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: YQKN2

Calculation Name: 1EL6-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1EL6

Chain ID: A

ChEMBL ID:

UniProt ID: P10929

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 209
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1894722.506954
FMO2-HF: Nuclear repulsion 1816391.034187
FMO2-HF: Total energy -78331.472767
FMO2-MP2: Total energy -78564.037889


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:11:ACE )


Summations of interaction energy for fragment #1(A:11:ACE )
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.
2.3783.2590.034-0.409-0.5060.001
Interaction energy analysis for fragmet #1(A:11:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.006
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].
3A13ARG 10.9060.9583.8611.2181.837-0.005-0.296-0.3170.000
4A14LEU 00.0840.0197.0930.1560.1560.0000.0000.0000.000
5A15ALA 00.0400.0469.9770.0410.0410.0000.0000.0000.000
6A16ASP -1-0.793-0.9076.642-1.943-1.9430.0000.0000.0000.000
7A17PHE 0-0.080-0.0467.0730.0840.0840.0000.0000.0000.000
8A18LEU 0-0.0270.00412.1600.1090.1090.0000.0000.0000.000
9A19GLY 00.0530.02615.064-0.016-0.0160.0000.0000.0000.000
10A20PHE 0-0.018-0.00317.9960.0100.0100.0000.0000.0000.000
11A21ARG 10.9410.96519.7260.1460.1460.0000.0000.0000.000
12A22PRO 00.0360.02622.3240.0060.0060.0000.0000.0000.000
13A23LYS 10.9680.98624.1290.1220.1220.0000.0000.0000.000
14A24THR 00.019-0.01227.4160.0010.0010.0000.0000.0000.000
15A25GLY 0-0.022-0.01930.2070.0040.0040.0000.0000.0000.000
16A26ASP -1-0.834-0.90125.368-0.143-0.1430.0000.0000.0000.000
17A27ILE 00.0020.02026.836-0.006-0.0060.0000.0000.0000.000
18A28ASP -1-0.891-0.94625.708-0.112-0.1120.0000.0000.0000.000
19A29VAL 0-0.0170.01220.2640.0030.0030.0000.0000.0000.000
20A30MET 00.001-0.01422.2420.0070.0070.0000.0000.0000.000
21A31ASN 0-0.041-0.01124.9440.0100.0100.0000.0000.0000.000
22A32ARG 10.8850.93924.9910.1110.1110.0000.0000.0000.000
23A33GLN 0-0.029-0.01420.030-0.011-0.0110.0000.0000.0000.000
24A34SER 0-0.036-0.03923.7580.0020.0020.0000.0000.0000.000
25A35VAL 00.0080.02220.145-0.019-0.0190.0000.0000.0000.000
26A36GLY 0-0.006-0.01617.7690.0100.0100.0000.0000.0000.000
27A37SER 0-0.095-0.04817.878-0.014-0.0140.0000.0000.0000.000
28A38VAL 0-0.0170.01314.846-0.031-0.0310.0000.0000.0000.000
29A39THR 00.0250.00212.4670.0210.0210.0000.0000.0000.000
30A40ILE 00.039-0.00611.738-0.032-0.0320.0000.0000.0000.000
31A41SER 00.0260.0088.1270.0500.0500.0000.0000.0000.000
32A42GLN 00.0370.0318.513-0.024-0.0240.0000.0000.0000.000
33A43LEU 0-0.0010.01410.7150.0470.0470.0000.0000.0000.000
34A44ALA 0-0.042-0.0159.0350.0510.0510.0000.0000.0000.000
35A45LYS 10.8180.9163.2143.5393.8010.039-0.113-0.1890.001
36A46GLY 0-0.0040.0059.0400.0400.0400.0000.0000.0000.000
37A47PHE 0-0.033-0.01712.1240.0320.0320.0000.0000.0000.000
38A48TYR 00.000-0.02913.684-0.010-0.0100.0000.0000.0000.000
39A49GLU -1-0.950-0.95616.622-0.190-0.1900.0000.0000.0000.000
40A50PRO 0-0.0100.00116.541-0.045-0.0450.0000.0000.0000.000
41A51ASN 0-0.020-0.03013.122-0.062-0.0620.0000.0000.0000.000
42A52ILE 00.014-0.00714.4330.0140.0140.0000.0000.0000.000
43A53GLU -1-0.900-0.9399.069-1.083-1.0830.0000.0000.0000.000
44A54SER 0-0.038-0.03212.1520.0460.0460.0000.0000.0000.000
45A55ALA 00.0580.02014.2290.0490.0490.0000.0000.0000.000
46A56ILE 0-0.037-0.01914.2490.0460.0460.0000.0000.0000.000
47A57ASN 0-0.021-0.01510.6810.0860.0860.0000.0000.0000.000
48A58ASP -1-0.816-0.90515.030-0.230-0.2300.0000.0000.0000.000
49A59VAL 0-0.010-0.01318.3580.0320.0320.0000.0000.0000.000
50A60HIS 0-0.047-0.01215.0080.0230.0230.0000.0000.0000.000
51A61ASN 00.008-0.01416.7880.0400.0400.0000.0000.0000.000
52A62PHE 0-0.053-0.01319.9320.0190.0190.0000.0000.0000.000
53A63SER 0-0.104-0.05721.6600.0180.0180.0000.0000.0000.000
54A64ILE 0-0.0240.01020.2770.0130.0130.0000.0000.0000.000
55A65LYS 10.9290.96223.4730.0890.0890.0000.0000.0000.000
56A66ASP -1-0.839-0.90725.121-0.075-0.0750.0000.0000.0000.000
57A67VAL 0-0.0080.00725.4320.0030.0030.0000.0000.0000.000
58A68GLY 00.0120.01227.9560.0000.0000.0000.0000.0000.000
59A69THR 0-0.082-0.06029.4360.0000.0000.0000.0000.0000.000
60A70ILE 0-0.003-0.00331.9830.0020.0020.0000.0000.0000.000
61A71ILE 0-0.0100.00530.769-0.003-0.0030.0000.0000.0000.000
62A72THR 0-0.011-0.00435.1860.0050.0050.0000.0000.0000.000
63A73ASN 0-0.0060.01236.9000.0000.0000.0000.0000.0000.000
64A74LYS 10.9930.97540.0480.0310.0310.0000.0000.0000.000
65A75THR 0-0.019-0.00139.2960.0020.0020.0000.0000.0000.000
66A76GLY 00.0470.03041.0010.0020.0020.0000.0000.0000.000
67A77VAL 0-0.029-0.01635.7590.0010.0010.0000.0000.0000.000
68A78SER 00.0350.01932.972-0.003-0.0030.0000.0000.0000.000
69A79PRO 0-0.031-0.03231.162-0.002-0.0020.0000.0000.0000.000
70A80GLU -1-0.826-0.89628.809-0.034-0.0340.0000.0000.0000.000
71A81GLY 0-0.0050.01126.851-0.001-0.0010.0000.0000.0000.000
72A82VAL 0-0.032-0.02027.9040.0050.0050.0000.0000.0000.000
73A83SER 00.0290.00724.732-0.007-0.0070.0000.0000.0000.000
74A84GLN 00.0030.01126.988-0.003-0.0030.0000.0000.0000.000
75A85THR 0-0.022-0.00828.4030.0020.0020.0000.0000.0000.000
76A86ASP -1-0.737-0.81729.266-0.028-0.0280.0000.0000.0000.000
77A87TYR 00.0320.01732.0200.0040.0040.0000.0000.0000.000
78A88TRP 0-0.040-0.02325.4800.0000.0000.0000.0000.0000.000
79A89ALA 00.0180.00033.0240.0030.0030.0000.0000.0000.000
80A90PHE 00.018-0.00531.2500.0000.0000.0000.0000.0000.000
81A91SER 0-0.023-0.01436.9450.0000.0000.0000.0000.0000.000
82A92GLY 00.0480.02839.1830.0000.0000.0000.0000.0000.000
83A93THR 0-0.023-0.02940.9700.0010.0010.0000.0000.0000.000
84A94VAL 0-0.0690.02336.200-0.001-0.0010.0000.0000.0000.000
85A95THR 0-0.009-0.04538.1330.0010.0010.0000.0000.0000.000
86A96ASP -1-0.801-0.94736.2540.0180.0180.0000.0000.0000.000
87A97ASP -1-0.948-0.94938.8810.0090.0090.0000.0000.0000.000
88A98SER 0-0.066-0.02138.3980.0000.0000.0000.0000.0000.000
89A99LEU 0-0.085-0.03935.7850.0020.0020.0000.0000.0000.000
90A100PRO 0-0.0100.01040.473-0.002-0.0020.0000.0000.0000.000
91A101PRO 00.010-0.00341.7130.0010.0010.0000.0000.0000.000
92A102GLY 00.0280.02741.0820.0010.0010.0000.0000.0000.000
93A103SER 0-0.047-0.04537.9360.0030.0030.0000.0000.0000.000
94A104PRO 0-0.040-0.01733.667-0.001-0.0010.0000.0000.0000.000
95A105ILE 00.0080.00032.2450.0010.0010.0000.0000.0000.000
96A106THR 0-0.018-0.00925.8040.0040.0040.0000.0000.0000.000
97A107VAL 0-0.009-0.00329.238-0.003-0.0030.0000.0000.0000.000
98A108LEU 00.0050.00723.5410.0030.0030.0000.0000.0000.000
99A109VAL 00.0280.02226.482-0.006-0.0060.0000.0000.0000.000
100A110PHE 00.010-0.00425.1420.0000.0000.0000.0000.0000.000
101A111GLY 0-0.013-0.00221.902-0.004-0.0040.0000.0000.0000.000
102A112LEU 0-0.016-0.00521.4750.0100.0100.0000.0000.0000.000
103A113PRO 00.003-0.00821.584-0.004-0.0040.0000.0000.0000.000
104A114VAL 00.0170.02224.6430.0040.0040.0000.0000.0000.000
105A115SER 0-0.029-0.00428.201-0.002-0.0020.0000.0000.0000.000
106A116ALA 00.020-0.00730.232-0.002-0.0020.0000.0000.0000.000
107A117THR 00.0480.01433.6520.0030.0030.0000.0000.0000.000
108A118THR 00.025-0.00536.884-0.002-0.0020.0000.0000.0000.000
109A119GLY 00.0160.00239.2460.0010.0010.0000.0000.0000.000
110A120MET 0-0.076-0.01036.289-0.001-0.0010.0000.0000.0000.000
111A121THR 00.0300.01440.454-0.002-0.0020.0000.0000.0000.000
112A122ALA 00.0540.02138.7430.0010.0010.0000.0000.0000.000
113A123ILE 00.0140.01138.1970.0010.0010.0000.0000.0000.000
114A124GLU -1-0.872-0.94638.7830.0190.0190.0000.0000.0000.000
115A125PHE 00.0250.00431.4290.0030.0030.0000.0000.0000.000
116A126VAL 00.0280.02534.0820.0020.0020.0000.0000.0000.000
117A127ALA 0-0.018-0.02033.8520.0010.0010.0000.0000.0000.000
118A128LYS 10.8760.94631.877-0.031-0.0310.0000.0000.0000.000
119A129VAL 00.0200.00929.2940.0040.0040.0000.0000.0000.000
120A130ARG 10.8750.92029.033-0.016-0.0160.0000.0000.0000.000
121A131VAL 0-0.0160.00127.7690.0020.0020.0000.0000.0000.000
122A132ALA 00.0570.03525.3410.0050.0050.0000.0000.0000.000
123A133LEU 0-0.011-0.00724.3360.0030.0030.0000.0000.0000.000
124A134GLN 0-0.034-0.01624.711-0.001-0.0010.0000.0000.0000.000
125A135GLU -1-0.927-0.96022.4160.0750.0750.0000.0000.0000.000
126A136ALA 0-0.021-0.00620.2120.0110.0110.0000.0000.0000.000
127A137ILE 0-0.019-0.00720.0540.0020.0020.0000.0000.0000.000
128A138ALA 0-0.034-0.01421.2510.0030.0030.0000.0000.0000.000
129A139SER 0-0.087-0.02316.5060.0110.0110.0000.0000.0000.000
130A140PHE 0-0.018-0.01316.1330.0070.0070.0000.0000.0000.000
131A141THR 00.0120.00215.941-0.011-0.0110.0000.0000.0000.000
132A142ALA 00.0040.00417.298-0.005-0.0050.0000.0000.0000.000
133A143ILE 0-0.033-0.03319.274-0.008-0.0080.0000.0000.0000.000
134A144ASN 0-0.012-0.00322.1620.0090.0090.0000.0000.0000.000
135A145SER 0-0.029-0.03124.0920.0050.0050.0000.0000.0000.000
136A146TYR 00.0150.00727.451-0.004-0.0040.0000.0000.0000.000
137A147LYS 10.9260.97230.1920.0000.0000.0000.0000.0000.000
138A148ASP -1-0.812-0.88033.9650.0140.0140.0000.0000.0000.000
139A149HIS 00.0190.01736.7080.0000.0000.0000.0000.0000.000
140A150PRO 0-0.051-0.02738.9700.0010.0010.0000.0000.0000.000
141A151THR 0-0.006-0.02142.1710.0000.0000.0000.0000.0000.000
142A152ASP -1-0.849-0.89241.3940.0010.0010.0000.0000.0000.000
143A153GLY 00.018-0.00340.5600.0000.0000.0000.0000.0000.000
144A154SER 0-0.102-0.07139.0430.0010.0010.0000.0000.0000.000
145A155LYS 10.8520.90936.5810.0040.0040.0000.0000.0000.000
146A156LEU 0-0.027-0.00931.8470.0020.0020.0000.0000.0000.000
147A157GLU -1-0.933-0.96732.912-0.007-0.0070.0000.0000.0000.000
148A158VAL 0-0.003-0.00626.9090.0040.0040.0000.0000.0000.000
149A159THR 00.0220.01926.974-0.005-0.0050.0000.0000.0000.000
150A160TYR 0-0.045-0.05222.9490.0060.0060.0000.0000.0000.000
151A161LEU 0-0.012-0.00518.465-0.001-0.0010.0000.0000.0000.000
152A162ASP -1-0.835-0.87119.494-0.070-0.0700.0000.0000.0000.000
153A163ASN 0-0.052-0.04221.3500.0030.0030.0000.0000.0000.000
154A164GLN 0-0.057-0.03118.445-0.004-0.0040.0000.0000.0000.000
155A165LYN 0-0.0100.03224.0780.0070.0070.0000.0000.0000.000
156A166HIS 10.7840.85921.5500.0590.0590.0000.0000.0000.000
157A167VAL 00.0510.03926.5890.0060.0060.0000.0000.0000.000
158A168LEU 0-0.039-0.02525.384-0.004-0.0040.0000.0000.0000.000
159A169SER 0-0.026-0.01328.9380.0020.0020.0000.0000.0000.000
160A170THR 00.015-0.00430.9650.0020.0020.0000.0000.0000.000
161A171TYR 0-0.075-0.03828.651-0.002-0.0020.0000.0000.0000.000
162A172SER 00.0270.01333.5550.0030.0030.0000.0000.0000.000
163A173THR 0-0.031-0.00930.5880.0000.0000.0000.0000.0000.000
164A174TYR 00.0600.02731.2170.0010.0010.0000.0000.0000.000
165A175GLY 00.0130.02535.7030.0010.0010.0000.0000.0000.000
166A176ILE 0-0.041-0.00334.824-0.001-0.0010.0000.0000.0000.000
167A177THR 0-0.027-0.02235.228-0.001-0.0010.0000.0000.0000.000
168A178ILE 0-0.015-0.00530.5380.0010.0010.0000.0000.0000.000
169A179SER 0-0.007-0.01333.515-0.003-0.0030.0000.0000.0000.000
170A180GLN 00.018-0.00929.2100.0010.0010.0000.0000.0000.000
171A181GLU -1-0.874-0.92433.048-0.011-0.0110.0000.0000.0000.000
172A182ILE 0-0.020-0.00631.6470.0020.0020.0000.0000.0000.000
173A183ILE 0-0.042-0.01333.9270.0010.0010.0000.0000.0000.000
174A184SER 0-0.017-0.02033.4930.0010.0010.0000.0000.0000.000
175A185GLU -1-0.913-0.96632.102-0.041-0.0410.0000.0000.0000.000
176A186SER 0-0.010-0.02227.4610.0000.0000.0000.0000.0000.000
177A187LYS 10.8280.91528.8130.0460.0460.0000.0000.0000.000
178A188PRO 00.0280.01127.085-0.002-0.0020.0000.0000.0000.000
179A189GLY 00.0360.01126.2950.0070.0070.0000.0000.0000.000
180A190TYR 00.0260.00523.089-0.005-0.0050.0000.0000.0000.000
181A191GLY 00.0270.00823.9820.0030.0030.0000.0000.0000.000
182A192THR 00.0250.03425.5230.0040.0040.0000.0000.0000.000
183A193TRP 0-0.087-0.06428.024-0.001-0.0010.0000.0000.0000.000
184A194ASN 00.0240.01231.8820.0040.0040.0000.0000.0000.000
185A195LEU 0-0.059-0.01835.316-0.002-0.0020.0000.0000.0000.000
186A196LEU 0-0.017-0.01237.7250.0020.0020.0000.0000.0000.000
187A197GLY 00.0280.01540.5620.0020.0020.0000.0000.0000.000
188A198ALA 0-0.038-0.02543.115-0.002-0.0020.0000.0000.0000.000
189A199GLN 00.0100.01245.4690.0000.0000.0000.0000.0000.000
190A200THR 0-0.002-0.00447.456-0.001-0.0010.0000.0000.0000.000
191A201VAL 0-0.002-0.01348.3400.0000.0000.0000.0000.0000.000
192A202THR 00.0070.00751.158-0.001-0.0010.0000.0000.0000.000
193A203LEU 0-0.040-0.01048.8180.0000.0000.0000.0000.0000.000
194A204ASP -1-0.854-0.93852.674-0.024-0.0240.0000.0000.0000.000
195A205ASN 0-0.049-0.01054.9640.0020.0020.0000.0000.0000.000
196A206GLN 0-0.026-0.01552.5290.0000.0000.0000.0000.0000.000
197A207GLN 00.0240.00757.3660.0000.0000.0000.0000.0000.000
198A208THR 0-0.034-0.01754.9870.0010.0010.0000.0000.0000.000
199A209PRO 00.0010.00554.238-0.001-0.0010.0000.0000.0000.000
200A210THR 0-0.017-0.01147.898-0.001-0.0010.0000.0000.0000.000
201A211VAL 0-0.0020.00947.1710.0000.0000.0000.0000.0000.000
202A212PHE 0-0.040-0.02243.559-0.002-0.0020.0000.0000.0000.000
203A213TYR 00.0300.01541.3990.0020.0020.0000.0000.0000.000
204A214HIS 10.8390.89139.3230.0270.0270.0000.0000.0000.000
205A215PHE 00.0420.02134.7990.0020.0020.0000.0000.0000.000
206A216GLU -1-0.854-0.94033.367-0.030-0.0300.0000.0000.0000.000
207A217ARG 10.7800.89622.5350.0660.0660.0000.0000.0000.000
208A218THR 0-0.001-0.02830.2270.0020.0020.0000.0000.0000.000
209A219ALA -1-0.803-0.87624.562-0.041-0.0410.0000.0000.0000.000