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: L7J79

Calculation Name: 3AEV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AEV

Chain ID: B

ChEMBL ID:

UniProt ID: O58655

Base Structure: X-ray

Registration Date: 2023-09-26

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1922499.249802
FMO2-HF: Nuclear repulsion 1850986.416443
FMO2-HF: Total energy -71512.833358
FMO2-MP2: Total energy -71727.139137


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(B:26:ASP)


Summations of interaction energy for fragment #1(B:26: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.
-35.601-30.7162.805-3.519-4.1680.014
Interaction energy analysis for fragmet #1(B:26:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.961 / q_NPA : -0.997
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].
3B28TRP0-0.018-0.0243.420-7.899-5.5020.056-1.083-1.3690.007
4B29GLU-1-0.890-0.9462.28035.85537.2822.735-2.089-2.0720.005
5B30GLU-1-0.915-0.9563.65343.03544.0960.014-0.347-0.7270.002
6B31PHE0-0.058-0.0105.600-7.017-7.0170.0000.0000.0000.000
7B32PHE0-0.071-0.0477.361-3.646-3.6460.0000.0000.0000.000
8B33LYS10.7490.9006.736-39.897-39.8970.0000.0000.0000.000
9B34GLN0-0.014-0.0048.831-2.188-2.1880.0000.0000.0000.000
10B35GLU-1-0.870-0.96210.04329.61229.6120.0000.0000.0000.000
11B36GLU-1-0.831-0.89113.39514.46514.4650.0000.0000.0000.000
12B37TYR0-0.058-0.05116.9270.0970.0970.0000.0000.0000.000
13B38VAL0-0.017-0.00918.827-0.866-0.8660.0000.0000.0000.000
14B39LYS10.8610.92222.194-12.247-12.2470.0000.0000.0000.000
15B40ILE0-0.056-0.01225.001-0.570-0.5700.0000.0000.0000.000
16B41PRO0-0.044-0.03427.703-0.002-0.0020.0000.0000.0000.000
17B42LYN00.1690.07230.3800.0590.0590.0000.0000.0000.000
18B43ASP-1-0.886-0.91931.4859.1099.1090.0000.0000.0000.000
19B44ARG10.7970.90430.705-9.528-9.5280.0000.0000.0000.000
20B45ILE00.0490.04026.6350.1670.1670.0000.0000.0000.000
21B46ALA0-0.002-0.00628.4050.1990.1990.0000.0000.0000.000
22B47VAL0-0.070-0.03530.1790.0400.0400.0000.0000.0000.000
23B48LEU00.0330.02023.663-0.024-0.0240.0000.0000.0000.000
24B49ILE00.0450.03624.7380.2790.2790.0000.0000.0000.000
25B50GLY00.0520.02826.4470.0520.0520.0000.0000.0000.000
26B51LYS10.9850.97028.826-8.535-8.5350.0000.0000.0000.000
27B52LYS10.9680.97628.416-9.910-9.9100.0000.0000.0000.000
28B53GLY00.0560.02724.8430.3560.3560.0000.0000.0000.000
29B54GLN0-0.072-0.03824.7180.2730.2730.0000.0000.0000.000
30B55THR00.0130.02026.245-0.050-0.0500.0000.0000.0000.000
31B56LYS10.8330.90818.341-15.690-15.6900.0000.0000.0000.000
32B57LYS10.9210.95721.383-12.258-12.2580.0000.0000.0000.000
33B58GLU-1-0.819-0.89122.20011.22711.2270.0000.0000.0000.000
34B59ILE00.0160.01421.7400.0210.0210.0000.0000.0000.000
35B60GLU-1-0.789-0.85317.31416.40716.4070.0000.0000.0000.000
36B61LYS10.8860.93119.191-11.458-11.4580.0000.0000.0000.000
37B62ARG10.8400.89921.127-10.607-10.6070.0000.0000.0000.000
38B63THR0-0.027-0.01120.0470.0490.0490.0000.0000.0000.000
39B64LYS10.8340.92216.386-14.885-14.8850.0000.0000.0000.000
40B65THR0-0.0210.00614.9551.0291.0290.0000.0000.0000.000
41B66LYS10.9360.98210.876-25.204-25.2040.0000.0000.0000.000
42B67ILE0-0.004-0.02314.7010.1940.1940.0000.0000.0000.000
43B68THR0-0.034-0.02514.9390.0090.0090.0000.0000.0000.000
44B69ILE0-0.005-0.01317.420-0.242-0.2420.0000.0000.0000.000
45B70ASP-1-0.810-0.89120.71314.11414.1140.0000.0000.0000.000
46B71SER0-0.068-0.06322.209-0.371-0.3710.0000.0000.0000.000
47B72GLU-1-0.930-0.93525.22410.55410.5540.0000.0000.0000.000
48B73THR0-0.057-0.04423.387-0.485-0.4850.0000.0000.0000.000
49B74GLY00.0170.00225.480-0.329-0.3290.0000.0000.0000.000
50B75GLU-1-0.842-0.86720.76414.22414.2240.0000.0000.0000.000
51B76VAL0-0.031-0.03419.8530.0650.0650.0000.0000.0000.000
52B77TRP00.0580.02514.718-0.221-0.2210.0000.0000.0000.000
53B78ILE0-0.055-0.02416.204-0.245-0.2450.0000.0000.0000.000
54B79THR00.0430.02110.8650.2670.2670.0000.0000.0000.000
55B80SER00.0330.02510.397-1.173-1.1730.0000.0000.0000.000
56B81THR0-0.056-0.0449.6571.4821.4820.0000.0000.0000.000
57B82LYS10.9360.9518.166-21.400-21.4000.0000.0000.0000.000
58B83GLU-1-0.836-0.90410.01217.47117.4710.0000.0000.0000.000
59B84THR0-0.071-0.04813.145-0.922-0.9220.0000.0000.0000.000
60B85GLU-1-0.849-0.90515.09914.34014.3400.0000.0000.0000.000
61B86ASP-1-0.808-0.88618.12612.84712.8470.0000.0000.0000.000
62B87PRO00.0310.00117.7830.5300.5300.0000.0000.0000.000
63B88LEU00.0230.00118.3920.4480.4480.0000.0000.0000.000
64B89ALA0-0.0050.00518.347-0.265-0.2650.0000.0000.0000.000
65B90VAL00.0240.01214.647-0.324-0.3240.0000.0000.0000.000
66B91TRP0-0.010-0.01616.605-0.564-0.5640.0000.0000.0000.000
67B92LYS10.9070.94521.139-12.675-12.6750.0000.0000.0000.000
68B93ALA0-0.023-0.00919.720-0.512-0.5120.0000.0000.0000.000
69B94ARG10.8220.88720.277-13.772-13.7720.0000.0000.0000.000
70B95ASP-1-0.798-0.88622.02811.61411.6140.0000.0000.0000.000
71B96ILE0-0.021-0.01524.762-0.541-0.5410.0000.0000.0000.000
72B97VAL0-0.0070.00121.925-0.460-0.4600.0000.0000.0000.000
73B98LEU00.0350.01625.288-0.488-0.4880.0000.0000.0000.000
74B99ALA0-0.001-0.00427.539-0.494-0.4940.0000.0000.0000.000
75B100ILE0-0.036-0.01227.309-0.435-0.4350.0000.0000.0000.000
76B101GLY00.0350.01929.050-0.316-0.3160.0000.0000.0000.000
77B102ARG10.8390.90430.168-9.746-9.7460.0000.0000.0000.000
78B103GLY0-0.0080.00133.228-0.345-0.3450.0000.0000.0000.000
79B104PHE0-0.019-0.00732.907-0.291-0.2910.0000.0000.0000.000
80B105SER0-0.008-0.01233.2850.2190.2190.0000.0000.0000.000
81B106PRO00.0820.02129.637-0.022-0.0220.0000.0000.0000.000
82B107GLU-1-0.948-0.96131.3288.4348.4340.0000.0000.0000.000
83B108ARG10.8420.88733.558-8.057-8.0570.0000.0000.0000.000
84B109ALA00.005-0.00229.766-0.013-0.0130.0000.0000.0000.000
85B110PHE00.004-0.00625.9730.2080.2080.0000.0000.0000.000
86B111ARG10.7730.87130.344-8.334-8.3340.0000.0000.0000.000
87B112LEU0-0.045-0.02628.201-0.074-0.0740.0000.0000.0000.000
88B113LEU0-0.058-0.01725.1390.3170.3170.0000.0000.0000.000
89B114ASN0-0.069-0.02928.3380.1700.1700.0000.0000.0000.000
90B115GLU-1-0.896-0.95229.40710.48310.4830.0000.0000.0000.000
91B116GLY0-0.029-0.00130.597-0.315-0.3150.0000.0000.0000.000
92B117GLU-1-0.855-0.91931.2928.3378.3370.0000.0000.0000.000
93B118TYR00.0250.00929.2040.1960.1960.0000.0000.0000.000
94B119LEU0-0.004-0.00928.610-0.352-0.3520.0000.0000.0000.000
95B120GLU-1-0.816-0.89731.3969.0059.0050.0000.0000.0000.000
96B121ILE0-0.027-0.03230.314-0.226-0.2260.0000.0000.0000.000
97B122ILE00.0060.01934.414-0.038-0.0380.0000.0000.0000.000
98B123ASN00.019-0.00535.5480.0370.0370.0000.0000.0000.000
99B124LEU0-0.023-0.01338.641-0.203-0.2030.0000.0000.0000.000
100B125THR0-0.073-0.04840.477-0.144-0.1440.0000.0000.0000.000
101B126ASP-1-0.823-0.90838.6838.1378.1370.0000.0000.0000.000
102B127ILE0-0.056-0.02142.368-0.131-0.1310.0000.0000.0000.000
103B128ILE0-0.083-0.04945.288-0.135-0.1350.0000.0000.0000.000
104B129ILE00.0820.05046.876-0.125-0.1250.0000.0000.0000.000
105B130GLY0-0.034-0.01648.802-0.105-0.1050.0000.0000.0000.000
106B131ASN00.0220.00550.230-0.163-0.1630.0000.0000.0000.000
107B132GLU-1-0.763-0.84352.9515.5875.5870.0000.0000.0000.000
108B133LYS10.9110.94552.508-5.412-5.4120.0000.0000.0000.000
109B134ASN00.018-0.01550.6620.0280.0280.0000.0000.0000.000
110B135ALA00.0330.01950.2500.0180.0180.0000.0000.0000.000
111B136LEU00.0630.03242.7820.0190.0190.0000.0000.0000.000
112B137PRO0-0.040-0.03046.9880.0240.0240.0000.0000.0000.000
113B138ARG10.8670.92748.254-5.910-5.9100.0000.0000.0000.000
114B139VAL00.0430.02346.587-0.057-0.0570.0000.0000.0000.000
115B140ARG10.9490.97542.887-7.277-7.2770.0000.0000.0000.000
116B141GLY00.0080.01046.7180.0230.0230.0000.0000.0000.000
117B142ARG10.7850.88349.858-6.158-6.1580.0000.0000.0000.000
118B143ILE00.0480.02644.534-0.063-0.0630.0000.0000.0000.000
119B144ILE00.0000.00344.969-0.008-0.0080.0000.0000.0000.000
120B145GLY00.0560.04047.884-0.050-0.0500.0000.0000.0000.000
121B146ARG10.9790.97751.383-5.607-5.6070.0000.0000.0000.000
122B147LYS10.9460.95951.788-5.688-5.6880.0000.0000.0000.000
123B148GLY00.0360.02148.7720.0410.0410.0000.0000.0000.000
124B149ARG10.9210.95649.037-5.786-5.7860.0000.0000.0000.000
125B150THR0-0.043-0.02349.380-0.033-0.0330.0000.0000.0000.000
126B151ARG10.8470.91442.571-7.233-7.2330.0000.0000.0000.000
127B152GLN00.0640.04946.158-0.045-0.0450.0000.0000.0000.000
128B153ILE0-0.027-0.01547.7540.0160.0160.0000.0000.0000.000
129B154ILE00.0260.00144.6620.0110.0110.0000.0000.0000.000
130B155GLU-1-0.747-0.80641.8767.5507.5500.0000.0000.0000.000
131B156GLU-1-0.905-0.96344.7576.4446.4440.0000.0000.0000.000
132B157MET0-0.073-0.02847.353-0.026-0.0260.0000.0000.0000.000
133B158SER0-0.052-0.03543.7740.0510.0510.0000.0000.0000.000
134B159GLY00.0350.01943.2480.0780.0780.0000.0000.0000.000
135B160ALA00.0080.02039.4710.1920.1920.0000.0000.0000.000
136B161SER0-0.038-0.01337.160-0.124-0.1240.0000.0000.0000.000
137B162VAL00.009-0.01338.4440.1290.1290.0000.0000.0000.000
138B163SER0-0.062-0.01236.717-0.189-0.1890.0000.0000.0000.000
139B164VAL0-0.004-0.01138.7660.0320.0320.0000.0000.0000.000
140B165TYR0-0.042-0.03934.339-0.071-0.0710.0000.0000.0000.000
141B166GLY00.0290.01838.3310.1330.1330.0000.0000.0000.000
142B167LYS10.9600.96137.401-8.516-8.5160.0000.0000.0000.000
143B168THR00.0530.05134.8570.0420.0420.0000.0000.0000.000
144B169VAL0-0.060-0.03138.188-0.128-0.1280.0000.0000.0000.000
145B170ALA00.0010.01134.3020.0830.0830.0000.0000.0000.000
146B171ILE00.000-0.01135.929-0.218-0.2180.0000.0000.0000.000
147B172ILE00.0350.01632.1420.2350.2350.0000.0000.0000.000
148B173GLY00.0440.02234.870-0.324-0.3240.0000.0000.0000.000
149B174ASN00.1140.06935.1030.1420.1420.0000.0000.0000.000
150B175PRO00.0570.01535.310-0.183-0.1830.0000.0000.0000.000
151B176ILE00.0260.01937.766-0.148-0.1480.0000.0000.0000.000
152B177GLN00.0380.02039.3090.0360.0360.0000.0000.0000.000
153B178ILE0-0.019-0.01234.966-0.159-0.1590.0000.0000.0000.000
154B179GLU-1-0.791-0.87839.5126.8676.8670.0000.0000.0000.000
155B180ILE0-0.0090.00442.025-0.186-0.1860.0000.0000.0000.000
156B181ALA00.001-0.00841.702-0.137-0.1370.0000.0000.0000.000
157B182LYS10.8710.93738.278-8.238-8.2380.0000.0000.0000.000
158B183THR0-0.007-0.00442.616-0.121-0.1210.0000.0000.0000.000
159B184ALA0-0.038-0.02146.040-0.150-0.1500.0000.0000.0000.000
160B185ILE0-0.009-0.01642.188-0.133-0.1330.0000.0000.0000.000
161B186GLU-1-0.875-0.94842.9197.2197.2190.0000.0000.0000.000
162B187LYS10.8550.93746.530-6.319-6.3190.0000.0000.0000.000
163B188LEU0-0.043-0.01548.590-0.147-0.1470.0000.0000.0000.000
164B189ALA0-0.008-0.00146.680-0.106-0.1060.0000.0000.0000.000
165B190ARG10.9620.97648.386-6.456-6.4560.0000.0000.0000.000
166B191GLY00.0200.02551.099-0.110-0.1100.0000.0000.0000.000
167B192SER0-0.034-0.01053.102-0.144-0.1440.0000.0000.0000.000
168B193PRO00.0230.02054.9280.0680.0680.0000.0000.0000.000
169B194HIS00.032-0.00852.322-0.071-0.0710.0000.0000.0000.000
170B195GLY00.0150.01955.7230.0310.0310.0000.0000.0000.000
171B196SER0-0.063-0.02756.6660.0290.0290.0000.0000.0000.000
172B197VAL00.0490.02350.7920.0440.0440.0000.0000.0000.000
173B198TYR00.0370.01952.1130.0520.0520.0000.0000.0000.000
174B199ARG11.0321.00954.598-5.278-5.2780.0000.0000.0000.000
175B200TYR0-0.017-0.00747.737-0.093-0.0930.0000.0000.0000.000
176B201LEU00.0520.00648.4100.0460.0460.0000.0000.0000.000
177B202GLU-1-0.935-0.97451.7075.7335.7330.0000.0000.0000.000
178B203ARG10.7230.82653.555-5.835-5.8350.0000.0000.0000.000
179B204ARG10.8660.92546.329-6.645-6.6450.0000.0000.0000.000
180B205LYS10.9490.99350.365-6.184-6.1840.0000.0000.0000.000
181B206LYS10.9030.95051.344-5.340-5.3400.0000.0000.0000.000
182B207ASP-1-0.820-0.86151.1595.8925.8920.0000.0000.0000.000
183B208LEU00.0100.01247.6270.1110.1110.0000.0000.0000.000