Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K22R3

Calculation Name: 3I82-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3I82

Chain ID: A

ChEMBL ID:

UniProt ID: P76541

Base Structure: X-ray

Registration Date: 2023-09-27

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2236583.339166
FMO2-HF: Nuclear repulsion 2157558.016851
FMO2-HF: Total energy -79025.322315
FMO2-MP2: Total energy -79255.087375


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:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-31.834-36.45430.522-13.667-12.237-0.054
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.034
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].
3A4LEU0-0.057-0.0403.544-2.242-1.0590.005-0.526-0.6620.001
4A5ASP-1-0.846-0.8891.861-19.964-19.91910.538-6.061-4.523-0.067
5A6LEU0-0.066-0.0514.5891.3501.428-0.001-0.012-0.0650.000
6A7ILE00.0050.0217.1200.1800.1800.0000.0000.0000.000
7A8ARG10.8430.9069.0540.1440.1440.0000.0000.0000.000
8A9PRO0-0.0100.01711.7900.1020.1020.0000.0000.0000.000
9A10SER0-0.045-0.04815.037-0.046-0.0460.0000.0000.0000.000
10A11VAL00.006-0.00518.0930.0110.0110.0000.0000.0000.000
11A12THR0-0.027-0.01721.0840.0080.0080.0000.0000.0000.000
12A13ALA0-0.053-0.03823.4260.0010.0010.0000.0000.0000.000
13A14MET00.0300.03527.114-0.009-0.0090.0000.0000.0000.000
14A15ARG10.8480.91929.486-0.046-0.0460.0000.0000.0000.000
15A16VAL00.0280.02433.248-0.003-0.0030.0000.0000.0000.000
16A17ILE0-0.0250.00535.9440.0020.0020.0000.0000.0000.000
17A18ALA00.000-0.01539.230-0.003-0.0030.0000.0000.0000.000
18A19SER00.0310.01241.591-0.004-0.0040.0000.0000.0000.000
19A20VAL0-0.031-0.00240.8600.0030.0030.0000.0000.0000.000
20A21ASN0-0.0040.00043.603-0.002-0.0020.0000.0000.0000.000
21A22ALA00.0520.01046.0380.0000.0000.0000.0000.0000.000
22A23ASP-1-0.855-0.91948.0050.0200.0200.0000.0000.0000.000
23A24PHE00.0400.01238.9460.0000.0000.0000.0000.0000.000
24A25ALA00.0280.01543.7170.0000.0000.0000.0000.0000.000
25A26ARG10.8590.92044.688-0.015-0.0150.0000.0000.0000.000
26A27GLU-1-0.851-0.92143.9440.0240.0240.0000.0000.0000.000
27A28LEU0-0.029-0.00338.6340.0010.0010.0000.0000.0000.000
28A29LYS10.7660.88241.360-0.022-0.0220.0000.0000.0000.000
29A30LEU0-0.0010.01240.044-0.002-0.0020.0000.0000.0000.000
30A31PRO00.0490.02442.0840.0000.0000.0000.0000.0000.000
31A32PRO0-0.033-0.01345.0650.0010.0010.0000.0000.0000.000
32A33HIS0-0.021-0.01941.9330.0030.0030.0000.0000.0000.000
33A34ILE0-0.0100.02939.3410.0000.0000.0000.0000.0000.000
34A35ARG10.8730.92242.9670.0020.0020.0000.0000.0000.000
35A36SER0-0.029-0.00840.0310.0020.0020.0000.0000.0000.000
36A37LEU00.015-0.00836.232-0.002-0.0020.0000.0000.0000.000
37A38GLY00.0100.00033.6820.0030.0030.0000.0000.0000.000
38A39LEU0-0.041-0.01531.9400.0000.0000.0000.0000.0000.000
39A40ILE00.029-0.00625.2620.0000.0000.0000.0000.0000.000
40A41SER00.0180.00425.668-0.006-0.0060.0000.0000.0000.000
41A42ALA00.0400.02520.460-0.003-0.0030.0000.0000.0000.000
42A43ASP-1-0.818-0.88816.9520.2190.2190.0000.0000.0000.000
43A44SER00.0360.02616.1640.0150.0150.0000.0000.0000.000
44A45ASP-1-0.766-0.86818.1530.0530.0530.0000.0000.0000.000
45A46ASP-1-0.771-0.87418.789-0.014-0.0140.0000.0000.0000.000
46A47VAL0-0.0110.00615.612-0.025-0.0250.0000.0000.0000.000
47A48THR0-0.008-0.03118.961-0.019-0.0190.0000.0000.0000.000
48A49TYR0-0.045-0.04722.088-0.011-0.0110.0000.0000.0000.000
49A50ILE0-0.012-0.00519.654-0.011-0.0110.0000.0000.0000.000
50A51ALA00.0110.01822.106-0.008-0.0080.0000.0000.0000.000
51A52ALA00.008-0.00623.9140.0000.0000.0000.0000.0000.000
52A53ASP-1-0.753-0.87726.654-0.077-0.0770.0000.0000.0000.000
53A54GLU-1-0.819-0.89825.162-0.127-0.1270.0000.0000.0000.000
54A55ALA00.0280.00727.3600.0000.0000.0000.0000.0000.000
55A56THR0-0.139-0.06329.5710.0030.0030.0000.0000.0000.000
56A57LYS10.7590.87627.1100.1170.1170.0000.0000.0000.000
57A58GLN0-0.112-0.05628.8910.0030.0030.0000.0000.0000.000
58A59ALA0-0.0040.01132.2110.0030.0030.0000.0000.0000.000
59A60MET0-0.068-0.03034.9520.0000.0000.0000.0000.0000.000
60A61VAL0-0.057-0.04432.8480.0060.0060.0000.0000.0000.000
61A62GLU-1-0.846-0.92734.772-0.023-0.0230.0000.0000.0000.000
62A63VAL0-0.008-0.00730.3810.0050.0050.0000.0000.0000.000
63A64VAL0-0.045-0.00333.5800.0010.0010.0000.0000.0000.000
64A65TYR00.001-0.02831.9690.0020.0020.0000.0000.0000.000
65A66GLY00.0410.01229.757-0.002-0.0020.0000.0000.0000.000
66A67ARG10.7950.91428.946-0.062-0.0620.0000.0000.0000.000
67A68SER00.0480.00623.898-0.003-0.0030.0000.0000.0000.000
68A69LEU0-0.079-0.03324.805-0.005-0.0050.0000.0000.0000.000
69A70TYR0-0.002-0.02224.6500.0040.0040.0000.0000.0000.000
70A71ALA0-0.038-0.01722.9650.0080.0080.0000.0000.0000.000
71A72GLY00.0570.04020.2950.0360.0360.0000.0000.0000.000
72A73ALA0-0.0060.00118.1740.0000.0000.0000.0000.0000.000
73A74ALA0-0.048-0.02016.8890.0000.0000.0000.0000.0000.000
74A75HIS0-0.095-0.05618.9340.0290.0290.0000.0000.0000.000
75A76GLY00.0540.04422.337-0.032-0.0320.0000.0000.0000.000
76A77PRO0-0.065-0.03424.2650.0050.0050.0000.0000.0000.000
77A78SER0-0.014-0.02826.283-0.005-0.0050.0000.0000.0000.000
78A79PRO00.0440.01623.2390.0010.0010.0000.0000.0000.000
79A80THR00.0060.00023.5620.0010.0010.0000.0000.0000.000
80A81ALA0-0.0320.00525.706-0.016-0.0160.0000.0000.0000.000
81A82GLY00.0410.03621.484-0.012-0.0120.0000.0000.0000.000
82A83GLU-1-0.801-0.91718.8110.2330.2330.0000.0000.0000.000
83A84VAL00.0180.01822.150-0.016-0.0160.0000.0000.0000.000
84A85LEU0-0.079-0.02324.9390.0030.0030.0000.0000.0000.000
85A86ILE00.0120.01426.730-0.006-0.0060.0000.0000.0000.000
86A87MET0-0.076-0.03929.2420.0020.0020.0000.0000.0000.000
87A88LEU00.0560.03430.118-0.004-0.0040.0000.0000.0000.000
88A89GLY00.003-0.01233.6440.0040.0040.0000.0000.0000.000
89A90GLY00.0710.01637.383-0.005-0.0050.0000.0000.0000.000
90A91PRO0-0.006-0.00139.2510.0040.0040.0000.0000.0000.000
91A92ASN00.0020.00041.1620.0020.0020.0000.0000.0000.000
92A93PRO00.027-0.01039.250-0.001-0.0010.0000.0000.0000.000
93A94ALA0-0.0250.00237.8600.0000.0000.0000.0000.0000.000
94A95GLU-1-0.818-0.90636.976-0.039-0.0390.0000.0000.0000.000
95A96VAL0-0.0020.00634.841-0.002-0.0020.0000.0000.0000.000
96A97ARG10.9130.94933.4700.0040.0040.0000.0000.0000.000
97A98ALA00.0660.05632.194-0.001-0.0010.0000.0000.0000.000
98A99GLY00.0310.01131.105-0.006-0.0060.0000.0000.0000.000
99A100LEU0-0.023-0.03829.116-0.003-0.0030.0000.0000.0000.000
100A101ASP-1-0.915-0.95227.579-0.033-0.0330.0000.0000.0000.000
101A102ALA0-0.033-0.01426.540-0.009-0.0090.0000.0000.0000.000
102A103MET0-0.045-0.01625.055-0.009-0.0090.0000.0000.0000.000
103A104ILE00.0250.00723.144-0.001-0.0010.0000.0000.0000.000
104A105ALA00.0010.00721.639-0.006-0.0060.0000.0000.0000.000
105A106HIS0-0.030-0.02120.603-0.031-0.0310.0000.0000.0000.000
106A107ILE0-0.0100.00118.921-0.013-0.0130.0000.0000.0000.000
107A108GLU-1-0.945-0.96917.175-0.029-0.0290.0000.0000.0000.000
108A109ASN0-0.110-0.06515.933-0.074-0.0740.0000.0000.0000.000
109A110GLY00.0500.02316.814-0.011-0.0110.0000.0000.0000.000
110A111ALA0-0.049-0.00315.781-0.057-0.0570.0000.0000.0000.000
111A112ALA0-0.002-0.02011.8600.0480.0480.0000.0000.0000.000
112A113PHE00.0410.02311.719-0.094-0.0940.0000.0000.0000.000
113A114GLN0-0.073-0.0448.1420.1310.1310.0000.0000.0000.000
114A115TRP00.0330.0273.9220.0790.4720.001-0.067-0.3280.000
115A116ALA0-0.011-0.0176.616-0.889-0.8890.0000.0000.0000.000
116A117ASN0-0.012-0.0545.849-0.002-0.0020.0000.0000.0000.000
117A118ASP-1-0.845-0.9262.075-2.585-0.6203.390-2.973-2.381-0.016
118A119ALA0-0.079-0.0363.1062.1942.1040.0030.548-0.462-0.002
119A120GLN0-0.057-0.0411.879-10.747-18.94116.586-4.576-3.8160.030
120A121ASP-1-0.875-0.8925.9800.6210.6210.0000.0000.0000.000
121A122THR0-0.018-0.0198.622-0.336-0.3360.0000.0000.0000.000
122A123ALA0-0.0130.0048.8850.0510.0510.0000.0000.0000.000
123A124PHE0-0.020-0.0189.195-0.014-0.0140.0000.0000.0000.000
124A125LEU0-0.0010.00912.478-0.068-0.0680.0000.0000.0000.000
125A126ALA00.0350.02114.8400.0380.0380.0000.0000.0000.000
126A127HIS00.0020.00116.209-0.096-0.0960.0000.0000.0000.000
127A128VAL00.000-0.00618.2810.0370.0370.0000.0000.0000.000
128A129VAL0-0.0010.01521.549-0.009-0.0090.0000.0000.0000.000
129A130SER0-0.021-0.02624.0550.0150.0150.0000.0000.0000.000
130A131ARG10.9240.96626.3140.1060.1060.0000.0000.0000.000
131A132THR00.0140.01327.9190.0040.0040.0000.0000.0000.000
132A133GLY00.0260.00529.5950.0020.0020.0000.0000.0000.000
133A134SER0-0.0100.00331.6380.0040.0040.0000.0000.0000.000
134A135TYR00.0180.01827.3710.0050.0050.0000.0000.0000.000
135A136LEU00.0500.01325.2260.0040.0040.0000.0000.0000.000
136A137SER0-0.091-0.05929.7570.0030.0030.0000.0000.0000.000
137A138SER0-0.023-0.01932.9640.0050.0050.0000.0000.0000.000
138A139THR0-0.080-0.04630.8800.0070.0070.0000.0000.0000.000
139A140ALA0-0.011-0.01133.439-0.005-0.0050.0000.0000.0000.000
140A141GLY00.0190.00934.4820.0000.0000.0000.0000.0000.000
141A142ILE0-0.041-0.02029.277-0.007-0.0070.0000.0000.0000.000
142A143THR00.006-0.00533.4750.0080.0080.0000.0000.0000.000
143A144LEU0-0.043-0.01333.992-0.007-0.0070.0000.0000.0000.000
144A145GLY0-0.047-0.02633.1790.0000.0000.0000.0000.0000.000
145A146ASP-1-0.861-0.91432.393-0.096-0.0960.0000.0000.0000.000
146A147PRO0-0.043-0.02827.723-0.003-0.0030.0000.0000.0000.000
147A148MET0-0.0020.00924.3670.0150.0150.0000.0000.0000.000
148A149ALA0-0.053-0.02022.203-0.021-0.0210.0000.0000.0000.000
149A150TYR0-0.041-0.06120.4710.0170.0170.0000.0000.0000.000
150A151LEU0-0.021-0.01519.103-0.033-0.0330.0000.0000.0000.000
151A152VAL00.0180.01117.4680.0290.0290.0000.0000.0000.000
152A153ALA00.0180.00916.083-0.026-0.0260.0000.0000.0000.000
153A154PRO00.0610.03914.833-0.004-0.0040.0000.0000.0000.000
154A155PRO00.004-0.00517.890-0.034-0.0340.0000.0000.0000.000
155A156LEU0-0.0190.00519.478-0.024-0.0240.0000.0000.0000.000
156A157GLU-1-0.800-0.92214.6680.1240.1240.0000.0000.0000.000
157A158ALA00.0000.00817.914-0.042-0.0420.0000.0000.0000.000
158A159THR0-0.037-0.03320.056-0.021-0.0210.0000.0000.0000.000
159A160TYR0-0.063-0.02419.025-0.001-0.0010.0000.0000.0000.000
160A161GLY00.0810.02519.458-0.018-0.0180.0000.0000.0000.000
161A162ILE0-0.033-0.01620.331-0.021-0.0210.0000.0000.0000.000
162A163ASP-1-0.841-0.90323.373-0.084-0.0840.0000.0000.0000.000
163A164ALA00.0260.00521.318-0.006-0.0060.0000.0000.0000.000
164A165ALA0-0.023-0.00121.780-0.016-0.0160.0000.0000.0000.000
165A166LEU0-0.026-0.01523.350-0.005-0.0050.0000.0000.0000.000
166A167LYS10.7850.88626.2410.0860.0860.0000.0000.0000.000
167A168SER0-0.098-0.04023.212-0.009-0.0090.0000.0000.0000.000
168A169ALA0-0.023-0.02425.026-0.011-0.0110.0000.0000.0000.000
169A170ASP-1-0.958-0.97026.969-0.102-0.1020.0000.0000.0000.000
170A171VAL0-0.036-0.02526.415-0.004-0.0040.0000.0000.0000.000
171A172GLN0-0.027-0.00929.6850.0090.0090.0000.0000.0000.000
172A173LEU00.0090.00127.813-0.007-0.0070.0000.0000.0000.000
173A174ALA0-0.0360.00029.7550.0070.0070.0000.0000.0000.000
174A175THR0-0.026-0.01828.8270.0090.0090.0000.0000.0000.000
175A176TYR00.0330.00625.405-0.005-0.0050.0000.0000.0000.000
176A177VAL00.0040.01326.1080.0070.0070.0000.0000.0000.000
177A178PRO00.0180.01425.8950.0030.0030.0000.0000.0000.000
178A179PRO0-0.0370.02023.7060.0070.0070.0000.0000.0000.000
179A180PRO0-0.061-0.03424.714-0.003-0.0030.0000.0000.0000.000
180A181SER00.0940.04322.886-0.006-0.0060.0000.0000.0000.000
181A182GLU-1-0.827-0.91925.4510.0840.0840.0000.0000.0000.000
182A183THR00.0390.01320.4590.0130.0130.0000.0000.0000.000
183A184ASN0-0.111-0.04420.7980.0150.0150.0000.0000.0000.000
184A185TYR00.0310.02315.0710.0220.0220.0000.0000.0000.000
185A186SER0-0.075-0.04620.432-0.013-0.0130.0000.0000.0000.000
186A187ALA00.0510.00720.969-0.008-0.0080.0000.0000.0000.000
187A188ALA0-0.004-0.00622.8970.0060.0060.0000.0000.0000.000
188A189PHE0-0.0240.00423.735-0.017-0.0170.0000.0000.0000.000
189A190LEU00.0040.00024.3900.0080.0080.0000.0000.0000.000
190A191THR00.0730.02227.169-0.011-0.0110.0000.0000.0000.000
191A192GLY00.0820.04129.7510.0000.0000.0000.0000.0000.000
192A193SER00.0090.00130.149-0.006-0.0060.0000.0000.0000.000
193A194GLN00.0700.02625.529-0.020-0.0200.0000.0000.0000.000
194A195ALA00.000-0.00325.165-0.017-0.0170.0000.0000.0000.000
195A196ALA00.0210.01624.597-0.018-0.0180.0000.0000.0000.000
196A197CYS00.0350.03024.279-0.003-0.0030.0000.0000.0000.000
197A198LYS10.9100.94815.7670.4920.4920.0000.0000.0000.000
198A199ALA0-0.016-0.00820.050-0.033-0.0330.0000.0000.0000.000
199A200ALA00.0430.02520.788-0.017-0.0170.0000.0000.0000.000
200A201CYS0-0.038-0.02017.7000.0050.0050.0000.0000.0000.000
201A202ASN0-0.0020.00516.161-0.065-0.0650.0000.0000.0000.000
202A203ALA00.0730.04316.467-0.029-0.0290.0000.0000.0000.000
203A204PHE0-0.037-0.00916.3570.0110.0110.0000.0000.0000.000
204A205THR0-0.006-0.02611.8760.0060.0060.0000.0000.0000.000
205A206ASP-1-0.922-0.95713.439-0.531-0.5310.0000.0000.0000.000
206A207ALA0-0.021-0.00115.0620.0280.0280.0000.0000.0000.000
207A208VAL0-0.001-0.00712.0700.0500.0500.0000.0000.0000.000
208A209LEU00.002-0.0018.6690.0430.0430.0000.0000.0000.000
209A210GLU-1-0.973-1.00011.725-0.126-0.1260.0000.0000.0000.000
210A211ILE0-0.030-0.00314.6060.0480.0480.0000.0000.0000.000
211A212ALA00.0020.0049.6580.0670.0670.0000.0000.0000.000
212A213ARG10.8680.94610.2620.4970.4970.0000.0000.0000.000
213A214ASN0-0.059-0.03112.0360.0780.0780.0000.0000.0000.000
214A215PRO00.0420.03814.052-0.026-0.0260.0000.0000.0000.000
215A216ILE0-0.050-0.03016.723-0.013-0.0130.0000.0000.0000.000
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