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: YZVN2

Calculation Name: 1EH1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EH1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WX76

Base Structure: X-ray

Registration Date: 2023-06-22

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1800638.599121
FMO2-HF: Nuclear repulsion 1728149.836954
FMO2-HF: Total energy -72488.762167
FMO2-MP2: Total energy -72704.54644


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.
-12.304-11.99111.291-6.097-5.508-0.036
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 : -0.011
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].
3A3LEU00.0820.0253.812-1.1391.402-0.023-1.381-1.1370.009
4A4LYS10.9640.9846.7401.8121.8120.0000.0000.0000.000
5A5GLU-1-0.832-0.8841.874-14.097-16.72511.315-4.668-4.019-0.045
6A6LEU00.0310.0344.8600.9220.9220.0000.0000.0000.000
7A7TYR00.0120.0115.6760.4550.4550.0000.0000.0000.000
8A8ALA0-0.0140.0007.6900.2730.2730.0000.0000.0000.000
9A9GLU-1-0.811-0.8905.4020.6000.6000.0000.0000.0000.000
10A10THR00.018-0.0118.4000.1970.1970.0000.0000.0000.000
11A11ARG10.9620.97110.8310.3910.3910.0000.0000.0000.000
12A12SER0-0.059-0.02011.4060.0640.0640.0000.0000.0000.000
13A13HIS00.0580.0138.8170.0040.0040.0000.0000.0000.000
14A14MET0-0.0190.01113.8970.0130.0130.0000.0000.0000.000
15A15GLN0-0.076-0.04916.177-0.011-0.0110.0000.0000.0000.000
16A16LYS10.8650.94215.483-0.009-0.0090.0000.0000.0000.000
17A17SER0-0.015-0.00317.7350.0190.0190.0000.0000.0000.000
18A18LEU0-0.029-0.01520.1400.0010.0010.0000.0000.0000.000
19A19GLU-1-0.805-0.89920.3790.0220.0220.0000.0000.0000.000
20A20VAL0-0.023-0.00821.5790.0070.0070.0000.0000.0000.000
21A21LEU0-0.026-0.00324.0880.0000.0000.0000.0000.0000.000
22A22GLU-1-0.839-0.94526.093-0.040-0.0400.0000.0000.0000.000
23A23HIS0-0.042-0.00927.093-0.003-0.0030.0000.0000.0000.000
24A24ASN00.005-0.01127.3760.0050.0050.0000.0000.0000.000
25A25LEU0-0.023-0.00530.028-0.003-0.0030.0000.0000.0000.000
26A26ALA0-0.039-0.02431.773-0.002-0.0020.0000.0000.0000.000
27A27GLY0-0.0280.00433.1620.0010.0010.0000.0000.0000.000
28A28LEU0-0.038-0.01434.8020.0020.0020.0000.0000.0000.000
29A29ARG10.7380.82437.317-0.024-0.0240.0000.0000.0000.000
30A30THR00.029-0.00338.5370.0000.0000.0000.0000.0000.000
31A31GLY00.0240.03041.2280.0020.0020.0000.0000.0000.000
32A32ARG10.8280.87443.027-0.012-0.0120.0000.0000.0000.000
33A33ALA0-0.0010.02744.0580.0020.0020.0000.0000.0000.000
34A34ASN0-0.021-0.00637.841-0.002-0.0020.0000.0000.0000.000
35A35PRO00.0800.04339.8970.0030.0030.0000.0000.0000.000
36A36ALA0-0.018-0.02635.9590.0040.0040.0000.0000.0000.000
37A37LEU0-0.0010.01137.5820.0050.0050.0000.0000.0000.000
38A38LEU00.024-0.00539.6160.0050.0050.0000.0000.0000.000
39A39LEU0-0.0160.00534.1010.0020.0020.0000.0000.0000.000
40A40HIS00.023-0.00831.6190.0080.0080.0000.0000.0000.000
41A41LEU0-0.0150.00736.6030.0060.0060.0000.0000.0000.000
42A42LYS10.9490.98334.674-0.092-0.0920.0000.0000.0000.000
43A43VAL00.0070.00340.092-0.002-0.0020.0000.0000.0000.000
44A44GLU-1-0.901-0.94743.3000.0650.0650.0000.0000.0000.000
45A45TYR0-0.061-0.06444.828-0.004-0.0040.0000.0000.0000.000
46A46TYR0-0.034-0.02445.3620.0030.0030.0000.0000.0000.000
47A47GLY0-0.0040.01246.3080.0030.0030.0000.0000.0000.000
48A48ALA00.0010.01341.3220.0050.0050.0000.0000.0000.000
49A49HIS0-0.036-0.02839.439-0.003-0.0030.0000.0000.0000.000
50A50VAL0-0.0020.00038.8290.0050.0050.0000.0000.0000.000
51A51PRO0-0.0060.00135.803-0.003-0.0030.0000.0000.0000.000
52A52LEU00.0510.02438.685-0.003-0.0030.0000.0000.0000.000
53A53ASN0-0.018-0.01436.177-0.002-0.0020.0000.0000.0000.000
54A54GLN0-0.036-0.01135.8280.0010.0010.0000.0000.0000.000
55A55ILE0-0.044-0.02440.1300.0000.0000.0000.0000.0000.000
56A56ALA0-0.035-0.01343.003-0.002-0.0020.0000.0000.0000.000
57A57THR0-0.037-0.02042.752-0.001-0.0010.0000.0000.0000.000
58A58VAL00.0220.01042.6160.0000.0000.0000.0000.0000.000
59A59THR0-0.0080.00142.943-0.002-0.0020.0000.0000.0000.000
60A60ALA00.0390.00544.1590.0020.0020.0000.0000.0000.000
61A61PRO0-0.040-0.00745.932-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.783-0.86948.517-0.010-0.0100.0000.0000.0000.000
63A63PRO0-0.025-0.04446.9270.0020.0020.0000.0000.0000.000
64A64ARG10.9370.97448.0230.0140.0140.0000.0000.0000.000
65A65THR0-0.048-0.02350.1320.0030.0030.0000.0000.0000.000
66A66LEU0-0.0100.00044.048-0.001-0.0010.0000.0000.0000.000
67A67VAL0-0.020-0.00447.8950.0020.0020.0000.0000.0000.000
68A68VAL00.007-0.00746.1140.0000.0000.0000.0000.0000.000
69A69GLN0-0.037-0.00647.453-0.001-0.0010.0000.0000.0000.000
70A70SER0-0.003-0.01747.2590.0030.0030.0000.0000.0000.000
71A71TRP00.0170.00946.622-0.001-0.0010.0000.0000.0000.000
72A72ASP-1-0.783-0.84449.5120.0300.0300.0000.0000.0000.000
73A73GLN00.0870.03451.2250.0010.0010.0000.0000.0000.000
74A74ASN00.005-0.02653.192-0.002-0.0020.0000.0000.0000.000
75A75ALA00.0280.01947.7310.0010.0010.0000.0000.0000.000
76A76LEU00.0210.02049.3220.0010.0010.0000.0000.0000.000
77A77LYS10.8280.91050.958-0.024-0.0240.0000.0000.0000.000
78A78ALA0-0.009-0.01749.0560.0000.0000.0000.0000.0000.000
79A79ILE00.0410.03545.8100.0020.0020.0000.0000.0000.000
80A80GLU-1-0.784-0.88947.7550.0210.0210.0000.0000.0000.000
81A81LYS10.7790.89250.266-0.032-0.0320.0000.0000.0000.000
82A82ALA00.0840.04045.0400.0030.0030.0000.0000.0000.000
83A83ILE0-0.041-0.01445.2330.0000.0000.0000.0000.0000.000
84A84ARG10.7350.88046.015-0.036-0.0360.0000.0000.0000.000
85A85ASP-1-0.802-0.91046.1250.0410.0410.0000.0000.0000.000
86A86SER00.0660.03342.6700.0050.0050.0000.0000.0000.000
87A87ASP-1-0.864-0.92442.5410.0280.0280.0000.0000.0000.000
88A88LEU00.015-0.00741.663-0.004-0.0040.0000.0000.0000.000
89A89GLY0-0.0040.02545.509-0.003-0.0030.0000.0000.0000.000
90A90LEU0-0.013-0.00645.970-0.003-0.0030.0000.0000.0000.000
91A91ASN0-0.020-0.02250.1570.0030.0030.0000.0000.0000.000
92A92PRO0-0.027-0.00550.321-0.002-0.0020.0000.0000.0000.000
93A93SER0-0.0100.01253.0420.0000.0000.0000.0000.0000.000
94A94ASN0-0.038-0.05355.322-0.001-0.0010.0000.0000.0000.000
95A95LYS10.9200.95556.327-0.007-0.0070.0000.0000.0000.000
96A96GLY00.0190.01556.648-0.001-0.0010.0000.0000.0000.000
97A97ASP-1-0.882-0.93152.6460.0090.0090.0000.0000.0000.000
98A98ALA00.041-0.00251.1900.0010.0010.0000.0000.0000.000
99A99LEU0-0.0490.00049.6640.0000.0000.0000.0000.0000.000
100A100TYR0-0.014-0.00951.258-0.002-0.0020.0000.0000.0000.000
101A101ILE0-0.001-0.01347.8640.0020.0020.0000.0000.0000.000
102A102ASN00.0290.01650.488-0.003-0.0030.0000.0000.0000.000
103A103ILE0-0.026-0.01346.8460.0030.0030.0000.0000.0000.000
104A104PRO0-0.049-0.01049.945-0.002-0.0020.0000.0000.0000.000
105A105PRO00.005-0.00349.9720.0000.0000.0000.0000.0000.000
106A106LEU00.0080.00044.6910.0020.0020.0000.0000.0000.000
107A107THR00.0420.01948.938-0.002-0.0020.0000.0000.0000.000
108A108GLU-1-0.836-0.90948.109-0.004-0.0040.0000.0000.0000.000
109A109GLU-1-0.881-0.93347.4930.0110.0110.0000.0000.0000.000
110A110ARG00.1330.07144.5690.0000.0000.0000.0000.0000.000
111A111ARG10.8730.93243.3290.0080.0080.0000.0000.0000.000
112A112LYS10.8130.91143.091-0.010-0.0100.0000.0000.0000.000
113A113ASP-1-0.858-0.93640.9700.0200.0200.0000.0000.0000.000
114A114LEU0-0.0320.00739.1850.0030.0030.0000.0000.0000.000
115A115VAL00.0140.01038.030-0.001-0.0010.0000.0000.0000.000
116A116ARG10.8540.90837.403-0.016-0.0160.0000.0000.0000.000
117A117ALA00.0330.02535.2050.0000.0000.0000.0000.0000.000
118A118VAL00.0180.01933.4210.0020.0020.0000.0000.0000.000
119A119ARG10.8580.90932.3590.0240.0240.0000.0000.0000.000
120A120GLN0-0.034-0.00131.205-0.007-0.0070.0000.0000.0000.000
121A121TYR00.0450.00829.0560.0030.0030.0000.0000.0000.000
122A122ALA0-0.004-0.00227.657-0.001-0.0010.0000.0000.0000.000
123A123GLU-1-0.801-0.88127.064-0.049-0.0490.0000.0000.0000.000
124A124GLU-1-0.901-0.95125.4930.0430.0430.0000.0000.0000.000
125A125GLY00.0080.01023.4890.0070.0070.0000.0000.0000.000
126A126ARG10.7540.82922.2270.0410.0410.0000.0000.0000.000
127A127VAL0-0.021-0.00421.841-0.013-0.0130.0000.0000.0000.000
128A128ALA00.0290.02319.2000.0010.0010.0000.0000.0000.000
129A129ILE00.0230.00617.624-0.004-0.0040.0000.0000.0000.000
130A130ARG10.8610.90717.4790.0440.0440.0000.0000.0000.000
131A131ASN00.0040.00416.405-0.024-0.0240.0000.0000.0000.000
132A132ILE00.0290.03212.533-0.002-0.0020.0000.0000.0000.000
133A133ARG10.9030.95512.7420.1630.1630.0000.0000.0000.000
134A134ARG10.7860.87713.420-0.103-0.1030.0000.0000.0000.000
135A135GLU-1-0.822-0.9069.8530.1220.1220.0000.0000.0000.000
136A136ALA0-0.009-0.0049.150-0.055-0.0550.0000.0000.0000.000
137A137LEU00.0280.0019.887-0.167-0.1670.0000.0000.0000.000
138A138ASP-1-0.879-0.92810.319-0.176-0.1760.0000.0000.0000.000
139A139LYS10.8170.8894.425-0.480-0.329-0.001-0.005-0.1450.000
140A140LEU00.0060.0096.958-0.284-0.2840.0000.0000.0000.000
141A141LYS10.8620.9339.1790.1830.1830.0000.0000.0000.000
142A142LYS10.8950.9416.6540.1810.1810.0000.0000.0000.000
143A143LEU00.0770.0414.031-0.1280.1210.000-0.043-0.2070.000
144A144ALA00.0340.0237.144-0.008-0.0080.0000.0000.0000.000
145A145LYS10.9200.95310.6840.2670.2670.0000.0000.0000.000
146A146GLU-1-1.000-0.9965.619-0.131-0.1310.0000.0000.0000.000
147A147LEU0-0.033-0.0246.610-0.004-0.0040.0000.0000.0000.000
148A148HIS0-0.079-0.02410.3780.0490.0490.0000.0000.0000.000
149A149LEU0-0.0290.0029.951-0.021-0.0210.0000.0000.0000.000
150A150SER0-0.008-0.04014.0520.1050.1050.0000.0000.0000.000
151A151GLU-1-0.878-0.95016.679-0.358-0.3580.0000.0000.0000.000
152A152ASP-1-0.875-0.94818.470-0.415-0.4150.0000.0000.0000.000
153A153GLU-1-0.863-0.89714.310-0.856-0.8560.0000.0000.0000.000
154A154THR0-0.039-0.02413.639-0.110-0.1100.0000.0000.0000.000
155A155LYS10.9110.95814.6410.3460.3460.0000.0000.0000.000
156A156ARG10.8400.92715.7390.6490.6490.0000.0000.0000.000
157A157ALA0-0.020-0.02211.384-0.009-0.0090.0000.0000.0000.000
158A158GLU-1-0.867-0.94913.310-0.469-0.4690.0000.0000.0000.000
159A159ALA00.0010.00315.3450.0450.0450.0000.0000.0000.000
160A160GLU-1-0.852-0.90712.990-0.582-0.5820.0000.0000.0000.000
161A161ILE0-0.005-0.00310.0570.0360.0360.0000.0000.0000.000
162A162GLN00.0230.02414.2040.0770.0770.0000.0000.0000.000
163A163LYS10.8360.92816.4710.5440.5440.0000.0000.0000.000
164A164ILE0-0.009-0.00112.8440.0260.0260.0000.0000.0000.000
165A165THR0-0.013-0.04616.7430.0530.0530.0000.0000.0000.000
166A166ASP-1-0.879-0.95418.376-0.184-0.1840.0000.0000.0000.000
167A167GLU-1-0.925-0.95219.433-0.306-0.3060.0000.0000.0000.000
168A168PHE0-0.006-0.01616.6690.0240.0240.0000.0000.0000.000
169A169ILE0-0.0300.00621.4110.0280.0280.0000.0000.0000.000
170A170ALA00.0330.02523.7990.0170.0170.0000.0000.0000.000
171A171LYS10.8780.94423.9260.0950.0950.0000.0000.0000.000
172A172ALA00.007-0.00624.3550.0160.0160.0000.0000.0000.000
173A173ASP-1-0.824-0.90326.167-0.066-0.0660.0000.0000.0000.000
174A174GLN0-0.044-0.01428.9490.0080.0080.0000.0000.0000.000
175A175LEU0-0.045-0.01826.5520.0060.0060.0000.0000.0000.000
176A176ALA00.0110.00630.3450.0070.0070.0000.0000.0000.000
177A177GLU-1-0.761-0.87332.165-0.057-0.0570.0000.0000.0000.000
178A178LYS10.8200.90033.0310.0670.0670.0000.0000.0000.000
179A179LYS10.8320.91134.3430.0150.0150.0000.0000.0000.000
180A180GLU-1-0.855-0.92936.243-0.022-0.0220.0000.0000.0000.000
181A181GLN0-0.049-0.03438.0280.0030.0030.0000.0000.0000.000
182A182GLU-1-0.801-0.87236.846-0.016-0.0160.0000.0000.0000.000
183A183ILE00.0010.00438.2020.0030.0030.0000.0000.0000.000
184A184LEU0-0.082-0.03541.9450.0030.0030.0000.0000.0000.000
185A185GLY0-0.031-0.01344.339-0.001-0.0010.0000.0000.0000.000