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: ZYKGN

Calculation Name: 3H25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H25

Chain ID: A

ChEMBL ID:

UniProt ID: Q52349

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2028261.951538
FMO2-HF: Nuclear repulsion 1954253.166916
FMO2-HF: Total energy -74008.784622
FMO2-MP2: Total energy -74223.880457


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:ASP)


Summations of interaction energy for fragment #1(A:4: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.
-130.02-125.23111.487-8.485-7.790.097
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.822 / q_NPA : -0.916
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].
3A6THR0-0.0090.0022.788-5.636-2.6710.182-1.413-1.7340.003
4A7LEU00.0280.0133.008-5.999-5.0660.045-0.213-0.7640.000
5A8GLN00.0310.0062.923-9.577-8.0340.239-0.756-1.0260.007
6A9ALA0-0.031-0.0026.197-3.734-3.7340.0000.0000.0000.000
7A10ILE00.0580.0307.231-2.401-2.4010.0000.0000.0000.000
8A11GLY00.0320.0208.750-2.239-2.2390.0000.0000.0000.000
9A12ARG10.8330.91210.177-23.251-23.2510.0000.0000.0000.000
10A13GLN00.0540.02912.215-0.608-0.6080.0000.0000.0000.000
11A14LEU0-0.007-0.00312.518-1.219-1.2190.0000.0000.0000.000
12A15LYS10.9440.97614.498-17.543-17.5430.0000.0000.0000.000
13A16ALA0-0.056-0.02716.216-0.879-0.8790.0000.0000.0000.000
14A17MET0-0.051-0.02817.970-0.445-0.4450.0000.0000.0000.000
15A18GLY0-0.0110.00019.014-0.704-0.7040.0000.0000.0000.000
16A19CYS0-0.061-0.00820.707-0.422-0.4220.0000.0000.0000.000
17A20GLU-1-0.911-0.95720.16712.68212.6820.0000.0000.0000.000
18A21ARG10.7390.83520.914-12.380-12.3800.0000.0000.0000.000
19A22PHE0-0.017-0.02918.217-0.126-0.1260.0000.0000.0000.000
20A23ASP-1-0.808-0.88820.57512.76712.7670.0000.0000.0000.000
21A24ILE0-0.035-0.03415.5620.6480.6480.0000.0000.0000.000
22A25GLY00.0440.01918.654-0.452-0.4520.0000.0000.0000.000
23A26VAL0-0.068-0.04916.6651.0061.0060.0000.0000.0000.000
24A27ARG10.9710.97819.087-13.086-13.0860.0000.0000.0000.000
25A28ASP-1-0.702-0.81420.43213.66213.6620.0000.0000.0000.000
26A29ALA0-0.053-0.02720.989-0.631-0.6310.0000.0000.0000.000
27A30THR0-0.048-0.03222.934-0.464-0.4640.0000.0000.0000.000
28A31THR0-0.039-0.06825.994-0.460-0.4600.0000.0000.0000.000
29A32GLY0-0.045-0.00525.837-0.394-0.3940.0000.0000.0000.000
30A33GLN00.000-0.00826.4390.1060.1060.0000.0000.0000.000
31A34MET0-0.0430.01922.0690.8900.8900.0000.0000.0000.000
32A35MET0-0.0070.00620.958-0.207-0.2070.0000.0000.0000.000
33A36ASN00.0420.02821.5960.8600.8600.0000.0000.0000.000
34A37ARG10.9140.97318.595-16.100-16.1000.0000.0000.0000.000
35A38GLU-1-0.767-0.85820.72212.46512.4650.0000.0000.0000.000
36A39TRP0-0.070-0.04016.0830.4790.4790.0000.0000.0000.000
37A40SER00.034-0.01319.6140.0980.0980.0000.0000.0000.000
38A41ALA00.0450.01016.2490.9640.9640.0000.0000.0000.000
39A42ALA00.001-0.00614.7371.3901.3900.0000.0000.0000.000
40A43GLU-1-0.758-0.84614.61815.99415.9940.0000.0000.0000.000
41A44VAL00.0000.00812.7141.1151.1150.0000.0000.0000.000
42A45LEU0-0.018-0.0079.0541.8291.8290.0000.0000.0000.000
43A46GLN0-0.0050.02510.4922.4432.4430.0000.0000.0000.000
44A47ASN0-0.065-0.04312.0580.7520.7520.0000.0000.0000.000
45A48THR00.025-0.0046.5120.1030.1030.0000.0000.0000.000
46A49PRO00.003-0.0097.8811.7431.7430.0000.0000.0000.000
47A50TRP00.0230.0098.830-0.444-0.4440.0000.0000.0000.000
48A51LEU00.0350.01910.788-0.735-0.7350.0000.0000.0000.000
49A52LYS10.8850.9331.795-110.671-111.32311.021-6.103-4.2660.087
50A53ARG10.9440.9889.121-21.048-21.0480.0000.0000.0000.000
51A54MET00.0090.00411.897-1.612-1.6120.0000.0000.0000.000
52A55ASN00.0130.01811.3230.7470.7470.0000.0000.0000.000
53A56ALA0-0.005-0.01111.095-1.247-1.2470.0000.0000.0000.000
54A57GLN0-0.077-0.05313.087-0.763-0.7630.0000.0000.0000.000
55A58GLY0-0.0100.01616.004-1.095-1.0950.0000.0000.0000.000
56A59ASN0-0.011-0.02016.384-1.691-1.6910.0000.0000.0000.000
57A60ASP-1-0.786-0.86715.82717.78317.7830.0000.0000.0000.000
58A61VAL00.008-0.00112.752-0.520-0.5200.0000.0000.0000.000
59A62TYR0-0.021-0.02215.6060.2470.2470.0000.0000.0000.000
60A63ILE0-0.038-0.02615.3380.4710.4710.0000.0000.0000.000
61A64ARG10.8450.91318.325-12.554-12.5540.0000.0000.0000.000
62A65PRO00.0250.01521.3740.3600.3600.0000.0000.0000.000
63A66ALA00.0200.01923.179-0.252-0.2520.0000.0000.0000.000
64A67GLU-1-0.795-0.89624.92710.04710.0470.0000.0000.0000.000
65A68GLN0-0.026-0.02128.569-0.327-0.3270.0000.0000.0000.000
66A69GLU-1-0.812-0.88024.75212.25212.2520.0000.0000.0000.000
67A70ARG10.8720.92927.834-9.704-9.7040.0000.0000.0000.000
68A71HIS00.0740.02526.2300.1560.1560.0000.0000.0000.000
69A72GLY00.0320.01227.852-0.389-0.3890.0000.0000.0000.000
70A73LEU0-0.058-0.01921.789-0.074-0.0740.0000.0000.0000.000
71A74VAL00.0190.00426.340-0.147-0.1470.0000.0000.0000.000
72A75LEU0-0.0330.00222.4580.2640.2640.0000.0000.0000.000
73A76VAL00.0230.01625.268-0.405-0.4050.0000.0000.0000.000
74A77ASP-1-0.815-0.91823.93113.05713.0570.0000.0000.0000.000
75A78ASP-1-0.932-0.94624.87810.53810.5380.0000.0000.0000.000
76A79LEU00.0450.02425.188-0.273-0.2730.0000.0000.0000.000
77A80SER0-0.021-0.05725.3140.5100.5100.0000.0000.0000.000
78A81GLU-1-0.835-0.92723.84712.85212.8520.0000.0000.0000.000
79A82PHE0-0.023-0.00226.1700.0010.0010.0000.0000.0000.000
80A83ASP-1-0.690-0.80228.6669.8989.8980.0000.0000.0000.000
81A84LEU0-0.084-0.04323.1080.0720.0720.0000.0000.0000.000
82A85ASP-1-0.949-0.98427.41610.82110.8210.0000.0000.0000.000
83A86ASP-1-0.838-0.91229.7248.8048.8040.0000.0000.0000.000
84A87MET0-0.051-0.02227.350-0.006-0.0060.0000.0000.0000.000
85A88LYS10.7620.87123.808-12.050-12.0500.0000.0000.0000.000
86A89ALA0-0.0210.00530.137-0.124-0.1240.0000.0000.0000.000
87A90GLU-1-0.842-0.87433.5478.1558.1550.0000.0000.0000.000
88A91GLY0-0.071-0.02133.283-0.169-0.1690.0000.0000.0000.000
89A92ARG10.7880.85430.735-8.516-8.5160.0000.0000.0000.000
90A93GLU-1-0.725-0.84427.15810.25310.2530.0000.0000.0000.000
91A94PRO00.0040.00523.1930.0690.0690.0000.0000.0000.000
92A95ALA0-0.071-0.03022.3860.1110.1110.0000.0000.0000.000
93A96LEU0-0.043-0.05516.8410.8080.8080.0000.0000.0000.000
94A97VAL00.0060.02318.695-0.415-0.4150.0000.0000.0000.000
95A98VAL0-0.025-0.03115.1391.1931.1930.0000.0000.0000.000
96A99GLU-1-0.819-0.91216.02915.56615.5660.0000.0000.0000.000
97A100THR00.011-0.00216.0761.0931.0930.0000.0000.0000.000
98A101SER00.000-0.03017.3600.7380.7380.0000.0000.0000.000
99A102PRO0-0.046-0.01217.358-0.287-0.2870.0000.0000.0000.000
100A103LYS10.9130.95319.324-13.125-13.1250.0000.0000.0000.000
101A104ASN00.0040.02520.927-0.971-0.9710.0000.0000.0000.000
102A105TYR0-0.071-0.06919.4771.3171.3170.0000.0000.0000.000
103A106GLN00.0340.04119.9770.1940.1940.0000.0000.0000.000
104A107ALA0-0.013-0.01521.0000.6890.6890.0000.0000.0000.000
105A108TRP00.0490.03019.615-0.474-0.4740.0000.0000.0000.000
106A109VAL00.0580.02623.2730.1750.1750.0000.0000.0000.000
107A110LYS10.8610.93125.279-11.264-11.2640.0000.0000.0000.000
108A111VAL00.0140.00727.297-0.187-0.1870.0000.0000.0000.000
109A112ALA00.008-0.00830.212-0.302-0.3020.0000.0000.0000.000
110A113ASP-1-0.868-0.92428.46010.69610.6960.0000.0000.0000.000
111A114ALA0-0.016-0.01129.1540.2420.2420.0000.0000.0000.000
112A115ALA00.0140.01031.630-0.300-0.3000.0000.0000.0000.000
113A116GLY0-0.0010.00232.5580.2260.2260.0000.0000.0000.000
114A117GLY00.0620.02033.0580.0770.0770.0000.0000.0000.000
115A118GLU-1-0.888-0.93134.0727.6867.6860.0000.0000.0000.000
116A119LEU0-0.0050.00535.954-0.057-0.0570.0000.0000.0000.000
117A120ARG10.8600.92329.389-10.235-10.2350.0000.0000.0000.000
118A121GLY00.0290.02332.6040.1740.1740.0000.0000.0000.000
119A122GLN00.0050.00134.4520.0580.0580.0000.0000.0000.000
120A123ILE00.009-0.00832.423-0.026-0.0260.0000.0000.0000.000
121A124ALA00.0180.01331.1850.0630.0630.0000.0000.0000.000
122A125ARG10.9230.96032.397-8.172-8.1720.0000.0000.0000.000
123A126THR0-0.054-0.02435.437-0.173-0.1730.0000.0000.0000.000
124A127LEU0-0.026-0.02230.0090.0040.0040.0000.0000.0000.000
125A128ALA00.0090.00332.0390.1080.1080.0000.0000.0000.000
126A129SER0-0.024-0.00132.948-0.104-0.1040.0000.0000.0000.000
127A130GLU-1-0.848-0.90834.7618.4488.4480.0000.0000.0000.000
128A131TYR0-0.058-0.07231.4870.0820.0820.0000.0000.0000.000
129A132ASP-1-0.951-0.95732.1168.6668.6660.0000.0000.0000.000
130A133ALA0-0.0090.00329.3000.2030.2030.0000.0000.0000.000
131A134ASP-1-0.853-0.93928.9829.7699.7690.0000.0000.0000.000
132A135PRO0-0.034-0.03130.8850.0850.0850.0000.0000.0000.000
133A136ALA0-0.065-0.02731.160-0.121-0.1210.0000.0000.0000.000
134A137SER0-0.040-0.02826.6740.0170.0170.0000.0000.0000.000
135A138ALA0-0.031-0.00128.8040.2350.2350.0000.0000.0000.000
136A139ASP-1-0.843-0.92930.2339.8349.8340.0000.0000.0000.000
137A140SER0-0.078-0.07029.5590.3280.3280.0000.0000.0000.000
138A141ARG10.7080.85426.559-10.616-10.6160.0000.0000.0000.000
139A142HIS00.0660.06625.0960.1910.1910.0000.0000.0000.000
140A143TYR0-0.083-0.06820.7670.4970.4970.0000.0000.0000.000
141A144GLY00.0550.03820.385-0.271-0.2710.0000.0000.0000.000
142A145ARG10.8110.88116.193-16.026-16.0260.0000.0000.0000.000
143A146LEU0-0.032-0.00711.659-0.001-0.0010.0000.0000.0000.000
144A147ALA00.011-0.00411.3810.8590.8590.0000.0000.0000.000
145A148GLY0-0.040-0.0237.6251.4701.4700.0000.0000.0000.000
146A149PHE0-0.002-0.0147.4724.6804.6800.0000.0000.0000.000
147A150THR0-0.009-0.00310.204-1.383-1.3830.0000.0000.0000.000
148A151ASN0-0.008-0.02612.513-0.797-0.7970.0000.0000.0000.000
149A152ARG10.8600.92314.346-19.753-19.7530.0000.0000.0000.000
150A153LYS10.8660.95518.299-13.527-13.5270.0000.0000.0000.000
151A154ASP-1-0.784-0.85219.64913.15013.1500.0000.0000.0000.000
152A155LYS10.9040.94019.776-10.420-10.4200.0000.0000.0000.000
153A163GLN0-0.085-0.04814.814-0.276-0.2760.0000.0000.0000.000
154A164PRO00.0390.03713.6221.4481.4480.0000.0000.0000.000
155A165TRP0-0.018-0.0167.7241.3081.3080.0000.0000.0000.000
156A166VAL00.0300.03211.642-1.089-1.0890.0000.0000.0000.000
157A167LEU0-0.052-0.02010.5682.6792.6790.0000.0000.0000.000
158A168LEU0-0.0230.00111.871-1.217-1.2170.0000.0000.0000.000
159A169ARG10.8780.93413.626-13.081-13.0810.0000.0000.0000.000
160A170GLU-1-0.843-0.92316.32913.25113.2510.0000.0000.0000.000
161A171SER00.000-0.00915.5280.4300.4300.0000.0000.0000.000
162A172LYS10.8950.93917.771-12.458-12.4580.0000.0000.0000.000
163A173GLY00.0340.02120.478-0.135-0.1350.0000.0000.0000.000
164A174LYS10.7310.89221.627-10.601-10.6010.0000.0000.0000.000
165A175THR0-0.006-0.01425.2060.2120.2120.0000.0000.0000.000
166A176ALA00.0340.02828.317-0.092-0.0920.0000.0000.0000.000
167A177THR0-0.040-0.06630.062-0.220-0.2200.0000.0000.0000.000
168A178ALA0-0.0060.00333.273-0.274-0.2740.0000.0000.0000.000
169A179GLY0-0.0150.00032.767-0.105-0.1050.0000.0000.0000.000
170A180PRO00.037-0.00533.515-0.112-0.1120.0000.0000.0000.000
171A181ALA00.0160.01236.522-0.188-0.1880.0000.0000.0000.000
172A182LEU00.0470.01333.361-0.173-0.1730.0000.0000.0000.000
173A183VAL0-0.036-0.01735.060-0.075-0.0750.0000.0000.0000.000
174A184GLN0-0.041-0.02337.601-0.063-0.0630.0000.0000.0000.000
175A185GLN00.0020.00840.262-0.045-0.0450.0000.0000.0000.000
176A186ALA00.0250.01438.269-0.143-0.1430.0000.0000.0000.000
177A187GLY00.0250.00540.353-0.088-0.0880.0000.0000.0000.000
178A188GLN0-0.044-0.02342.463-0.237-0.2370.0000.0000.0000.000
179A189GLN00.0140.00541.394-0.029-0.0290.0000.0000.0000.000
180A190ILE0-0.0020.00739.623-0.070-0.0700.0000.0000.0000.000
181A191GLU-1-0.798-0.87644.2246.2636.2630.0000.0000.0000.000
182A192GLN0-0.0020.00247.439-0.242-0.2420.0000.0000.0000.000
183A193ALA0-0.012-0.01146.263-0.131-0.1310.0000.0000.0000.000
184A194GLN0-0.038-0.01247.431-0.064-0.0640.0000.0000.0000.000
185A195ARG10.8060.87849.187-6.157-6.1570.0000.0000.0000.000
186A196GLN0-0.085-0.02351.455-0.202-0.2020.0000.0000.0000.000
187A197GLN0-0.061-0.03452.3040.1730.1730.0000.0000.0000.000
188A198GLU-1-0.943-0.95553.8365.4785.4780.0000.0000.0000.000