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: 52JRZ

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1801642.252888
FMO2-HF: Nuclear repulsion 1729155.349328
FMO2-HF: Total energy -72486.90356
FMO2-MP2: Total energy -72702.847346


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.
-12.06-14.47115.877-7.482-5.984-0.045
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 : 0.009 / q_NPA : -0.015
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].
3A3LEU00.0890.0283.812-1.0381.230-0.021-1.219-1.0280.008
4A4LYS10.9510.9796.7441.7251.7250.0000.0000.0000.000
5A5GLU-1-0.880-0.9341.750-15.378-20.41915.898-6.219-4.638-0.053
6A6LEU00.0430.0344.8590.6630.6630.0000.0000.0000.000
7A7TYR00.0140.0175.6730.4200.4200.0000.0000.0000.000
8A8ALA0-0.0120.0037.6820.2560.2560.0000.0000.0000.000
9A9GLU-1-0.867-0.9155.839-0.458-0.4580.0000.0000.0000.000
10A10THR00.014-0.0118.4040.2490.2490.0000.0000.0000.000
11A11ARG10.9600.97310.8280.6420.6420.0000.0000.0000.000
12A12SER0-0.081-0.03111.2710.1210.1210.0000.0000.0000.000
13A13HIS00.0860.0279.0430.0760.0760.0000.0000.0000.000
14A14MET0-0.0050.01114.0200.0500.0500.0000.0000.0000.000
15A15GLN0-0.019-0.00716.1840.0090.0090.0000.0000.0000.000
16A16LYS10.9080.95614.9200.3270.3270.0000.0000.0000.000
17A17SER0-0.0140.00017.9530.0380.0380.0000.0000.0000.000
18A18LEU0-0.029-0.01320.3570.0190.0190.0000.0000.0000.000
19A19GLU-1-0.874-0.93621.193-0.168-0.1680.0000.0000.0000.000
20A20VAL0-0.030-0.00821.4700.0180.0180.0000.0000.0000.000
21A21LEU0-0.032-0.00924.1640.0120.0120.0000.0000.0000.000
22A22GLU-1-0.899-0.96925.398-0.145-0.1450.0000.0000.0000.000
23A23HIS0-0.044-0.01027.2260.0050.0050.0000.0000.0000.000
24A24ASN00.020-0.00227.0570.0100.0100.0000.0000.0000.000
25A25LEU0-0.027-0.00630.1890.0060.0060.0000.0000.0000.000
26A26ALA0-0.052-0.03631.9710.0050.0050.0000.0000.0000.000
27A27GLY0-0.0210.00833.2520.0040.0040.0000.0000.0000.000
28A28LEU0-0.043-0.01334.8360.0060.0060.0000.0000.0000.000
29A29ARG10.7480.82137.3640.0250.0250.0000.0000.0000.000
30A30THR00.0410.01938.7000.0020.0020.0000.0000.0000.000
31A31GLY00.0480.03741.2920.0030.0030.0000.0000.0000.000
32A32ARG10.8080.91443.0590.0350.0350.0000.0000.0000.000
33A33ALA0-0.0020.02544.1600.0010.0010.0000.0000.0000.000
34A34ASN00.003-0.00537.588-0.002-0.0020.0000.0000.0000.000
35A35PRO00.0610.03639.7740.0030.0030.0000.0000.0000.000
36A36ALA0-0.014-0.02936.1150.0030.0030.0000.0000.0000.000
37A37LEU00.0050.01037.8650.0020.0020.0000.0000.0000.000
38A38LEU00.023-0.01239.7990.0040.0040.0000.0000.0000.000
39A39LEU0-0.0180.01634.3320.0020.0020.0000.0000.0000.000
40A40HIS00.009-0.01431.7550.0060.0060.0000.0000.0000.000
41A41LEU0-0.0180.01036.6970.0040.0040.0000.0000.0000.000
42A42LYS10.9470.98234.2720.0000.0000.0000.0000.0000.000
43A43VAL00.0170.00939.9410.0010.0010.0000.0000.0000.000
44A44GLU-1-0.910-0.96643.1590.0050.0050.0000.0000.0000.000
45A45TYR0-0.045-0.02344.671-0.002-0.0020.0000.0000.0000.000
46A46TYR0-0.027-0.02445.2060.0020.0020.0000.0000.0000.000
47A47GLY0-0.0170.00346.0400.0020.0020.0000.0000.0000.000
48A48ALA0-0.0040.01641.0340.0020.0020.0000.0000.0000.000
49A49HIS00.0340.01238.977-0.004-0.0040.0000.0000.0000.000
50A50VAL0-0.026-0.00738.6470.0000.0000.0000.0000.0000.000
51A51PRO0-0.006-0.00135.9960.0000.0000.0000.0000.0000.000
52A52LEU00.0590.02738.783-0.001-0.0010.0000.0000.0000.000
53A53ASN00.001-0.00936.1510.0010.0010.0000.0000.0000.000
54A54GLN0-0.032-0.00936.2610.0010.0010.0000.0000.0000.000
55A55ILE0-0.053-0.02340.2150.0020.0020.0000.0000.0000.000
56A56ALA0-0.036-0.02143.1550.0010.0010.0000.0000.0000.000
57A57THR0-0.044-0.01842.677-0.004-0.0040.0000.0000.0000.000
58A58VAL00.0160.01042.7590.0020.0020.0000.0000.0000.000
59A59THR0-0.0070.00242.954-0.004-0.0040.0000.0000.0000.000
60A60ALA00.0450.00444.1980.0030.0030.0000.0000.0000.000
61A61PRO0-0.049-0.00645.942-0.002-0.0020.0000.0000.0000.000
62A62ASP-1-0.807-0.89348.528-0.044-0.0440.0000.0000.0000.000
63A63PRO0-0.023-0.05146.9780.0010.0010.0000.0000.0000.000
64A64ARG10.9160.95848.0300.0460.0460.0000.0000.0000.000
65A65THR0-0.0090.01550.1050.0030.0030.0000.0000.0000.000
66A66LEU0-0.0070.00244.230-0.003-0.0030.0000.0000.0000.000
67A67VAL0-0.032-0.00947.9060.0030.0030.0000.0000.0000.000
68A68VAL00.016-0.00746.369-0.002-0.0020.0000.0000.0000.000
69A69GLN0-0.0300.00147.5120.0000.0000.0000.0000.0000.000
70A70SER0-0.006-0.02047.306-0.001-0.0010.0000.0000.0000.000
71A71TRP00.0180.00846.5820.0020.0020.0000.0000.0000.000
72A72ASP-1-0.810-0.89349.595-0.013-0.0130.0000.0000.0000.000
73A73GLN00.0430.01151.3070.0000.0000.0000.0000.0000.000
74A74ASN0-0.006-0.02653.1100.0000.0000.0000.0000.0000.000
75A75ALA00.0310.02247.9320.0010.0010.0000.0000.0000.000
76A76LEU00.0360.02249.4360.0000.0000.0000.0000.0000.000
77A77LYS10.8390.92951.1760.0130.0130.0000.0000.0000.000
78A78ALA0-0.004-0.01748.9240.0000.0000.0000.0000.0000.000
79A79ILE00.0420.03746.1720.0000.0000.0000.0000.0000.000
80A80GLU-1-0.814-0.91547.770-0.017-0.0170.0000.0000.0000.000
81A81LYS10.7480.87250.1830.0080.0080.0000.0000.0000.000
82A82ALA00.0620.03944.8480.0020.0020.0000.0000.0000.000
83A83ILE0-0.045-0.01845.292-0.001-0.0010.0000.0000.0000.000
84A84ARG10.8000.92145.9160.0080.0080.0000.0000.0000.000
85A85ASP-1-0.807-0.93245.556-0.008-0.0080.0000.0000.0000.000
86A86SER00.0500.03442.5750.0010.0010.0000.0000.0000.000
87A87ASP-1-0.856-0.93642.287-0.024-0.0240.0000.0000.0000.000
88A88LEU0-0.016-0.04741.728-0.002-0.0020.0000.0000.0000.000
89A89GLY00.0170.03045.388-0.002-0.0020.0000.0000.0000.000
90A90LEU0-0.011-0.00346.032-0.002-0.0020.0000.0000.0000.000
91A91ASN0-0.015-0.01650.1780.0030.0030.0000.0000.0000.000
92A92PRO0-0.020-0.01250.505-0.001-0.0010.0000.0000.0000.000
93A93SER0-0.0050.02453.2100.0010.0010.0000.0000.0000.000
94A94ASN0-0.010-0.03155.592-0.001-0.0010.0000.0000.0000.000
95A95LYS10.9190.95556.5870.0220.0220.0000.0000.0000.000
96A96GLY00.0100.01156.786-0.001-0.0010.0000.0000.0000.000
97A97ASP-1-0.892-0.94552.262-0.030-0.0300.0000.0000.0000.000
98A98ALA00.0520.00251.227-0.001-0.0010.0000.0000.0000.000
99A99LEU0-0.0420.00550.2440.0010.0010.0000.0000.0000.000
100A100TYR0-0.015-0.00651.454-0.003-0.0030.0000.0000.0000.000
101A101ILE00.014-0.01148.1520.0020.0020.0000.0000.0000.000
102A102ASN00.0510.02050.621-0.004-0.0040.0000.0000.0000.000
103A103ILE0-0.037-0.00846.8840.0020.0020.0000.0000.0000.000
104A104PRO0-0.062-0.01750.072-0.001-0.0010.0000.0000.0000.000
105A105PRO0-0.001-0.00850.131-0.001-0.0010.0000.0000.0000.000
106A106LEU00.0250.01244.8910.0030.0030.0000.0000.0000.000
107A107THR00.0530.01649.0750.0000.0000.0000.0000.0000.000
108A108GLU-1-0.909-0.97748.315-0.037-0.0370.0000.0000.0000.000
109A109GLU-1-1.004-0.99346.781-0.020-0.0200.0000.0000.0000.000
110A110ARG00.1680.09344.622-0.002-0.0020.0000.0000.0000.000
111A111ARG10.9601.00043.5150.0390.0390.0000.0000.0000.000
112A112LYS10.9150.96843.3980.0230.0230.0000.0000.0000.000
113A113ASP-1-0.923-0.98741.234-0.026-0.0260.0000.0000.0000.000
114A114LEU0-0.0050.01439.365-0.001-0.0010.0000.0000.0000.000
115A115VAL00.0220.01438.305-0.004-0.0040.0000.0000.0000.000
116A116ARG10.8880.95437.8030.0250.0250.0000.0000.0000.000
117A117ALA00.0320.02035.473-0.002-0.0020.0000.0000.0000.000
118A118VAL00.0210.02533.708-0.003-0.0030.0000.0000.0000.000
119A119ARG10.9450.96332.7410.0610.0610.0000.0000.0000.000
120A120GLN0-0.032-0.00431.647-0.005-0.0050.0000.0000.0000.000
121A121TYR00.0650.01729.351-0.001-0.0010.0000.0000.0000.000
122A122ALA0-0.009-0.00428.021-0.008-0.0080.0000.0000.0000.000
123A123GLU-1-0.873-0.95027.544-0.103-0.1030.0000.0000.0000.000
124A124GLU-1-0.927-0.95925.848-0.049-0.0490.0000.0000.0000.000
125A125GLY00.0060.01123.878-0.005-0.0050.0000.0000.0000.000
126A126ARG10.7570.85422.6930.0930.0930.0000.0000.0000.000
127A127VAL0-0.028-0.00322.085-0.014-0.0140.0000.0000.0000.000
128A128ALA00.0160.01419.601-0.002-0.0020.0000.0000.0000.000
129A129ILE00.0380.01118.075-0.018-0.0180.0000.0000.0000.000
130A130ARG10.9130.94817.8650.1040.1040.0000.0000.0000.000
131A131ASN00.0210.00316.807-0.012-0.0120.0000.0000.0000.000
132A132ILE00.0230.03013.047-0.005-0.0050.0000.0000.0000.000
133A133ARG10.8790.94613.0930.1840.1840.0000.0000.0000.000
134A134ARG10.9020.94813.9150.0240.0240.0000.0000.0000.000
135A135GLU-1-0.922-0.96310.195-0.093-0.0930.0000.0000.0000.000
136A136ALA00.0100.0059.396-0.013-0.0130.0000.0000.0000.000
137A137LEU00.001-0.0119.881-0.078-0.0780.0000.0000.0000.000
138A138ASP-1-0.925-0.95010.392-0.045-0.0450.0000.0000.0000.000
139A139LYS10.8160.8734.7140.3560.473-0.001-0.002-0.1140.000
140A140LEU00.0150.0197.177-0.034-0.0340.0000.0000.0000.000
141A141LYS10.9570.9859.1430.0380.0380.0000.0000.0000.000
142A142LYS10.8530.9187.271-0.196-0.1960.0000.0000.0000.000
143A143LEU00.1040.0554.121-0.1230.1220.001-0.042-0.2040.000
144A144ALA00.0340.0207.150-0.032-0.0320.0000.0000.0000.000
145A145LYS10.9040.94610.689-0.111-0.1110.0000.0000.0000.000
146A146GLU-1-0.994-0.9976.0851.7581.7580.0000.0000.0000.000
147A147LEU0-0.028-0.0216.560-0.018-0.0180.0000.0000.0000.000
148A148HIS0-0.080-0.02010.142-0.077-0.0770.0000.0000.0000.000
149A149LEU0-0.0180.00610.026-0.048-0.0480.0000.0000.0000.000
150A150SER00.004-0.00514.0680.0770.0770.0000.0000.0000.000
151A151GLU-1-0.932-0.98816.679-0.223-0.2230.0000.0000.0000.000
152A152ASP-1-0.843-0.93218.458-0.294-0.2940.0000.0000.0000.000
153A153GLU-1-0.917-0.95314.352-0.606-0.6060.0000.0000.0000.000
154A154THR0-0.038-0.01313.606-0.081-0.0810.0000.0000.0000.000
155A155LYS10.9650.98114.6260.2080.2080.0000.0000.0000.000
156A156ARG10.8320.92115.8990.5570.5570.0000.0000.0000.000
157A157ALA00.0350.00111.424-0.021-0.0210.0000.0000.0000.000
158A158GLU-1-0.912-0.96813.301-0.332-0.3320.0000.0000.0000.000
159A159ALA0-0.0110.00115.3320.0170.0170.0000.0000.0000.000
160A160GLU-1-0.883-0.92712.812-0.619-0.6190.0000.0000.0000.000
161A161ILE0-0.004-0.00310.2930.0030.0030.0000.0000.0000.000
162A162GLN00.0070.00914.1960.0570.0570.0000.0000.0000.000
163A163LYS10.9380.98116.9450.5430.5430.0000.0000.0000.000
164A164ILE0-0.021-0.00312.8670.0120.0120.0000.0000.0000.000
165A165THR0-0.017-0.04516.6840.0390.0390.0000.0000.0000.000
166A166ASP-1-0.877-0.95018.369-0.224-0.2240.0000.0000.0000.000
167A167GLU-1-0.948-0.96519.555-0.361-0.3610.0000.0000.0000.000
168A168PHE0-0.019-0.02217.0690.0160.0160.0000.0000.0000.000
169A169ILE0-0.0370.00321.4100.0260.0260.0000.0000.0000.000
170A170ALA00.0460.03123.7930.0180.0180.0000.0000.0000.000
171A171LYS10.8900.94823.9550.1960.1960.0000.0000.0000.000
172A172ALA00.004-0.00724.3720.0140.0140.0000.0000.0000.000
173A173ASP-1-0.817-0.90826.164-0.122-0.1220.0000.0000.0000.000
174A174GLN0-0.017-0.00328.9620.0030.0030.0000.0000.0000.000
175A175LEU0-0.021-0.01526.6330.0070.0070.0000.0000.0000.000
176A176ALA00.0000.00230.3500.0090.0090.0000.0000.0000.000
177A177GLU-1-0.876-0.95432.162-0.096-0.0960.0000.0000.0000.000
178A178LYS10.9660.99232.7470.1180.1180.0000.0000.0000.000
179A179LYS10.8880.96334.5040.0770.0770.0000.0000.0000.000
180A180GLU-1-0.931-0.97936.243-0.066-0.0660.0000.0000.0000.000
181A181GLN0-0.037-0.02138.2870.0040.0040.0000.0000.0000.000
182A182GLU-1-0.935-0.96237.344-0.074-0.0740.0000.0000.0000.000
183A183ILE0-0.017-0.01238.1520.0050.0050.0000.0000.0000.000
184A184LEU0-0.124-0.04542.0310.0050.0050.0000.0000.0000.000
185A185GLY0-0.025-0.01244.3360.0010.0010.0000.0000.0000.000