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: ZVLRN

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 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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2795895.722241
FMO2-HF: Nuclear repulsion 2708778.474025
FMO2-HF: Total energy -87117.248216
FMO2-MP2: Total energy -87373.775729


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.
-15.938-10.2923.194-3.488-5.3520.011
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 : 0.026 / q_NPA : 0.002
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].
3A34LEU00.0510.0373.579-2.6080.0370.038-1.285-1.3970.003
4A35TRP00.0730.0202.243-8.204-5.3673.156-2.177-3.8160.008
5A36SER0-0.087-0.0614.093-1.751-1.5870.000-0.026-0.1390.000
6A37PHE00.0380.0346.287-0.566-0.5660.0000.0000.0000.000
7A38TRP00.0720.0217.288-0.556-0.5560.0000.0000.0000.000
8A39ARG10.9460.9725.125-0.416-0.4160.0000.0000.0000.000
9A40ALA0-0.0030.0209.767-0.189-0.1890.0000.0000.0000.000
10A41ALA00.0240.00611.849-0.126-0.1260.0000.0000.0000.000
11A42ILE00.008-0.00311.155-0.102-0.1020.0000.0000.0000.000
12A43ALA00.0080.00913.906-0.080-0.0800.0000.0000.0000.000
13A44GLU-1-0.708-0.81515.7980.2790.2790.0000.0000.0000.000
14A45PHE0-0.0280.01117.400-0.045-0.0450.0000.0000.0000.000
15A46ILE00.0180.00117.833-0.039-0.0390.0000.0000.0000.000
16A47ALA00.0180.01019.746-0.033-0.0330.0000.0000.0000.000
17A48THR0-0.006-0.03621.682-0.028-0.0280.0000.0000.0000.000
18A49LEU0-0.0190.00422.843-0.019-0.0190.0000.0000.0000.000
19A50LEU00.012-0.00722.859-0.020-0.0200.0000.0000.0000.000
20A51PHE0-0.014-0.00625.775-0.015-0.0150.0000.0000.0000.000
21A52LEU0-0.0240.01227.555-0.012-0.0120.0000.0000.0000.000
22A53TYR00.0030.01828.786-0.011-0.0110.0000.0000.0000.000
23A54ILE00.0350.01029.805-0.009-0.0090.0000.0000.0000.000
24A55THR0-0.035-0.02031.465-0.008-0.0080.0000.0000.0000.000
25A56VAL00.0250.00833.384-0.008-0.0080.0000.0000.0000.000
26A57ALA00.0070.00734.552-0.006-0.0060.0000.0000.0000.000
27A58THR0-0.040-0.02535.779-0.008-0.0080.0000.0000.0000.000
28A59VAL0-0.017-0.01137.800-0.005-0.0050.0000.0000.0000.000
29A60ILE0-0.0340.00638.999-0.004-0.0040.0000.0000.0000.000
30A61GLY00.0350.01740.204-0.004-0.0040.0000.0000.0000.000
31A62HIS0-0.012-0.00141.859-0.006-0.0060.0000.0000.0000.000
32A63SER0-0.042-0.05143.256-0.003-0.0030.0000.0000.0000.000
33A64LYS10.8070.89644.004-0.054-0.0540.0000.0000.0000.000
34A65GLU-1-0.845-0.88546.7080.0430.0430.0000.0000.0000.000
35A66THR0-0.063-0.03748.946-0.001-0.0010.0000.0000.0000.000
36A67VAL00.0010.00452.381-0.002-0.0020.0000.0000.0000.000
37A68VAL00.0420.00752.5000.0020.0020.0000.0000.0000.000
38A69CYS0-0.060-0.03651.389-0.001-0.0010.0000.0000.0000.000
39A70GLY00.0360.03750.703-0.001-0.0010.0000.0000.0000.000
40A71SER0-0.029-0.03045.8070.0010.0010.0000.0000.0000.000
41A72VAL00.0180.00341.162-0.001-0.0010.0000.0000.0000.000
42A73GLY00.0450.02944.4100.0000.0000.0000.0000.0000.000
43A74LEU00.020-0.01143.4060.0030.0030.0000.0000.0000.000
44A75LEU00.0250.02442.2980.0040.0040.0000.0000.0000.000
45A76GLY00.0550.02740.8970.0020.0020.0000.0000.0000.000
46A77ILE0-0.0020.00238.5390.0040.0040.0000.0000.0000.000
47A78ALA0-0.015-0.00837.4800.0060.0060.0000.0000.0000.000
48A79TRP00.0100.00136.8720.0050.0050.0000.0000.0000.000
49A80ALA00.0020.01434.8150.0030.0030.0000.0000.0000.000
50A81PHE0-0.007-0.02632.7550.0070.0070.0000.0000.0000.000
51A82GLY00.0000.00331.9130.0080.0080.0000.0000.0000.000
52A83GLY00.0130.00031.5080.0040.0040.0000.0000.0000.000
53A84MET0-0.012-0.00227.739-0.001-0.0010.0000.0000.0000.000
54A85ILE00.0050.01226.9190.0090.0090.0000.0000.0000.000
55A86PHE00.0160.00526.6210.0070.0070.0000.0000.0000.000
56A87VAL00.0440.01726.0610.0030.0030.0000.0000.0000.000
57A88LEU00.0090.01123.2130.0050.0050.0000.0000.0000.000
58A89VAL00.0040.01921.9750.0160.0160.0000.0000.0000.000
59A90TYR0-0.029-0.01321.8280.0060.0060.0000.0000.0000.000
60A91CYS0-0.067-0.02420.514-0.009-0.0090.0000.0000.0000.000
61A92THR0-0.030-0.03917.5030.0170.0170.0000.0000.0000.000
62A93ALA00.0330.02817.1690.0400.0400.0000.0000.0000.000
63A94GLY00.0500.02016.4120.0100.0100.0000.0000.0000.000
64A95ILE0-0.092-0.04412.5100.0130.0130.0000.0000.0000.000
65A96SER0-0.014-0.04812.3210.0960.0960.0000.0000.0000.000
66A97GLY00.0440.04014.6170.0370.0370.0000.0000.0000.000
67A98GLY0-0.0230.00217.899-0.036-0.0360.0000.0000.0000.000
68A99HIS00.004-0.00919.489-0.011-0.0110.0000.0000.0000.000
69A100ILE0-0.010-0.01121.269-0.025-0.0250.0000.0000.0000.000
70A101ASN00.019-0.00123.175-0.013-0.0130.0000.0000.0000.000
71A102PRO00.0440.02824.1990.0050.0050.0000.0000.0000.000
72A103ALA00.0380.01925.2460.0050.0050.0000.0000.0000.000
73A104VAL0-0.0120.00623.928-0.005-0.0050.0000.0000.0000.000
74A105THR00.002-0.01020.2790.0010.0010.0000.0000.0000.000
75A106PHE0-0.017-0.00422.9570.0110.0110.0000.0000.0000.000
76A107GLY00.0450.01925.562-0.004-0.0040.0000.0000.0000.000
77A108LEU0-0.012-0.01722.111-0.008-0.0080.0000.0000.0000.000
78A109PHE0-0.026-0.00921.1810.0020.0020.0000.0000.0000.000
79A110LEU0-0.0120.00822.972-0.006-0.0060.0000.0000.0000.000
80A111ALA0-0.059-0.02425.613-0.012-0.0120.0000.0000.0000.000
81A112ARG10.9030.94521.819-0.196-0.1960.0000.0000.0000.000
82A113LYS10.9070.96820.567-0.145-0.1450.0000.0000.0000.000
83A114VAL00.001-0.01017.5060.0240.0240.0000.0000.0000.000
84A115GLU-1-0.773-0.85412.9150.6680.6680.0000.0000.0000.000
85A116LEU00.0280.01117.1220.0340.0340.0000.0000.0000.000
86A117LEU00.0250.01113.818-0.005-0.0050.0000.0000.0000.000
87A118ARG10.8340.88910.506-0.833-0.8330.0000.0000.0000.000
88A119ALA00.0290.01115.374-0.020-0.0200.0000.0000.0000.000
89A120LEU00.0350.00819.089-0.024-0.0240.0000.0000.0000.000
90A121VAL0-0.0040.00513.643-0.020-0.0200.0000.0000.0000.000
91A122TYR0-0.044-0.04913.5340.0300.0300.0000.0000.0000.000
92A123MET0-0.0240.00618.056-0.042-0.0420.0000.0000.0000.000
93A124ILE00.0290.01919.448-0.034-0.0340.0000.0000.0000.000
94A125ALA0-0.0030.00017.100-0.029-0.0290.0000.0000.0000.000
95A126GLN0-0.003-0.02919.229-0.046-0.0460.0000.0000.0000.000
96A127CYS0-0.038-0.02422.118-0.036-0.0360.0000.0000.0000.000
97A128LEU00.0130.00620.293-0.022-0.0220.0000.0000.0000.000
98A129GLY00.0430.02322.409-0.018-0.0180.0000.0000.0000.000
99A130ALA0-0.001-0.00923.209-0.023-0.0230.0000.0000.0000.000
100A131ILE0-0.003-0.00126.629-0.018-0.0180.0000.0000.0000.000
101A132CYS0-0.044-0.01924.607-0.013-0.0130.0000.0000.0000.000
102A133GLY00.0140.01226.841-0.014-0.0140.0000.0000.0000.000
103A134VAL00.001-0.01428.190-0.013-0.0130.0000.0000.0000.000
104A135GLY00.0260.01530.462-0.010-0.0100.0000.0000.0000.000
105A136LEU0-0.011-0.00327.263-0.010-0.0100.0000.0000.0000.000
106A137VAL0-0.0110.00931.619-0.009-0.0090.0000.0000.0000.000
107A138LYS10.8240.91834.638-0.105-0.1050.0000.0000.0000.000
108A139ALA0-0.032-0.01733.949-0.006-0.0060.0000.0000.0000.000
109A140PHE0-0.018-0.01431.674-0.005-0.0050.0000.0000.0000.000
110A141MET00.0100.01137.153-0.006-0.0060.0000.0000.0000.000
111A142LYS10.9781.00039.872-0.075-0.0750.0000.0000.0000.000
112A143GLY00.0000.00540.8630.0010.0010.0000.0000.0000.000
113A144PRO00.0770.01742.8790.0010.0010.0000.0000.0000.000
114A145TYR00.0030.00736.2040.0010.0010.0000.0000.0000.000
115A146ASN00.002-0.02141.1170.0060.0060.0000.0000.0000.000
116A147GLN0-0.0200.00043.1880.0010.0010.0000.0000.0000.000
117A148PHE00.0030.00843.809-0.002-0.0020.0000.0000.0000.000
118A149GLY00.0200.01642.7820.0020.0020.0000.0000.0000.000
119A150GLY00.0410.00139.0290.0050.0050.0000.0000.0000.000
120A151GLY00.0120.00037.1450.0070.0070.0000.0000.0000.000
121A152ALA0-0.015-0.00236.9070.0070.0070.0000.0000.0000.000
122A153ASN0-0.040-0.01435.7990.0040.0040.0000.0000.0000.000
123A154SER0-0.026-0.02438.8230.0000.0000.0000.0000.0000.000
124A155VAL0-0.053-0.02042.000-0.001-0.0010.0000.0000.0000.000
125A156ALA00.0490.03144.908-0.002-0.0020.0000.0000.0000.000
126A157LEU0-0.002-0.01647.4070.0000.0000.0000.0000.0000.000
127A158GLY00.0490.02651.141-0.002-0.0020.0000.0000.0000.000
128A159TYR0-0.029-0.00548.210-0.001-0.0010.0000.0000.0000.000
129A160ASN00.0420.03549.6550.0040.0040.0000.0000.0000.000
130A161LYS10.9430.93045.174-0.080-0.0800.0000.0000.0000.000
131A162GLY00.0410.03144.8150.0040.0040.0000.0000.0000.000
132A163THR0-0.003-0.01345.5330.0010.0010.0000.0000.0000.000
133A164ALA00.0180.01443.0340.0010.0010.0000.0000.0000.000
134A165LEU0-0.020-0.00539.5060.0040.0040.0000.0000.0000.000
135A166GLY00.0250.01340.7980.0040.0040.0000.0000.0000.000
136A167ALA00.0300.01641.8730.0010.0010.0000.0000.0000.000
137A168GLU-1-0.720-0.84436.8660.1130.1130.0000.0000.0000.000
138A169ILE0-0.0490.00936.9050.0070.0070.0000.0000.0000.000
139A170ILE00.0210.00637.4370.0040.0040.0000.0000.0000.000
140A171GLY00.0380.00337.8100.0000.0000.0000.0000.0000.000
141A172THR0-0.025-0.03731.9430.0050.0050.0000.0000.0000.000
142A173PHE0-0.0230.00633.3690.0060.0060.0000.0000.0000.000
143A174VAL00.0310.01534.7960.0010.0010.0000.0000.0000.000
144A175LEU0-0.0220.01129.8510.0000.0000.0000.0000.0000.000
145A176VAL00.013-0.00428.7990.0030.0030.0000.0000.0000.000
146A177TYR00.0360.02030.4160.0020.0020.0000.0000.0000.000
147A178THR0-0.029-0.01531.618-0.005-0.0050.0000.0000.0000.000
148A179VAL0-0.022-0.02225.7740.0000.0000.0000.0000.0000.000
149A180PHE0-0.050-0.03927.1970.0050.0050.0000.0000.0000.000
150A181SER0-0.038-0.01828.948-0.005-0.0050.0000.0000.0000.000
151A182ALA0-0.0170.00027.994-0.009-0.0090.0000.0000.0000.000
152A183THR0-0.068-0.01524.0680.0080.0080.0000.0000.0000.000
153A184ASP-1-0.745-0.86322.3150.0550.0550.0000.0000.0000.000
154A185PRO0-0.005-0.00423.0770.0120.0120.0000.0000.0000.000
155A186LYS10.8930.93622.230-0.035-0.0350.0000.0000.0000.000
156A187ARG10.8400.91818.810-0.051-0.0510.0000.0000.0000.000
157A188SER00.0560.02615.5380.0040.0040.0000.0000.0000.000
158A189ALA0-0.0060.01814.129-0.037-0.0370.0000.0000.0000.000
159A190ARG10.8520.9227.790-0.425-0.4250.0000.0000.0000.000
160A191ASP-1-0.851-0.9006.4890.0180.0180.0000.0000.0000.000
161A192SER0-0.053-0.0429.1410.2690.2690.0000.0000.0000.000
162A193HIS00.0370.01612.366-0.094-0.0940.0000.0000.0000.000
163A194VAL00.0230.02015.503-0.028-0.0280.0000.0000.0000.000
164A195PRO0-0.0170.00517.324-0.009-0.0090.0000.0000.0000.000
165A196ILE0-0.018-0.01717.9950.0120.0120.0000.0000.0000.000
166A197LEU00.0000.00520.573-0.014-0.0140.0000.0000.0000.000
167A198ALA00.010-0.00123.607-0.006-0.0060.0000.0000.0000.000
168A199PRO00.0040.00625.2390.0010.0010.0000.0000.0000.000
169A200LEU00.0180.00327.0400.0020.0020.0000.0000.0000.000
170A201PRO00.0330.00830.1040.0000.0000.0000.0000.0000.000
171A202ILE00.0440.03226.4160.0010.0010.0000.0000.0000.000
172A203GLY00.0150.01130.2710.0020.0020.0000.0000.0000.000
173A204PHE00.026-0.00431.484-0.003-0.0030.0000.0000.0000.000
174A205ALA00.0180.02033.059-0.003-0.0030.0000.0000.0000.000
175A206VAL0-0.016-0.00930.683-0.001-0.0010.0000.0000.0000.000
176A207PHE00.0080.00734.036-0.001-0.0010.0000.0000.0000.000
177A208MET00.0140.00436.825-0.003-0.0030.0000.0000.0000.000
178A209VAL00.0140.02436.749-0.002-0.0020.0000.0000.0000.000
179A210HIS10.8420.92734.158-0.104-0.1040.0000.0000.0000.000
180A211LEU0-0.025-0.00839.091-0.002-0.0020.0000.0000.0000.000
181A212ALA0-0.0080.00842.121-0.003-0.0030.0000.0000.0000.000
182A213THR0-0.011-0.01740.135-0.002-0.0020.0000.0000.0000.000
183A214ILE0-0.052-0.01739.6910.0020.0020.0000.0000.0000.000
184A215PRO00.013-0.00242.4580.0010.0010.0000.0000.0000.000
185A216ILE0-0.0270.01643.927-0.002-0.0020.0000.0000.0000.000
186A217THR0-0.008-0.03440.004-0.001-0.0010.0000.0000.0000.000
187A218GLY00.0370.03140.4290.0050.0050.0000.0000.0000.000
188A219THR0-0.027-0.03136.3420.0010.0010.0000.0000.0000.000
189A220GLY00.0260.01934.9730.0020.0020.0000.0000.0000.000
190A221ILE0-0.048-0.04332.6650.0050.0050.0000.0000.0000.000
191A222ASN0-0.013-0.01626.9820.0150.0150.0000.0000.0000.000
192A223PRO00.0600.03628.683-0.002-0.0020.0000.0000.0000.000
193A224ALA00.0330.02225.914-0.002-0.0020.0000.0000.0000.000
194A225ARG10.7760.89327.997-0.125-0.1250.0000.0000.0000.000
195A226SER0-0.007-0.01730.502-0.009-0.0090.0000.0000.0000.000
196A227PHE0-0.0020.01428.870-0.006-0.0060.0000.0000.0000.000
197A228GLY00.0180.00029.680-0.003-0.0030.0000.0000.0000.000
198A229ALA00.0200.00530.410-0.006-0.0060.0000.0000.0000.000
199A230ALA0-0.0050.00633.865-0.008-0.0080.0000.0000.0000.000
200A231VAL0-0.013-0.01030.692-0.006-0.0060.0000.0000.0000.000
201A232ILE0-0.0310.00631.030-0.006-0.0060.0000.0000.0000.000
202A233PHE0-0.036-0.01634.654-0.009-0.0090.0000.0000.0000.000
203A234ASN0-0.0220.00537.528-0.003-0.0030.0000.0000.0000.000
204A235SER00.0240.01338.987-0.006-0.0060.0000.0000.0000.000
205A236ASN00.0380.01341.7090.0050.0050.0000.0000.0000.000
206A237LYS10.8890.95043.142-0.076-0.0760.0000.0000.0000.000
207A238VAL0-0.023-0.00838.3800.0010.0010.0000.0000.0000.000
208A239TRP0-0.011-0.02333.9840.0090.0090.0000.0000.0000.000
209A240ASP-1-0.892-0.95239.9660.0900.0900.0000.0000.0000.000
210A241ASP-1-0.779-0.88641.5340.0840.0840.0000.0000.0000.000
211A242GLN0-0.006-0.00733.8270.0110.0110.0000.0000.0000.000
212A243TRP00.0340.00436.2720.0080.0080.0000.0000.0000.000
213A244ILE00.0040.01336.9580.0040.0040.0000.0000.0000.000
214A245PHE0-0.023-0.01834.8120.0010.0010.0000.0000.0000.000
215A246TRP0-0.021-0.01027.5370.0150.0150.0000.0000.0000.000
216A247VAL00.0220.00233.3000.0040.0040.0000.0000.0000.000
217A248GLY00.0380.01335.773-0.001-0.0010.0000.0000.0000.000
218A249PRO00.016-0.00732.2660.0000.0000.0000.0000.0000.000
219A250PHE00.011-0.00427.0470.0060.0060.0000.0000.0000.000
220A251ILE00.0270.02132.1670.0010.0010.0000.0000.0000.000
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