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: R5LN8

Calculation Name: 2Y2C-A-Xray372

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: 2023-03-14

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1938633.75738
FMO2-HF: Nuclear repulsion 1868877.858752
FMO2-HF: Total energy -69755.898628
FMO2-MP2: Total energy -69960.604095


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:2:LEU)


Summations of interaction energy for fragment #1(A:2:LEU)
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.
-11.897-19.99323.753-5.413-10.2440.014
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.016
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].
3A4ASP-1-0.806-0.8823.790-2.249-0.354-0.021-0.820-1.0550.001
4A5GLU-1-0.934-0.9646.2390.8630.8630.0000.0000.0000.000
5A6GLY00.0310.0298.5210.0500.0500.0000.0000.0000.000
6A7TRP0-0.029-0.0257.2410.0790.0790.0000.0000.0000.000
7A8LEU0-0.005-0.0142.592-0.9050.8860.724-0.986-1.5300.004
8A9ALA0-0.001-0.0201.805-1.648-12.68220.391-5.123-4.2340.007
9A10GLU-1-0.955-0.9842.728-4.767-5.6580.2692.138-1.5160.002
10A11ALA0-0.0490.0004.680-0.939-0.882-0.001-0.008-0.0470.000
11A12ARG10.7740.8567.310-0.718-0.7180.0000.0000.0000.000
12A13ARG10.8170.9036.083-1.889-1.8890.0000.0000.0000.000
13A14VAL0-0.014-0.00711.941-0.176-0.1760.0000.0000.0000.000
14A15PRO0-0.015-0.01514.3920.0050.0050.0000.0000.0000.000
15A16SER00.006-0.01016.142-0.094-0.0940.0000.0000.0000.000
16A17PRO0-0.010-0.01318.9520.0100.0100.0000.0000.0000.000
17A18HIS0-0.063-0.03721.279-0.051-0.0510.0000.0000.0000.000
18A19TYR00.0220.01517.3080.0420.0420.0000.0000.0000.000
19A20ASP-1-0.793-0.85120.6310.2520.2520.0000.0000.0000.000
20A21CYS00.009-0.00719.9980.0420.0420.0000.0000.0000.000
21A22ARG10.8020.90514.187-0.479-0.4790.0000.0000.0000.000
22A23PRO0-0.031-0.01920.591-0.014-0.0140.0000.0000.0000.000
23A24ASP-1-0.929-0.97122.7360.1400.1400.0000.0000.0000.000
24A25ASP-1-0.947-0.95419.9850.1710.1710.0000.0000.0000.000
25A26GLU-1-0.837-0.86719.2680.1770.1770.0000.0000.0000.000
26A27ASN0-0.003-0.01215.1000.0440.0440.0000.0000.0000.000
27A28PRO00.0010.00812.915-0.028-0.0280.0000.0000.0000.000
28A29SER0-0.021-0.02414.867-0.016-0.0160.0000.0000.0000.000
29A30LEU0-0.042-0.01216.648-0.026-0.0260.0000.0000.0000.000
30A31LEU00.0030.02311.7600.0500.0500.0000.0000.0000.000
31A32VAL0-0.017-0.02415.122-0.059-0.0590.0000.0000.0000.000
32A33VAL00.000-0.00615.2650.0570.0570.0000.0000.0000.000
33A34HIS10.8290.91717.391-0.398-0.3980.0000.0000.0000.000
34A35ASN0-0.095-0.04418.7300.0170.0170.0000.0000.0000.000
35A36ILE00.0570.03020.199-0.010-0.0100.0000.0000.0000.000
36A37SER00.007-0.00822.423-0.003-0.0030.0000.0000.0000.000
37A38LEU0-0.0600.01224.743-0.012-0.0120.0000.0000.0000.000
38A39PRO00.042-0.00626.7110.0090.0090.0000.0000.0000.000
39A40PRO00.0170.01028.7870.0030.0030.0000.0000.0000.000
40A41GLY0-0.024-0.01128.164-0.012-0.0120.0000.0000.0000.000
41A42GLU-1-0.952-0.96428.3300.1320.1320.0000.0000.0000.000
42A43PHE0-0.013-0.03023.2890.0180.0180.0000.0000.0000.000
43A44GLY00.004-0.00122.395-0.017-0.0170.0000.0000.0000.000
44A45GLY00.0010.01623.2980.0030.0030.0000.0000.0000.000
45A46PRO00.0280.00922.4180.0300.0300.0000.0000.0000.000
46A47TRP00.028-0.00523.2800.0210.0210.0000.0000.0000.000
47A48ILE00.0470.03319.721-0.003-0.0030.0000.0000.0000.000
48A49ASP-1-0.765-0.85718.2010.5240.5240.0000.0000.0000.000
49A50ALA00.0180.02820.5230.0070.0070.0000.0000.0000.000
50A51LEU0-0.011-0.00223.858-0.008-0.0080.0000.0000.0000.000
51A52PHE0-0.024-0.01118.558-0.009-0.0090.0000.0000.0000.000
52A53THR0-0.038-0.01719.7800.0180.0180.0000.0000.0000.000
53A54GLY00.0010.00622.213-0.017-0.0170.0000.0000.0000.000
54A55THR0-0.072-0.04024.535-0.026-0.0260.0000.0000.0000.000
55A56ILE0-0.051-0.01227.083-0.011-0.0110.0000.0000.0000.000
56A57ASP-1-0.772-0.89528.5090.1350.1350.0000.0000.0000.000
57A58PRO0-0.025-0.01931.960-0.001-0.0010.0000.0000.0000.000
58A59ASN0-0.074-0.05934.292-0.011-0.0110.0000.0000.0000.000
59A60ALA0-0.0220.01032.176-0.006-0.0060.0000.0000.0000.000
60A61HIS00.0440.01332.896-0.003-0.0030.0000.0000.0000.000
61A62PRO00.0050.00334.7770.0030.0030.0000.0000.0000.000
62A63TYR0-0.011-0.01129.733-0.004-0.0040.0000.0000.0000.000
63A64PHE00.027-0.00529.2850.0080.0080.0000.0000.0000.000
64A65ALA00.0370.02732.7890.0060.0060.0000.0000.0000.000
65A66GLY0-0.026-0.01035.5070.0000.0000.0000.0000.0000.000
66A67ILE0-0.015-0.01628.4840.0020.0020.0000.0000.0000.000
67A68ALA00.0170.01930.5250.0130.0130.0000.0000.0000.000
68A69HIS0-0.069-0.02531.6480.0050.0050.0000.0000.0000.000
69A70LEU0-0.050-0.01827.5380.0010.0010.0000.0000.0000.000
70A71ARG10.9240.97026.957-0.223-0.2230.0000.0000.0000.000
71A72VAL0-0.015-0.00523.585-0.002-0.0020.0000.0000.0000.000
72A73SER0-0.003-0.01718.9070.0080.0080.0000.0000.0000.000
73A74ALA00.0300.01916.517-0.034-0.0340.0000.0000.0000.000
74A75HIS00.0180.00711.7490.0080.0080.0000.0000.0000.000
75A76CYS0-0.049-0.0309.8830.3010.3010.0000.0000.0000.000
76A77LEU00.0350.03812.590-0.158-0.1580.0000.0000.0000.000
77A78ILE0-0.034-0.00610.5680.1020.1020.0000.0000.0000.000
78A79ARG10.8520.90013.861-0.436-0.4360.0000.0000.0000.000
79A80ARG10.8430.90116.203-0.204-0.2040.0000.0000.0000.000
80A81ASP-1-0.871-0.92816.4350.2540.2540.0000.0000.0000.000
81A82GLY0-0.017-0.01413.691-0.044-0.0440.0000.0000.0000.000
82A83GLU-1-0.792-0.86311.9140.5920.5920.0000.0000.0000.000
83A84ILE0-0.0060.0007.6940.0050.0050.0000.0000.0000.000
84A85VAL00.0080.01810.1300.1480.1480.0000.0000.0000.000
85A86GLN0-0.001-0.0217.9450.6880.6880.0000.0000.0000.000
86A87TYR0-0.008-0.04211.376-0.064-0.0640.0000.0000.0000.000
87A88VAL0-0.030-0.01013.350-0.100-0.1000.0000.0000.0000.000
88A89PRO00.0220.03911.0690.1840.1840.0000.0000.0000.000
89A90PHE00.021-0.0245.846-0.304-0.3040.0000.0000.0000.000
90A91ASP-1-0.798-0.88011.1350.4470.4470.0000.0000.0000.000
91A92LYS10.8260.90813.683-0.600-0.6000.0000.0000.0000.000
92A93ARG10.7720.84715.897-0.216-0.2160.0000.0000.0000.000
93A94ALA00.0240.02216.365-0.013-0.0130.0000.0000.0000.000
94A95TRP0-0.102-0.06718.401-0.047-0.0470.0000.0000.0000.000
95A96HIS00.1240.06718.192-0.020-0.0200.0000.0000.0000.000
96A97ALA0-0.0030.00521.266-0.023-0.0230.0000.0000.0000.000
97A98GLY00.0220.01023.120-0.024-0.0240.0000.0000.0000.000
98A99VAL00.0020.00226.5810.0000.0000.0000.0000.0000.000
99A100SER00.000-0.00625.7630.0050.0050.0000.0000.0000.000
100A101SER00.006-0.00727.695-0.004-0.0040.0000.0000.0000.000
101A102TYR00.035-0.00521.4980.0060.0060.0000.0000.0000.000
102A103GLN0-0.035-0.01623.747-0.009-0.0090.0000.0000.0000.000
103A104GLY00.0170.01727.795-0.006-0.0060.0000.0000.0000.000
104A105ARG10.7940.87222.931-0.174-0.1740.0000.0000.0000.000
105A106GLU-1-0.912-0.97227.0570.1320.1320.0000.0000.0000.000
106A107ARG10.9380.96026.367-0.140-0.1400.0000.0000.0000.000
107A108CYS00.0790.04422.0880.0060.0060.0000.0000.0000.000
108A109ASN00.0070.04320.4280.0360.0360.0000.0000.0000.000
109A110ASP-1-0.829-0.90719.6890.2530.2530.0000.0000.0000.000
110A111PHE00.0210.02818.8500.0190.0190.0000.0000.0000.000
111A112SER0-0.040-0.05416.9170.0090.0090.0000.0000.0000.000
112A113ILE00.0110.00010.4170.0330.0330.0000.0000.0000.000
113A114GLY0-0.0080.01014.351-0.055-0.0550.0000.0000.0000.000
114A115ILE0-0.018-0.02210.5060.1100.1100.0000.0000.0000.000
115A116GLU-1-0.853-0.95214.1690.2910.2910.0000.0000.0000.000
116A117LEU0-0.012-0.00414.3170.0510.0510.0000.0000.0000.000
117A118GLU-1-0.732-0.84417.2300.2550.2550.0000.0000.0000.000
118A119GLY00.007-0.00319.789-0.021-0.0210.0000.0000.0000.000
119A120THR00.0000.00422.5760.0030.0030.0000.0000.0000.000
120A121ASP-1-0.729-0.85124.7990.1620.1620.0000.0000.0000.000
121A122THR0-0.042-0.03226.731-0.006-0.0060.0000.0000.0000.000
122A123LEU0-0.0340.00725.514-0.012-0.0120.0000.0000.0000.000
123A124ALA00.0180.01323.6660.0100.0100.0000.0000.0000.000
124A125TYR0-0.004-0.00518.6730.0150.0150.0000.0000.0000.000
125A126THR0-0.024-0.02917.961-0.023-0.0230.0000.0000.0000.000
126A127ASP-1-0.797-0.89317.3070.0370.0370.0000.0000.0000.000
127A128ALA00.0070.00614.135-0.013-0.0130.0000.0000.0000.000
128A129GLN0-0.007-0.02012.933-0.014-0.0140.0000.0000.0000.000
129A130TYR00.0150.01413.0370.0540.0540.0000.0000.0000.000
130A131GLN0-0.002-0.00110.729-0.017-0.0170.0000.0000.0000.000
131A132GLN0-0.002-0.0038.557-0.160-0.1600.0000.0000.0000.000
132A133LEU00.0240.0118.0810.1850.1850.0000.0000.0000.000
133A134ALA00.0030.0178.9980.1190.1190.0000.0000.0000.000
134A135ALA00.0020.0174.483-0.0740.001-0.001-0.005-0.0680.000
135A136VAL00.008-0.0024.2560.1250.4060.000-0.037-0.2440.000
136A137THR0-0.007-0.0285.5930.1400.1400.0000.0000.0000.000
137A138ASN00.004-0.0035.4300.0050.0050.0000.0000.0000.000
138A139ALA00.0100.0182.330-0.382-0.6922.383-0.603-1.4700.000
139A140LEU0-0.014-0.0123.728-0.518-0.4780.0090.031-0.0800.000
140A141ILE0-0.023-0.0017.277-0.182-0.1820.0000.0000.0000.000
141A142THR0-0.034-0.0195.594-0.153-0.1530.0000.0000.0000.000
142A143ARG10.8490.9337.547-0.196-0.1960.0000.0000.0000.000
143A144TYR0-0.029-0.0239.128-0.055-0.0550.0000.0000.0000.000
144A145PRO00.0730.03911.8300.0440.0440.0000.0000.0000.000
145A146ALA0-0.010-0.00612.9810.0020.0020.0000.0000.0000.000
146A147ILE00.0380.01411.3020.0020.0020.0000.0000.0000.000
147A148ALA0-0.0040.00613.0930.0060.0060.0000.0000.0000.000
148A149ASN0-0.070-0.03114.310-0.026-0.0260.0000.0000.0000.000
149A150ASN0-0.067-0.01616.707-0.015-0.0150.0000.0000.0000.000
150A151MET00.0200.01714.1790.0530.0530.0000.0000.0000.000
151A152THR0-0.026-0.01317.309-0.038-0.0380.0000.0000.0000.000
152A153GLY00.0840.04419.0440.0350.0350.0000.0000.0000.000
153A154HIS00.000-0.02021.348-0.002-0.0020.0000.0000.0000.000
154A155CYS0-0.069-0.03922.928-0.015-0.0150.0000.0000.0000.000
155A156ASN0-0.034-0.01523.723-0.005-0.0050.0000.0000.0000.000
156A157ILE0-0.0280.00022.179-0.007-0.0070.0000.0000.0000.000
157A158ALA0-0.025-0.01726.073-0.002-0.0020.0000.0000.0000.000
158A159PRO00.0540.04128.3760.0020.0020.0000.0000.0000.000
159A160GLU-1-0.929-0.97430.5350.1000.1000.0000.0000.0000.000
160A161ARG10.8180.91327.212-0.180-0.1800.0000.0000.0000.000
161A162LYS10.8050.90725.476-0.212-0.2120.0000.0000.0000.000
162A163THR00.004-0.02628.070-0.006-0.0060.0000.0000.0000.000
163A164ASP-1-0.796-0.87322.8990.2350.2350.0000.0000.0000.000
164A165PRO0-0.041-0.02520.0510.0000.0000.0000.0000.0000.000
165A166GLY00.1070.05722.510-0.007-0.0070.0000.0000.0000.000
166A167PRO0-0.034-0.03824.5700.0020.0020.0000.0000.0000.000
167A168SER0-0.0340.00424.433-0.005-0.0050.0000.0000.0000.000
168A169PHE0-0.041-0.01716.1480.0010.0010.0000.0000.0000.000
169A170ASP-1-0.818-0.91120.5060.0500.0500.0000.0000.0000.000
170A171TRP00.049-0.00417.1780.0000.0000.0000.0000.0000.000
171A172ALA0-0.0270.00118.773-0.004-0.0040.0000.0000.0000.000
172A173ARG10.8370.90316.858-0.045-0.0450.0000.0000.0000.000
173A174PHE0-0.007-0.01511.557-0.021-0.0210.0000.0000.0000.000
174A175ARG10.9430.95814.083-0.113-0.1130.0000.0000.0000.000
175A176ALA0-0.0270.00515.283-0.019-0.0190.0000.0000.0000.000
176A177LEU0-0.041-0.01611.407-0.033-0.0330.0000.0000.0000.000
177A178VAL0-0.021-0.01510.524-0.031-0.0310.0000.0000.0000.000
178A179THR0-0.062-0.02610.156-0.030-0.0300.0000.0000.0000.000
179A180PRO0-0.0110.0099.170-0.013-0.0130.0000.0000.0000.000