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: 94292

Calculation Name: 5EIQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EIQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IYS5

Base Structure: X-ray

Registration Date: 2023-06-26

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1796208.046678
FMO2-HF: Nuclear repulsion 1723940.453195
FMO2-HF: Total energy -72267.593483
FMO2-MP2: Total energy -72479.400497


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:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-13.935-12.4174.193-2.289-3.4220.023
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.001
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].
3A5HIS10.8910.9512.073-14.345-12.9354.194-2.285-3.3190.023
4A6PRO00.0430.0216.223-0.078-0.0780.0000.0000.0000.000
5A7LYS10.8880.9489.563-0.059-0.0590.0000.0000.0000.000
6A8PRO00.0000.01412.6750.0030.0030.0000.0000.0000.000
7A9TRP0-0.032-0.01715.124-0.027-0.0270.0000.0000.0000.000
8A10LEU0-0.007-0.01218.8180.0110.0110.0000.0000.0000.000
9A11GLY00.0220.01321.686-0.010-0.0100.0000.0000.0000.000
10A12ALA00.015-0.00225.2340.0030.0030.0000.0000.0000.000
11A13GLN0-0.064-0.00828.747-0.004-0.0040.0000.0000.0000.000
12A14PRO00.0590.02431.5660.0010.0010.0000.0000.0000.000
13A15ALA00.0290.00632.9830.0000.0000.0000.0000.0000.000
14A16THR0-0.010-0.00829.2930.0010.0010.0000.0000.0000.000
15A17VAL0-0.0120.00332.045-0.002-0.0020.0000.0000.0000.000
16A18VAL0-0.013-0.01335.1490.0000.0000.0000.0000.0000.000
17A19THR00.0620.03437.6980.0000.0000.0000.0000.0000.000
18A20PRO0-0.065-0.04439.5370.0030.0030.0000.0000.0000.000
19A21GLY00.0280.02439.592-0.001-0.0010.0000.0000.0000.000
20A22VAL0-0.051-0.01236.7360.0010.0010.0000.0000.0000.000
21A23ASN00.0330.01935.524-0.001-0.0010.0000.0000.0000.000
22A24VAL0-0.019-0.01030.3550.0010.0010.0000.0000.0000.000
23A25THR0-0.033-0.00828.0370.0030.0030.0000.0000.0000.000
24A26LEU0-0.006-0.00325.1060.0010.0010.0000.0000.0000.000
25A27ARG10.8260.89523.935-0.106-0.1060.0000.0000.0000.000
26A28CYS0-0.0040.01217.8780.0130.0130.0000.0000.0000.000
27A29ARG10.8630.92417.864-0.211-0.2110.0000.0000.0000.000
28A30ALA00.0170.00413.019-0.008-0.0080.0000.0000.0000.000
29A31PRO0-0.040-0.02210.942-0.022-0.0220.0000.0000.0000.000
30A32GLN00.0170.0097.1910.2650.2650.0000.0000.0000.000
31A33PRO00.0030.00112.4010.0230.0230.0000.0000.0000.000
32A34ALA0-0.021-0.00912.0650.1620.1620.0000.0000.0000.000
33A35TRP00.0180.00312.931-0.064-0.0640.0000.0000.0000.000
34A36ARG10.8410.88914.065-0.222-0.2220.0000.0000.0000.000
35A37PHE0-0.003-0.02114.4440.0640.0640.0000.0000.0000.000
36A38GLY00.0230.00316.686-0.029-0.0290.0000.0000.0000.000
37A39LEU0-0.024-0.01218.1900.0120.0120.0000.0000.0000.000
38A40PHE00.001-0.01016.164-0.002-0.0020.0000.0000.0000.000
39A41LYS10.8830.94621.025-0.060-0.0600.0000.0000.0000.000
40A42PRO0-0.039-0.04122.544-0.002-0.0020.0000.0000.0000.000
41A43GLY0-0.018-0.00722.385-0.003-0.0030.0000.0000.0000.000
42A44GLU-1-0.845-0.90822.3170.0520.0520.0000.0000.0000.000
43A45ILE0-0.014-0.01517.3810.0060.0060.0000.0000.0000.000
44A46ALA0-0.003-0.00118.0860.0060.0060.0000.0000.0000.000
45A47PRO0-0.050-0.02718.2590.0030.0030.0000.0000.0000.000
46A48LEU00.0370.04020.700-0.006-0.0060.0000.0000.0000.000
47A49LEU0-0.016-0.01223.028-0.003-0.0030.0000.0000.0000.000
48A50PHE0-0.024-0.02919.4260.0140.0140.0000.0000.0000.000
49A51ARG10.9370.98119.901-0.143-0.1430.0000.0000.0000.000
50A52ASP-1-0.751-0.83018.7540.2050.2050.0000.0000.0000.000
51A53VAL0-0.032-0.02818.364-0.020-0.0200.0000.0000.0000.000
52A54SER0-0.038-0.00716.923-0.002-0.0020.0000.0000.0000.000
53A55SER00.0650.03617.223-0.018-0.0180.0000.0000.0000.000
54A56GLU-1-0.809-0.88715.5300.3460.3460.0000.0000.0000.000
55A57LEU0-0.041-0.02117.120-0.004-0.0040.0000.0000.0000.000
56A58ALA0-0.0030.01319.461-0.002-0.0020.0000.0000.0000.000
57A59GLU-1-0.831-0.90021.2260.1120.1120.0000.0000.0000.000
58A60PHE0-0.019-0.02720.346-0.001-0.0010.0000.0000.0000.000
59A61PHE00.0100.00826.162-0.002-0.0020.0000.0000.0000.000
60A62LEU0-0.031-0.01428.355-0.002-0.0020.0000.0000.0000.000
61A63GLU-1-0.908-0.96431.7040.0550.0550.0000.0000.0000.000
62A64GLU-1-0.958-0.97235.3370.0370.0370.0000.0000.0000.000
63A65VAL0-0.067-0.01833.752-0.001-0.0010.0000.0000.0000.000
64A66THR00.0820.02436.181-0.004-0.0040.0000.0000.0000.000
65A67PRO00.020-0.01735.8020.0030.0030.0000.0000.0000.000
66A68ALA0-0.0200.00834.3140.0010.0010.0000.0000.0000.000
67A69GLN00.0570.04231.4180.0000.0000.0000.0000.0000.000
68A70GLY00.0650.05530.9690.0060.0060.0000.0000.0000.000
69A71GLY00.0110.02029.742-0.001-0.0010.0000.0000.0000.000
70A72SER0-0.076-0.07725.1010.0030.0030.0000.0000.0000.000
71A73TYR0-0.062-0.05023.5980.0000.0000.0000.0000.0000.000
72A74ARG10.9200.96017.907-0.101-0.1010.0000.0000.0000.000
73A76CYS0-0.0060.00912.9560.0040.0040.0000.0000.0000.000
74A77TYR00.021-0.0169.2000.0510.0510.0000.0000.0000.000
75A78ARG10.8400.9119.695-0.190-0.1900.0000.0000.0000.000
76A79ARG10.8980.9537.744-1.264-1.2640.0000.0000.0000.000
77A80PRO00.0230.0009.649-0.013-0.0130.0000.0000.0000.000
78A81ASP-1-0.872-0.9367.2671.3271.3270.0000.0000.0000.000
79A82TRP0-0.086-0.0325.4610.0130.121-0.001-0.004-0.1030.000
80A83GLY00.0770.0286.269-0.180-0.1800.0000.0000.0000.000
81A84PRO00.0500.0088.2720.1920.1920.0000.0000.0000.000
82A85GLY00.0350.02111.6520.0870.0870.0000.0000.0000.000
83A86VAL0-0.069-0.0185.364-0.020-0.0200.0000.0000.0000.000
84A87TRP00.0430.0188.8580.2180.2180.0000.0000.0000.000
85A88SER0-0.028-0.0078.110-0.016-0.0160.0000.0000.0000.000
86A89GLN0-0.049-0.0218.126-0.112-0.1120.0000.0000.0000.000
87A90PRO00.0680.01310.7260.0390.0390.0000.0000.0000.000
88A91SER0-0.0030.00714.393-0.004-0.0040.0000.0000.0000.000
89A92ASP-1-0.866-0.91717.0660.1120.1120.0000.0000.0000.000
90A93VAL0-0.021-0.02019.7750.0060.0060.0000.0000.0000.000
91A94LEU0-0.0120.01822.658-0.001-0.0010.0000.0000.0000.000
92A95GLU-1-0.856-0.92025.2930.0580.0580.0000.0000.0000.000
93A96LEU0-0.022-0.00228.5060.0000.0000.0000.0000.0000.000
94A97LEU0-0.037-0.02430.873-0.003-0.0030.0000.0000.0000.000
95A98VAL00.0290.01334.4490.0010.0010.0000.0000.0000.000
96A99THR0-0.049-0.03837.020-0.003-0.0030.0000.0000.0000.000
97A100GLU-1-0.812-0.91840.4810.0340.0340.0000.0000.0000.000
98A101GLU-1-0.905-0.94843.7150.0260.0260.0000.0000.0000.000
99A102LEU0-0.052-0.02439.5800.0010.0010.0000.0000.0000.000
100A103PRO00.011-0.00740.044-0.002-0.0020.0000.0000.0000.000
101A104ARG10.9030.97243.276-0.021-0.0210.0000.0000.0000.000
102A105PRO0-0.055-0.01244.6650.0000.0000.0000.0000.0000.000
103A106SER0-0.073-0.04345.541-0.002-0.0020.0000.0000.0000.000
104A107LEU00.033-0.00247.6580.0010.0010.0000.0000.0000.000
105A108VAL0-0.0110.00248.717-0.001-0.0010.0000.0000.0000.000
106A109ALA00.0450.01951.4940.0010.0010.0000.0000.0000.000
107A110LEU0-0.071-0.04247.6430.0000.0000.0000.0000.0000.000
108A111PRO00.002-0.00450.473-0.001-0.0010.0000.0000.0000.000
109A112GLY00.0230.01752.5970.0010.0010.0000.0000.0000.000
110A113PRO0-0.033-0.01654.2050.0000.0000.0000.0000.0000.000
111A114VAL00.0190.00756.452-0.001-0.0010.0000.0000.0000.000
112A115VAL0-0.019-0.00758.7310.0000.0000.0000.0000.0000.000
113A116GLY00.0510.01861.215-0.001-0.0010.0000.0000.0000.000
114A117PRO0-0.016-0.01763.7660.0010.0010.0000.0000.0000.000
115A118GLY00.0210.01765.2530.0000.0000.0000.0000.0000.000
116A119ALA00.0120.02361.1150.0000.0000.0000.0000.0000.000
117A120ASN00.001-0.02057.3270.0000.0000.0000.0000.0000.000
118A121VAL00.0350.02656.0000.0000.0000.0000.0000.0000.000
119A122SER0-0.0060.00550.4110.0010.0010.0000.0000.0000.000
120A123LEU00.0240.02651.705-0.001-0.0010.0000.0000.0000.000
121A124ARG10.8510.89643.201-0.026-0.0260.0000.0000.0000.000
122A125CYS0-0.0670.00246.8910.0000.0000.0000.0000.0000.000
123A126ALA00.005-0.01442.8900.0020.0020.0000.0000.0000.000
124A127GLY00.0820.04341.416-0.001-0.0010.0000.0000.0000.000
125A128ARG10.9020.93837.316-0.029-0.0290.0000.0000.0000.000
126A129LEU00.0310.02335.0520.0020.0020.0000.0000.0000.000
127A130ARG10.9060.94131.020-0.053-0.0530.0000.0000.0000.000
128A131ASN0-0.024-0.02231.501-0.001-0.0010.0000.0000.0000.000
129A132MET00.0310.04435.9470.0000.0000.0000.0000.0000.000
130A133SER00.002-0.00139.4240.0000.0000.0000.0000.0000.000
131A134PHE00.014-0.00140.701-0.001-0.0010.0000.0000.0000.000
132A135VAL00.0110.00245.5370.0000.0000.0000.0000.0000.000
133A136LEU0-0.0090.00149.281-0.001-0.0010.0000.0000.0000.000
134A137TYR00.0470.00652.0850.0000.0000.0000.0000.0000.000
135A138ARG10.8790.93455.637-0.018-0.0180.0000.0000.0000.000
136A139GLU-1-0.888-0.95358.7160.0190.0190.0000.0000.0000.000
137A140GLY0-0.001-0.00261.6830.0000.0000.0000.0000.0000.000
138A141VAL0-0.082-0.04160.5360.0000.0000.0000.0000.0000.000
139A142ALA00.0150.01160.1650.0000.0000.0000.0000.0000.000
140A143ALA0-0.0070.00357.8180.0010.0010.0000.0000.0000.000
141A144PRO00.0090.00753.1520.0000.0000.0000.0000.0000.000
142A145LEU0-0.038-0.01755.3020.0000.0000.0000.0000.0000.000
143A146GLN0-0.051-0.04051.4100.0010.0010.0000.0000.0000.000
144A147TYR00.0500.02643.9050.0000.0000.0000.0000.0000.000
145A148ARG10.8490.91343.931-0.030-0.0300.0000.0000.0000.000
146A149HIS0-0.0260.01038.0790.0020.0020.0000.0000.0000.000
147A150SER0-0.031-0.04139.629-0.001-0.0010.0000.0000.0000.000
148A151ALA00.0350.03034.1590.0020.0020.0000.0000.0000.000
149A152GLN00.0540.02034.7350.0040.0040.0000.0000.0000.000
150A153PRO0-0.0050.01235.6230.0000.0000.0000.0000.0000.000
151A154TRP0-0.020-0.03338.033-0.001-0.0010.0000.0000.0000.000
152A155ALA00.0220.04641.6880.0010.0010.0000.0000.0000.000
153A156ASP-1-0.746-0.83944.4870.0260.0260.0000.0000.0000.000
154A157PHE00.011-0.00547.2840.0010.0010.0000.0000.0000.000
155A158THR00.0090.01550.673-0.001-0.0010.0000.0000.0000.000
156A159LEU0-0.0030.00553.3800.0000.0000.0000.0000.0000.000
157A160LEU00.024-0.00357.0300.0000.0000.0000.0000.0000.000
158A161GLY00.0650.02859.9690.0000.0000.0000.0000.0000.000
159A162ALA0-0.020-0.01962.5450.0000.0000.0000.0000.0000.000
160A163ARG10.9200.95262.079-0.017-0.0170.0000.0000.0000.000
161A164ALA00.0170.02860.5820.0000.0000.0000.0000.0000.000
162A165PRO00.0220.02461.2470.0000.0000.0000.0000.0000.000
163A166GLY00.0280.01762.6350.0000.0000.0000.0000.0000.000
164A167THR00.0080.00759.8460.0000.0000.0000.0000.0000.000
165A168TYR0-0.015-0.02255.6450.0000.0000.0000.0000.0000.000
166A169SER00.0330.01753.9980.0000.0000.0000.0000.0000.000
167A171TYR00.0660.03347.929-0.001-0.0010.0000.0000.0000.000
168A172TYR0-0.045-0.05540.4210.0010.0010.0000.0000.0000.000
169A173HIS00.0140.00143.183-0.002-0.0020.0000.0000.0000.000
170A174THR00.0480.01138.3570.0000.0000.0000.0000.0000.000
171A175PRO0-0.058-0.01637.168-0.002-0.0020.0000.0000.0000.000
172A176SER00.0000.00537.1100.0000.0000.0000.0000.0000.000
173A177ALA0-0.0140.01539.689-0.001-0.0010.0000.0000.0000.000
174A178PRO00.0290.01437.7980.0030.0030.0000.0000.0000.000
175A179TYR00.0420.00740.5720.0000.0000.0000.0000.0000.000
176A180VAL00.0380.02039.975-0.001-0.0010.0000.0000.0000.000
177A181LEU0-0.017-0.01243.0180.0010.0010.0000.0000.0000.000
178A182SER0-0.0090.00744.3150.0000.0000.0000.0000.0000.000
179A183GLN0-0.0130.00545.599-0.002-0.0020.0000.0000.0000.000
180A184ARG10.9410.95848.342-0.019-0.0190.0000.0000.0000.000
181A185SER0-0.005-0.00249.7600.0000.0000.0000.0000.0000.000
182A186GLU-1-0.860-0.91950.8640.0190.0190.0000.0000.0000.000
183A187VAL0-0.022-0.01853.6650.0000.0000.0000.0000.0000.000
184A188LEU0-0.0080.00653.8210.0000.0000.0000.0000.0000.000
185A189VAL0-0.003-0.00656.9490.0000.0000.0000.0000.0000.000
186A190ILE0-0.0160.00357.3290.0000.0000.0000.0000.0000.000