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: 3J34L

Calculation Name: 2I6X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I6X

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MWA6

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2533571.767234
FMO2-HF: Nuclear repulsion 2449189.754446
FMO2-HF: Total energy -84382.012788
FMO2-MP2: Total energy -84627.529257


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-8.061-2.4110.404-2.58-3.472-0.007
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004
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].
3A2ILE0-0.0190.0132.837-0.6691.7050.060-1.212-1.2210.002
4A3ARG10.8970.9433.3730.9411.7740.060-0.318-0.575-0.002
5A4ASN0-0.031-0.0355.5250.5770.5770.0000.0000.0000.000
6A5ILE00.0140.0228.064-0.139-0.1390.0000.0000.0000.000
7A6VAL0-0.021-0.01410.9890.0940.0940.0000.0000.0000.000
8A7PHE00.0200.00413.144-0.015-0.0150.0000.0000.0000.000
9A8ASP-1-0.736-0.87417.139-0.195-0.1950.0000.0000.0000.000
10A9LEU0-0.044-0.03620.6070.0080.0080.0000.0000.0000.000
11A10GLY0-0.015-0.01623.2600.0100.0100.0000.0000.0000.000
12A11GLY00.0840.05724.488-0.013-0.0130.0000.0000.0000.000
13A12VAL0-0.056-0.02718.3850.0060.0060.0000.0000.0000.000
14A13LEU0-0.035-0.03118.5840.0110.0110.0000.0000.0000.000
15A14ILE0-0.049-0.02622.3120.0190.0190.0000.0000.0000.000
16A15HIS0-0.080-0.01926.099-0.014-0.0140.0000.0000.0000.000
17A16LEU0-0.024-0.03527.8030.0070.0070.0000.0000.0000.000
18A17ASN00.0870.03030.5740.0010.0010.0000.0000.0000.000
19A18ARG10.9650.97734.2070.0910.0910.0000.0000.0000.000
20A19GLU-1-0.887-0.94135.942-0.073-0.0730.0000.0000.0000.000
21A20GLU-1-0.815-0.87837.865-0.045-0.0450.0000.0000.0000.000
22A21SER0-0.012-0.02737.3390.0020.0020.0000.0000.0000.000
23A22ILE0-0.011-0.01039.3560.0030.0030.0000.0000.0000.000
24A23ARG10.8350.91141.7170.0490.0490.0000.0000.0000.000
25A24ARG10.8160.90039.8190.0540.0540.0000.0000.0000.000
26A25PHE00.0790.01639.3700.0030.0030.0000.0000.0000.000
27A26LYS10.9340.98344.6090.0560.0560.0000.0000.0000.000
28A27ALA0-0.043-0.01047.2940.0020.0020.0000.0000.0000.000
29A28ILE0-0.060-0.02245.0230.0030.0030.0000.0000.0000.000
30A29GLY0-0.070-0.04649.2430.0000.0000.0000.0000.0000.000
31A30VAL00.0300.02344.9330.0000.0000.0000.0000.0000.000
32A31ALA0-0.016-0.02046.895-0.001-0.0010.0000.0000.0000.000
33A32ASP-1-0.912-0.93947.485-0.055-0.0550.0000.0000.0000.000
34A33ILE0-0.044-0.02641.215-0.003-0.0030.0000.0000.0000.000
35A34GLU-1-0.950-0.98341.476-0.070-0.0700.0000.0000.0000.000
36A35GLU-1-0.904-0.96541.153-0.069-0.0690.0000.0000.0000.000
37A36MET0-0.064-0.02141.784-0.004-0.0040.0000.0000.0000.000
38A37LEU0-0.030-0.01837.120-0.004-0.0040.0000.0000.0000.000
39A38ASP-1-0.887-0.93936.882-0.099-0.0990.0000.0000.0000.000
40A39PRO0-0.044-0.01533.730-0.001-0.0010.0000.0000.0000.000
41A40TYR00.0330.02435.850-0.003-0.0030.0000.0000.0000.000
42A41LEU0-0.041-0.00636.0440.0000.0000.0000.0000.0000.000
43A42GLN0-0.053-0.02334.210-0.010-0.0100.0000.0000.0000.000
44A43LYS10.9370.94737.8110.0860.0860.0000.0000.0000.000
45A44GLY00.0700.03540.4110.0000.0000.0000.0000.0000.000
46A45LEU00.0100.00340.141-0.003-0.0030.0000.0000.0000.000
47A46PHE00.0750.02637.4310.0000.0000.0000.0000.0000.000
48A47LEU00.0490.03733.859-0.003-0.0030.0000.0000.0000.000
49A48ASP-1-0.870-0.93435.893-0.095-0.0950.0000.0000.0000.000
50A49LEU0-0.033-0.00836.193-0.001-0.0010.0000.0000.0000.000
51A50GLU-1-0.914-0.95631.575-0.135-0.1350.0000.0000.0000.000
52A51SER0-0.0110.00932.089-0.006-0.0060.0000.0000.0000.000
53A52GLY00.0500.04033.538-0.003-0.0030.0000.0000.0000.000
54A53ARG10.8440.94635.4030.0970.0970.0000.0000.0000.000
55A54LYS10.7800.88238.3320.0840.0840.0000.0000.0000.000
56A55SER00.0430.02038.930-0.002-0.0020.0000.0000.0000.000
57A56GLU-1-0.725-0.84239.041-0.061-0.0610.0000.0000.0000.000
58A57GLU-1-0.901-0.95440.646-0.051-0.0510.0000.0000.0000.000
59A58GLU-1-0.879-0.93442.953-0.070-0.0700.0000.0000.0000.000
60A59PHE0-0.001-0.00641.0590.0010.0010.0000.0000.0000.000
61A60ARG10.8620.92643.3160.0570.0570.0000.0000.0000.000
62A61THR0-0.034-0.00945.4330.0040.0040.0000.0000.0000.000
63A62GLU-1-0.891-0.95046.052-0.057-0.0570.0000.0000.0000.000
64A63LEU00.0020.00243.9660.0010.0010.0000.0000.0000.000
65A64SER00.0170.00347.1450.0030.0030.0000.0000.0000.000
66A65ARG10.7890.88050.3270.0550.0550.0000.0000.0000.000
67A66TYR0-0.053-0.02947.7690.0010.0010.0000.0000.0000.000
68A67ILE0-0.0040.00348.9310.0010.0010.0000.0000.0000.000
69A68GLY0-0.049-0.00251.8830.0020.0020.0000.0000.0000.000
70A69LYS10.8950.92552.6330.0430.0430.0000.0000.0000.000
71A70GLU-1-0.940-0.96151.976-0.044-0.0440.0000.0000.0000.000
72A71LEU0-0.0220.00446.7870.0010.0010.0000.0000.0000.000
73A72THR00.0470.01548.026-0.001-0.0010.0000.0000.0000.000
74A73TYR0-0.032-0.06738.4420.0000.0000.0000.0000.0000.000
75A74GLN0-0.006-0.00743.160-0.001-0.0010.0000.0000.0000.000
76A75GLN00.0540.02243.740-0.001-0.0010.0000.0000.0000.000
77A76VAL00.0470.03940.746-0.001-0.0010.0000.0000.0000.000
78A77TYR00.0050.00636.774-0.004-0.0040.0000.0000.0000.000
79A78ASP-1-0.947-0.97539.054-0.048-0.0480.0000.0000.0000.000
80A79ALA00.0190.00940.4990.0000.0000.0000.0000.0000.000
81A80LEU00.0040.00536.221-0.002-0.0020.0000.0000.0000.000
82A81LEU0-0.011-0.01534.754-0.004-0.0040.0000.0000.0000.000
83A82GLY0-0.050-0.01135.9450.0020.0020.0000.0000.0000.000
84A83PHE0-0.011-0.01232.7960.0000.0000.0000.0000.0000.000
85A84LEU0-0.059-0.02430.458-0.005-0.0050.0000.0000.0000.000
86A85GLU-1-0.937-0.94931.696-0.056-0.0560.0000.0000.0000.000
87A86GLU-1-0.922-0.96627.787-0.047-0.0470.0000.0000.0000.000
88A87ILE0-0.027-0.00326.684-0.011-0.0110.0000.0000.0000.000
89A88SER00.0360.01523.0720.0100.0100.0000.0000.0000.000
90A89ALA00.0380.00523.429-0.005-0.0050.0000.0000.0000.000
91A90GLU-1-0.921-0.96221.448-0.026-0.0260.0000.0000.0000.000
92A91LYS10.8730.94718.9770.1310.1310.0000.0000.0000.000
93A92PHE00.010-0.00518.378-0.018-0.0180.0000.0000.0000.000
94A93ASP-1-0.896-0.94019.262-0.002-0.0020.0000.0000.0000.000
95A94TYR0-0.031-0.02010.9920.0310.0310.0000.0000.0000.000
96A95ILE00.0030.02314.6240.0050.0050.0000.0000.0000.000
97A96ASP-1-0.871-0.93414.954-0.007-0.0070.0000.0000.0000.000
98A97SER0-0.131-0.08614.3990.0290.0290.0000.0000.0000.000
99A98LEU0-0.012-0.0129.4260.0400.0400.0000.0000.0000.000
100A99ARG10.8580.94310.6840.1040.1040.0000.0000.0000.000
101A100PRO0-0.052-0.02812.147-0.026-0.0260.0000.0000.0000.000
102A101ASP-1-0.954-0.9676.9060.7010.7010.0000.0000.0000.000
103A102TYR0-0.042-0.0173.711-0.0160.1660.000-0.020-0.1620.000
104A103ARG10.8400.9388.3660.5640.5640.0000.0000.0000.000
105A104LEU0-0.0010.00610.914-0.111-0.1110.0000.0000.0000.000
106A105PHE00.002-0.01612.4840.0530.0530.0000.0000.0000.000
107A106LEU00.0090.02216.280-0.010-0.0100.0000.0000.0000.000
108A107LEU00.004-0.01019.3440.0030.0030.0000.0000.0000.000
109A108SER0-0.028-0.00721.0340.0050.0050.0000.0000.0000.000
110A109ASN00.0240.00324.212-0.004-0.0040.0000.0000.0000.000
111A110THR00.0310.01327.6460.0100.0100.0000.0000.0000.000
112A111ASN00.0780.02429.8180.0070.0070.0000.0000.0000.000
113A112PRO00.044-0.01332.5700.0000.0000.0000.0000.0000.000
114A113TYR0-0.014-0.01134.6660.0020.0020.0000.0000.0000.000
115A114VAL00.0180.00629.6690.0040.0040.0000.0000.0000.000
116A115LEU00.0110.00827.8640.0010.0010.0000.0000.0000.000
117A116ASP-1-0.832-0.88631.232-0.067-0.0670.0000.0000.0000.000
118A117LEU0-0.077-0.02731.8210.0050.0050.0000.0000.0000.000
119A118ALA00.018-0.00227.6620.0050.0050.0000.0000.0000.000
120A119MET0-0.020-0.00227.7650.0000.0000.0000.0000.0000.000
121A120SER0-0.044-0.01630.4710.0090.0090.0000.0000.0000.000
122A121PRO0-0.007-0.02031.401-0.001-0.0010.0000.0000.0000.000
123A122ARG10.8640.91333.0320.0320.0320.0000.0000.0000.000
124A123PHE00.0240.04125.2850.0000.0000.0000.0000.0000.000
125A124LEU00.0840.03924.7530.0000.0000.0000.0000.0000.000
126A125PRO0-0.0040.00228.3830.0050.0050.0000.0000.0000.000
127A126SER0-0.020-0.01626.0270.0030.0030.0000.0000.0000.000
128A127GLY0-0.021-0.00229.1500.0050.0050.0000.0000.0000.000
129A128ARG10.7720.88020.4160.0340.0340.0000.0000.0000.000
130A129THR00.0300.01826.819-0.005-0.0050.0000.0000.0000.000
131A130LEU00.0570.02823.2650.0000.0000.0000.0000.0000.000
132A131ASP-1-0.900-0.97522.605-0.133-0.1330.0000.0000.0000.000
133A132SER0-0.064-0.02321.931-0.002-0.0020.0000.0000.0000.000
134A133PHE0-0.011-0.01018.7620.0150.0150.0000.0000.0000.000
135A134PHE0-0.031-0.00916.719-0.013-0.0130.0000.0000.0000.000
136A135ASP-1-0.889-0.95314.144-0.199-0.1990.0000.0000.0000.000
137A136LYS10.8590.92517.4030.2060.2060.0000.0000.0000.000
138A137VAL00.0260.01419.240-0.027-0.0270.0000.0000.0000.000
139A138TYR0-0.063-0.06718.395-0.001-0.0010.0000.0000.0000.000
140A139ALA00.0340.01123.102-0.006-0.0060.0000.0000.0000.000
141A140SER00.045-0.01526.3880.0070.0070.0000.0000.0000.000
142A141CYS0-0.065-0.01328.6090.0040.0040.0000.0000.0000.000
143A142GLN0-0.074-0.05027.8960.0010.0010.0000.0000.0000.000
144A143MET0-0.0360.00124.060-0.001-0.0010.0000.0000.0000.000
145A144GLY0-0.0300.00529.5370.0010.0010.0000.0000.0000.000
146A145LYS10.7890.88927.8180.1780.1780.0000.0000.0000.000
147A146TYR0-0.013-0.02228.4080.0040.0040.0000.0000.0000.000
148A147LYS10.7860.93322.2440.2390.2390.0000.0000.0000.000
149A148PRO00.0260.00225.7620.0160.0160.0000.0000.0000.000
150A149ASN00.0060.00626.460-0.011-0.0110.0000.0000.0000.000
151A150GLU-1-0.865-0.95524.538-0.276-0.2760.0000.0000.0000.000
152A151ASP-1-0.909-0.96024.658-0.203-0.2030.0000.0000.0000.000
153A152ILE0-0.0080.00023.994-0.008-0.0080.0000.0000.0000.000
154A153PHE00.0280.00119.277-0.006-0.0060.0000.0000.0000.000
155A154LEU0-0.010-0.01020.622-0.026-0.0260.0000.0000.0000.000
156A155GLU-1-0.862-0.91422.332-0.192-0.1920.0000.0000.0000.000
157A156MET00.0250.02517.2640.0050.0050.0000.0000.0000.000
158A157ILE0-0.0180.00917.080-0.016-0.0160.0000.0000.0000.000
159A158ALA0-0.047-0.02118.437-0.010-0.0100.0000.0000.0000.000
160A159ASP-1-0.864-0.89720.874-0.212-0.2120.0000.0000.0000.000
161A160SER0-0.027-0.01315.926-0.013-0.0130.0000.0000.0000.000
162A161GLY00.0220.00215.995-0.007-0.0070.0000.0000.0000.000
163A162MET0-0.081-0.01712.513-0.073-0.0730.0000.0000.0000.000
164A163LYS10.9850.98310.9300.9520.9520.0000.0000.0000.000
165A164PRO00.0580.04411.541-0.162-0.1620.0000.0000.0000.000
166A165GLU-1-0.852-0.92110.568-1.017-1.0170.0000.0000.0000.000
167A166GLU-1-0.979-0.9867.268-2.134-2.1340.0000.0000.0000.000
168A167THR0-0.044-0.0477.634-0.112-0.1120.0000.0000.0000.000
169A168LEU0-0.0030.0098.8030.0360.0360.0000.0000.0000.000
170A169PHE0-0.044-0.03510.5650.0960.0960.0000.0000.0000.000
171A170ILE0-0.006-0.01112.3030.0150.0150.0000.0000.0000.000
172A171ASP-1-0.708-0.86716.097-0.221-0.2210.0000.0000.0000.000
173A172ASP-1-0.798-0.89519.841-0.196-0.1960.0000.0000.0000.000
174A173GLY00.0080.00222.7280.0170.0170.0000.0000.0000.000
175A174PRO0-0.003-0.01223.498-0.022-0.0220.0000.0000.0000.000
176A175ALA0-0.042-0.02324.293-0.015-0.0150.0000.0000.0000.000
177A176ASN00.007-0.01122.442-0.004-0.0040.0000.0000.0000.000
178A177VAL00.0710.02919.107-0.027-0.0270.0000.0000.0000.000
179A178ALA0-0.025-0.01120.259-0.029-0.0290.0000.0000.0000.000
180A179THR0-0.069-0.05822.463-0.006-0.0060.0000.0000.0000.000
181A180ALA00.0150.01617.334-0.012-0.0120.0000.0000.0000.000
182A181GLU-1-0.849-0.90516.916-0.558-0.5580.0000.0000.0000.000
183A182ARG10.8710.94918.8680.2430.2430.0000.0000.0000.000
184A183LEU0-0.051-0.02919.4350.0040.0040.0000.0000.0000.000
185A184GLY0-0.0260.00016.655-0.021-0.0210.0000.0000.0000.000
186A185PHE0-0.063-0.04013.589-0.097-0.0970.0000.0000.0000.000
187A186HIS00.0450.0409.3440.1840.1840.0000.0000.0000.000
188A187THR0-0.081-0.06312.3270.0500.0500.0000.0000.0000.000
189A188TYR0-0.071-0.04913.836-0.016-0.0160.0000.0000.0000.000
190A189CYS0-0.077-0.02615.7080.0150.0150.0000.0000.0000.000
191A190PRO0-0.047-0.01018.1880.0160.0160.0000.0000.0000.000
192A191ASP-1-0.850-0.93020.545-0.141-0.1410.0000.0000.0000.000
193A192ASN00.0490.00423.716-0.003-0.0030.0000.0000.0000.000
194A193GLY00.0020.01425.1350.0100.0100.0000.0000.0000.000
195A194GLU-1-0.886-0.92320.403-0.157-0.1570.0000.0000.0000.000
196A195ASN00.004-0.01320.141-0.019-0.0190.0000.0000.0000.000
197A196TRP00.0400.01114.9360.0040.0040.0000.0000.0000.000
198A197ILE00.0530.03515.258-0.029-0.0290.0000.0000.0000.000
199A198PRO0-0.0440.00514.298-0.007-0.0070.0000.0000.0000.000
200A199ALA00.0070.00013.9150.0100.0100.0000.0000.0000.000
201A200ILE00.0730.03310.805-0.049-0.0490.0000.0000.0000.000
202A201THR0-0.031-0.0479.729-0.064-0.0640.0000.0000.0000.000
203A202ARG10.8420.9109.3090.1590.1590.0000.0000.0000.000
204A203LEU00.0100.0118.7260.0450.0450.0000.0000.0000.000
205A204LEU00.0160.0155.216-0.261-0.2610.0000.0000.0000.000
206A205ARG10.8850.9453.982-0.583-0.3320.000-0.044-0.2070.000
207A206GLU-1-0.977-0.9675.534-0.413-0.4130.0000.0000.0000.000
208A207GLN00.0270.0092.749-4.464-2.4540.284-0.986-1.307-0.007