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: Q1JGY

Calculation Name: 1YXY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YXY

Chain ID: A

ChEMBL ID:

UniProt ID: P65522

Base Structure: X-ray

Registration Date: 2023-06-19

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2700311.771943
FMO2-HF: Nuclear repulsion 2613523.815179
FMO2-HF: Total energy -86787.956765
FMO2-MP2: Total energy -87039.578215


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:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-170.675-168.66513.116-7.079-8.046-0.075
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.896 / q_NPA : 0.932
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].
3A6THR00.0780.0253.822-2.105-0.741-0.013-0.578-0.7730.003
4A7LYS10.9220.9556.26320.63720.6370.0000.0000.0000.000
5A8GLU-1-0.938-0.9638.725-17.312-17.3120.0000.0000.0000.000
6A9LYS10.8680.9138.30319.46019.4600.0000.0000.0000.000
7A10LEU0-0.0090.0086.5900.7190.7190.0000.0000.0000.000
8A11MET0-0.015-0.0258.8641.0731.0730.0000.0000.0000.000
9A12GLU-1-0.899-0.93412.331-16.285-16.2850.0000.0000.0000.000
10A13GLN0-0.044-0.01810.6500.9070.9070.0000.0000.0000.000
11A14LEU0-0.025-0.02410.8380.6070.6070.0000.0000.0000.000
12A15LYS10.9770.99114.08913.53213.5320.0000.0000.0000.000
13A16GLY0-0.037-0.00817.1710.1890.1890.0000.0000.0000.000
14A17GLY00.0250.02518.4590.4590.4590.0000.0000.0000.000
15A18ILE0-0.048-0.02819.2560.1110.1110.0000.0000.0000.000
16A19ILE0-0.0060.00913.996-0.433-0.4330.0000.0000.0000.000
17A20VAL00.0500.01216.7790.6270.6270.0000.0000.0000.000
18A21SER00.0070.01217.411-0.941-0.9410.0000.0000.0000.000
19A22CYS0-0.051-0.00618.3180.9700.9700.0000.0000.0000.000
20A23GLN00.028-0.00319.499-0.399-0.3990.0000.0000.0000.000
21A24ALA00.0480.02221.7550.5900.5900.0000.0000.0000.000
22A25LEU0-0.017-0.00422.738-0.384-0.3840.0000.0000.0000.000
23A26PRO00.0360.00325.0810.3950.3950.0000.0000.0000.000
24A27GLY00.0140.01428.2500.1250.1250.0000.0000.0000.000
25A28GLH0-0.095-0.09226.9810.1540.1540.0000.0000.0000.000
26A29PRO00.008-0.00530.616-0.075-0.0750.0000.0000.0000.000
27A30LEU0-0.006-0.00227.1240.0900.0900.0000.0000.0000.000
28A31TYR0-0.0040.00924.601-0.614-0.6140.0000.0000.0000.000
29A32SER00.0010.00826.2640.4990.4990.0000.0000.0000.000
30A33GLU-1-0.908-0.96125.821-10.822-10.8220.0000.0000.0000.000
31A34THR0-0.034-0.02625.977-0.230-0.2300.0000.0000.0000.000
32A35GLY0-0.0260.01423.119-0.334-0.3340.0000.0000.0000.000
33A36GLY00.010-0.01922.5280.6280.6280.0000.0000.0000.000
34A37ILE0-0.040-0.02223.8570.2660.2660.0000.0000.0000.000
35A38MET00.0050.00119.9340.0760.0760.0000.0000.0000.000
36A39PRO00.0430.02918.569-0.155-0.1550.0000.0000.0000.000
37A40LEU00.0060.00519.6330.0240.0240.0000.0000.0000.000
38A41MET0-0.0220.00321.5700.3470.3470.0000.0000.0000.000
39A42ALA00.0400.00616.6970.0880.0880.0000.0000.0000.000
40A43LYS10.8210.89718.69212.00812.0080.0000.0000.0000.000
41A44ALA0-0.0030.00020.1310.1930.1930.0000.0000.0000.000
42A45ALA00.002-0.00119.0570.2570.2570.0000.0000.0000.000
43A46GLN00.0570.04015.913-0.669-0.6690.0000.0000.0000.000
44A47GLU-1-0.875-0.92418.679-11.772-11.7720.0000.0000.0000.000
45A48ALA0-0.055-0.01722.0680.4070.4070.0000.0000.0000.000
46A49GLY0-0.0110.00520.1970.3510.3510.0000.0000.0000.000
47A50ALA0-0.080-0.02917.816-0.129-0.1290.0000.0000.0000.000
48A51VAL00.0160.00914.579-0.389-0.3890.0000.0000.0000.000
49A52GLY00.0460.00812.597-1.237-1.2370.0000.0000.0000.000
50A53ILE0-0.0260.00012.4621.2391.2390.0000.0000.0000.000
51A54ARG10.7400.83212.70915.34515.3450.0000.0000.0000.000
52A55ALA00.0170.00414.3211.1011.1010.0000.0000.0000.000
53A56ASN00.0720.02115.110-1.084-1.0840.0000.0000.0000.000
54A57SER0-0.023-0.00916.0560.5780.5780.0000.0000.0000.000
55A58VAL00.0750.01912.864-0.575-0.5750.0000.0000.0000.000
56A59ARG10.7810.87814.55913.42813.4280.0000.0000.0000.000
57A60ASP-1-0.796-0.88717.101-15.334-15.3340.0000.0000.0000.000
58A61ILE0-0.0210.00110.613-0.271-0.2710.0000.0000.0000.000
59A62LYS10.9520.97710.79826.07726.0770.0000.0000.0000.000
60A63GLU-1-0.817-0.90813.831-14.841-14.8410.0000.0000.0000.000
61A64ILE0-0.014-0.01613.3200.5700.5700.0000.0000.0000.000
62A65GLN0-0.032-0.0407.6701.5481.5480.0000.0000.0000.000
63A66ALA0-0.048-0.00512.059-0.129-0.1290.0000.0000.0000.000
64A67ILE0-0.090-0.04414.9360.8960.8960.0000.0000.0000.000
65A68THR0-0.063-0.04412.6910.7030.7030.0000.0000.0000.000
66A69ASP-1-0.881-0.92910.118-22.411-22.4110.0000.0000.0000.000
67A70LEU0-0.081-0.0279.419-0.826-0.8260.0000.0000.0000.000
68A71PRO0-0.023-0.0027.517-1.534-1.5340.0000.0000.0000.000
69A72ILE00.008-0.0147.9651.4301.4300.0000.0000.0000.000
70A73ILE0-0.011-0.0078.352-2.126-2.1260.0000.0000.0000.000
71A74GLY00.018-0.00410.4281.4841.4840.0000.0000.0000.000
72A75ILE0-0.043-0.01711.940-0.042-0.0420.0000.0000.0000.000
73A76ILE00.008-0.01013.383-0.011-0.0110.0000.0000.0000.000
74A77LYS10.8490.93616.50914.15514.1550.0000.0000.0000.000
75A78LYS10.8670.93520.19214.17014.1700.0000.0000.0000.000
76A79ASP-1-0.863-0.92722.099-11.884-11.8840.0000.0000.0000.000
77A80TYR0-0.106-0.09519.8480.0170.0170.0000.0000.0000.000
78A81PRO00.0340.04225.8360.1380.1380.0000.0000.0000.000
79A82PRO0-0.040-0.04329.591-0.088-0.0880.0000.0000.0000.000
80A83GLN00.0100.00827.5090.0820.0820.0000.0000.0000.000
81A84GLU-1-0.843-0.91728.360-10.155-10.1550.0000.0000.0000.000
82A85PRO0-0.050-0.01122.956-0.153-0.1530.0000.0000.0000.000
83A86PHE00.0620.02322.714-0.095-0.0950.0000.0000.0000.000
84A87ILE0-0.039-0.01617.711-0.467-0.4670.0000.0000.0000.000
85A88THR0-0.032-0.03713.560-0.125-0.1250.0000.0000.0000.000
86A89ALA00.0320.03116.856-0.249-0.2490.0000.0000.0000.000
87A90THR00.009-0.01018.2660.3210.3210.0000.0000.0000.000
88A91MET00.0550.00713.610-1.516-1.5160.0000.0000.0000.000
89A92THR00.0110.01914.064-1.568-1.5680.0000.0000.0000.000
90A93GLU-1-0.758-0.82814.205-17.951-17.9510.0000.0000.0000.000
91A94VAL00.0230.00810.332-1.744-1.7440.0000.0000.0000.000
92A95ASP-1-0.754-0.8469.735-28.115-28.1150.0000.0000.0000.000
93A96GLN0-0.043-0.0249.085-2.671-2.6710.0000.0000.0000.000
94A97LEU0-0.023-0.0129.196-1.699-1.6990.0000.0000.0000.000
95A98ALA00.0250.0175.557-3.791-3.7910.0000.0000.0000.000
96A99ALA0-0.062-0.0254.489-11.463-11.366-0.001-0.008-0.0870.000
97A100LEU0-0.050-0.0246.383-0.197-0.1970.0000.0000.0000.000
98A101ASN0-0.0280.0071.754-42.094-44.56313.045-5.606-4.971-0.072
99A102ILE00.0330.0283.9035.2905.557-0.001-0.016-0.2500.000
100A103ALA00.0100.0043.459-4.835-4.3090.008-0.105-0.4290.000
101A104VAL0-0.022-0.0114.542-1.291-1.186-0.001-0.005-0.0990.000
102A105ILE00.0130.0287.0630.7450.7450.0000.0000.0000.000
103A106ALA0-0.0010.0029.9040.8560.8560.0000.0000.0000.000
104A107MET00.0170.00412.368-0.093-0.0930.0000.0000.0000.000
105A108ASP-1-0.760-0.83516.351-12.717-12.7170.0000.0000.0000.000
106A109CYS0-0.074-0.03517.978-0.550-0.5500.0000.0000.0000.000
107A110THR0-0.040-0.04520.6690.5970.5970.0000.0000.0000.000
108A111LYS10.8580.92924.4419.7409.7400.0000.0000.0000.000
109A112ARG10.7630.86425.21511.82411.8240.0000.0000.0000.000
110A113ASP-1-0.885-0.93426.829-10.426-10.4260.0000.0000.0000.000
111A114ARG10.8120.87919.61414.66414.6640.0000.0000.0000.000
112A115HIS0-0.045-0.02724.3730.0640.0640.0000.0000.0000.000
113A116ASP-1-0.811-0.89420.844-14.305-14.3050.0000.0000.0000.000
114A117GLY0-0.024-0.00424.2740.0450.0450.0000.0000.0000.000
115A118LEU0-0.063-0.01120.4870.2280.2280.0000.0000.0000.000
116A119ASP-1-0.775-0.85524.212-12.560-12.5600.0000.0000.0000.000
117A120ILE00.0500.00819.445-0.527-0.5270.0000.0000.0000.000
118A121ALA00.0200.01120.099-0.806-0.8060.0000.0000.0000.000
119A122SER0-0.052-0.07219.680-0.745-0.7450.0000.0000.0000.000
120A123PHE00.0020.01516.151-0.792-0.7920.0000.0000.0000.000
121A124ILE00.0100.00414.975-1.172-1.1720.0000.0000.0000.000
122A125ARG10.9240.95314.70312.75912.7590.0000.0000.0000.000
123A126GLN0-0.010-0.00115.328-1.154-1.1540.0000.0000.0000.000
124A127VAL0-0.013-0.00710.750-1.297-1.2970.0000.0000.0000.000
125A128LYS10.8220.8908.47224.59524.5950.0000.0000.0000.000
126A129GLU-1-0.944-0.96011.070-20.565-20.5650.0000.0000.0000.000
127A130LYS10.7640.88510.30423.34823.3480.0000.0000.0000.000
128A131TYR0-0.092-0.0936.089-3.731-3.7310.0000.0000.0000.000
129A132PRO00.0600.0417.514-1.653-1.6530.0000.0000.0000.000
130A133ASN0-0.093-0.0533.5833.0893.3560.005-0.047-0.2240.000
131A134GLN0-0.062-0.0173.166-16.096-14.3150.075-0.704-1.152-0.006
132A135LEU0-0.0100.0044.8045.8385.910-0.001-0.010-0.0610.000
133A136LEU00.010-0.0057.176-0.837-0.8370.0000.0000.0000.000
134A137MET0-0.010-0.01710.4811.0751.0750.0000.0000.0000.000
135A138ALA00.0330.00513.183-0.058-0.0580.0000.0000.0000.000
136A139ASP-1-0.785-0.86016.822-15.841-15.8410.0000.0000.0000.000
137A140ILE0-0.031-0.01719.1450.3060.3060.0000.0000.0000.000
138A141SER0-0.042-0.05422.4400.2820.2820.0000.0000.0000.000
139A142THR0-0.015-0.03026.0150.4630.4630.0000.0000.0000.000
140A143PHE00.0520.00125.870-0.355-0.3550.0000.0000.0000.000
141A144ASP-1-0.901-0.95226.132-10.712-10.7120.0000.0000.0000.000
142A145GLU-1-0.652-0.77224.202-11.628-11.6280.0000.0000.0000.000
143A146GLY00.0200.01321.793-0.573-0.5730.0000.0000.0000.000
144A147LEU0-0.009-0.00521.678-0.536-0.5360.0000.0000.0000.000
145A148VAL0-0.004-0.00322.904-0.361-0.3610.0000.0000.0000.000
146A149ALA00.0180.00218.633-0.446-0.4460.0000.0000.0000.000
147A150HIS0-0.008-0.01218.009-1.184-1.1840.0000.0000.0000.000
148A151GLN0-0.034-0.01818.823-0.572-0.5720.0000.0000.0000.000
149A152ALA0-0.061-0.01718.836-0.007-0.0070.0000.0000.0000.000
150A153GLY00.0000.00415.597-0.640-0.6400.0000.0000.0000.000
151A154ILE0-0.057-0.01913.740-1.497-1.4970.0000.0000.0000.000
152A155ASP-1-0.824-0.8929.968-24.428-24.4280.0000.0000.0000.000
153A156PHE00.019-0.0119.0410.8610.8610.0000.0000.0000.000
154A157VAL00.0200.02514.162-0.247-0.2470.0000.0000.0000.000
155A158GLY00.0630.03017.5700.2120.2120.0000.0000.0000.000
156A159THR0-0.023-0.02818.6340.1710.1710.0000.0000.0000.000
157A160THR0-0.076-0.05519.8140.7400.7400.0000.0000.0000.000
158A161LEU00.0110.00822.1920.3310.3310.0000.0000.0000.000
159A162SER0-0.047-0.03824.6630.5060.5060.0000.0000.0000.000
160A163GLY0-0.046-0.02327.281-0.010-0.0100.0000.0000.0000.000
161A164TYR0-0.069-0.03626.7650.2150.2150.0000.0000.0000.000
162A165THR00.0160.01627.640-0.041-0.0410.0000.0000.0000.000
163A166PRO00.0420.00530.4400.1480.1480.0000.0000.0000.000
164A167TYR0-0.043-0.05428.0830.3330.3330.0000.0000.0000.000
165A168SER0-0.0120.00729.7280.0370.0370.0000.0000.0000.000
166A169ARG10.8640.93431.1179.2889.2880.0000.0000.0000.000
167A170GLN0-0.006-0.01532.250-0.129-0.1290.0000.0000.0000.000
168A171GLU-1-0.940-0.96334.811-8.186-8.1860.0000.0000.0000.000
169A172ALA00.0210.00833.506-0.296-0.2960.0000.0000.0000.000
170A173GLY00.0430.02831.7340.1090.1090.0000.0000.0000.000
171A174PRO00.0380.02727.370-0.098-0.0980.0000.0000.0000.000
172A175ASP-1-0.817-0.90527.434-9.537-9.5370.0000.0000.0000.000
173A176VAL0-0.003-0.02727.671-0.231-0.2310.0000.0000.0000.000
174A177ALA00.0210.02328.852-0.077-0.0770.0000.0000.0000.000
175A178LEU0-0.0160.01325.424-0.072-0.0720.0000.0000.0000.000
176A179ILE00.0290.00223.286-0.278-0.2780.0000.0000.0000.000
177A180GLU-1-0.842-0.90024.892-9.360-9.3600.0000.0000.0000.000
178A181ALA0-0.015-0.00627.205-0.052-0.0520.0000.0000.0000.000
179A182LEU0-0.011-0.01622.207-0.074-0.0740.0000.0000.0000.000
180A183CYS0-0.020-0.00922.850-0.386-0.3860.0000.0000.0000.000
181A184LYS10.8370.90223.8959.2179.2170.0000.0000.0000.000
182A185ALA0-0.055-0.01624.9720.1510.1510.0000.0000.0000.000
183A186GLY0-0.0220.00623.065-0.085-0.0850.0000.0000.0000.000
184A187ILE0-0.031-0.00718.956-0.552-0.5520.0000.0000.0000.000
185A188ALA0-0.0010.00015.1770.2450.2450.0000.0000.0000.000
186A189VAL00.002-0.00416.695-0.580-0.5800.0000.0000.0000.000
187A190ILE0-0.001-0.00312.766-0.056-0.0560.0000.0000.0000.000
188A191ALA00.0070.01117.3420.1530.1530.0000.0000.0000.000
189A192GLU-1-0.770-0.87217.926-15.325-15.3250.0000.0000.0000.000
190A193GLY00.0630.04121.3390.1870.1870.0000.0000.0000.000
191A194LYS10.8400.92024.50710.04710.0470.0000.0000.0000.000
192A195ILE0-0.0100.01023.1010.3700.3700.0000.0000.0000.000
193A196HIS00.001-0.01726.825-0.303-0.3030.0000.0000.0000.000
194A197SER0-0.028-0.01129.6050.1500.1500.0000.0000.0000.000
195A198PRO00.0450.00928.309-0.263-0.2630.0000.0000.0000.000
196A199GLU-1-0.867-0.94129.157-8.815-8.8150.0000.0000.0000.000
197A200GLU-1-0.889-0.94329.077-9.319-9.3190.0000.0000.0000.000
198A201ALA00.0270.01024.972-0.181-0.1810.0000.0000.0000.000
199A202LYS10.8320.90325.7928.9018.9010.0000.0000.0000.000
200A203LYS10.9720.98727.9308.7978.7970.0000.0000.0000.000
201A204ILE00.008-0.00623.496-0.021-0.0210.0000.0000.0000.000
202A205ASN0-0.007-0.00122.768-0.596-0.5960.0000.0000.0000.000
203A206ASP-1-0.856-0.91724.454-9.566-9.5660.0000.0000.0000.000
204A207LEU0-0.069-0.02825.3210.1750.1750.0000.0000.0000.000
205A208GLY0-0.046-0.00623.178-0.004-0.0040.0000.0000.0000.000
206A209VAL0-0.026-0.01219.912-0.279-0.2790.0000.0000.0000.000
207A210ALA0-0.042-0.02314.979-0.066-0.0660.0000.0000.0000.000
208A211GLY00.0240.00915.875-0.548-0.5480.0000.0000.0000.000
209A212ILE00.0050.00516.9830.4590.4590.0000.0000.0000.000
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