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: LZ649

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1795468.128277
FMO2-HF: Nuclear repulsion 1723200.997348
FMO2-HF: Total energy -72267.130929
FMO2-MP2: Total energy -72478.850605


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.
-6.7-3.7730.155-1.193-1.8890.006
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 : 0.015 / q_NPA : -0.008
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].
3A5HIS10.9330.9753.212-7.389-4.5630.156-1.189-1.7930.006
4A6PRO00.0360.0166.1430.0690.0690.0000.0000.0000.000
5A7LYS10.9230.9779.5230.0470.0470.0000.0000.0000.000
6A8PRO00.0050.01712.6030.0060.0060.0000.0000.0000.000
7A9TRP0-0.032-0.01315.040-0.017-0.0170.0000.0000.0000.000
8A10LEU0-0.004-0.01518.7430.0110.0110.0000.0000.0000.000
9A11GLY00.0150.00621.592-0.006-0.0060.0000.0000.0000.000
10A12ALA00.004-0.00925.1450.0030.0030.0000.0000.0000.000
11A13GLN0-0.0250.01028.649-0.003-0.0030.0000.0000.0000.000
12A14PRO00.0420.01731.4710.0010.0010.0000.0000.0000.000
13A15ALA00.0350.01132.898-0.001-0.0010.0000.0000.0000.000
14A16THR0-0.016-0.01329.2220.0010.0010.0000.0000.0000.000
15A17VAL0-0.0110.00531.953-0.001-0.0010.0000.0000.0000.000
16A18VAL0-0.020-0.01335.0660.0000.0000.0000.0000.0000.000
17A19THR00.0540.03037.7220.0000.0000.0000.0000.0000.000
18A20PRO0-0.050-0.03939.7570.0020.0020.0000.0000.0000.000
19A21GLY00.0350.02739.850-0.001-0.0010.0000.0000.0000.000
20A22VAL0-0.046-0.01036.6300.0010.0010.0000.0000.0000.000
21A23ASN00.0350.02235.7780.0000.0000.0000.0000.0000.000
22A24VAL0-0.006-0.00630.4770.0000.0000.0000.0000.0000.000
23A25THR0-0.036-0.01128.0270.0020.0020.0000.0000.0000.000
24A26LEU0-0.0050.00125.181-0.001-0.0010.0000.0000.0000.000
25A27ARG10.8740.92923.794-0.058-0.0580.0000.0000.0000.000
26A28CYS0-0.0130.01018.0370.0080.0080.0000.0000.0000.000
27A29ARG10.8830.94617.935-0.099-0.0990.0000.0000.0000.000
28A30ALA00.0140.00612.897-0.014-0.0140.0000.0000.0000.000
29A31PRO0-0.039-0.01810.883-0.007-0.0070.0000.0000.0000.000
30A32GLN00.0170.0057.3950.2140.2140.0000.0000.0000.000
31A33PRO00.0140.00612.3490.0180.0180.0000.0000.0000.000
32A34ALA0-0.027-0.01512.1090.1180.1180.0000.0000.0000.000
33A35TRP00.0390.01513.176-0.044-0.0440.0000.0000.0000.000
34A36ARG10.8380.90114.292-0.186-0.1860.0000.0000.0000.000
35A37PHE0-0.010-0.02914.6840.0390.0390.0000.0000.0000.000
36A38GLY00.0190.00116.925-0.014-0.0140.0000.0000.0000.000
37A39LEU0-0.019-0.01018.4180.0010.0010.0000.0000.0000.000
38A40PHE00.006-0.00716.1580.0000.0000.0000.0000.0000.000
39A41LYS10.8860.97021.002-0.030-0.0300.0000.0000.0000.000
40A42PRO0-0.044-0.04222.517-0.002-0.0020.0000.0000.0000.000
41A43GLY0-0.010-0.00322.3540.0000.0000.0000.0000.0000.000
42A44GLU-1-0.857-0.92122.3110.0260.0260.0000.0000.0000.000
43A45ILE0-0.018-0.01517.3770.0020.0020.0000.0000.0000.000
44A46ALA0-0.007-0.00518.0710.0040.0040.0000.0000.0000.000
45A47PRO0-0.055-0.02818.3560.0010.0010.0000.0000.0000.000
46A48LEU00.0490.04520.750-0.002-0.0020.0000.0000.0000.000
47A49LEU0-0.020-0.01623.2130.0000.0000.0000.0000.0000.000
48A50PHE0-0.033-0.02919.5960.0080.0080.0000.0000.0000.000
49A51ARG10.9420.98020.127-0.096-0.0960.0000.0000.0000.000
50A52ASP-1-0.759-0.84118.9780.1660.1660.0000.0000.0000.000
51A53VAL0-0.037-0.03118.597-0.015-0.0150.0000.0000.0000.000
52A54SER0-0.040-0.00917.1720.0020.0020.0000.0000.0000.000
53A55SER00.0680.04117.403-0.017-0.0170.0000.0000.0000.000
54A56GLU-1-0.830-0.91415.3410.1950.1950.0000.0000.0000.000
55A57LEU0-0.057-0.02917.032-0.010-0.0100.0000.0000.0000.000
56A58ALA00.0050.01619.7650.0040.0040.0000.0000.0000.000
57A59GLU-1-0.876-0.93921.4190.0640.0640.0000.0000.0000.000
58A60PHE0-0.017-0.02520.4910.0010.0010.0000.0000.0000.000
59A61PHE00.0130.00726.427-0.002-0.0020.0000.0000.0000.000
60A62LEU0-0.034-0.01628.503-0.001-0.0010.0000.0000.0000.000
61A63GLU-1-0.918-0.96931.9580.0340.0340.0000.0000.0000.000
62A64GLU-1-0.967-0.97935.5900.0220.0220.0000.0000.0000.000
63A65VAL0-0.058-0.01333.924-0.001-0.0010.0000.0000.0000.000
64A66THR00.0980.04936.399-0.002-0.0020.0000.0000.0000.000
65A67PRO00.018-0.02135.8380.0010.0010.0000.0000.0000.000
66A68ALA0-0.0190.00834.2770.0000.0000.0000.0000.0000.000
67A69GLN00.0410.02131.4920.0000.0000.0000.0000.0000.000
68A70GLY00.0570.05331.0100.0030.0030.0000.0000.0000.000
69A71GLY00.0100.00529.7270.0000.0000.0000.0000.0000.000
70A72SER0-0.077-0.07725.0390.0020.0020.0000.0000.0000.000
71A73TYR0-0.030-0.03823.6150.0010.0010.0000.0000.0000.000
72A74ARG10.9330.97117.762-0.031-0.0310.0000.0000.0000.000
73A76CYS0-0.0110.01513.184-0.013-0.0130.0000.0000.0000.000
74A77TYR00.019-0.0219.1340.0370.0370.0000.0000.0000.000
75A78ARG10.9340.9609.928-0.226-0.2260.0000.0000.0000.000
76A79ARG10.8950.9487.954-0.963-0.9630.0000.0000.0000.000
77A80PRO00.010-0.0119.7870.0300.0300.0000.0000.0000.000
78A81ASP-1-0.885-0.9378.1051.1981.1980.0000.0000.0000.000
79A82TRP0-0.099-0.0355.7260.1190.220-0.001-0.004-0.0960.000
80A83GLY00.0510.0216.402-0.266-0.2660.0000.0000.0000.000
81A84PRO00.0310.0018.3640.1260.1260.0000.0000.0000.000
82A85GLY00.0220.00811.7050.0650.0650.0000.0000.0000.000
83A86VAL0-0.061-0.0185.552-0.032-0.0320.0000.0000.0000.000
84A87TRP00.0290.0158.9060.2020.2020.0000.0000.0000.000
85A88SER0-0.031-0.0158.256-0.054-0.0540.0000.0000.0000.000
86A89GLN0-0.049-0.0197.591-0.003-0.0030.0000.0000.0000.000
87A90PRO00.0720.00810.6910.0390.0390.0000.0000.0000.000
88A91SER0-0.0210.00114.360-0.006-0.0060.0000.0000.0000.000
89A92ASP-1-0.884-0.93517.0660.0260.0260.0000.0000.0000.000
90A93VAL0-0.034-0.02519.7750.0040.0040.0000.0000.0000.000
91A94LEU00.0000.02322.622-0.001-0.0010.0000.0000.0000.000
92A95GLU-1-0.886-0.93925.2930.0240.0240.0000.0000.0000.000
93A96LEU0-0.027-0.00728.4720.0000.0000.0000.0000.0000.000
94A97LEU0-0.037-0.02530.842-0.002-0.0020.0000.0000.0000.000
95A98VAL00.0280.01334.4170.0010.0010.0000.0000.0000.000
96A99THR0-0.057-0.04336.991-0.002-0.0020.0000.0000.0000.000
97A100GLU-1-0.822-0.92740.4500.0180.0180.0000.0000.0000.000
98A101GLU-1-0.959-0.97543.6980.0130.0130.0000.0000.0000.000
99A102LEU0-0.050-0.02339.3630.0000.0000.0000.0000.0000.000
100A103PRO00.006-0.00840.012-0.001-0.0010.0000.0000.0000.000
101A104ARG11.0261.03543.238-0.009-0.0090.0000.0000.0000.000
102A105PRO0-0.055-0.00544.7250.0000.0000.0000.0000.0000.000
103A106SER0-0.083-0.04845.712-0.001-0.0010.0000.0000.0000.000
104A107LEU00.043-0.00547.6580.0000.0000.0000.0000.0000.000
105A108VAL0-0.0110.00548.8750.0000.0000.0000.0000.0000.000
106A109ALA00.0450.02151.4940.0000.0000.0000.0000.0000.000
107A110LEU0-0.077-0.04647.5480.0000.0000.0000.0000.0000.000
108A111PRO00.002-0.00250.4730.0000.0000.0000.0000.0000.000
109A112GLY00.0240.01652.5850.0000.0000.0000.0000.0000.000
110A113PRO0-0.032-0.01554.1910.0000.0000.0000.0000.0000.000
111A114VAL00.0210.00856.4400.0000.0000.0000.0000.0000.000
112A115VAL0-0.020-0.00858.6020.0000.0000.0000.0000.0000.000
113A116GLY00.0480.01661.2020.0000.0000.0000.0000.0000.000
114A117PRO0-0.016-0.01563.7520.0000.0000.0000.0000.0000.000
115A118GLY00.0250.01765.2370.0000.0000.0000.0000.0000.000
116A119ALA00.0160.02561.0570.0000.0000.0000.0000.0000.000
117A120ASN0-0.005-0.02857.2880.0000.0000.0000.0000.0000.000
118A121VAL00.0320.02656.1500.0000.0000.0000.0000.0000.000
119A122SER0-0.0010.00850.3010.0000.0000.0000.0000.0000.000
120A123LEU00.0160.01851.7000.0000.0000.0000.0000.0000.000
121A124ARG10.8720.92943.164-0.010-0.0100.0000.0000.0000.000
122A125CYS0-0.0490.00646.9410.0000.0000.0000.0000.0000.000
123A126ALA0-0.008-0.01542.8840.0010.0010.0000.0000.0000.000
124A127GLY00.0750.03941.4160.0000.0000.0000.0000.0000.000
125A128ARG10.9110.94337.291-0.012-0.0120.0000.0000.0000.000
126A129LEU00.0360.02534.8150.0010.0010.0000.0000.0000.000
127A130ARG10.9120.94731.024-0.021-0.0210.0000.0000.0000.000
128A131ASN0-0.028-0.02231.5660.0000.0000.0000.0000.0000.000
129A132MET00.0350.04135.9470.0010.0010.0000.0000.0000.000
130A133SER0-0.002-0.00339.4240.0000.0000.0000.0000.0000.000
131A134PHE00.0160.00040.8030.0000.0000.0000.0000.0000.000
132A135VAL00.003-0.00445.5370.0000.0000.0000.0000.0000.000
133A136LEU0-0.0150.00149.2810.0000.0000.0000.0000.0000.000
134A137TYR00.0390.00652.1050.0000.0000.0000.0000.0000.000
135A138ARG10.9230.95755.637-0.008-0.0080.0000.0000.0000.000
136A139GLU-1-0.904-0.95959.0900.0090.0090.0000.0000.0000.000
137A140GLY0-0.003-0.00461.6830.0000.0000.0000.0000.0000.000
138A141VAL0-0.090-0.04660.5760.0000.0000.0000.0000.0000.000
139A142ALA00.0180.01260.1650.0000.0000.0000.0000.0000.000
140A143ALA0-0.0060.00557.7600.0000.0000.0000.0000.0000.000
141A144PRO00.0120.00853.1110.0000.0000.0000.0000.0000.000
142A145LEU0-0.045-0.02255.2750.0000.0000.0000.0000.0000.000
143A146GLN0-0.048-0.03651.3740.0000.0000.0000.0000.0000.000
144A147TYR00.0470.02343.6560.0000.0000.0000.0000.0000.000
145A148ARG10.9020.95244.093-0.013-0.0130.0000.0000.0000.000
146A149HIS0-0.0140.01837.9730.0010.0010.0000.0000.0000.000
147A150SER0-0.034-0.04139.675-0.001-0.0010.0000.0000.0000.000
148A151ALA00.0430.03434.1150.0010.0010.0000.0000.0000.000
149A152GLN00.0320.00334.9070.0010.0010.0000.0000.0000.000
150A153PRO0-0.0020.01735.6090.0000.0000.0000.0000.0000.000
151A154TRP00.000-0.02637.919-0.001-0.0010.0000.0000.0000.000
152A155ALA00.0170.04141.6880.0010.0010.0000.0000.0000.000
153A156ASP-1-0.775-0.87344.4870.0110.0110.0000.0000.0000.000
154A157PHE0-0.027-0.03247.2670.0000.0000.0000.0000.0000.000
155A158THR0-0.007-0.00150.6540.0000.0000.0000.0000.0000.000
156A159LEU00.0100.01753.3620.0000.0000.0000.0000.0000.000
157A160LEU00.0280.00057.0120.0000.0000.0000.0000.0000.000
158A161GLY00.0590.03059.9510.0000.0000.0000.0000.0000.000
159A162ALA0-0.018-0.01962.5280.0000.0000.0000.0000.0000.000
160A163ARG10.9090.94462.004-0.008-0.0080.0000.0000.0000.000
161A164ALA0-0.0040.02360.5570.0000.0000.0000.0000.0000.000
162A165PRO00.0150.01361.2470.0000.0000.0000.0000.0000.000
163A166GLY00.0290.01762.6350.0000.0000.0000.0000.0000.000
164A167THR00.0000.00759.9710.0000.0000.0000.0000.0000.000
165A168TYR0-0.011-0.02255.6020.0000.0000.0000.0000.0000.000
166A169SER00.0330.01753.9980.0000.0000.0000.0000.0000.000
167A171TYR00.0740.03847.9430.0000.0000.0000.0000.0000.000
168A172TYR0-0.044-0.05840.6830.0000.0000.0000.0000.0000.000
169A173HIS00.0140.00843.156-0.001-0.0010.0000.0000.0000.000
170A174THR00.0350.00438.3550.0000.0000.0000.0000.0000.000
171A175PRO0-0.054-0.02137.239-0.001-0.0010.0000.0000.0000.000
172A176SER00.0020.00636.9120.0000.0000.0000.0000.0000.000
173A177ALA0-0.0140.01639.620-0.001-0.0010.0000.0000.0000.000
174A178PRO00.0310.01437.7170.0010.0010.0000.0000.0000.000
175A179TYR00.0440.01140.4840.0000.0000.0000.0000.0000.000
176A180VAL00.0370.02140.0510.0000.0000.0000.0000.0000.000
177A181LEU0-0.027-0.01942.9280.0000.0000.0000.0000.0000.000
178A182SER0-0.0170.00944.2940.0000.0000.0000.0000.0000.000
179A183GLN00.0700.04545.5990.0000.0000.0000.0000.0000.000
180A184ARG10.9470.96348.325-0.009-0.0090.0000.0000.0000.000
181A185SER0-0.017-0.00449.6980.0000.0000.0000.0000.0000.000
182A186GLU-1-0.974-0.98950.8550.0080.0080.0000.0000.0000.000
183A187VAL0-0.019-0.01653.6240.0000.0000.0000.0000.0000.000
184A188LEU00.0030.00953.9280.0000.0000.0000.0000.0000.000
185A189VAL0-0.005-0.00656.9490.0000.0000.0000.0000.0000.000
186A190ILE0-0.0110.00357.3110.0000.0000.0000.0000.0000.000