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: 2NR7R

Calculation Name: 3CN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CN5

Chain ID: A

ChEMBL ID:

UniProt ID: Q41372

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2780249.118115
FMO2-HF: Nuclear repulsion 2693132.718875
FMO2-HF: Total energy -87116.39924
FMO2-MP2: Total energy -87372.981509


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:32:LEU)


Summations of interaction energy for fragment #1(A:32: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.
-22.582-16.4776.052-4.947-7.210.035
Interaction energy analysis for fragmet #1(A:32:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.007
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].
3A34LEU00.0020.0162.790-5.197-1.4061.005-2.049-2.7470.021
4A35TRP00.0570.0102.074-9.991-7.9265.041-2.839-4.2670.014
5A36SER0-0.104-0.1033.894-2.223-1.9740.006-0.059-0.1960.000
6A37PHE0-0.0200.0056.251-0.821-0.8210.0000.0000.0000.000
7A38TRP00.0560.0116.698-0.815-0.8150.0000.0000.0000.000
8A39ARG10.9340.9615.599-1.244-1.2440.0000.0000.0000.000
9A40ALA00.0110.0259.815-0.258-0.2580.0000.0000.0000.000
10A41ALA00.0210.00811.734-0.178-0.1780.0000.0000.0000.000
11A42ILE00.0030.00211.226-0.131-0.1310.0000.0000.0000.000
12A43ALA00.0000.00213.893-0.107-0.1070.0000.0000.0000.000
13A44GLU-1-0.697-0.79515.8100.3590.3590.0000.0000.0000.000
14A45PHE0-0.0250.01317.279-0.060-0.0600.0000.0000.0000.000
15A46ILE00.0280.00817.995-0.051-0.0510.0000.0000.0000.000
16A47ALA00.0200.01519.815-0.043-0.0430.0000.0000.0000.000
17A48THR00.005-0.02721.677-0.041-0.0410.0000.0000.0000.000
18A49LEU0-0.0100.00822.991-0.027-0.0270.0000.0000.0000.000
19A50LEU0-0.007-0.01923.175-0.027-0.0270.0000.0000.0000.000
20A51PHE0-0.013-0.00425.808-0.022-0.0220.0000.0000.0000.000
21A52LEU0-0.038-0.00827.513-0.017-0.0170.0000.0000.0000.000
22A53TYR00.0030.01428.859-0.015-0.0150.0000.0000.0000.000
23A54ILE00.0310.00529.909-0.013-0.0130.0000.0000.0000.000
24A55THR0-0.033-0.01731.683-0.012-0.0120.0000.0000.0000.000
25A56VAL00.0300.01233.436-0.010-0.0100.0000.0000.0000.000
26A57ALA00.0110.01334.695-0.009-0.0090.0000.0000.0000.000
27A58THR0-0.032-0.01535.932-0.010-0.0100.0000.0000.0000.000
28A59VAL0-0.027-0.01637.948-0.007-0.0070.0000.0000.0000.000
29A60ILE0-0.035-0.01938.845-0.006-0.0060.0000.0000.0000.000
30A61GLY00.008-0.00640.465-0.006-0.0060.0000.0000.0000.000
31A62HIS00.0090.00042.244-0.006-0.0060.0000.0000.0000.000
32A63SER0-0.047-0.02843.553-0.004-0.0040.0000.0000.0000.000
33A64LYS10.9250.95343.795-0.078-0.0780.0000.0000.0000.000
34A65GLU-1-0.956-0.96646.9810.0610.0610.0000.0000.0000.000
35A66THR0-0.029-0.01248.9910.0000.0000.0000.0000.0000.000
36A67VAL0-0.0080.00652.719-0.002-0.0020.0000.0000.0000.000
37A68VAL00.0440.00752.6820.0020.0020.0000.0000.0000.000
38A69CYS0-0.075-0.04751.552-0.001-0.0010.0000.0000.0000.000
39A70GLY00.0620.05250.816-0.001-0.0010.0000.0000.0000.000
40A71SER0-0.0110.00445.9840.0010.0010.0000.0000.0000.000
41A72VAL0-0.005-0.01041.374-0.001-0.0010.0000.0000.0000.000
42A73GLY00.0460.02944.7170.0000.0000.0000.0000.0000.000
43A74LEU00.037-0.01643.8770.0040.0040.0000.0000.0000.000
44A75LEU00.0080.02142.7980.0050.0050.0000.0000.0000.000
45A76GLY00.0560.02241.3670.0030.0030.0000.0000.0000.000
46A77ILE00.0030.00338.7970.0060.0060.0000.0000.0000.000
47A78ALA0-0.015-0.00937.8710.0080.0080.0000.0000.0000.000
48A79TRP00.001-0.00236.7400.0080.0080.0000.0000.0000.000
49A80ALA00.0160.02835.1930.0060.0060.0000.0000.0000.000
50A81PHE0-0.034-0.03232.7340.0110.0110.0000.0000.0000.000
51A82GLY00.0060.00032.1090.0100.0100.0000.0000.0000.000
52A83GLY00.0200.00031.9810.0050.0050.0000.0000.0000.000
53A84MET00.0000.00227.7290.0020.0020.0000.0000.0000.000
54A85ILE0-0.0040.01327.2490.0140.0140.0000.0000.0000.000
55A86PHE00.0090.00526.9930.0110.0110.0000.0000.0000.000
56A87VAL00.0340.01426.2020.0060.0060.0000.0000.0000.000
57A88LEU00.005-0.00123.4250.0100.0100.0000.0000.0000.000
58A89VAL00.0010.00522.3030.0260.0260.0000.0000.0000.000
59A90TYR0-0.033-0.01522.2720.0120.0120.0000.0000.0000.000
60A91CYS0-0.056-0.02020.794-0.004-0.0040.0000.0000.0000.000
61A92THR0-0.016-0.01317.8940.0220.0220.0000.0000.0000.000
62A93ALA00.0430.03917.4530.0570.0570.0000.0000.0000.000
63A94GLY00.0200.00216.7630.0200.0200.0000.0000.0000.000
64A95ILE0-0.084-0.03812.2390.0350.0350.0000.0000.0000.000
65A96SER0-0.060-0.09212.7570.1230.1230.0000.0000.0000.000
66A97GLY00.0570.04015.0870.0300.0300.0000.0000.0000.000
67A98GLY0-0.042-0.00518.243-0.049-0.0490.0000.0000.0000.000
68A99HIS0-0.004-0.00819.420-0.015-0.0150.0000.0000.0000.000
69A100ILE0-0.009-0.00821.386-0.033-0.0330.0000.0000.0000.000
70A101ASN00.017-0.01023.279-0.022-0.0220.0000.0000.0000.000
71A102PRO00.0460.03224.1210.0060.0060.0000.0000.0000.000
72A103ALA00.0320.01225.1820.0030.0030.0000.0000.0000.000
73A104VAL00.0010.01623.823-0.009-0.0090.0000.0000.0000.000
74A105THR0-0.022-0.02720.1760.0030.0030.0000.0000.0000.000
75A106PHE0-0.0150.00022.7990.0080.0080.0000.0000.0000.000
76A107GLY00.0490.02325.317-0.007-0.0070.0000.0000.0000.000
77A108LEU0-0.001-0.01321.826-0.010-0.0100.0000.0000.0000.000
78A109PHE0-0.039-0.01221.2590.0000.0000.0000.0000.0000.000
79A110LEU0-0.0020.01123.006-0.012-0.0120.0000.0000.0000.000
80A111ALA0-0.065-0.01625.495-0.017-0.0170.0000.0000.0000.000
81A112ARG10.9010.94222.089-0.199-0.1990.0000.0000.0000.000
82A113LYS10.9560.98420.374-0.182-0.1820.0000.0000.0000.000
83A114VAL0-0.020-0.01017.1490.0420.0420.0000.0000.0000.000
84A115GLU-1-0.898-0.95013.7500.5650.5650.0000.0000.0000.000
85A116LEU00.0410.01217.3630.0450.0450.0000.0000.0000.000
86A117LEU00.0530.01613.6450.0010.0010.0000.0000.0000.000
87A118ARG10.9410.97210.168-1.065-1.0650.0000.0000.0000.000
88A119ALA00.0240.01115.150-0.017-0.0170.0000.0000.0000.000
89A120LEU00.006-0.00118.743-0.026-0.0260.0000.0000.0000.000
90A121VAL00.0150.01413.589-0.017-0.0170.0000.0000.0000.000
91A122TYR0-0.050-0.03913.7690.0620.0620.0000.0000.0000.000
92A123MET0-0.0120.00718.114-0.047-0.0470.0000.0000.0000.000
93A124ILE00.0270.02119.409-0.037-0.0370.0000.0000.0000.000
94A125ALA00.0030.00217.108-0.030-0.0300.0000.0000.0000.000
95A126GLN0-0.009-0.03419.245-0.061-0.0610.0000.0000.0000.000
96A127CYS0-0.021-0.01422.164-0.042-0.0420.0000.0000.0000.000
97A128LEU00.0090.00620.174-0.027-0.0270.0000.0000.0000.000
98A129GLY00.0360.01822.467-0.021-0.0210.0000.0000.0000.000
99A130ALA00.002-0.00923.306-0.027-0.0270.0000.0000.0000.000
100A131ILE00.0010.00526.642-0.021-0.0210.0000.0000.0000.000
101A132CYS0-0.025-0.00924.776-0.017-0.0170.0000.0000.0000.000
102A133GLY00.0150.01926.965-0.016-0.0160.0000.0000.0000.000
103A134VAL0-0.004-0.01228.422-0.017-0.0170.0000.0000.0000.000
104A135GLY00.0190.00930.580-0.014-0.0140.0000.0000.0000.000
105A136LEU0-0.012-0.00727.359-0.012-0.0120.0000.0000.0000.000
106A137VAL00.0070.01531.672-0.011-0.0110.0000.0000.0000.000
107A138LYS10.8900.94934.557-0.131-0.1310.0000.0000.0000.000
108A139ALA0-0.035-0.02233.993-0.008-0.0080.0000.0000.0000.000
109A140PHE0-0.013-0.00632.329-0.007-0.0070.0000.0000.0000.000
110A141MET0-0.0080.01137.215-0.008-0.0080.0000.0000.0000.000
111A142LYS10.9901.00240.224-0.096-0.0960.0000.0000.0000.000
112A143GLY0-0.017-0.00741.1170.0000.0000.0000.0000.0000.000
113A144PRO00.0600.01442.7510.0000.0000.0000.0000.0000.000
114A145TYR00.0090.01536.2990.0000.0000.0000.0000.0000.000
115A146ASN0-0.009-0.02941.1510.0060.0060.0000.0000.0000.000
116A147GLN00.0030.01543.2320.0010.0010.0000.0000.0000.000
117A148PHE0-0.012-0.00443.971-0.002-0.0020.0000.0000.0000.000
118A149GLY00.0240.02442.9900.0010.0010.0000.0000.0000.000
119A150GLY00.0310.00939.3950.0050.0050.0000.0000.0000.000
120A151GLY00.004-0.00637.0040.0090.0090.0000.0000.0000.000
121A152ALA0-0.0150.00436.7710.0090.0090.0000.0000.0000.000
122A153ASN0-0.044-0.01035.8660.0050.0050.0000.0000.0000.000
123A154SER0-0.026-0.01938.9880.0000.0000.0000.0000.0000.000
124A155VAL0-0.071-0.03742.116-0.001-0.0010.0000.0000.0000.000
125A156ALA00.0340.02645.073-0.002-0.0020.0000.0000.0000.000
126A157LEU00.012-0.01247.630-0.001-0.0010.0000.0000.0000.000
127A158GLY00.0290.01851.280-0.001-0.0010.0000.0000.0000.000
128A159TYR00.0200.02448.428-0.001-0.0010.0000.0000.0000.000
129A160ASN00.0220.00449.7690.0040.0040.0000.0000.0000.000
130A161LYS10.9890.96245.185-0.089-0.0890.0000.0000.0000.000
131A162GLY00.0370.03444.9250.0040.0040.0000.0000.0000.000
132A163THR00.0200.01445.7550.0010.0010.0000.0000.0000.000
133A164ALA00.0090.01342.9810.0020.0020.0000.0000.0000.000
134A165LEU0-0.014-0.00139.3560.0050.0050.0000.0000.0000.000
135A166GLY00.0170.00840.9420.0050.0050.0000.0000.0000.000
136A167ALA00.014-0.00142.0090.0020.0020.0000.0000.0000.000
137A168GLU-1-0.712-0.84436.7320.1420.1420.0000.0000.0000.000
138A169ILE0-0.0300.00537.1370.0080.0080.0000.0000.0000.000
139A170ILE00.0260.00737.4940.0040.0040.0000.0000.0000.000
140A171GLY00.0290.01538.0650.0000.0000.0000.0000.0000.000
141A172THR0-0.008-0.02232.0750.0070.0070.0000.0000.0000.000
142A173PHE0-0.0320.00233.4970.0080.0080.0000.0000.0000.000
143A174VAL00.0270.01334.9040.0010.0010.0000.0000.0000.000
144A175LEU0-0.0180.00429.6080.0020.0020.0000.0000.0000.000
145A176VAL00.014-0.00928.8440.0060.0060.0000.0000.0000.000
146A177TYR00.0260.02330.4600.0020.0020.0000.0000.0000.000
147A178THR0-0.019-0.00431.542-0.006-0.0060.0000.0000.0000.000
148A179VAL0-0.013-0.01525.8370.0000.0000.0000.0000.0000.000
149A180PHE0-0.036-0.03326.8160.0060.0060.0000.0000.0000.000
150A181SER0-0.030-0.01328.799-0.007-0.0070.0000.0000.0000.000
151A182ALA0-0.038-0.00228.061-0.009-0.0090.0000.0000.0000.000
152A183THR0-0.096-0.04924.2740.0070.0070.0000.0000.0000.000
153A184ASP-1-0.829-0.92622.3920.0830.0830.0000.0000.0000.000
154A185PRO0-0.042-0.01522.7650.0120.0120.0000.0000.0000.000
155A186LYS10.9180.95122.288-0.042-0.0420.0000.0000.0000.000
156A187ARG10.9280.97819.078-0.076-0.0760.0000.0000.0000.000
157A188SER00.0500.02415.5310.0220.0220.0000.0000.0000.000
158A189ALA0-0.0100.00214.312-0.032-0.0320.0000.0000.0000.000
159A190ARG10.9660.9758.685-0.597-0.5970.0000.0000.0000.000
160A191ASP-1-0.875-0.8916.4410.3010.3010.0000.0000.0000.000
161A192SER0-0.103-0.0609.1700.2820.2820.0000.0000.0000.000
162A193HIS00.0610.02211.991-0.105-0.1050.0000.0000.0000.000
163A194VAL0-0.0050.01015.021-0.027-0.0270.0000.0000.0000.000
164A195PRO00.0070.01717.165-0.008-0.0080.0000.0000.0000.000
165A196ILE00.0100.00117.5440.0230.0230.0000.0000.0000.000
166A197LEU0-0.017-0.00120.515-0.021-0.0210.0000.0000.0000.000
167A198ALA00.013-0.00123.906-0.002-0.0020.0000.0000.0000.000
168A199PRO00.0320.01225.535-0.001-0.0010.0000.0000.0000.000
169A200LEU00.0010.00427.4890.0010.0010.0000.0000.0000.000
170A201PRO00.0330.01130.350-0.001-0.0010.0000.0000.0000.000
171A202ILE00.0450.02226.792-0.001-0.0010.0000.0000.0000.000
172A203GLY00.0110.00930.5450.0020.0020.0000.0000.0000.000
173A204PHE00.025-0.00231.709-0.004-0.0040.0000.0000.0000.000
174A205ALA00.0310.02833.328-0.005-0.0050.0000.0000.0000.000
175A206VAL0-0.012-0.00830.932-0.002-0.0020.0000.0000.0000.000
176A207PHE00.0130.00234.310-0.003-0.0030.0000.0000.0000.000
177A208MET00.0040.00137.054-0.006-0.0060.0000.0000.0000.000
178A209VAL00.0120.02336.728-0.004-0.0040.0000.0000.0000.000
179A210HIS10.8380.91734.441-0.134-0.1340.0000.0000.0000.000
180A211LEU0-0.014-0.00239.470-0.003-0.0030.0000.0000.0000.000
181A212ALA0-0.0200.00642.344-0.004-0.0040.0000.0000.0000.000
182A213THR0-0.010-0.01640.346-0.003-0.0030.0000.0000.0000.000
183A214ILE0-0.069-0.02640.2840.0020.0020.0000.0000.0000.000
184A215PRO00.0130.00142.7180.0010.0010.0000.0000.0000.000
185A216ILE0-0.0090.02044.188-0.001-0.0010.0000.0000.0000.000
186A217THR0-0.011-0.02339.965-0.001-0.0010.0000.0000.0000.000
187A218GLY00.0260.02640.5350.0050.0050.0000.0000.0000.000
188A219THR0-0.041-0.04436.4640.0000.0000.0000.0000.0000.000
189A220GLY0-0.0050.00135.1380.0040.0040.0000.0000.0000.000
190A221ILE0-0.059-0.05532.7470.0080.0080.0000.0000.0000.000
191A222ASN0-0.015-0.01827.2160.0190.0190.0000.0000.0000.000
192A223PRO00.0560.03428.629-0.002-0.0020.0000.0000.0000.000
193A224ALA00.0340.01625.737-0.003-0.0030.0000.0000.0000.000
194A225ARG10.8300.92427.828-0.159-0.1590.0000.0000.0000.000
195A226SER0-0.020-0.02830.308-0.010-0.0100.0000.0000.0000.000
196A227PHE00.0120.01228.101-0.008-0.0080.0000.0000.0000.000
197A228GLY00.0220.00529.917-0.005-0.0050.0000.0000.0000.000
198A229ALA0-0.001-0.00730.495-0.007-0.0070.0000.0000.0000.000
199A230ALA0-0.0110.00434.043-0.009-0.0090.0000.0000.0000.000
200A231VAL0-0.011-0.01130.611-0.008-0.0080.0000.0000.0000.000
201A232ILE0-0.066-0.01731.357-0.008-0.0080.0000.0000.0000.000
202A233PHE0-0.069-0.03934.790-0.010-0.0100.0000.0000.0000.000
203A234ASN0-0.0380.00037.596-0.005-0.0050.0000.0000.0000.000
204A235SER00.0330.01739.036-0.007-0.0070.0000.0000.0000.000
205A236ASN00.0770.01741.5290.0080.0080.0000.0000.0000.000
206A237LYS10.9120.97543.439-0.092-0.0920.0000.0000.0000.000
207A238VAL0-0.015-0.01538.5610.0010.0010.0000.0000.0000.000
208A239TRP0-0.006-0.00933.5370.0100.0100.0000.0000.0000.000
209A240ASP-1-0.912-0.94539.8260.1060.1060.0000.0000.0000.000
210A241ASP-1-0.814-0.92441.5060.1020.1020.0000.0000.0000.000
211A242GLN0-0.010-0.00933.4800.0150.0150.0000.0000.0000.000
212A243TRP00.0570.01936.3130.0100.0100.0000.0000.0000.000
213A244ILE00.0150.01836.9140.0040.0040.0000.0000.0000.000
214A245PHE0-0.031-0.02035.0060.0010.0010.0000.0000.0000.000
215A246TRP0-0.018-0.00827.3730.0170.0170.0000.0000.0000.000
216A247VAL00.005-0.01233.1130.0050.0050.0000.0000.0000.000
217A248GLY00.0240.00935.517-0.001-0.0010.0000.0000.0000.000
218A249PRO00.002-0.01032.056-0.001-0.0010.0000.0000.0000.000
219A250PHE00.0170.00026.9760.0070.0070.0000.0000.0000.000
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