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: V5QK1

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 OptAll
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 -1798651.016047
FMO2-HF: Nuclear repulsion 1726161.294405
FMO2-HF: Total energy -72489.721642
FMO2-MP2: Total energy -72705.355421


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.
-10.935-12.61111.52-5.27-4.573-0.036
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 : -0.018 / q_NPA : -0.012
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].
3A3LEU00.0660.0123.884-0.8271.151-0.011-1.090-0.8770.006
4A4LYS10.9420.9846.5312.0432.0430.0000.0000.0000.000
5A5GLU-1-0.773-0.8551.813-12.808-17.08511.531-4.107-3.147-0.042
6A6LEU00.0210.0294.7050.8420.988-0.001-0.009-0.1360.000
7A7TYR00.0340.0195.9810.5540.5540.0000.0000.0000.000
8A8ALA0-0.0090.0017.9160.2910.2910.0000.0000.0000.000
9A9GLU-1-0.821-0.8935.5200.6040.6040.0000.0000.0000.000
10A10THR00.006-0.0188.7070.1850.1850.0000.0000.0000.000
11A11ARG10.9600.97611.2290.3320.3320.0000.0000.0000.000
12A12SER0-0.054-0.01711.5120.0600.0600.0000.0000.0000.000
13A13HIS00.0360.0008.9670.0060.0060.0000.0000.0000.000
14A14MET0-0.0260.01814.0310.0090.0090.0000.0000.0000.000
15A15GLN0-0.034-0.02316.485-0.020-0.0200.0000.0000.0000.000
16A16LYS10.7880.88515.429-0.115-0.1150.0000.0000.0000.000
17A17SER00.006-0.00617.6120.0110.0110.0000.0000.0000.000
18A18LEU0-0.024-0.00820.071-0.003-0.0030.0000.0000.0000.000
19A19GLU-1-0.757-0.86520.1410.0960.0960.0000.0000.0000.000
20A20VAL0-0.0050.00221.7380.0050.0050.0000.0000.0000.000
21A21LEU0-0.0100.01224.129-0.003-0.0030.0000.0000.0000.000
22A22GLU-1-0.857-0.94226.012-0.018-0.0180.0000.0000.0000.000
23A23HIS0-0.029-0.01026.974-0.004-0.0040.0000.0000.0000.000
24A24ASN00.000-0.00927.7530.0060.0060.0000.0000.0000.000
25A25LEU0-0.033-0.01629.934-0.004-0.0040.0000.0000.0000.000
26A26ALA0-0.042-0.02031.570-0.005-0.0050.0000.0000.0000.000
27A27GLY0-0.038-0.00432.7450.0000.0000.0000.0000.0000.000
28A28LEU0-0.033-0.01334.4500.0010.0010.0000.0000.0000.000
29A29ARG10.7350.82537.068-0.035-0.0350.0000.0000.0000.000
30A30THR00.029-0.01338.800-0.001-0.0010.0000.0000.0000.000
31A31GLY00.010-0.00141.2250.0020.0020.0000.0000.0000.000
32A32ARG10.7960.87243.258-0.024-0.0240.0000.0000.0000.000
33A33ALA00.0020.01944.3470.0030.0030.0000.0000.0000.000
34A34ASN0-0.0120.01438.089-0.001-0.0010.0000.0000.0000.000
35A35PRO00.0890.03140.1300.0040.0040.0000.0000.0000.000
36A36ALA0-0.018-0.02135.8070.0050.0050.0000.0000.0000.000
37A37LEU0-0.0130.00437.4710.0060.0060.0000.0000.0000.000
38A38LEU00.0290.00339.4730.0040.0040.0000.0000.0000.000
39A39LEU0-0.0220.00234.0710.0030.0030.0000.0000.0000.000
40A40HIS00.0360.01031.6930.0100.0100.0000.0000.0000.000
41A41LEU0-0.0140.01336.6560.0070.0070.0000.0000.0000.000
42A42LYS10.9370.97534.960-0.123-0.1230.0000.0000.0000.000
43A43VAL0-0.017-0.01040.213-0.004-0.0040.0000.0000.0000.000
44A44GLU-1-0.867-0.93143.4410.0880.0880.0000.0000.0000.000
45A45TYR0-0.057-0.06444.691-0.005-0.0050.0000.0000.0000.000
46A46TYR0-0.046-0.02945.4650.0030.0030.0000.0000.0000.000
47A47GLY00.0360.03646.2500.0020.0020.0000.0000.0000.000
48A48ALA0-0.017-0.00341.3130.0070.0070.0000.0000.0000.000
49A49HIS0-0.048-0.03339.598-0.002-0.0020.0000.0000.0000.000
50A50VAL00.0100.00338.9230.0060.0060.0000.0000.0000.000
51A51PRO00.0050.00935.712-0.004-0.0040.0000.0000.0000.000
52A52LEU00.0390.01438.577-0.003-0.0030.0000.0000.0000.000
53A53ASN0-0.051-0.04935.866-0.002-0.0020.0000.0000.0000.000
54A54GLN0-0.024-0.00635.3780.0010.0010.0000.0000.0000.000
55A55ILE0-0.052-0.01939.9350.0000.0000.0000.0000.0000.000
56A56ALA0-0.026-0.00543.114-0.004-0.0040.0000.0000.0000.000
57A57THR0-0.043-0.02542.7470.0010.0010.0000.0000.0000.000
58A58VAL00.0000.00742.217-0.002-0.0020.0000.0000.0000.000
59A59THR0-0.017-0.01142.973-0.003-0.0030.0000.0000.0000.000
60A60ALA00.0470.01944.7950.0020.0020.0000.0000.0000.000
61A61PRO0-0.040-0.01346.490-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.748-0.87449.535-0.003-0.0030.0000.0000.0000.000
63A63PRO0-0.044-0.02747.2810.0020.0020.0000.0000.0000.000
64A64ARG10.8880.95248.3990.0050.0050.0000.0000.0000.000
65A65THR0-0.041-0.01750.0250.0030.0030.0000.0000.0000.000
66A66LEU0-0.0070.00044.325-0.001-0.0010.0000.0000.0000.000
67A67VAL0-0.016-0.00947.8560.0010.0010.0000.0000.0000.000
68A68VAL0-0.004-0.01645.8110.0010.0010.0000.0000.0000.000
69A69GLN0-0.0130.00047.7190.0000.0000.0000.0000.0000.000
70A70SER0-0.015-0.03647.2860.0040.0040.0000.0000.0000.000
71A71TRP00.0210.01446.472-0.002-0.0020.0000.0000.0000.000
72A72ASP-1-0.760-0.82849.2830.0500.0500.0000.0000.0000.000
73A73GLN00.0780.03151.0190.0000.0000.0000.0000.0000.000
74A74ASN0-0.027-0.03752.895-0.003-0.0030.0000.0000.0000.000
75A75ALA00.0570.03147.5370.0010.0010.0000.0000.0000.000
76A76LEU0-0.0090.01349.2490.0010.0010.0000.0000.0000.000
77A77LYS10.8480.91451.094-0.039-0.0390.0000.0000.0000.000
78A78ALA0-0.013-0.00648.6350.0000.0000.0000.0000.0000.000
79A79ILE00.0410.01545.7060.0010.0010.0000.0000.0000.000
80A80GLU-1-0.825-0.91047.8970.0340.0340.0000.0000.0000.000
81A81LYS10.8390.91050.471-0.046-0.0460.0000.0000.0000.000
82A82ALA00.0650.04845.1610.0020.0020.0000.0000.0000.000
83A83ILE0-0.043-0.01045.2800.0010.0010.0000.0000.0000.000
84A84ARG10.7570.87846.434-0.053-0.0530.0000.0000.0000.000
85A85ASP-1-0.842-0.92646.0500.0580.0580.0000.0000.0000.000
86A86SER00.0420.01142.6180.0060.0060.0000.0000.0000.000
87A87ASP-1-0.844-0.90642.6910.0420.0420.0000.0000.0000.000
88A88LEU00.0290.01341.696-0.005-0.0050.0000.0000.0000.000
89A89GLY00.0180.03545.543-0.004-0.0040.0000.0000.0000.000
90A90LEU0-0.016-0.01346.013-0.003-0.0030.0000.0000.0000.000
91A91ASN0-0.027-0.01550.0940.0030.0030.0000.0000.0000.000
92A92PRO0-0.024-0.01150.203-0.002-0.0020.0000.0000.0000.000
93A93SER00.0100.01052.938-0.001-0.0010.0000.0000.0000.000
94A94ASN0-0.027-0.03755.337-0.001-0.0010.0000.0000.0000.000
95A95LYS10.9030.95756.210-0.018-0.0180.0000.0000.0000.000
96A96GLY00.0190.00556.986-0.002-0.0020.0000.0000.0000.000
97A97ASP-1-0.853-0.91852.3910.0250.0250.0000.0000.0000.000
98A98ALA00.0170.00851.5140.0020.0020.0000.0000.0000.000
99A99LEU0-0.055-0.01049.488-0.001-0.0010.0000.0000.0000.000
100A100TYR00.005-0.00551.385-0.002-0.0020.0000.0000.0000.000
101A101ILE00.003-0.00547.8970.0010.0010.0000.0000.0000.000
102A102ASN00.0190.01950.963-0.003-0.0030.0000.0000.0000.000
103A103ILE0-0.027-0.01647.1020.0030.0030.0000.0000.0000.000
104A104PRO0-0.032-0.00649.810-0.003-0.0030.0000.0000.0000.000
105A105PRO00.005-0.00849.8550.0000.0000.0000.0000.0000.000
106A106LEU0-0.021-0.00844.6860.0020.0020.0000.0000.0000.000
107A107THR00.0250.00648.579-0.002-0.0020.0000.0000.0000.000
108A108GLU-1-0.791-0.90548.1470.0010.0010.0000.0000.0000.000
109A109GLU-1-0.866-0.90447.6250.0140.0140.0000.0000.0000.000
110A110ARG00.1180.07544.7710.0000.0000.0000.0000.0000.000
111A111ARG10.8140.90843.3870.0040.0040.0000.0000.0000.000
112A112LYS10.8260.90242.801-0.012-0.0120.0000.0000.0000.000
113A113ASP-1-0.846-0.92140.6600.0270.0270.0000.0000.0000.000
114A114LEU0-0.028-0.00538.9140.0020.0020.0000.0000.0000.000
115A115VAL00.0240.01137.879-0.001-0.0010.0000.0000.0000.000
116A116ARG10.8370.90937.116-0.022-0.0220.0000.0000.0000.000
117A117ALA00.0230.02034.7350.0000.0000.0000.0000.0000.000
118A118VAL00.0010.00833.1270.0020.0020.0000.0000.0000.000
119A119ARG10.8530.89832.1770.0250.0250.0000.0000.0000.000
120A120GLN0-0.0260.00430.890-0.012-0.0120.0000.0000.0000.000
121A121TYR00.0600.01928.7280.0010.0010.0000.0000.0000.000
122A122ALA0-0.008-0.00227.355-0.001-0.0010.0000.0000.0000.000
123A123GLU-1-0.769-0.85226.532-0.065-0.0650.0000.0000.0000.000
124A124GLU-1-0.895-0.95425.2700.0510.0510.0000.0000.0000.000
125A125GLY00.0300.01923.0300.0050.0050.0000.0000.0000.000
126A126ARG10.7740.85021.9550.0450.0450.0000.0000.0000.000
127A127VAL0-0.030-0.02021.779-0.022-0.0220.0000.0000.0000.000
128A128ALA00.0190.02018.938-0.005-0.0050.0000.0000.0000.000
129A129ILE00.001-0.00317.500-0.014-0.0140.0000.0000.0000.000
130A130ARG10.8410.88817.3200.0440.0440.0000.0000.0000.000
131A131ASN0-0.018-0.00716.124-0.036-0.0360.0000.0000.0000.000
132A132ILE00.0200.02112.239-0.022-0.0220.0000.0000.0000.000
133A133ARG10.7950.87312.5270.2010.2010.0000.0000.0000.000
134A134ARG10.7970.89113.023-0.056-0.0560.0000.0000.0000.000
135A135GLU-1-0.820-0.9049.8670.0600.0600.0000.0000.0000.000
136A136ALA00.0020.0058.889-0.118-0.1180.0000.0000.0000.000
137A137LEU00.020-0.0019.551-0.242-0.2420.0000.0000.0000.000
138A138ASP-1-0.884-0.93710.135-0.311-0.3110.0000.0000.0000.000
139A139LYS10.8280.8954.411-0.509-0.354-0.001-0.005-0.1480.000
140A140LEU00.0000.0096.885-0.375-0.3750.0000.0000.0000.000
141A141LYS10.8710.9349.1230.3230.3230.0000.0000.0000.000
142A142LYS10.8080.8986.5250.6180.6180.0000.0000.0000.000
143A143LEU00.0440.0193.782-0.0760.2460.002-0.059-0.2650.000
144A144ALA00.0360.0096.901-0.018-0.0180.0000.0000.0000.000
145A145LYS10.9400.97210.5350.5250.5250.0000.0000.0000.000
146A146GLU-1-0.926-0.9555.396-0.737-0.7370.0000.0000.0000.000
147A147LEU0-0.026-0.0226.7560.0260.0260.0000.0000.0000.000
148A148HIS0-0.075-0.02610.3010.1250.1250.0000.0000.0000.000
149A149LEU0-0.0240.00710.1580.0130.0130.0000.0000.0000.000
150A150SER0-0.023-0.04514.2320.1250.1250.0000.0000.0000.000
151A151GLU-1-0.845-0.92616.602-0.500-0.5000.0000.0000.0000.000
152A152ASP-1-0.889-0.95018.279-0.537-0.5370.0000.0000.0000.000
153A153GLU-1-0.851-0.88814.156-1.081-1.0810.0000.0000.0000.000
154A154THR0-0.055-0.03713.590-0.138-0.1380.0000.0000.0000.000
155A155LYS10.8750.93314.5980.4840.4840.0000.0000.0000.000
156A156ARG10.8390.91815.7540.7600.7600.0000.0000.0000.000
157A157ALA0-0.011-0.01711.6370.0050.0050.0000.0000.0000.000
158A158GLU-1-0.836-0.92513.656-0.619-0.6190.0000.0000.0000.000
159A159ALA00.0100.00215.5070.0650.0650.0000.0000.0000.000
160A160GLU-1-0.847-0.89713.260-0.623-0.6230.0000.0000.0000.000
161A161ILE00.000-0.00310.5320.0550.0550.0000.0000.0000.000
162A162GLN00.0130.04114.6130.0800.0800.0000.0000.0000.000
163A163LYS10.8190.91916.7610.5970.5970.0000.0000.0000.000
164A164ILE00.0280.01213.2740.0440.0440.0000.0000.0000.000
165A165THR0-0.024-0.04816.9870.0630.0630.0000.0000.0000.000
166A166ASP-1-0.798-0.89218.596-0.215-0.2150.0000.0000.0000.000
167A167GLU-1-0.916-0.95919.383-0.328-0.3280.0000.0000.0000.000
168A168PHE0-0.010-0.01317.4970.0350.0350.0000.0000.0000.000
169A169ILE0-0.043-0.00621.5060.0310.0310.0000.0000.0000.000
170A170ALA00.0410.02624.1620.0210.0210.0000.0000.0000.000
171A171LYS10.8450.92324.0060.0780.0780.0000.0000.0000.000
172A172ALA00.0300.00224.4990.0180.0180.0000.0000.0000.000
173A173ASP-1-0.819-0.90326.451-0.068-0.0680.0000.0000.0000.000
174A174GLN0-0.037-0.01129.1970.0130.0130.0000.0000.0000.000
175A175LEU0-0.047-0.02426.9470.0070.0070.0000.0000.0000.000
176A176ALA00.0240.01630.7010.0090.0090.0000.0000.0000.000
177A177GLU-1-0.776-0.87032.447-0.056-0.0560.0000.0000.0000.000
178A178LYS10.8180.89933.6570.0640.0640.0000.0000.0000.000
179A179LYS10.8790.92634.2480.0000.0000.0000.0000.0000.000
180A180GLU-1-0.838-0.90936.245-0.020-0.0200.0000.0000.0000.000
181A181GLN0-0.063-0.04838.0780.0030.0030.0000.0000.0000.000
182A182GLU-1-0.801-0.88236.797-0.002-0.0020.0000.0000.0000.000
183A183ILE0-0.0140.00938.2220.0040.0040.0000.0000.0000.000
184A184LEU0-0.014-0.00442.0020.0020.0020.0000.0000.0000.000
185A185GLY0-0.039-0.00944.1090.0010.0010.0000.0000.0000.000