.8680.9320.9320.0000.0000.0000.000
30A33ILE0-0.038-0.0047.5821.5491.5490.0000.0000.0000.000
31A34LYS10.8350.8929.275-22.261-22.2610.0000.0000.0000.000
32A35VAL00.0280.0218.8742.1852.1850.0000.0000.0000.000
33A36THR0-0.076-0.0339.898-0.582-0.5820.0000.0000.0000.000
34A37VAL00.0260.01811.5610.5530.5530.0000.0000.0000.000
35A38GLU-1-0.907-0.95511.73220.27520.2750.0000.0000.0000.000
36A39HIS10.8890.94515.583-13.498-13.4980.0000.0000.0000.000
37A40PRO00.0170.01615.593-0.736-0.7360.0000.0000.0000.000
38A41ASP-1-0.821-0.93218.72511.52711.5270.0000.0000.0000.000
39A42LYS10.7840.89420.916-10.667-10.6670.0000.0000.0000.000
40A43LEU00.0640.02917.5260.1920.1920.0000.0000.0000.000
41A44GLU-1-0.777-0.88018.46712.33412.3340.0000.0000.0000.000
42A45GLU-1-0.926-0.95320.70711.30611.3060.0000.0000.0000.000
43A46LYS10.8390.90417.279-13.024-13.0240.0000.0000.0000.000
44A47PHE00.0340.02712.7940.5770.5770.0000.0000.0000.000
45A48PRO0-0.030-0.02715.3670.8170.8170.0000.0000.0000.000
46A49GLN0-0.063-0.02617.2040.2570.2570.0000.0000.0000.000
47A50VAL00.0080.01711.9610.2140.2140.0000.0000.0000.000
48A51ALA00.0210.02511.3641.4131.4130.0000.0000.0000.000
49A52ALA0-0.028-0.02012.1151.0121.0120.0000.0000.0000.000
50A53THR0-0.063-0.03612.277-1.077-1.0770.0000.0000.0000.000
51A54GLY0-0.027-0.0178.8571.0051.0050.0000.0000.0000.000
52A55ASP-1-0.851-0.9007.07330.13230.1320.0000.0000.0000.000
53A56GLY0-0.065-0.0448.692-1.496-1.4960.0000.0000.0000.000
54A57PRO0-0.065-0.0177.8572.1382.1380.0000.0000.0000.000
55A58ASP-1-0.709-0.8225.52337.62437.6240.0000.0000.0000.000
56A59ILE0-0.035-0.0308.467-1.436-1.4360.0000.0000.0000.000
57A60ILE0-0.0180.00112.176-0.170-0.1700.0000.0000.0000.000
58A61PHE00.019-0.00315.253-0.617-0.6170.0000.0000.0000.000
59A62TRP0-0.018-0.03018.714-0.103-0.1030.0000.0000.0000.000
60A63ALA00.0160.02721.640-0.056-0.0560.0000.0000.0000.000
61A64HIS00.0390.00024.1150.3140.3140.0000.0000.0000.000
62A65ASP-1-0.903-0.95325.16710.59710.5970.0000.0000.0000.000
63A66ARG10.9120.95623.019-11.543-11.5430.0000.0000.0000.000
64A67PHE0-0.006-0.01119.0960.3480.3480.0000.0000.0000.000
65A68GLY00.0280.02622.3620.3380.3380.0000.0000.0000.000
66A69GLY0-0.020-0.01324.614-0.013-0.0130.0000.0000.0000.000
67A70TYR0-0.007-0.03718.8260.0190.0190.0000.0000.0000.000
68A71ALA00.0100.01120.1190.4910.4910.0000.0000.0000.000
69A72GLN0-0.036-0.00921.459-0.238-0.2380.0000.0000.0000.000
70A73SER0-0.066-0.02320.554-0.327-0.3270.0000.0000.0000.000
71A74GLY0-0.009-0.01219.3370.6210.6210.0000.0000.0000.000
72A75LEU0-0.0060.00415.7560.7420.7420.0000.0000.0000.000
73A76LEU0-0.058-0.01814.6841.1111.1110.0000.0000.0000.000
74A77ALA0-0.021-0.02212.877-0.298-0.2980.0000.0000.0000.000
75A78GLU-1-0.838-0.89915.04312.82712.8270.0000.0000.0000.000
76A79ILE0-0.033-0.01015.9330.7230.7230.0000.0000.0000.000
77A80THR00.003-0.01217.529-0.640-0.6400.0000.0000.0000.000
78A81PRO00.0050.03819.1430.2790.2790.0000.0000.0000.000
79A82ASP-1-0.847-0.93321.25511.34711.3470.0000.0000.0000.000
80A83LYS10.8480.87524.135-9.261-9.2610.0000.0000.0000.000
81A84ALA00.0120.01126.857-0.247-0.2470.0000.0000.0000.000
82A85PHE00.0290.01522.025-0.189-0.1890.0000.0000.0000.000
83A86GLN0-0.065-0.03724.750-0.423-0.4230.0000.0000.0000.000
84A87ASP-1-0.809-0.86626.7938.9768.9760.0000.0000.0000.000
85A88LYS10.9680.99523.725-11.754-11.7540.0000.0000.0000.000
86A89LEU00.0030.01024.362-0.094-0.0940.0000.0000.0000.000
87A90TYR00.0300.01828.598-0.281-0.2810.0000.0000.0000.000
88A91PRO00.0160.00430.3760.2310.2310.0000.0000.0000.000
89A92PHE00.0380.01031.0120.2140.2140.0000.0000.0000.000
90A93THR0-0.026-0.02228.1530.1960.1960.0000.0000.0000.000
91A94TRP00.0400.00422.4750.4770.4770.0000.0000.0000.000
92A95ASP-1-0.827-0.89227.2719.4649.4640.0000.0000.0000.000
93A96ALA0-0.0150.00527.760-0.068-0.0680.0000.0000.0000.000
94A97VAL0-0.067-0.02723.0340.2450.2450.0000.0000.0000.000
95A98ARG10.9080.94224.205-9.733-9.7330.0000.0000.0000.000
96A99TYR00.0630.02324.388-0.180-0.1800.0000.0000.0000.000
97A100ASN0-0.046-0.02325.810-0.109-0.1090.0000.0000.0000.000
98A101GLY00.0460.03028.0700.0420.0420.0000.0000.0000.000
99A102LYS10.8010.90122.540-12.623-12.6230.0000.0000.0000.000
100A103LEU0-0.0050.00222.379-0.145-0.1450.0000.0000.0000.000
101A104ILE0-0.004-0.01419.5150.5230.5230.0000.0000.0000.000
102A105ALA0-0.023-0.00718.5770.6640.6640.0000.0000.0000.000
103A106TYR0-0.015-0.04616.271-0.371-0.3710.0000.0000.0000.000
104A107PRO0-0.0090.01220.6470.1630.1630.0000.0000.0000.000
105A108ILE0-0.027-0.01620.0410.1580.1580.0000.0000.0000.000
106A109ALA00.0010.00224.219-0.291-0.2910.0000.0000.0000.000
107A110VAL0-0.031-0.02927.4910.1130.1130.0000.0000.0000.000
108A111GLU-1-0.908-0.94930.6938.9518.9510.0000.0000.0000.000
109A112ALA00.009-0.01633.0580.0040.0040.0000.0000.0000.000
110A113LEU0-0.0240.01336.581-0.100-0.1000.0000.0000.0000.000
111A114SER00.0050.00239.898-0.004-0.0040.0000.0000.0000.000
112A115LEU00.0040.00142.631-0.024-0.0240.0000.0000.0000.000
113A116ILE0-0.043-0.02142.4060.0300.0300.0000.0000.0000.000
114A117TYR00.0140.00846.819-0.055-0.0550.0000.0000.0000.000
115A118ASN00.0620.04450.0940.0340.0340.0000.0000.0000.000
116A119LYS10.8910.92648.343-6.285-6.2850.0000.0000.0000.000
117A120ASP-1-0.868-0.92653.8265.4835.4830.0000.0000.0000.000
118A121LEU0-0.076-0.03655.827-0.104-0.1040.0000.0000.0000.000
119A122LEU0-0.042-0.02854.571-0.092-0.0920.0000.0000.0000.000
120A123PRO00.0120.01355.0800.1070.1070.0000.0000.0000.000
121A124ASN0-0.064-0.03555.1790.1110.1110.0000.0000.0000.000
122A125PRO0-0.0010.01351.289-0.069-0.0690.0000.0000.0000.000
123A126PRO00.0210.01653.935-0.009-0.0090.0000.0000.0000.000
124A127LYS10.9770.98150.175-5.851-5.8510.0000.0000.0000.000
125A128THR0-0.077-0.03452.7520.0680.0680.0000.0000.0000.000
126A129TRP00.050-0.00148.375-0.111-0.1110.0000.0000.0000.000
127A130GLU-1-0.803-0.91054.5875.4325.4320.0000.0000.0000.000
128A131GLU-1-0.840-0.90157.0535.2505.2500.0000.0000.0000.000
129A132ILE0-0.011-0.01053.447-0.052-0.0520.0000.0000.0000.000
130A133PRO00.0070.00557.954-0.052-0.0520.0000.0000.0000.000
131A134ALA0-0.020-0.01660.714-0.049-0.0490.0000.0000.0000.000
132A135LEU00.0680.04057.172-0.046-0.0460.0000.0000.0000.000
133A136ASP-1-0.748-0.84459.1975.1265.1260.0000.0000.0000.000
134A137LYS10.8730.92260.912-4.836-4.8360.0000.0000.0000.000
135A138GLU-1-0.890-0.91963.5414.7714.7710.0000.0000.0000.000
136A139LEU00.012-0.01358.522-0.047-0.0470.0000.0000.0000.000
137A140LYS10.8590.92559.537-5.114-5.1140.0000.0000.0000.000
138A141ALA0-0.052-0.01163.963-0.045-0.0450.0000.0000.0000.000
139A142LYS10.8070.90163.213-4.904-4.9040.0000.0000.0000.000
140A143GLY0-0.017-0.00463.7850.0470.0470.0000.0000.0000.000
141A144LYS10.8280.91358.348-5.137-5.1370.0000.0000.0000.000
142A145SER00.0480.01355.687-0.069-0.0690.0000.0000.0000.000
143A146ALA0-0.005-0.00256.8450.0480.0480.0000.0000.0000.000
144A147LEU0-0.029-0.01449.9320.0850.0850.0000.0000.0000.000
145A148MET0-0.0060.01351.473-0.088-0.0880.0000.0000.0000.000
146A149PHE00.0380.00946.1130.0960.0960.0000.0000.0000.000
147A150ASN00.0160.00542.231-0.202-0.2020.0000.0000.0000.000
148A151LEU00.016-0.00345.6130.0900.0900.0000.0000.0000.000
149A152GLN0-0.055-0.04745.252-0.005-0.0050.0000.0000.0000.000
150A153GLU-1-0.791-0.85639.0547.6307.6300.0000.0000.0000.000
151A154PRO00.0060.00240.400-0.080-0.0800.0000.0000.0000.000
152A155TYR0-0.005-0.00535.539-0.089-0.0890.0000.0000.0000.000
153A156PHE00.0570.01139.5590.0280.0280.0000.0000.0000.000
154A157THR0-0.0030.00542.832-0.107-0.1070.0000.0000.0000.000
155A158TRP0-0.061-0.03141.166-0.214-0.2140.0000.0000.0000.000
156A159PRO00.0200.01442.059-0.106-0.1060.0000.0000.0000.000
157A160LEU00.0100.02344.457-0.057-0.0570.0000.0000.0000.000
158A161ILE0-0.059-0.02346.526-0.109-0.1090.0000.0000.0000.000
159A162ALA00.0380.00644.144-0.092-0.0920.0000.0000.0000.000
160A163ALA0-0.0010.01946.0980.0000.0000.0000.0000.0000.000
161A164ASP-1-0.804-0.90347.8555.7545.7540.0000.0000.0000.000
162A165GLY0-0.012-0.01648.354-0.065-0.0650.0000.0000.0000.000
163A166GLY0-0.0420.02246.3850.0420.0420.0000.0000.0000.000
164A167TYR0-0.061-0.06941.508-0.006-0.0060.0000.0000.0000.000
165A168ALA0-0.006-0.01138.374-0.088-0.0880.0000.0000.0000.000
166A169PHE00.003-0.01936.636-0.060-0.0600.0000.0000.0000.000
167A170LYS10.8360.92438.522-6.889-6.8890.0000.0000.0000.000
168A171TYR0-0.020-0.03931.7610.2410.2410.0000.0000.0000.000
169A172GLU-1-0.897-0.94836.6678.1808.1800.0000.0000.0000.000
170A173ASN0-0.055-0.03334.553-0.042-0.0420.0000.0000.0000.000
171A174GLY00.0200.02031.0790.2480.2480.0000.0000.0000.000
172A175LYS10.8340.91030.604-8.925-8.9250.0000.0000.0000.000
173A176TYR00.0750.03131.257-0.132-0.1320.0000.0000.0000.000
174A177ASP-1-0.831-0.91035.1077.6887.6880.0000.0000.0000.000
175A178ILE0-0.035-0.02334.733-0.162-0.1620.0000.0000.0000.000
176A179LYS10.8410.90937.948-7.074-7.0740.0000.0000.0000.000
177A180ASP-1-0.812-0.84741.1636.7436.7430.0000.0000.0000.000
178A181VAL00.0550.01441.2090.1670.1670.0000.0000.0000.000
179A182GLY0-0.0160.01343.440-0.189-0.1890.0000.0000.0000.000
180A183VAL00.006-0.00943.813-0.021-0.0210.0000.0000.0000.000
181A184ASP-1-0.873-0.93846.5846.0616.0610.0000.0000.0000.000
182A185ASN0-0.016-0.01647.610-0.216-0.2160.0000.0000.0000.000
183A186ALA00.023-0.01751.080-0.001-0.0010.0000.0000.0000.000
184A187GLY00.0510.04251.123-0.070-0.0700.0000.0000.0000.000
185A188ALA00.0360.01948.300-0.023-0.0230.0000.0000.0000.000
186A189LYS10.8360.90550.125-5.663-5.6630.0000.0000.0000.000
187A190ALA00.0010.02953.553-0.087-0.0870.0000.0000.0000.000
188A191GLY00.0600.02751.060-0.054-0.0540.0000.0000.0000.000
189A192LEU0-0.006-0.01250.194-0.037-0.0370.0000.0000.0000.000
190A193THR0-0.027-0.01952.435-0.076-0.0760.0000.0000.0000.000
191A194PHE00.0240.02554.436-0.079-0.0790.0000.0000.0000.000
192A195LEU00.0180.01149.783-0.051-0.0510.0000.0000.0000.000
193A196VAL00.018-0.01653.883-0.064-0.0640.0000.0000.0000.000
194A197ASP-1-0.802-0.90056.0025.0355.0350.0000.0000.0000.000
195A198LEU0-0.0180.00554.264-0.101-0.1010.0000.0000.0000.000
196A199ILE0-0.024-0.00653.470-0.062-0.0620.0000.0000.0000.000
197A200LYS10.8140.90457.866-5.178-5.1780.0000.0000.0000.000
198A201ASN0-0.140-0.08561.105-0.163-0.1630.0000.0000.0000.000
199A202LYS10.9210.96260.718-4.826-4.8260.0000.0000.0000.000
200A203HIS0-0.027-0.02558.586-0.085-0.0850.0000.0000.0000.000
201A204MET0-0.031-0.00250.9760.0740.0740.0000.0000.0000.000
202A205ASN0-0.033-0.02155.143-0.143-0.1430.0000.0000.0000.000
203A206ALA00.0530.02853.5630.1080.1080.0000.0000.0000.000
204A207ASP-1-0.891-0.92052.0045.6825.6820.0000.0000.0000.000
205A208THR0-0.004-0.00849.6130.0130.0130.0000.0000.0000.000
206A209ASP-1-0.797-0.91745.7466.5886.5880.0000.0000.0000.000
207A210TYR0-0.086-0.04140.164-0.018-0.0180.0000.0000.0000.000
208A211SER00.0330.00944.1260.0010.0010.0000.0000.0000.000
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