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: 98N22

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2539647.220948
FMO2-HF: Nuclear repulsion 2455263.602447
FMO2-HF: Total energy -84383.618501
FMO2-MP2: Total energy -84629.079869


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.
-13.278-6.9565.53-5.233-6.617-0.004
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 : 0.020 / q_NPA : 0.005
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].
3A2ILE0-0.0040.0072.992-0.2681.9960.023-1.146-1.1400.003
4A3ARG10.8070.8713.5201.7602.3930.039-0.233-0.439-0.001
5A4ASN0-0.024-0.0135.8240.6000.6000.0000.0000.0000.000
6A5ILE00.0110.0128.194-0.147-0.1470.0000.0000.0000.000
7A6VAL0-0.023-0.01211.1860.0910.0910.0000.0000.0000.000
8A7PHE00.0590.03013.221-0.019-0.0190.0000.0000.0000.000
9A8ASP-1-0.700-0.81017.460-0.209-0.2090.0000.0000.0000.000
10A9LEU0-0.014-0.02521.0310.0030.0030.0000.0000.0000.000
11A10GLY0-0.008-0.01523.6010.0130.0130.0000.0000.0000.000
12A11GLY00.0790.05824.108-0.017-0.0170.0000.0000.0000.000
13A12VAL0-0.056-0.02818.5540.0070.0070.0000.0000.0000.000
14A13LEU0-0.022-0.01918.8490.0090.0090.0000.0000.0000.000
15A14ILE0-0.039-0.01222.4070.0180.0180.0000.0000.0000.000
16A15HIS0-0.058-0.02326.245-0.011-0.0110.0000.0000.0000.000
17A16LEU0-0.019-0.01528.0860.0060.0060.0000.0000.0000.000
18A17ASN0-0.022-0.01730.5690.0020.0020.0000.0000.0000.000
19A18ARG10.8910.92534.2550.0910.0910.0000.0000.0000.000
20A19GLU-1-0.843-0.92435.986-0.080-0.0800.0000.0000.0000.000
21A20GLU-1-0.741-0.81137.809-0.051-0.0510.0000.0000.0000.000
22A21SER0-0.041-0.02837.2350.0020.0020.0000.0000.0000.000
23A22ILE00.004-0.00739.3000.0040.0040.0000.0000.0000.000
24A23ARG10.7950.86841.7180.0550.0550.0000.0000.0000.000
25A24ARG10.7750.87240.6640.0610.0610.0000.0000.0000.000
26A25PHE00.0830.01439.5280.0030.0030.0000.0000.0000.000
27A26LYS10.8310.92544.5930.0640.0640.0000.0000.0000.000
28A27ALA0-0.055-0.01547.2860.0020.0020.0000.0000.0000.000
29A28ILE0-0.023-0.00645.2000.0030.0030.0000.0000.0000.000
30A29GLY0-0.018-0.00649.1510.0010.0010.0000.0000.0000.000
31A30VAL0-0.0040.01345.2390.0000.0000.0000.0000.0000.000
32A31ALA0-0.002-0.00846.940-0.002-0.0020.0000.0000.0000.000
33A32ASP-1-0.801-0.88847.563-0.060-0.0600.0000.0000.0000.000
34A33ILE0-0.048-0.02241.432-0.003-0.0030.0000.0000.0000.000
35A34GLU-1-0.825-0.90241.690-0.075-0.0750.0000.0000.0000.000
36A35GLU-1-0.928-0.96241.314-0.074-0.0740.0000.0000.0000.000
37A36MET0-0.058-0.02841.496-0.004-0.0040.0000.0000.0000.000
38A37LEU0-0.009-0.00437.235-0.004-0.0040.0000.0000.0000.000
39A38ASP-1-0.873-0.91936.954-0.104-0.1040.0000.0000.0000.000
40A39PRO00.002-0.01633.748-0.002-0.0020.0000.0000.0000.000
41A40TYR0-0.042-0.00435.751-0.004-0.0040.0000.0000.0000.000
42A41LEU0-0.0270.00535.9820.0020.0020.0000.0000.0000.000
43A42GLN0-0.016-0.01334.211-0.011-0.0110.0000.0000.0000.000
44A43LYS10.8920.93638.0950.0890.0890.0000.0000.0000.000
45A44GLY00.0730.03741.2610.0010.0010.0000.0000.0000.000
46A45LEU0-0.006-0.00240.428-0.005-0.0050.0000.0000.0000.000
47A46PHE00.0930.03137.671-0.001-0.0010.0000.0000.0000.000
48A47LEU00.0650.05134.236-0.004-0.0040.0000.0000.0000.000
49A48ASP-1-0.824-0.87136.183-0.101-0.1010.0000.0000.0000.000
50A49LEU0-0.038-0.01336.264-0.002-0.0020.0000.0000.0000.000
51A50GLU-1-0.862-0.92431.617-0.150-0.1500.0000.0000.0000.000
52A51SER0-0.016-0.02832.202-0.007-0.0070.0000.0000.0000.000
53A52GLY00.0280.02233.721-0.004-0.0040.0000.0000.0000.000
54A53ARG10.7740.88635.7500.1040.1040.0000.0000.0000.000
55A54LYS10.8050.90038.6000.0900.0900.0000.0000.0000.000
56A55SER00.005-0.02839.090-0.003-0.0030.0000.0000.0000.000
57A56GLU-1-0.718-0.82939.539-0.068-0.0680.0000.0000.0000.000
58A57GLU-1-0.807-0.89141.117-0.057-0.0570.0000.0000.0000.000
59A58GLU-1-0.842-0.87443.376-0.078-0.0780.0000.0000.0000.000
60A59PHE0-0.013-0.00840.9940.0010.0010.0000.0000.0000.000
61A60ARG10.7910.86943.3260.0650.0650.0000.0000.0000.000
62A61THR0-0.034-0.01445.3610.0040.0040.0000.0000.0000.000
63A62GLU-1-0.832-0.89246.253-0.061-0.0610.0000.0000.0000.000
64A63LEU0-0.0020.00143.5470.0010.0010.0000.0000.0000.000
65A64SER00.010-0.00947.1550.0030.0030.0000.0000.0000.000
66A65ARG10.7380.82750.2890.0600.0600.0000.0000.0000.000
67A66TYR0-0.114-0.07848.7870.0010.0010.0000.0000.0000.000
68A67ILE0-0.019-0.00849.3530.0010.0010.0000.0000.0000.000
69A68GLY0-0.050-0.00752.1800.0020.0020.0000.0000.0000.000
70A69LYS10.8020.87052.3380.0490.0490.0000.0000.0000.000
71A70GLU-1-0.897-0.95451.329-0.052-0.0520.0000.0000.0000.000
72A71LEU0-0.047-0.00946.8860.0010.0010.0000.0000.0000.000
73A72THR00.037-0.00348.253-0.002-0.0020.0000.0000.0000.000
74A73TYR0-0.048-0.06638.5500.0010.0010.0000.0000.0000.000
75A74GLN00.0160.00243.171-0.001-0.0010.0000.0000.0000.000
76A75GLN00.0440.04243.546-0.001-0.0010.0000.0000.0000.000
77A76VAL00.0260.02041.183-0.001-0.0010.0000.0000.0000.000
78A77TYR00.0050.00836.409-0.002-0.0020.0000.0000.0000.000
79A78ASP-1-0.885-0.93738.913-0.058-0.0580.0000.0000.0000.000
80A79ALA00.009-0.00240.061-0.001-0.0010.0000.0000.0000.000
81A80LEU0-0.0190.00435.561-0.003-0.0030.0000.0000.0000.000
82A81LEU00.011-0.00435.098-0.004-0.0040.0000.0000.0000.000
83A82GLY0-0.033-0.00235.6840.0000.0000.0000.0000.0000.000
84A83PHE0-0.002-0.01232.6770.0010.0010.0000.0000.0000.000
85A84LEU0-0.062-0.02530.076-0.005-0.0050.0000.0000.0000.000
86A85GLU-1-0.870-0.90731.954-0.066-0.0660.0000.0000.0000.000
87A86GLU-1-0.845-0.90526.772-0.077-0.0770.0000.0000.0000.000
88A87ILE0-0.0120.00026.547-0.012-0.0120.0000.0000.0000.000
89A88SER00.011-0.04122.9240.0060.0060.0000.0000.0000.000
90A89ALA0-0.017-0.00223.048-0.009-0.0090.0000.0000.0000.000
91A90GLU-1-0.850-0.91721.513-0.056-0.0560.0000.0000.0000.000
92A91LYS10.8490.93318.7410.1420.1420.0000.0000.0000.000
93A92PHE00.0220.00918.087-0.026-0.0260.0000.0000.0000.000
94A93ASP-1-0.915-0.96018.934-0.049-0.0490.0000.0000.0000.000
95A94TYR0-0.052-0.04111.571-0.020-0.0200.0000.0000.0000.000
96A95ILE00.0080.01714.405-0.005-0.0050.0000.0000.0000.000
97A96ASP-1-0.822-0.88514.587-0.087-0.0870.0000.0000.0000.000
98A97SER0-0.127-0.08214.4890.0210.0210.0000.0000.0000.000
99A98LEU00.0150.0089.0130.0350.0350.0000.0000.0000.000
100A99ARG10.8280.90610.6740.1330.1330.0000.0000.0000.000
101A100PRO0-0.084-0.04211.755-0.025-0.0250.0000.0000.0000.000
102A101ASP-1-0.952-0.9666.9200.4260.4260.0000.0000.0000.000
103A102TYR0-0.051-0.0343.670-0.1310.1110.004-0.035-0.2100.000
104A103ARG10.8360.9258.2050.6960.6960.0000.0000.0000.000
105A104LEU0-0.0010.00711.101-0.099-0.0990.0000.0000.0000.000
106A105PHE00.000-0.01313.0660.0540.0540.0000.0000.0000.000
107A106LEU0-0.0080.00416.653-0.009-0.0090.0000.0000.0000.000
108A107LEU00.015-0.00619.3990.0100.0100.0000.0000.0000.000
109A108SER0-0.062-0.04121.2490.0030.0030.0000.0000.0000.000
110A109ASN0-0.007-0.01024.323-0.008-0.0080.0000.0000.0000.000
111A110THR00.0510.02127.6630.0110.0110.0000.0000.0000.000
112A111ASN00.0720.01729.8420.0070.0070.0000.0000.0000.000
113A112PRO00.0500.00632.8460.0000.0000.0000.0000.0000.000
114A113TYR0-0.001-0.02334.5450.0000.0000.0000.0000.0000.000
115A114VAL00.0270.01529.7440.0040.0040.0000.0000.0000.000
116A115LEU0-0.0030.00128.309-0.001-0.0010.0000.0000.0000.000
117A116ASP-1-0.838-0.90231.279-0.082-0.0820.0000.0000.0000.000
118A117LEU0-0.054-0.01831.8690.0050.0050.0000.0000.0000.000
119A118ALA00.0290.02727.7520.0040.0040.0000.0000.0000.000
120A119MET0-0.019-0.00327.712-0.004-0.0040.0000.0000.0000.000
121A120SER0-0.013-0.00830.6310.0090.0090.0000.0000.0000.000
122A121PRO00.004-0.00831.669-0.002-0.0020.0000.0000.0000.000
123A122ARG10.7950.86633.0100.0490.0490.0000.0000.0000.000
124A123PHE00.0330.05724.7740.0010.0010.0000.0000.0000.000
125A124LEU00.0870.04724.4880.0000.0000.0000.0000.0000.000
126A125PRO0-0.010-0.01628.3830.0050.0050.0000.0000.0000.000
127A126SER0-0.014-0.00225.7630.0040.0040.0000.0000.0000.000
128A127GLY0-0.029-0.01428.8510.0030.0030.0000.0000.0000.000
129A128ARG10.7350.83820.6340.0750.0750.0000.0000.0000.000
130A129THR00.0270.01427.223-0.004-0.0040.0000.0000.0000.000
131A130LEU00.0500.03022.955-0.002-0.0020.0000.0000.0000.000
132A131ASP-1-0.855-0.95322.684-0.177-0.1770.0000.0000.0000.000
133A132SER0-0.063-0.02621.822-0.006-0.0060.0000.0000.0000.000
134A133PHE0-0.029-0.02119.0520.0140.0140.0000.0000.0000.000
135A134PHE0-0.0050.00016.718-0.020-0.0200.0000.0000.0000.000
136A135ASP-1-0.838-0.91414.188-0.292-0.2920.0000.0000.0000.000
137A136LYS10.8120.88917.7520.2370.2370.0000.0000.0000.000
138A137VAL00.0030.01019.670-0.030-0.0300.0000.0000.0000.000
139A138TYR0-0.076-0.06718.8370.0000.0000.0000.0000.0000.000
140A139ALA00.0380.01523.582-0.006-0.0060.0000.0000.0000.000
141A140SER00.0490.00326.7120.0040.0040.0000.0000.0000.000
142A141CYS0-0.074-0.02428.8760.0050.0050.0000.0000.0000.000
143A142GLN0-0.076-0.04328.6580.0020.0020.0000.0000.0000.000
144A143MET0-0.0280.00624.305-0.002-0.0020.0000.0000.0000.000
145A144GLY0-0.0310.00529.8160.0000.0000.0000.0000.0000.000
146A145LYS10.7500.87228.2270.1880.1880.0000.0000.0000.000
147A146TYR0-0.022-0.04328.8500.0050.0050.0000.0000.0000.000
148A147LYS10.7700.87922.2900.2600.2600.0000.0000.0000.000
149A148PRO00.0240.00726.0850.0150.0150.0000.0000.0000.000
150A149ASN00.0050.01126.672-0.011-0.0110.0000.0000.0000.000
151A150GLU-1-0.803-0.90524.800-0.270-0.2700.0000.0000.0000.000
152A151ASP-1-0.886-0.95124.882-0.220-0.2200.0000.0000.0000.000
153A152ILE00.0030.00224.248-0.008-0.0080.0000.0000.0000.000
154A153PHE00.0330.01219.239-0.007-0.0070.0000.0000.0000.000
155A154LEU0-0.017-0.00921.031-0.026-0.0260.0000.0000.0000.000
156A155GLU-1-0.845-0.91122.669-0.206-0.2060.0000.0000.0000.000
157A156MET00.0250.02717.5610.0030.0030.0000.0000.0000.000
158A157ILE0-0.0370.00817.369-0.016-0.0160.0000.0000.0000.000
159A158ALA0-0.057-0.02818.929-0.010-0.0100.0000.0000.0000.000
160A159ASP-1-0.846-0.87721.631-0.232-0.2320.0000.0000.0000.000
161A160SER00.020-0.00216.396-0.014-0.0140.0000.0000.0000.000
162A161GLY0-0.004-0.00116.231-0.024-0.0240.0000.0000.0000.000
163A162MET0-0.064-0.01512.892-0.077-0.0770.0000.0000.0000.000
164A163LYS10.8290.90110.1331.2231.2230.0000.0000.0000.000
165A164PRO00.0200.03312.273-0.128-0.1280.0000.0000.0000.000
166A165GLU-1-0.781-0.89510.717-1.094-1.0940.0000.0000.0000.000
167A166GLU-1-0.794-0.8517.528-2.032-2.0320.0000.0000.0000.000
168A167THR0-0.019-0.0338.141-0.099-0.0990.0000.0000.0000.000
169A168LEU0-0.0100.0108.8340.0280.0280.0000.0000.0000.000
170A169PHE0-0.019-0.02310.6630.0880.0880.0000.0000.0000.000
171A170ILE0-0.004-0.00912.1220.0170.0170.0000.0000.0000.000
172A171ASP-1-0.739-0.87016.200-0.244-0.2440.0000.0000.0000.000
173A172ASP-1-0.795-0.89619.986-0.204-0.2040.0000.0000.0000.000
174A173GLY00.0380.02422.9070.0180.0180.0000.0000.0000.000
175A174PRO0-0.010-0.02423.996-0.019-0.0190.0000.0000.0000.000
176A175ALA0-0.029-0.01824.487-0.015-0.0150.0000.0000.0000.000
177A176ASN0-0.020-0.02922.7810.0020.0020.0000.0000.0000.000
178A177VAL00.0530.02619.164-0.025-0.0250.0000.0000.0000.000
179A178ALA0-0.007-0.00520.650-0.028-0.0280.0000.0000.0000.000
180A179THR0-0.056-0.05122.8360.0090.0090.0000.0000.0000.000
181A180ALA00.0100.01517.553-0.014-0.0140.0000.0000.0000.000
182A181GLU-1-0.821-0.89216.635-0.561-0.5610.0000.0000.0000.000
183A182ARG10.7160.86418.9400.2550.2550.0000.0000.0000.000
184A183LEU0-0.044-0.02319.8460.0110.0110.0000.0000.0000.000
185A184GLY0-0.021-0.00717.132-0.024-0.0240.0000.0000.0000.000
186A185PHE0-0.040-0.03513.932-0.098-0.0980.0000.0000.0000.000
187A186HIS00.0080.0139.5930.1910.1910.0000.0000.0000.000
188A187THR0-0.093-0.07712.7090.0290.0290.0000.0000.0000.000
189A188TYR0-0.090-0.07813.841-0.019-0.0190.0000.0000.0000.000
190A189CYS0-0.087-0.03515.7040.0150.0150.0000.0000.0000.000
191A190PRO0-0.036-0.00418.1750.0160.0160.0000.0000.0000.000
192A191ASP-1-0.833-0.93220.530-0.133-0.1330.0000.0000.0000.000
193A192ASN00.003-0.00823.760-0.009-0.0090.0000.0000.0000.000
194A193GLY00.0080.00525.0920.0120.0120.0000.0000.0000.000
195A194GLU-1-0.860-0.89919.613-0.185-0.1850.0000.0000.0000.000
196A195ASN0-0.056-0.05020.061-0.025-0.0250.0000.0000.0000.000
197A196TRP00.0270.00415.0540.0020.0020.0000.0000.0000.000
198A197ILE00.0270.03515.323-0.030-0.0300.0000.0000.0000.000
199A198PRO0-0.045-0.01914.157-0.007-0.0070.0000.0000.0000.000
200A199ALA00.0060.00813.7310.0100.0100.0000.0000.0000.000
201A200ILE00.0850.04210.725-0.055-0.0550.0000.0000.0000.000
202A201THR00.0130.0079.576-0.087-0.0870.0000.0000.0000.000
203A202ARG10.8570.9369.8070.2130.2130.0000.0000.0000.000
204A203LEU00.0140.0078.7820.0530.0530.0000.0000.0000.000
205A204LEU00.0140.0135.321-0.295-0.2950.0000.0000.0000.000
206A205ARG10.7990.9013.888-0.753-0.4730.001-0.065-0.2170.000
207A206GLU-1-0.850-0.8935.074-0.564-0.463-0.001-0.017-0.0820.000
208A207GLN0-0.072-0.0532.396-10.186-7.3845.464-3.737-4.529-0.006