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: LNM69

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535483.443891
FMO2-HF: Nuclear repulsion 2451100.381628
FMO2-HF: Total energy -84383.062263
FMO2-MP2: Total energy -84628.573292


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.
-8.552-2.0241.75-3.642-4.637-0.012
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 : -0.002 / 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].
3A2ILE0-0.0190.0072.807-0.8841.7120.063-1.345-1.3140.002
4A3ARG10.8180.8893.4221.6192.4500.057-0.314-0.574-0.002
5A4ASN0-0.030-0.0305.5220.5630.5630.0000.0000.0000.000
6A5ILE00.0160.0218.081-0.136-0.1360.0000.0000.0000.000
7A6VAL0-0.025-0.01610.9730.0880.0880.0000.0000.0000.000
8A7PHE00.0340.01213.002-0.013-0.0130.0000.0000.0000.000
9A8ASP-1-0.665-0.80217.141-0.188-0.1880.0000.0000.0000.000
10A9LEU0-0.043-0.03820.6160.0080.0080.0000.0000.0000.000
11A10GLY0-0.013-0.01423.2640.0090.0090.0000.0000.0000.000
12A11GLY00.0690.04624.509-0.013-0.0130.0000.0000.0000.000
13A12VAL0-0.055-0.02618.3890.0060.0060.0000.0000.0000.000
14A13LEU0-0.019-0.02218.7420.0100.0100.0000.0000.0000.000
15A14ILE0-0.048-0.02722.3300.0180.0180.0000.0000.0000.000
16A15HIS0-0.030-0.01326.117-0.013-0.0130.0000.0000.0000.000
17A16LEU0-0.012-0.02527.8350.0070.0070.0000.0000.0000.000
18A17ASN00.0340.00830.6040.0010.0010.0000.0000.0000.000
19A18ARG10.9780.99034.2410.0850.0850.0000.0000.0000.000
20A19GLU-1-0.860-0.93935.974-0.071-0.0710.0000.0000.0000.000
21A20GLU-1-0.751-0.81137.864-0.043-0.0430.0000.0000.0000.000
22A21SER0-0.018-0.02237.3120.0020.0020.0000.0000.0000.000
23A22ILE0-0.013-0.01239.3770.0030.0030.0000.0000.0000.000
24A23ARG10.7890.86141.7430.0460.0460.0000.0000.0000.000
25A24ARG10.7950.90440.3690.0510.0510.0000.0000.0000.000
26A25PHE00.0670.00439.5320.0020.0020.0000.0000.0000.000
27A26LYS10.8540.93844.6250.0560.0560.0000.0000.0000.000
28A27ALA0-0.045-0.00847.3140.0020.0020.0000.0000.0000.000
29A28ILE0-0.029-0.00845.0860.0020.0020.0000.0000.0000.000
30A29GLY0-0.067-0.04749.2530.0000.0000.0000.0000.0000.000
31A30VAL00.0330.02944.9630.0000.0000.0000.0000.0000.000
32A31ALA0-0.005-0.01146.914-0.001-0.0010.0000.0000.0000.000
33A32ASP-1-0.833-0.89847.563-0.053-0.0530.0000.0000.0000.000
34A33ILE0-0.028-0.02241.278-0.003-0.0030.0000.0000.0000.000
35A34GLU-1-0.879-0.94941.679-0.064-0.0640.0000.0000.0000.000
36A35GLU-1-0.937-0.96741.184-0.067-0.0670.0000.0000.0000.000
37A36MET0-0.064-0.02441.809-0.004-0.0040.0000.0000.0000.000
38A37LEU0-0.029-0.02137.137-0.003-0.0030.0000.0000.0000.000
39A38ASP-1-0.903-0.93536.908-0.096-0.0960.0000.0000.0000.000
40A39PRO0-0.037-0.01533.657-0.001-0.0010.0000.0000.0000.000
41A40TYR00.0370.02135.879-0.002-0.0020.0000.0000.0000.000
42A41LEU0-0.040-0.00835.8910.0010.0010.0000.0000.0000.000
43A42GLN0-0.048-0.01634.169-0.011-0.0110.0000.0000.0000.000
44A43LYS10.9430.95437.8540.0830.0830.0000.0000.0000.000
45A44GLY00.0640.03340.4230.0000.0000.0000.0000.0000.000
46A45LEU0-0.002-0.00340.142-0.004-0.0040.0000.0000.0000.000
47A46PHE00.0860.03237.4860.0000.0000.0000.0000.0000.000
48A47LEU00.0620.04434.032-0.003-0.0030.0000.0000.0000.000
49A48ASP-1-0.832-0.88135.887-0.091-0.0910.0000.0000.0000.000
50A49LEU0-0.032-0.00836.264-0.001-0.0010.0000.0000.0000.000
51A50GLU-1-0.882-0.93331.535-0.132-0.1320.0000.0000.0000.000
52A51SER0-0.021-0.02132.075-0.005-0.0050.0000.0000.0000.000
53A52GLY00.0310.02833.553-0.003-0.0030.0000.0000.0000.000
54A53ARG10.7930.90235.4340.0940.0940.0000.0000.0000.000
55A54LYS10.8010.90138.3600.0800.0800.0000.0000.0000.000
56A55SER00.025-0.02638.967-0.002-0.0020.0000.0000.0000.000
57A56GLU-1-0.715-0.82439.104-0.058-0.0580.0000.0000.0000.000
58A57GLU-1-0.818-0.90840.690-0.049-0.0490.0000.0000.0000.000
59A58GLU-1-0.847-0.88242.897-0.068-0.0680.0000.0000.0000.000
60A59PHE0-0.017-0.01341.0910.0010.0010.0000.0000.0000.000
61A60ARG10.7960.87543.3030.0550.0550.0000.0000.0000.000
62A61THR0-0.028-0.00245.4210.0040.0040.0000.0000.0000.000
63A62GLU-1-0.846-0.90246.069-0.054-0.0540.0000.0000.0000.000
64A63LEU0-0.0040.00543.7090.0010.0010.0000.0000.0000.000
65A64SER00.021-0.00347.1430.0020.0020.0000.0000.0000.000
66A65ARG10.7340.82450.3230.0530.0530.0000.0000.0000.000
67A66TYR0-0.108-0.06848.4770.0000.0000.0000.0000.0000.000
68A67ILE0-0.0080.00349.0900.0010.0010.0000.0000.0000.000
69A68GLY0-0.055-0.00551.8900.0020.0020.0000.0000.0000.000
70A69LYS10.8450.90252.1260.0420.0420.0000.0000.0000.000
71A70GLU-1-0.941-0.95951.649-0.044-0.0440.0000.0000.0000.000
72A71LEU0-0.050-0.00846.6440.0010.0010.0000.0000.0000.000
73A72THR00.0620.00048.043-0.001-0.0010.0000.0000.0000.000
74A73TYR0-0.036-0.06738.4880.0010.0010.0000.0000.0000.000
75A74GLN0-0.005-0.00643.149-0.001-0.0010.0000.0000.0000.000
76A75GLN00.0520.03843.735-0.001-0.0010.0000.0000.0000.000
77A76VAL00.0330.03140.903-0.001-0.0010.0000.0000.0000.000
78A77TYR00.0070.00836.442-0.002-0.0020.0000.0000.0000.000
79A78ASP-1-0.912-0.96739.053-0.047-0.0470.0000.0000.0000.000
80A79ALA00.0140.00240.5060.0000.0000.0000.0000.0000.000
81A80LEU00.0060.00635.763-0.002-0.0020.0000.0000.0000.000
82A81LEU0-0.010-0.02134.967-0.004-0.0040.0000.0000.0000.000
83A82GLY0-0.0330.00035.9560.0010.0010.0000.0000.0000.000
84A83PHE0-0.019-0.01832.8740.0000.0000.0000.0000.0000.000
85A84LEU0-0.060-0.02230.164-0.005-0.0050.0000.0000.0000.000
86A85GLU-1-0.935-0.94331.710-0.051-0.0510.0000.0000.0000.000
87A86GLU-1-0.858-0.91526.859-0.052-0.0520.0000.0000.0000.000
88A87ILE0-0.0080.00126.577-0.011-0.0110.0000.0000.0000.000
89A88SER0-0.012-0.03122.9910.0100.0100.0000.0000.0000.000
90A89ALA0-0.015-0.01023.441-0.005-0.0050.0000.0000.0000.000
91A90GLU-1-0.848-0.91921.929-0.027-0.0270.0000.0000.0000.000
92A91LYS10.8680.94218.9980.1220.1220.0000.0000.0000.000
93A92PHE00.013-0.00318.386-0.017-0.0170.0000.0000.0000.000
94A93ASP-1-0.907-0.94919.252-0.004-0.0040.0000.0000.0000.000
95A94TYR0-0.047-0.03911.652-0.011-0.0110.0000.0000.0000.000
96A95ILE00.0140.01814.6090.0060.0060.0000.0000.0000.000
97A96ASP-1-0.837-0.89914.930-0.015-0.0150.0000.0000.0000.000
98A97SER0-0.137-0.08014.3920.0300.0300.0000.0000.0000.000
99A98LEU0-0.003-0.0059.2890.0400.0400.0000.0000.0000.000
100A99ARG10.8370.91510.7450.0960.0960.0000.0000.0000.000
101A100PRO0-0.061-0.03212.108-0.027-0.0270.0000.0000.0000.000
102A101ASP-1-0.955-0.9697.0460.6360.6360.0000.0000.0000.000
103A102TYR0-0.039-0.0193.833-0.0800.0930.000-0.019-0.1540.000
104A103ARG10.8400.9328.4000.5630.5630.0000.0000.0000.000
105A104LEU0-0.0100.00310.947-0.105-0.1050.0000.0000.0000.000
106A105PHE0-0.005-0.01712.6860.0490.0490.0000.0000.0000.000
107A106LEU00.0080.02216.319-0.009-0.0090.0000.0000.0000.000
108A107LEU00.015-0.00819.3690.0030.0030.0000.0000.0000.000
109A108SER0-0.030-0.02421.0190.0060.0060.0000.0000.0000.000
110A109ASN00.0170.00224.204-0.008-0.0080.0000.0000.0000.000
111A110THR00.0380.01627.6430.0100.0100.0000.0000.0000.000
112A111ASN00.0690.03529.8110.0050.0050.0000.0000.0000.000
113A112PRO00.067-0.00432.5540.0000.0000.0000.0000.0000.000
114A113TYR0-0.017-0.01834.7060.0020.0020.0000.0000.0000.000
115A114VAL00.0270.00929.6660.0040.0040.0000.0000.0000.000
116A115LEU0-0.0020.00628.0850.0010.0010.0000.0000.0000.000
117A116ASP-1-0.821-0.88431.262-0.065-0.0650.0000.0000.0000.000
118A117LEU0-0.082-0.03531.9940.0050.0050.0000.0000.0000.000
119A118ALA00.0160.00927.7270.0050.0050.0000.0000.0000.000
120A119MET0-0.0140.00127.923-0.001-0.0010.0000.0000.0000.000
121A120SER0-0.045-0.01930.5090.0090.0090.0000.0000.0000.000
122A121PRO0-0.006-0.02131.464-0.001-0.0010.0000.0000.0000.000
123A122ARG10.8640.91033.0950.0290.0290.0000.0000.0000.000
124A123PHE00.0210.04725.0970.0000.0000.0000.0000.0000.000
125A124LEU00.0880.03924.6980.0010.0010.0000.0000.0000.000
126A125PRO0-0.0040.00028.4370.0040.0040.0000.0000.0000.000
127A126SER0-0.017-0.01126.0240.0020.0020.0000.0000.0000.000
128A127GLY0-0.023-0.00529.1290.0040.0040.0000.0000.0000.000
129A128ARG10.7440.85620.3910.0300.0300.0000.0000.0000.000
130A129THR00.0310.01526.873-0.005-0.0050.0000.0000.0000.000
131A130LEU00.0560.03123.0240.0000.0000.0000.0000.0000.000
132A131ASP-1-0.896-0.97322.660-0.129-0.1290.0000.0000.0000.000
133A132SER0-0.068-0.03321.969-0.002-0.0020.0000.0000.0000.000
134A133PHE0-0.014-0.00818.9080.0140.0140.0000.0000.0000.000
135A134PHE0-0.018-0.00416.604-0.012-0.0120.0000.0000.0000.000
136A135ASP-1-0.856-0.92114.003-0.208-0.2080.0000.0000.0000.000
137A136LYS10.8090.88117.4190.2080.2080.0000.0000.0000.000
138A137VAL00.0320.01919.270-0.026-0.0260.0000.0000.0000.000
139A138TYR0-0.063-0.05818.3070.0010.0010.0000.0000.0000.000
140A139ALA00.0320.00823.131-0.005-0.0050.0000.0000.0000.000
141A140SER00.046-0.00226.4260.0060.0060.0000.0000.0000.000
142A141CYS0-0.073-0.03328.6450.0050.0050.0000.0000.0000.000
143A142GLN0-0.071-0.04628.0700.0010.0010.0000.0000.0000.000
144A143MET0-0.0280.00824.0170.0000.0000.0000.0000.0000.000
145A144GLY0-0.0320.00229.532-0.001-0.0010.0000.0000.0000.000
146A145LYS10.7750.87727.8230.1660.1660.0000.0000.0000.000
147A146TYR0-0.041-0.04628.4250.0040.0040.0000.0000.0000.000
148A147LYS10.7610.88822.3920.2300.2300.0000.0000.0000.000
149A148PRO00.009-0.00725.7700.0150.0150.0000.0000.0000.000
150A149ASN00.0040.00326.468-0.011-0.0110.0000.0000.0000.000
151A150GLU-1-0.797-0.91724.340-0.265-0.2650.0000.0000.0000.000
152A151ASP-1-0.896-0.95424.664-0.200-0.2000.0000.0000.0000.000
153A152ILE0-0.0030.00423.940-0.007-0.0070.0000.0000.0000.000
154A153PHE00.0250.00119.024-0.006-0.0060.0000.0000.0000.000
155A154LEU0-0.019-0.00920.623-0.026-0.0260.0000.0000.0000.000
156A155GLU-1-0.864-0.91222.315-0.185-0.1850.0000.0000.0000.000
157A156MET00.0260.02817.2380.0040.0040.0000.0000.0000.000
158A157ILE0-0.0180.01016.963-0.014-0.0140.0000.0000.0000.000
159A158ALA0-0.045-0.02018.406-0.011-0.0110.0000.0000.0000.000
160A159ASP-1-0.853-0.88120.836-0.208-0.2080.0000.0000.0000.000
161A160SER0-0.004-0.00815.878-0.011-0.0110.0000.0000.0000.000
162A161GLY00.0150.00515.960-0.008-0.0080.0000.0000.0000.000
163A162MET0-0.076-0.01712.489-0.072-0.0720.0000.0000.0000.000
164A163LYS10.8890.9299.3671.2201.2200.0000.0000.0000.000
165A164PRO00.0440.03511.522-0.156-0.1560.0000.0000.0000.000
166A165GLU-1-0.824-0.91110.404-1.056-1.0560.0000.0000.0000.000
167A166GLU-1-0.829-0.8817.203-2.094-2.0940.0000.0000.0000.000
168A167THR0-0.025-0.0367.642-0.114-0.1140.0000.0000.0000.000
169A168LEU0-0.0080.0088.7840.0320.0320.0000.0000.0000.000
170A169PHE0-0.039-0.03310.5830.0890.0890.0000.0000.0000.000
171A170ILE00.005-0.00412.3330.0140.0140.0000.0000.0000.000
172A171ASP-1-0.724-0.85616.127-0.217-0.2170.0000.0000.0000.000
173A172ASP-1-0.789-0.88719.872-0.185-0.1850.0000.0000.0000.000
174A173GLY00.0230.01322.7710.0170.0170.0000.0000.0000.000
175A174PRO00.000-0.01023.535-0.021-0.0210.0000.0000.0000.000
176A175ALA0-0.047-0.02724.335-0.014-0.0140.0000.0000.0000.000
177A176ASN0-0.014-0.03322.527-0.002-0.0020.0000.0000.0000.000
178A177VAL00.0530.01919.104-0.026-0.0260.0000.0000.0000.000
179A178ALA0-0.009-0.00320.294-0.029-0.0290.0000.0000.0000.000
180A179THR0-0.039-0.03922.494-0.006-0.0060.0000.0000.0000.000
181A180ALA00.0120.01917.376-0.013-0.0130.0000.0000.0000.000
182A181GLU-1-0.853-0.90516.829-0.533-0.5330.0000.0000.0000.000
183A182ARG10.7570.88618.9010.2400.2400.0000.0000.0000.000
184A183LEU0-0.050-0.03119.4350.0040.0040.0000.0000.0000.000
185A184GLY0-0.029-0.00316.657-0.022-0.0220.0000.0000.0000.000
186A185PHE0-0.059-0.04113.598-0.098-0.0980.0000.0000.0000.000
187A186HIS00.0290.0269.2970.1940.1940.0000.0000.0000.000
188A187THR0-0.079-0.06612.3670.0490.0490.0000.0000.0000.000
189A188TYR0-0.090-0.07513.892-0.015-0.0150.0000.0000.0000.000
190A189CYS0-0.081-0.03615.7660.0140.0140.0000.0000.0000.000
191A190PRO0-0.039-0.00318.2110.0150.0150.0000.0000.0000.000
192A191ASP-1-0.847-0.93820.604-0.128-0.1280.0000.0000.0000.000
193A192ASN00.0150.00223.768-0.003-0.0030.0000.0000.0000.000
194A193GLY0-0.0020.00625.1710.0090.0090.0000.0000.0000.000
195A194GLU-1-0.858-0.89219.782-0.158-0.1580.0000.0000.0000.000
196A195ASN0-0.061-0.05220.116-0.019-0.0190.0000.0000.0000.000
197A196TRP00.0430.00915.0770.0030.0030.0000.0000.0000.000
198A197ILE00.0380.03415.389-0.026-0.0260.0000.0000.0000.000
199A198PRO0-0.041-0.00914.357-0.004-0.0040.0000.0000.0000.000
200A199ALA00.004-0.00213.9930.0110.0110.0000.0000.0000.000
201A200ILE00.0830.04010.826-0.048-0.0480.0000.0000.0000.000
202A201THR0-0.011-0.0169.796-0.050-0.0500.0000.0000.0000.000
203A202ARG10.8450.9219.3820.1580.1580.0000.0000.0000.000
204A203LEU00.0160.0158.8160.0430.0430.0000.0000.0000.000
205A204LEU00.0160.0185.279-0.249-0.2490.0000.0000.0000.000
206A205ARG10.8380.9234.061-0.502-0.2780.000-0.034-0.1910.000
207A206GLU-1-0.981-0.9765.540-0.453-0.4530.0000.0000.0000.000
208A207GLN00.0400.0182.521-5.604-2.9001.630-1.930-2.404-0.012