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: MMG7Z

Calculation Name: 2Y2C-A-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y2C

Chain ID: A

ChEMBL ID:

UniProt ID: P82974

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 181
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1947214.769745
FMO2-HF: Nuclear repulsion 1877288.87899
FMO2-HF: Total energy -69925.890755
FMO2-MP2: Total energy -70131.165078


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:1:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
27.64-17.54389.568-35.428-8.955-0.064
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : -0.203
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].
3A3LEU 0-0.089-0.0543.2273.3581.662-0.1813.159-1.2820.005
4A4ASP -1-0.865-0.9176.3160.3800.3800.0000.0000.0000.000
5A5GLU -1-0.940-0.9767.760-0.043-0.0430.0000.0000.0000.000
6A6GLY 00.0300.03810.4170.0270.0270.0000.0000.0000.000
7A7TRP 0-0.046-0.0397.800-0.033-0.0330.0000.0000.0000.000
8A8LEU 0-0.013-0.0132.703-0.664-0.1540.236-0.268-0.4780.000
9A9ALA 0-0.013-0.0201.9502.3980.1086.504-2.269-1.944-0.006
10A10GLU -1-0.919-0.7931.64821.310-17.06982.773-39.197-5.196-0.061
11A11ALA 0-0.0730.0013.0041.395-1.9330.2363.147-0.055-0.002
12A12ARG 10.8540.9125.604-0.144-0.1440.0000.0000.0000.000
13A13ARG 10.8990.9556.539-0.685-0.6850.0000.0000.0000.000
14A14VAL 0-0.018-0.00610.9330.0040.0040.0000.0000.0000.000
15A15PRO 0-0.020-0.01914.058-0.042-0.0420.0000.0000.0000.000
16A16SER 00.009-0.02115.7570.0020.0020.0000.0000.0000.000
17A17PRO 0-0.012-0.01318.536-0.010-0.0100.0000.0000.0000.000
18A18HIS 0-0.072-0.02820.997-0.003-0.0030.0000.0000.0000.000
19A19TYR 00.0060.00217.773-0.018-0.0180.0000.0000.0000.000
20A20ASP -1-0.781-0.85621.055-0.057-0.0570.0000.0000.0000.000
21A21CYS 0-0.010-0.02121.280-0.010-0.0100.0000.0000.0000.000
22A22ARG 10.8090.90715.9800.2120.2120.0000.0000.0000.000
23A23PRO 0-0.030-0.01922.6830.0040.0040.0000.0000.0000.000
24A24ASP -1-0.917-0.96425.319-0.091-0.0910.0000.0000.0000.000
25A25ASP -1-0.958-0.95822.678-0.095-0.0950.0000.0000.0000.000
26A26GLU -1-0.834-0.88022.128-0.152-0.1520.0000.0000.0000.000
27A27ASN 0-0.036-0.03218.407-0.020-0.0200.0000.0000.0000.000
28A28PRO 0-0.0110.00315.6740.0130.0130.0000.0000.0000.000
29A29SER 0-0.024-0.02617.952-0.023-0.0230.0000.0000.0000.000
30A30LEU 0-0.035-0.00919.1780.0000.0000.0000.0000.0000.000
31A31LEU 00.0030.02213.905-0.009-0.0090.0000.0000.0000.000
32A32VAL 0-0.018-0.02517.1150.0270.0270.0000.0000.0000.000
33A33VAL 00.000-0.00716.480-0.010-0.0100.0000.0000.0000.000
34A34HIS 10.8390.92117.9930.1430.1430.0000.0000.0000.000
35A35ASN 0-0.099-0.04718.780-0.004-0.0040.0000.0000.0000.000
36A36ILE 00.0630.03319.2020.0070.0070.0000.0000.0000.000
37A37SER 0-0.004-0.00721.2460.0060.0060.0000.0000.0000.000
38A38LEU 0-0.0440.01423.013-0.002-0.0020.0000.0000.0000.000
39A39PRO 00.054-0.00324.9210.0070.0070.0000.0000.0000.000
40A40PRO 00.0090.00827.0990.0000.0000.0000.0000.0000.000
41A41GLY 0-0.025-0.01226.8970.0020.0020.0000.0000.0000.000
42A42GLU -1-0.974-0.97126.5290.0200.0200.0000.0000.0000.000
43A43PHE 0-0.010-0.02521.399-0.005-0.0050.0000.0000.0000.000
44A44GLY 00.004-0.00320.4100.0050.0050.0000.0000.0000.000
45A45GLY 0-0.0120.00821.3180.0110.0110.0000.0000.0000.000
46A46PRO 00.0350.01320.5920.0040.0040.0000.0000.0000.000
47A47TRP 00.0310.00021.575-0.001-0.0010.0000.0000.0000.000
48A48ILE 00.0530.03418.151-0.005-0.0050.0000.0000.0000.000
49A49ASP -1-0.767-0.86816.5190.0950.0950.0000.0000.0000.000
50A50ALA 00.0060.01818.973-0.005-0.0050.0000.0000.0000.000
51A51LEU 0-0.015-0.00322.390-0.005-0.0050.0000.0000.0000.000
52A52PHE 0-0.021-0.00917.171-0.007-0.0070.0000.0000.0000.000
53A53THR 0-0.048-0.01318.906-0.003-0.0030.0000.0000.0000.000
54A54GLY 0-0.001-0.00221.3390.0020.0020.0000.0000.0000.000
55A55THR 0-0.070-0.03223.4700.0020.0020.0000.0000.0000.000
56A56ILE 0-0.052-0.01325.3590.0040.0040.0000.0000.0000.000
57A57ASP -1-0.809-0.91727.1150.0240.0240.0000.0000.0000.000
58A58PRO 0-0.027-0.02230.440-0.002-0.0020.0000.0000.0000.000
59A59ASN 0-0.023-0.03332.815-0.004-0.0040.0000.0000.0000.000
60A60ALA 0-0.0330.00830.4870.0000.0000.0000.0000.0000.000
61A61HIS 00.0520.02431.115-0.001-0.0010.0000.0000.0000.000
62A62PRO 00.0160.00633.062-0.002-0.0020.0000.0000.0000.000
63A63TYR 0-0.015-0.02328.502-0.002-0.0020.0000.0000.0000.000
64A64PHE 00.012-0.00927.415-0.004-0.0040.0000.0000.0000.000
65A65ALA 00.0490.03331.263-0.001-0.0010.0000.0000.0000.000
66A66GLY 0-0.029-0.01134.090-0.001-0.0010.0000.0000.0000.000
67A67ILE 0-0.013-0.02227.098-0.004-0.0040.0000.0000.0000.000
68A68ALA 00.0200.02329.426-0.001-0.0010.0000.0000.0000.000
69A69HIS 0-0.072-0.02330.685-0.002-0.0020.0000.0000.0000.000
70A70LEU 0-0.066-0.02227.061-0.003-0.0030.0000.0000.0000.000
71A71ARG 10.9550.98126.4240.0210.0210.0000.0000.0000.000
72A72VAL 0-0.014-0.00423.054-0.007-0.0070.0000.0000.0000.000
73A73SER 0-0.002-0.00818.5180.0060.0060.0000.0000.0000.000
74A74ALA 00.0440.02416.191-0.011-0.0110.0000.0000.0000.000
75A75HIS 00.0040.00012.3080.0070.0070.0000.0000.0000.000
76A76CYS 0-0.019-0.0208.4760.0150.0150.0000.0000.0000.000
77A77LEU 00.0380.03911.751-0.001-0.0010.0000.0000.0000.000
78A78ILE 0-0.040-0.00710.2080.0130.0130.0000.0000.0000.000
79A79ARG 10.8580.90412.484-0.086-0.0860.0000.0000.0000.000
80A80ARG 10.8470.90514.6490.0030.0030.0000.0000.0000.000
81A81ASP -1-0.871-0.93114.3910.1430.1430.0000.0000.0000.000
82A82GLY 0-0.026-0.01912.0510.0240.0240.0000.0000.0000.000
83A83GLU -1-0.844-0.91810.0100.2690.2690.0000.0000.0000.000
84A84ILE 0-0.012-0.0036.327-0.114-0.1140.0000.0000.0000.000
85A85VAL 00.0020.0168.2700.1670.1670.0000.0000.0000.000
86A86GLN 00.020-0.0037.711-0.130-0.1300.0000.0000.0000.000
87A87TYR 0-0.021-0.03510.3700.0620.0620.0000.0000.0000.000
88A88VAL 0-0.037-0.01713.0620.0180.0180.0000.0000.0000.000
89A89PRO 00.0240.04311.862-0.056-0.0560.0000.0000.0000.000
90A90PHE 00.027-0.0217.3500.0310.0310.0000.0000.0000.000
91A91ASP -1-0.830-0.91512.914-0.160-0.1600.0000.0000.0000.000
92A92LYS 10.8730.95215.7780.1160.1160.0000.0000.0000.000
93A93ARG 10.7810.87217.4090.0550.0550.0000.0000.0000.000
94A94ALA 00.0190.02016.9210.0180.0180.0000.0000.0000.000
95A95TRP 0-0.111-0.07019.0510.0030.0030.0000.0000.0000.000
96A96HIS 00.1090.05519.2340.0170.0170.0000.0000.0000.000
97A97ALA 00.0040.00621.5570.0050.0050.0000.0000.0000.000
98A98GLY 0-0.009-0.00423.8550.0080.0080.0000.0000.0000.000
99A99VAL 0-0.003-0.00927.259-0.005-0.0050.0000.0000.0000.000
100A100SER 0-0.009-0.00527.026-0.004-0.0040.0000.0000.0000.000
101A101SER 00.013-0.00229.1110.0000.0000.0000.0000.0000.000
102A102TYR 00.0470.00524.570-0.001-0.0010.0000.0000.0000.000
103A103GLN 0-0.034-0.01927.421-0.003-0.0030.0000.0000.0000.000
104A104GLY 00.0150.01630.2650.0020.0020.0000.0000.0000.000
105A105ARG 10.7950.88325.5590.1250.1250.0000.0000.0000.000
106A106GLU -1-0.916-0.97429.111-0.068-0.0680.0000.0000.0000.000
107A107ARG 10.9280.95627.8970.0590.0590.0000.0000.0000.000
108A108CYS 00.0710.04023.747-0.006-0.0060.0000.0000.0000.000
109A109ASN 00.0130.04221.791-0.021-0.0210.0000.0000.0000.000
110A110ASP -1-0.839-0.91821.388-0.106-0.1060.0000.0000.0000.000
111A111PHE 00.0240.02621.284-0.010-0.0100.0000.0000.0000.000
112A112SER 0-0.032-0.04419.032-0.021-0.0210.0000.0000.0000.000
113A113ILE 00.009-0.00512.4430.0070.0070.0000.0000.0000.000
114A114GLY 0-0.0050.01115.8720.0000.0000.0000.0000.0000.000
115A115ILE 0-0.017-0.02110.867-0.011-0.0110.0000.0000.0000.000
116A116GLU -1-0.858-0.95614.332-0.069-0.0690.0000.0000.0000.000
117A117LEU 0-0.015-0.00614.4830.0010.0010.0000.0000.0000.000
118A118GLU -1-0.730-0.85216.5470.0460.0460.0000.0000.0000.000
119A119GLY 00.002-0.00618.6120.0010.0010.0000.0000.0000.000
120A120THR 0-0.0010.00421.7670.0000.0000.0000.0000.0000.000
121A121ASP -1-0.722-0.84624.670-0.060-0.0600.0000.0000.0000.000
122A122THR 0-0.048-0.03226.821-0.003-0.0030.0000.0000.0000.000
123A123LEU 0-0.0310.00624.5100.0030.0030.0000.0000.0000.000
124A124ALA 00.0160.01023.897-0.007-0.0070.0000.0000.0000.000
125A125TYR 0-0.019-0.01918.5770.0080.0080.0000.0000.0000.000
126A126THR 0-0.020-0.02716.934-0.006-0.0060.0000.0000.0000.000
127A127ASP -1-0.849-0.93917.417-0.043-0.0430.0000.0000.0000.000
128A128ALA 00.0050.00613.443-0.023-0.0230.0000.0000.0000.000
129A129GLN 0-0.004-0.01112.738-0.028-0.0280.0000.0000.0000.000
130A130TYR 00.0020.01413.229-0.055-0.0550.0000.0000.0000.000
131A131GLN 0-0.014-0.00711.798-0.080-0.0800.0000.0000.0000.000
132A132GLN 00.0250.0146.960-0.185-0.1850.0000.0000.0000.000
133A133LEU 00.0150.0098.659-0.197-0.1970.0000.0000.0000.000
134A134ALA 0-0.0020.00810.672-0.117-0.1170.0000.0000.0000.000
135A135ALA 00.0050.0196.345-0.093-0.0930.0000.0000.0000.000
136A136VAL 00.0140.0005.829-0.458-0.4580.0000.0000.0000.000
137A137THR 0-0.005-0.0237.323-0.034-0.0340.0000.0000.0000.000
138A138ASN 00.0170.0059.2660.0930.0930.0000.0000.0000.000
139A139ALA 00.0020.0115.8510.0470.0470.0000.0000.0000.000
140A140LEU 0-0.024-0.0167.8010.2460.2460.0000.0000.0000.000
141A141ILE 0-0.0130.00210.5020.1470.1470.0000.0000.0000.000
142A142THR 0-0.025-0.00410.0320.1240.1240.0000.0000.0000.000
143A143ARG 10.8920.96311.1870.4360.4360.0000.0000.0000.000
144A144TYR 0-0.033-0.03212.6040.1210.1210.0000.0000.0000.000
145A145PRO 00.0740.04415.524-0.001-0.0010.0000.0000.0000.000
146A146ALA 0-0.011-0.01317.3960.0190.0190.0000.0000.0000.000
147A147ILE 00.0380.01814.1970.0210.0210.0000.0000.0000.000
148A148ALA 0-0.0050.00417.5270.0100.0100.0000.0000.0000.000
149A149ASN 0-0.073-0.03218.3970.0250.0250.0000.0000.0000.000
150A150ASN 0-0.070-0.01420.1550.0430.0430.0000.0000.0000.000
151A151MET 00.0190.01117.108-0.036-0.0360.0000.0000.0000.000
152A152THR 0-0.025-0.00819.8270.0250.0250.0000.0000.0000.000
153A153GLY 00.0850.03820.677-0.014-0.0140.0000.0000.0000.000
154A154HIS 00.005-0.03622.4510.0050.0050.0000.0000.0000.000
155A155CYS 0-0.021-0.01123.8940.0050.0050.0000.0000.0000.000
156A156ASN 0-0.060-0.02225.352-0.004-0.0040.0000.0000.0000.000
157A157ILE 0-0.0140.02323.8240.0020.0020.0000.0000.0000.000
158A158ALA 0-0.031-0.02127.5860.0050.0050.0000.0000.0000.000
159A159PRO 00.0620.04329.4470.0030.0030.0000.0000.0000.000
160A160GLU -1-0.940-0.97731.741-0.052-0.0520.0000.0000.0000.000
161A161ARG 10.8460.93027.9700.0650.0650.0000.0000.0000.000
162A162LYS 10.8490.92426.1530.0620.0620.0000.0000.0000.000
163A163THR 0-0.010-0.03428.381-0.002-0.0020.0000.0000.0000.000
164A164ASP -1-0.808-0.87122.993-0.086-0.0860.0000.0000.0000.000
165A165PRO 0-0.054-0.04120.924-0.005-0.0050.0000.0000.0000.000
166A166GLY 00.0980.05723.0590.0060.0060.0000.0000.0000.000
167A167PRO 0-0.043-0.03925.493-0.007-0.0070.0000.0000.0000.000
168A168SER 0-0.0250.00524.659-0.006-0.0060.0000.0000.0000.000
169A169PHE 0-0.042-0.01717.612-0.004-0.0040.0000.0000.0000.000
170A170ASP -1-0.829-0.92421.949-0.098-0.0980.0000.0000.0000.000
171A171TRP 00.037-0.00419.479-0.021-0.0210.0000.0000.0000.000
172A172ALA 0-0.0270.00421.381-0.017-0.0170.0000.0000.0000.000
173A173ARG 10.9160.96018.7310.0710.0710.0000.0000.0000.000
174A174PHE 0-0.014-0.01513.659-0.004-0.0040.0000.0000.0000.000
175A175ARG 10.9600.96417.0470.1490.1490.0000.0000.0000.000
176A176ALA 0-0.0290.00318.927-0.013-0.0130.0000.0000.0000.000
177A177LEU 0-0.041-0.01814.4700.0060.0060.0000.0000.0000.000
178A178VAL 0-0.013-0.00714.153-0.063-0.0630.0000.0000.0000.000
179A179THR 0-0.086-0.04514.1270.0320.0320.0000.0000.0000.000
180A180PRO 0-0.006-0.00112.9440.0460.0460.0000.0000.0000.000
181A181NME 00.0010.01316.179-0.004-0.0040.0000.0000.0000.000