Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YY2J2

Calculation Name: 2EJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EJB

Chain ID: A

ChEMBL ID:

UniProt ID: O66811

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1861395.038543
FMO2-HF: Nuclear repulsion 1792807.823928
FMO2-HF: Total energy -68587.214615
FMO2-MP2: Total energy -68786.927101


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-15.55-11.213.496-8.13-9.716-0.011
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.037
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].
3A3LYS10.9750.9913.595-0.9111.335-0.008-1.148-1.0900.005
4A4ILE00.0240.0196.1710.0760.0760.0000.0000.0000.000
5A5ALA00.0030.0148.6310.0770.0770.0000.0000.0000.000
6A6LEU00.0040.01012.0960.0030.0030.0000.0000.0000.000
7A7CYS0-0.036-0.01214.178-0.009-0.0090.0000.0000.0000.000
8A8ILE00.0370.02317.1590.0020.0020.0000.0000.0000.000
9A9THR0-0.041-0.05220.270-0.009-0.0090.0000.0000.0000.000
10A10GLY00.021-0.00723.9100.0020.0020.0000.0000.0000.000
11A11ALA0-0.025-0.01826.521-0.002-0.0020.0000.0000.0000.000
12A12SER0-0.035-0.02827.0900.0020.0020.0000.0000.0000.000
13A13GLY00.032-0.00226.2520.0020.0020.0000.0000.0000.000
14A14VAL0-0.038-0.02423.2690.0050.0050.0000.0000.0000.000
15A15ILE00.0290.01721.7290.0060.0060.0000.0000.0000.000
16A16TYR00.016-0.00120.8100.0070.0070.0000.0000.0000.000
17A17GLY00.0400.02317.9780.0080.0080.0000.0000.0000.000
18A18ILE0-0.055-0.02216.6940.0150.0150.0000.0000.0000.000
19A19LYS10.8390.89216.454-0.044-0.0440.0000.0000.0000.000
20A20LEU00.0220.01213.2990.0120.0120.0000.0000.0000.000
21A21LEU0-0.019-0.01111.4470.0190.0190.0000.0000.0000.000
22A22GLN0-0.023-0.02011.5760.0450.0450.0000.0000.0000.000
23A23VAL00.0800.04311.8280.0310.0310.0000.0000.0000.000
24A24LEU0-0.019-0.0118.259-0.001-0.0010.0000.0000.0000.000
25A25GLU-1-0.798-0.8937.0590.4810.4810.0000.0000.0000.000
26A26GLU-1-0.932-0.9627.4480.2380.2380.0000.0000.0000.000
27A27LEU0-0.088-0.0367.792-0.032-0.0320.0000.0000.0000.000
28A28ASP-1-0.886-0.9273.536-0.0120.3850.027-0.130-0.2950.000
29A29PHE0-0.040-0.0202.482-6.235-3.0402.303-2.482-3.017-0.028
30A30SER0-0.046-0.0472.351-4.840-7.96810.668-3.707-3.8320.016
31A31VAL0-0.006-0.0034.496-1.657-1.4410.030-0.143-0.1040.002
32A32ASP-1-0.765-0.7908.179-0.221-0.2210.0000.0000.0000.000
33A33LEU00.009-0.01210.899-0.010-0.0100.0000.0000.0000.000
34A34VAL00.0140.00814.027-0.028-0.0280.0000.0000.0000.000
35A35ILE00.0130.00617.2460.0080.0080.0000.0000.0000.000
36A36SER00.0030.00920.245-0.009-0.0090.0000.0000.0000.000
37A37ARG10.9260.93023.9390.0090.0090.0000.0000.0000.000
38A38ASN0-0.025-0.02526.487-0.001-0.0010.0000.0000.0000.000
39A39ALA00.0410.02223.4250.0010.0010.0000.0000.0000.000
40A40LYS10.9080.96321.7070.0150.0150.0000.0000.0000.000
41A41VAL0-0.003-0.00325.3560.0000.0000.0000.0000.0000.000
42A42VAL00.0460.03427.4660.0000.0000.0000.0000.0000.000
43A43LEU00.0100.00422.2940.0010.0010.0000.0000.0000.000
44A44LYS10.8870.94826.4310.0050.0050.0000.0000.0000.000
45A45GLU-1-0.963-0.98228.9170.0030.0030.0000.0000.0000.000
46A46GLU-1-0.845-0.88628.2960.0250.0250.0000.0000.0000.000
47A54VAL0-0.024-0.02619.5540.0030.0030.0000.0000.0000.000
48A55LEU00.0150.01218.144-0.001-0.0010.0000.0000.0000.000
49A56LYS10.9050.94814.556-0.044-0.0440.0000.0000.0000.000
50A57GLY00.0240.02014.290-0.017-0.0170.0000.0000.0000.000
51A58LEU0-0.038-0.02010.777-0.010-0.0100.0000.0000.0000.000
52A59LYS10.8280.8976.297-0.569-0.5690.0000.0000.0000.000
53A60ASN0-0.035-0.0253.058-2.603-1.2640.477-0.519-1.296-0.006
54A61VAL00.0340.0255.2700.3690.454-0.001-0.001-0.0820.000
55A62ARG10.8300.8828.5100.0820.0820.0000.0000.0000.000
56A63ILE0-0.007-0.00910.3830.0350.0350.0000.0000.0000.000
57A64HIS0-0.022-0.01411.854-0.040-0.0400.0000.0000.0000.000
58A65GLU-1-0.863-0.93616.623-0.022-0.0220.0000.0000.0000.000
59A66GLU-1-0.805-0.89020.399-0.007-0.0070.0000.0000.0000.000
60A67ASN0-0.019-0.02122.3620.0040.0040.0000.0000.0000.000
61A68ASP-1-0.814-0.88919.436-0.077-0.0770.0000.0000.0000.000
62A69PHE0-0.022-0.01920.828-0.002-0.0020.0000.0000.0000.000
63A70THR0-0.078-0.05321.007-0.003-0.0030.0000.0000.0000.000
64A71SER00.0220.00816.074-0.013-0.0130.0000.0000.0000.000
65A72PRO0-0.028-0.03313.2150.0020.0020.0000.0000.0000.000
66A73LEU00.0290.01612.5220.0070.0070.0000.0000.0000.000
67A74ALA0-0.0010.01815.8510.0150.0150.0000.0000.0000.000
68A75SER0-0.014-0.01117.6290.0090.0090.0000.0000.0000.000
69A76GLY00.0670.02717.277-0.009-0.0090.0000.0000.0000.000
70A77SER0-0.002-0.00717.324-0.002-0.0020.0000.0000.0000.000
71A78ARG10.9060.95013.7020.1570.1570.0000.0000.0000.000
72A79LEU00.049-0.00112.915-0.025-0.0250.0000.0000.0000.000
73A80VAL00.0240.01213.745-0.001-0.0010.0000.0000.0000.000
74A81HIS0-0.066-0.01410.0120.0560.0560.0000.0000.0000.000
75A82TYR0-0.144-0.0919.333-0.110-0.1100.0000.0000.0000.000
76A83ARG10.8470.9257.165-0.145-0.1450.0000.0000.0000.000
77A84GLY00.017-0.0079.9990.0470.0470.0000.0000.0000.000
78A85VAL0-0.048-0.02012.088-0.020-0.0200.0000.0000.0000.000
79A86TYR00.012-0.01211.6370.0060.0060.0000.0000.0000.000
80A87VAL0-0.014-0.01315.933-0.003-0.0030.0000.0000.0000.000
81A88VAL0-0.0130.02817.696-0.002-0.0020.0000.0000.0000.000
82A89PRO00.0560.01919.5240.0040.0040.0000.0000.0000.000
83A90CYS00.0160.00922.583-0.005-0.0050.0000.0000.0000.000
84A91SER0-0.009-0.00124.239-0.001-0.0010.0000.0000.0000.000
85A92THR00.0840.02327.7890.0000.0000.0000.0000.0000.000
86A93ASN0-0.009-0.00430.405-0.001-0.0010.0000.0000.0000.000
87A94THR00.0420.02324.166-0.002-0.0020.0000.0000.0000.000
88A95LEU00.0140.01426.9510.0000.0000.0000.0000.0000.000
89A96SER00.0020.00027.8990.0010.0010.0000.0000.0000.000
90A97CYS0-0.085-0.03828.483-0.001-0.0010.0000.0000.0000.000
91A98ILE00.0480.02222.998-0.001-0.0010.0000.0000.0000.000
92A99ALA0-0.0170.01327.1510.0000.0000.0000.0000.0000.000
93A100ASN0-0.078-0.05529.5640.0010.0010.0000.0000.0000.000
94A101GLY00.0110.02728.986-0.001-0.0010.0000.0000.0000.000
95A102ILE0-0.052-0.01230.073-0.003-0.0030.0000.0000.0000.000
96A103ASN00.008-0.02826.4090.0030.0030.0000.0000.0000.000
97A104LYS10.9430.97328.7440.0020.0020.0000.0000.0000.000
98A105ASN0-0.035-0.03725.064-0.001-0.0010.0000.0000.0000.000
99A106LEU00.0350.02818.1780.0030.0030.0000.0000.0000.000
100A107ILE00.010-0.00920.5030.0010.0010.0000.0000.0000.000
101A108HIS0-0.0050.00421.8600.0010.0010.0000.0000.0000.000
102A109ARG10.8540.93021.7980.0240.0240.0000.0000.0000.000
103A110VAL00.006-0.01116.8190.0000.0000.0000.0000.0000.000
104A111GLY00.0230.02219.7050.0030.0030.0000.0000.0000.000
105A112GLU-1-0.821-0.90521.687-0.003-0.0030.0000.0000.0000.000
106A113VAL0-0.031-0.02418.6800.0030.0030.0000.0000.0000.000
107A114ALA00.0310.01318.2380.0030.0030.0000.0000.0000.000
108A115LEU00.0180.01719.5070.0090.0090.0000.0000.0000.000
109A116LYS10.7860.88122.8840.0080.0080.0000.0000.0000.000
110A117GLU-1-0.876-0.91419.0860.0080.0080.0000.0000.0000.000
111A118ARG10.8750.94619.497-0.038-0.0380.0000.0000.0000.000
112A119VAL0-0.0090.00914.4280.0120.0120.0000.0000.0000.000
113A120PRO00.0190.00614.395-0.006-0.0060.0000.0000.0000.000
114A121LEU00.0200.01716.152-0.011-0.0110.0000.0000.0000.000
115A122VAL0-0.017-0.00716.5840.0040.0040.0000.0000.0000.000
116A123LEU00.004-0.00918.927-0.003-0.0030.0000.0000.0000.000
117A124LEU00.0090.01421.0810.0020.0020.0000.0000.0000.000
118A125VAL0-0.007-0.00422.855-0.003-0.0030.0000.0000.0000.000
119A126ARG10.9220.96726.558-0.021-0.0210.0000.0000.0000.000
120A127GLU-1-0.884-0.96228.7980.0170.0170.0000.0000.0000.000
121A128ALA0-0.0560.00532.4380.0020.0020.0000.0000.0000.000
122A129PRO00.0360.00335.816-0.001-0.0010.0000.0000.0000.000
123A130TYR0-0.010-0.00631.2030.0000.0000.0000.0000.0000.000
124A131ASN00.0410.01836.8270.0000.0000.0000.0000.0000.000
125A132GLU-1-0.852-0.95537.5860.0180.0180.0000.0000.0000.000
126A133ILE00.0420.02435.6430.0010.0010.0000.0000.0000.000
127A134HIS0-0.009-0.00233.4410.0020.0020.0000.0000.0000.000
128A135LEU00.0310.00932.7610.0020.0020.0000.0000.0000.000
129A136GLU-1-0.906-0.95133.6480.0230.0230.0000.0000.0000.000
130A137ASN0-0.023-0.01630.8710.0010.0010.0000.0000.0000.000
131A138MET0-0.024-0.00428.7450.0020.0020.0000.0000.0000.000
132A139LEU00.0240.02829.1300.0030.0030.0000.0000.0000.000
133A140LYS10.8770.94030.639-0.018-0.0180.0000.0000.0000.000
134A141ILE00.007-0.00124.6550.0010.0010.0000.0000.0000.000
135A142THR0-0.021-0.02626.2680.0030.0030.0000.0000.0000.000
136A143ARG10.9190.96226.979-0.030-0.0300.0000.0000.0000.000
137A144MET0-0.080-0.03026.6500.0000.0000.0000.0000.0000.000
138A145GLY0-0.0010.01023.7730.0010.0010.0000.0000.0000.000
139A146GLY0-0.0240.00421.8350.0050.0050.0000.0000.0000.000
140A147VAL0-0.013-0.01720.5660.0010.0010.0000.0000.0000.000
141A148VAL00.000-0.01022.122-0.002-0.0020.0000.0000.0000.000
142A149VAL0-0.015-0.00920.9150.0020.0020.0000.0000.0000.000
143A150PRO00.0180.03024.058-0.002-0.0020.0000.0000.0000.000
144A151ALA0-0.003-0.00925.4640.0030.0030.0000.0000.0000.000
145A152SER0-0.057-0.04126.379-0.003-0.0030.0000.0000.0000.000
146A153PRO0-0.0110.00126.8010.0020.0020.0000.0000.0000.000
147A154ALA00.0080.01827.860-0.002-0.0020.0000.0000.0000.000
148A155PHE00.034-0.01129.5470.0000.0000.0000.0000.0000.000
149A156TYR0-0.030-0.01228.214-0.001-0.0010.0000.0000.0000.000
150A157HIS00.010-0.01024.379-0.003-0.0030.0000.0000.0000.000
151A158LYS10.9210.97429.414-0.035-0.0350.0000.0000.0000.000
152A159PRO0-0.0030.01728.7860.0000.0000.0000.0000.0000.000
153A160GLN00.0140.00030.144-0.001-0.0010.0000.0000.0000.000
154A161SER0-0.014-0.00728.413-0.002-0.0020.0000.0000.0000.000
155A162ILE00.022-0.01727.7400.0020.0020.0000.0000.0000.000
156A163ASP-1-0.783-0.87423.3160.0510.0510.0000.0000.0000.000
157A164ASP-1-0.763-0.86924.1310.0430.0430.0000.0000.0000.000
158A165MET0-0.052-0.02825.2070.0030.0030.0000.0000.0000.000
159A166ILE0-0.021-0.01221.1940.0030.0030.0000.0000.0000.000
160A167ASN00.0560.02120.1940.0100.0100.0000.0000.0000.000
161A168PHE00.0110.02520.3570.0050.0050.0000.0000.0000.000
162A169VAL0-0.007-0.00921.4710.0040.0040.0000.0000.0000.000
163A170VAL0-0.001-0.00716.0330.0030.0030.0000.0000.0000.000
164A171GLY00.0550.02816.9240.0060.0060.0000.0000.0000.000
165A172LYS10.8670.93217.961-0.074-0.0740.0000.0000.0000.000
166A173LEU0-0.004-0.00716.6580.0030.0030.0000.0000.0000.000
167A174LEU00.0260.03811.5440.0010.0010.0000.0000.0000.000
168A175ASP-1-0.798-0.88214.4450.1060.1060.0000.0000.0000.000
169A176VAL0-0.075-0.02616.9100.0100.0100.0000.0000.0000.000
170A177LEU0-0.016-0.00312.1940.0040.0040.0000.0000.0000.000
171A178ARG10.8770.92612.358-0.108-0.1080.0000.0000.0000.000
172A179ILE0-0.048-0.0109.0680.0340.0340.0000.0000.0000.000
173A180GLU-1-0.930-0.95710.1040.2410.2410.0000.0000.0000.000
174A181HIS0-0.008-0.02711.663-0.015-0.0150.0000.0000.0000.000
175A182ASN0-0.002-0.00714.2210.0040.0040.0000.0000.0000.000
176A183LEU0-0.0300.00515.685-0.010-0.0100.0000.0000.0000.000