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: JQ619

Calculation Name: 2R55-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R55

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NSY2

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptAll
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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541949.704265
FMO2-HF: Nuclear repulsion 2457212.81611
FMO2-HF: Total energy -84736.888155
FMO2-MP2: Total energy -84979.286319


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:PHE)


Summations of interaction energy for fragment #1(A:2:PHE)
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.
-10.216-2.5123.358-3.189-7.8720.003
Interaction energy analysis for fragmet #1(A:2:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.013
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].
3A4SER0-0.011-0.0063.232-3.480-1.1800.061-0.941-1.419-0.001
4A5MET0-0.0020.0002.633-1.4090.1210.626-0.653-1.502-0.001
5A6ALA00.0340.0223.293-1.4300.1790.406-0.664-1.3510.005
6A7ALA00.0600.0315.432-0.476-0.302-0.001-0.013-0.1600.000
7A8GLN0-0.050-0.0147.6110.0300.0300.0000.0000.0000.000
8A9MET00.0090.0007.326-0.004-0.0040.0000.0000.0000.000
9A10SER0-0.022-0.0298.3960.0190.0190.0000.0000.0000.000
10A11GLU-1-0.771-0.87110.722-0.099-0.0990.0000.0000.0000.000
11A12ALA00.0330.01913.2250.0190.0190.0000.0000.0000.000
12A13VAL0-0.047-0.02012.6090.0190.0190.0000.0000.0000.000
13A14ALA00.0200.01015.0710.0200.0200.0000.0000.0000.000
14A15GLU-1-0.956-0.97216.935-0.120-0.1200.0000.0000.0000.000
15A16LYS10.7960.88417.9250.2440.2440.0000.0000.0000.000
16A17MET0-0.0280.01418.2330.0160.0160.0000.0000.0000.000
17A18LEU0-0.008-0.00120.7750.0150.0150.0000.0000.0000.000
18A19GLN0-0.029-0.01422.8680.0150.0150.0000.0000.0000.000
19A20TYR0-0.025-0.02820.9460.0050.0050.0000.0000.0000.000
20A21ARG10.7350.82824.9890.0840.0840.0000.0000.0000.000
21A22ARG10.8970.94825.2860.0870.0870.0000.0000.0000.000
22A23ASP-1-0.811-0.87528.172-0.096-0.0960.0000.0000.0000.000
23A24THR00.0290.01030.372-0.001-0.0010.0000.0000.0000.000
24A25ALA00.0180.01332.8400.0010.0010.0000.0000.0000.000
25A26GLY00.0180.01132.292-0.006-0.0060.0000.0000.0000.000
26A27TRP0-0.024-0.01926.7900.0000.0000.0000.0000.0000.000
27A28LYS10.8380.91633.6810.0790.0790.0000.0000.0000.000
28A29ILE00.0390.02035.184-0.005-0.0050.0000.0000.0000.000
29A30CYS0-0.077-0.02334.436-0.002-0.0020.0000.0000.0000.000
30A31ARG10.8490.90535.8180.0730.0730.0000.0000.0000.000
31A32GLU-1-0.883-0.94437.141-0.060-0.0600.0000.0000.0000.000
32A33GLY00.0080.00339.2040.0010.0010.0000.0000.0000.000
33A34ASN0-0.017-0.02440.4050.0010.0010.0000.0000.0000.000
34A35GLY00.0120.01938.111-0.002-0.0020.0000.0000.0000.000
35A36VAL0-0.035-0.00733.275-0.002-0.0020.0000.0000.0000.000
36A37SER00.0060.01634.7880.0020.0020.0000.0000.0000.000
37A38VAL0-0.030-0.02832.062-0.005-0.0050.0000.0000.0000.000
38A39SER0-0.026-0.01432.0120.0040.0040.0000.0000.0000.000
39A40TRP00.017-0.00130.496-0.007-0.0070.0000.0000.0000.000
40A41ARG10.7870.89226.3810.1190.1190.0000.0000.0000.000
41A42PRO00.0480.01929.234-0.006-0.0060.0000.0000.0000.000
42A43SER0-0.019-0.02223.392-0.004-0.0040.0000.0000.0000.000
43A44VAL0-0.027-0.02023.1080.0090.0090.0000.0000.0000.000
44A45GLU-1-0.829-0.89619.004-0.232-0.2320.0000.0000.0000.000
45A46PHE0-0.001-0.00520.694-0.012-0.0120.0000.0000.0000.000
46A47PRO0-0.008-0.01823.0320.0090.0090.0000.0000.0000.000
47A48GLY00.0140.04025.6590.0100.0100.0000.0000.0000.000
48A49ASN0-0.034-0.02427.1260.0030.0030.0000.0000.0000.000
49A50LEU0-0.0020.00923.486-0.009-0.0090.0000.0000.0000.000
50A51TYR0-0.005-0.02926.1420.0110.0110.0000.0000.0000.000
51A52ARG10.8620.92526.3600.0770.0770.0000.0000.0000.000
52A53GLY00.000-0.00628.1350.0070.0070.0000.0000.0000.000
53A54GLU-1-0.720-0.84229.114-0.077-0.0770.0000.0000.0000.000
54A55GLY00.0370.02331.5940.0040.0040.0000.0000.0000.000
55A56ILE00.0180.02732.450-0.002-0.0020.0000.0000.0000.000
56A57VAL00.0070.00130.3050.0000.0000.0000.0000.0000.000
57A58TYR0-0.005-0.00833.7860.0020.0020.0000.0000.0000.000
58A59GLY00.034-0.00933.4690.0020.0020.0000.0000.0000.000
59A60THR0-0.020-0.02531.773-0.002-0.0020.0000.0000.0000.000
60A61LEU00.0460.01826.465-0.004-0.0040.0000.0000.0000.000
61A62GLU-1-0.807-0.91724.008-0.050-0.0500.0000.0000.0000.000
62A63GLU-1-0.775-0.83426.151-0.045-0.0450.0000.0000.0000.000
63A64VAL0-0.001-0.01727.183-0.006-0.0060.0000.0000.0000.000
64A65TRP00.0530.02417.821-0.012-0.0120.0000.0000.0000.000
65A66ASP-1-0.805-0.90222.939-0.089-0.0890.0000.0000.0000.000
66A67CYS0-0.069-0.01923.695-0.004-0.0040.0000.0000.0000.000
67A68VAL0-0.006-0.02422.031-0.008-0.0080.0000.0000.0000.000
68A69LYS10.7520.89118.7490.0670.0670.0000.0000.0000.000
69A70PRO00.0060.01214.5890.0040.0040.0000.0000.0000.000
70A71ALA00.028-0.00915.076-0.017-0.0170.0000.0000.0000.000
71A72VAL0-0.0100.00014.4560.0220.0220.0000.0000.0000.000
72A73GLY00.0120.00716.7020.0200.0200.0000.0000.0000.000
73A74GLY00.0120.01618.229-0.011-0.0110.0000.0000.0000.000
74A75LEU00.0420.00721.1910.0050.0050.0000.0000.0000.000
75A76ARG10.8670.92719.9670.1590.1590.0000.0000.0000.000
76A77VAL0-0.005-0.00921.5450.0040.0040.0000.0000.0000.000
77A78LYS10.9140.97224.1780.0700.0700.0000.0000.0000.000
78A79TRP0-0.052-0.03524.8630.0070.0070.0000.0000.0000.000
79A80ASP-1-0.746-0.84524.657-0.123-0.1230.0000.0000.0000.000
80A81GLU-1-0.776-0.84327.084-0.086-0.0860.0000.0000.0000.000
81A82ASN0-0.067-0.03425.6400.0010.0010.0000.0000.0000.000
82A83VAL0-0.032-0.02621.727-0.013-0.0130.0000.0000.0000.000
83A84THR0-0.033-0.02223.6710.0060.0060.0000.0000.0000.000
84A85GLY00.001-0.00221.5580.0100.0100.0000.0000.0000.000
85A86PHE0-0.045-0.02014.782-0.013-0.0130.0000.0000.0000.000
86A87GLU-1-0.781-0.88015.023-0.176-0.1760.0000.0000.0000.000
87A88ILE00.010-0.00510.793-0.047-0.0470.0000.0000.0000.000
88A89ILE0-0.0250.0018.4140.0470.0470.0000.0000.0000.000
89A90GLN00.0320.0133.009-1.635-0.6460.195-0.406-0.7790.002
90A91SER00.0240.0086.713-0.257-0.2570.0000.0000.0000.000
91A92ILE0-0.051-0.0162.328-1.645-0.6702.073-0.503-2.545-0.002
92A93THR0-0.050-0.0374.5310.2250.283-0.001-0.005-0.0520.000
93A94ASP-1-0.919-0.9547.592-0.072-0.0720.0000.0000.0000.000
94A95THR00.0290.01410.555-0.001-0.0010.0000.0000.0000.000
95A96LEU0-0.030-0.0125.732-0.003-0.0030.0000.0000.0000.000
96A97CYS0-0.065-0.0206.947-0.087-0.0870.0000.0000.0000.000
97A98VAL00.0350.0274.711-0.086-0.017-0.001-0.004-0.0640.000
98A99SER0-0.049-0.0247.4570.1380.1380.0000.0000.0000.000
99A100ARG10.8640.89311.1800.1990.1990.0000.0000.0000.000
100A101THR00.0080.01314.0290.0390.0390.0000.0000.0000.000
101A102SER0-0.0130.00317.557-0.008-0.0080.0000.0000.0000.000
102A103THR00.0210.00920.7180.0100.0100.0000.0000.0000.000
103A104PRO00.0200.01224.0040.0020.0020.0000.0000.0000.000
104A105SER0-0.022-0.01327.592-0.003-0.0030.0000.0000.0000.000
105A106ALA00.0370.01329.8330.0040.0040.0000.0000.0000.000
106A107ALA00.0220.00131.5480.0020.0020.0000.0000.0000.000
107A108MET00.0170.00334.4300.0010.0010.0000.0000.0000.000
108A109LYS10.8830.93333.4550.0750.0750.0000.0000.0000.000
109A110LEU0-0.0080.01233.488-0.002-0.0020.0000.0000.0000.000
110A111ILE00.0020.01727.989-0.003-0.0030.0000.0000.0000.000
111A112SER00.0460.02529.078-0.001-0.0010.0000.0000.0000.000
112A113PRO00.0150.01425.972-0.006-0.0060.0000.0000.0000.000
113A114ARG10.8570.93122.3280.1410.1410.0000.0000.0000.000
114A115ASP-1-0.774-0.87318.601-0.219-0.2190.0000.0000.0000.000
115A116PHE00.0000.01016.1500.0020.0020.0000.0000.0000.000
116A117VAL00.013-0.00910.0360.0150.0150.0000.0000.0000.000
117A118ASP-1-0.794-0.88411.320-0.391-0.3910.0000.0000.0000.000
118A119LEU0-0.038-0.0015.261-0.069-0.0690.0000.0000.0000.000
119A120VAL0-0.028-0.0278.6560.1140.1140.0000.0000.0000.000
120A121LEU00.0200.01110.267-0.051-0.0510.0000.0000.0000.000
121A122VAL0-0.018-0.00811.9040.0330.0330.0000.0000.0000.000
122A123LYS10.8550.91714.2000.1070.1070.0000.0000.0000.000
123A124ARG10.8590.92816.7480.0520.0520.0000.0000.0000.000
124A125TYR00.0220.00619.5400.0020.0020.0000.0000.0000.000
125A126GLU-1-0.890-0.95023.051-0.008-0.0080.0000.0000.0000.000
126A127ASP-1-0.875-0.89926.122-0.045-0.0450.0000.0000.0000.000
127A128GLY00.004-0.00326.1860.0030.0030.0000.0000.0000.000
128A129THR0-0.070-0.07423.592-0.006-0.0060.0000.0000.0000.000
129A130ILE0-0.060-0.01820.3520.0000.0000.0000.0000.0000.000
130A131SER0-0.006-0.01019.071-0.006-0.0060.0000.0000.0000.000
131A132SER00.000-0.00916.734-0.006-0.0060.0000.0000.0000.000
132A133ASN0-0.029-0.01614.7930.0220.0220.0000.0000.0000.000
133A134ALA00.0340.00412.964-0.037-0.0370.0000.0000.0000.000
134A135THR00.0170.00311.4940.0600.0600.0000.0000.0000.000
135A136HIS0-0.049-0.03711.391-0.076-0.0760.0000.0000.0000.000
136A137VAL0-0.047-0.0326.394-0.045-0.0450.0000.0000.0000.000
137A138GLU-1-0.933-0.9529.094-0.447-0.4470.0000.0000.0000.000
138A139HIS00.030-0.0195.275-0.116-0.1160.0000.0000.0000.000
139A140PRO00.0140.0027.2120.1300.1300.0000.0000.0000.000
140A141LEU0-0.0270.0009.7380.0820.0820.0000.0000.0000.000
141A142CYS0-0.087-0.03111.5130.0560.0560.0000.0000.0000.000
142A143PRO00.0940.05412.906-0.031-0.0310.0000.0000.0000.000
143A144PRO0-0.007-0.02215.3230.0070.0070.0000.0000.0000.000
144A145LYS10.8330.93517.0630.2050.2050.0000.0000.0000.000
145A146PRO00.015-0.00220.4740.0020.0020.0000.0000.0000.000
146A147GLY0-0.003-0.00924.2820.0040.0040.0000.0000.0000.000
147A148PHE0-0.070-0.02521.8500.0050.0050.0000.0000.0000.000
148A149VAL0-0.027-0.01123.091-0.003-0.0030.0000.0000.0000.000
149A150ARG10.8180.91414.5880.3070.3070.0000.0000.0000.000
150A151GLY00.0270.01719.4400.0090.0090.0000.0000.0000.000
151A152PHE0-0.012-0.02715.372-0.029-0.0290.0000.0000.0000.000
152A153ASN0-0.015-0.00715.9140.0520.0520.0000.0000.0000.000
153A154HIS00.0450.05215.879-0.051-0.0510.0000.0000.0000.000
154A155PRO00.009-0.00716.1580.0050.0050.0000.0000.0000.000
155A156CYS0-0.0190.00516.9690.0280.0280.0000.0000.0000.000
156A157GLY00.0540.01617.644-0.018-0.0180.0000.0000.0000.000
157A158CYS0-0.073-0.04219.5550.0180.0180.0000.0000.0000.000
158A159PHE00.0340.02021.272-0.006-0.0060.0000.0000.0000.000
159A160CYS0-0.023-0.00424.0000.0030.0030.0000.0000.0000.000
160A161GLU-1-0.718-0.82725.779-0.070-0.0700.0000.0000.0000.000
161A162PRO00.0240.02027.8640.0020.0020.0000.0000.0000.000
162A163LEU00.0370.01030.8540.0000.0000.0000.0000.0000.000
163A164PRO0-0.0020.00134.3380.0020.0020.0000.0000.0000.000
164A165GLY0-0.006-0.00837.1130.0020.0020.0000.0000.0000.000
165A166GLU-1-0.847-0.92538.076-0.033-0.0330.0000.0000.0000.000
166A167PRO00.0020.00337.426-0.002-0.0020.0000.0000.0000.000
167A168THR0-0.026-0.00836.4300.0000.0000.0000.0000.0000.000
168A169LYS10.7420.87234.9420.0310.0310.0000.0000.0000.000
169A170THR0-0.0120.00428.6520.0020.0020.0000.0000.0000.000
170A171ASN0-0.063-0.03731.1040.0000.0000.0000.0000.0000.000
171A172LEU0-0.019-0.00525.910-0.003-0.0030.0000.0000.0000.000
172A173VAL00.0260.01327.0010.0020.0020.0000.0000.0000.000
173A174THR0-0.022-0.01824.338-0.005-0.0050.0000.0000.0000.000
174A175PHE00.0280.01222.2430.0060.0060.0000.0000.0000.000
175A176PHE0-0.004-0.00222.059-0.013-0.0130.0000.0000.0000.000
176A177HIS00.0190.01320.2980.0190.0190.0000.0000.0000.000
177A178THR0-0.017-0.01220.707-0.010-0.0100.0000.0000.0000.000
178A179ASP-1-0.844-0.91120.776-0.176-0.1760.0000.0000.0000.000
179A180LEU0-0.023-0.02921.585-0.010-0.0100.0000.0000.0000.000
180A181SER00.0240.02621.3010.0050.0050.0000.0000.0000.000
181A182GLY0-0.027-0.01423.7800.0130.0130.0000.0000.0000.000
182A183TYR0-0.009-0.01526.0040.0010.0010.0000.0000.0000.000
183A184LEU0-0.002-0.00228.1230.0060.0060.0000.0000.0000.000
184A185PRO00.0160.01331.408-0.001-0.0010.0000.0000.0000.000
185A186GLN00.0420.00530.250-0.007-0.0070.0000.0000.0000.000
186A187ASN00.0490.02533.450-0.004-0.0040.0000.0000.0000.000
187A188VAL0-0.033-0.00432.8580.0030.0030.0000.0000.0000.000
188A189VAL00.0300.01628.5120.0000.0000.0000.0000.0000.000
189A190ASP-1-0.814-0.91031.249-0.102-0.1020.0000.0000.0000.000
190A191SER0-0.050-0.03333.2730.0050.0050.0000.0000.0000.000
191A192PHE0-0.055-0.02426.9540.0070.0070.0000.0000.0000.000
192A193PHE00.0810.03724.9380.0040.0040.0000.0000.0000.000
193A194PRO00.0490.02629.8810.0010.0010.0000.0000.0000.000
194A195ARG10.8560.92332.6500.0800.0800.0000.0000.0000.000
195A196SER0-0.003-0.00128.3530.0020.0020.0000.0000.0000.000
196A197MET00.0430.05226.2700.0020.0020.0000.0000.0000.000
197A198THR0-0.014-0.01829.8890.0040.0040.0000.0000.0000.000
198A199ARG10.7570.83632.4050.0790.0790.0000.0000.0000.000
199A200PHE00.0750.03824.0350.0030.0030.0000.0000.0000.000
200A201TYR00.023-0.01028.1890.0030.0030.0000.0000.0000.000
201A202ALA00.0020.01131.4350.0040.0040.0000.0000.0000.000
202A203ASN0-0.071-0.04430.231-0.001-0.0010.0000.0000.0000.000
203A204LEU00.0370.03327.3080.0030.0030.0000.0000.0000.000
204A205GLN0-0.022-0.02130.2380.0050.0050.0000.0000.0000.000
205A206LYS10.8790.93833.7160.0560.0560.0000.0000.0000.000
206A207ALA0-0.023-0.02129.8260.0030.0030.0000.0000.0000.000
207A208VAL00.0190.00430.3880.0030.0030.0000.0000.0000.000
208A209LYS10.8750.94432.5640.0450.0450.0000.0000.0000.000
209A210GLN00.0280.03634.2490.0000.0000.0000.0000.0000.000
210A211PHE0-0.0230.00328.9690.0020.0020.0000.0000.0000.000
211A212HIS0-0.101-0.06134.6460.0030.0030.0000.0000.0000.000
212A213GLU-1-0.994-0.99338.201-0.034-0.0340.0000.0000.0000.000