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: 66K9Z

Calculation Name: 3L8I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BUL8

Base Structure: X-ray

Registration Date: 2023-06-19

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2150926.841739
FMO2-HF: Nuclear repulsion 2070735.582654
FMO2-HF: Total energy -80191.259085
FMO2-MP2: Total energy -80426.351586


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:15:THR)


Summations of interaction energy for fragment #1(A:15:THR)
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.
-1.5070.561-0.02-1.17-0.8790.003
Interaction energy analysis for fragmet #1(A:15:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.008
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].
3A17MET00.0430.0133.8730.4822.550-0.020-1.170-0.8790.003
4A18VAL00.0190.0146.329-0.456-0.4560.0000.0000.0000.000
5A19SER00.030-0.0137.535-0.212-0.2120.0000.0000.0000.000
6A20MET0-0.057-0.0219.339-0.217-0.2170.0000.0000.0000.000
7A21PRO00.0240.00310.759-0.141-0.1410.0000.0000.0000.000
8A22LEU00.0350.02812.213-0.131-0.1310.0000.0000.0000.000
9A23TYR0-0.013-0.02610.260-0.080-0.0800.0000.0000.0000.000
10A24ALA0-0.016-0.00714.569-0.088-0.0880.0000.0000.0000.000
11A25VAL0-0.0060.00316.290-0.081-0.0810.0000.0000.0000.000
12A26MET0-0.0030.00417.606-0.056-0.0560.0000.0000.0000.000
13A27TYR0-0.017-0.00515.232-0.067-0.0670.0000.0000.0000.000
14A28PRO0-0.0190.00418.786-0.049-0.0490.0000.0000.0000.000
15A29VAL00.0550.03121.853-0.041-0.0410.0000.0000.0000.000
16A30PHE0-0.008-0.01820.746-0.039-0.0390.0000.0000.0000.000
17A31ASN00.007-0.00320.998-0.027-0.0270.0000.0000.0000.000
18A32GLU-1-0.953-0.97824.8500.3120.3120.0000.0000.0000.000
19A33LEU0-0.0120.00027.099-0.028-0.0280.0000.0000.0000.000
20A34GLU-1-0.821-0.88926.0860.2850.2850.0000.0000.0000.000
21A35ARG10.8890.92729.666-0.193-0.1930.0000.0000.0000.000
22A36VAL0-0.0250.00832.227-0.013-0.0130.0000.0000.0000.000
23A37ASN00.0400.01631.771-0.007-0.0070.0000.0000.0000.000
24A38LEU00.0660.05228.3760.0120.0120.0000.0000.0000.000
25A39SER0-0.019-0.01328.5830.0140.0140.0000.0000.0000.000
26A40ALA00.0360.02228.5850.0090.0090.0000.0000.0000.000
27A41ALA00.0650.03225.9440.0160.0160.0000.0000.0000.000
28A42GLN0-0.045-0.02324.2000.0270.0270.0000.0000.0000.000
29A43THR0-0.012-0.01323.5530.0210.0210.0000.0000.0000.000
30A44LEU0-0.003-0.00223.6610.0100.0100.0000.0000.0000.000
31A45ARG10.8030.87220.057-0.342-0.3420.0000.0000.0000.000
32A46ALA0-0.0090.00318.9700.0490.0490.0000.0000.0000.000
33A47ALA0-0.009-0.00319.2270.0180.0180.0000.0000.0000.000
34A48PHE00.0390.00717.3490.0020.0020.0000.0000.0000.000
35A49ILE0-0.027-0.01414.1370.0650.0650.0000.0000.0000.000
36A50LYS10.7690.87614.359-0.185-0.1850.0000.0000.0000.000
37A51ALA00.0410.01715.638-0.003-0.0030.0000.0000.0000.000
38A52GLU-1-0.698-0.79210.8861.0431.0430.0000.0000.0000.000
39A53LYS10.9060.94610.537-0.504-0.5040.0000.0000.0000.000
40A54GLU-1-0.838-0.90011.3530.1950.1950.0000.0000.0000.000
41A55ASN0-0.082-0.03212.780-0.146-0.1460.0000.0000.0000.000
42A56PRO00.0120.0027.5730.0530.0530.0000.0000.0000.000
43A57GLY00.0270.0119.751-0.107-0.1070.0000.0000.0000.000
44A58LEU0-0.0040.00411.684-0.102-0.1020.0000.0000.0000.000
45A59THR0-0.019-0.05214.097-0.081-0.0810.0000.0000.0000.000
46A60GLN00.0250.01013.880-0.016-0.0160.0000.0000.0000.000
47A61ASP-1-0.853-0.91515.7120.1930.1930.0000.0000.0000.000
48A62ILE00.000-0.00417.781-0.057-0.0570.0000.0000.0000.000
49A63ILE00.008-0.00417.101-0.037-0.0370.0000.0000.0000.000
50A64MET0-0.042-0.01918.964-0.027-0.0270.0000.0000.0000.000
51A65LYS10.8800.93420.576-0.255-0.2550.0000.0000.0000.000
52A66ILE0-0.0060.00122.827-0.024-0.0240.0000.0000.0000.000
53A67LEU0-0.025-0.01322.285-0.023-0.0230.0000.0000.0000.000
54A68GLU-1-0.875-0.93824.4310.1570.1570.0000.0000.0000.000
55A69LYS10.8270.91527.653-0.171-0.1710.0000.0000.0000.000
56A70LYS10.9460.99129.827-0.167-0.1670.0000.0000.0000.000
57A71SER00.011-0.01731.3710.0000.0000.0000.0000.0000.000
58A72VAL00.0270.02133.747-0.006-0.0060.0000.0000.0000.000
59A73GLU-1-0.861-0.92631.4600.1590.1590.0000.0000.0000.000
60A74VAL0-0.068-0.03134.1390.0000.0000.0000.0000.0000.000
61A75ASN00.0110.01136.522-0.004-0.0040.0000.0000.0000.000
62A76PHE00.0240.02535.748-0.007-0.0070.0000.0000.0000.000
63A77THR0-0.009-0.02935.918-0.001-0.0010.0000.0000.0000.000
64A78GLU-1-0.902-0.94438.4480.0920.0920.0000.0000.0000.000
65A79SER0-0.006-0.01641.617-0.006-0.0060.0000.0000.0000.000
66A80LEU0-0.023-0.00638.265-0.004-0.0040.0000.0000.0000.000
67A81LEU0-0.093-0.02542.285-0.002-0.0020.0000.0000.0000.000
68A82ARG10.7640.83443.921-0.088-0.0880.0000.0000.0000.000
69A83MET0-0.0080.00543.716-0.003-0.0030.0000.0000.0000.000
70A84ALA00.002-0.00244.839-0.003-0.0030.0000.0000.0000.000
71A85ALA0-0.017-0.01446.932-0.001-0.0010.0000.0000.0000.000
72A86ASP-1-0.890-0.94750.4830.0680.0680.0000.0000.0000.000
73A87ASP-1-0.775-0.89051.1350.0720.0720.0000.0000.0000.000
74A88VAL0-0.085-0.06052.932-0.001-0.0010.0000.0000.0000.000
75A89GLU-1-0.947-0.95755.4220.0590.0590.0000.0000.0000.000
76A90GLU-1-0.902-0.91550.8270.0800.0800.0000.0000.0000.000
77A91TYR0-0.124-0.10248.9560.0010.0010.0000.0000.0000.000
78A92MET00.003-0.00954.553-0.001-0.0010.0000.0000.0000.000
79A93ILE0-0.077-0.03357.967-0.001-0.0010.0000.0000.0000.000
80A94GLU-1-0.803-0.88960.3900.0590.0590.0000.0000.0000.000
81A95ARG10.8020.89463.601-0.055-0.0550.0000.0000.0000.000
82A96PRO00.0550.00765.9100.0010.0010.0000.0000.0000.000
83A97GLU-1-0.854-0.90167.2850.0490.0490.0000.0000.0000.000
84A98PRO00.0470.02266.9200.0020.0020.0000.0000.0000.000
85A99GLU-1-0.766-0.88464.4640.0510.0510.0000.0000.0000.000
86A100PHE00.0140.00060.5970.0020.0020.0000.0000.0000.000
87A101GLN00.0210.02062.3110.0010.0010.0000.0000.0000.000
88A102ASP-1-0.746-0.83962.9110.0570.0570.0000.0000.0000.000
89A103LEU0-0.028-0.01256.6800.0020.0020.0000.0000.0000.000
90A104ASN0-0.001-0.01958.3170.0040.0040.0000.0000.0000.000
91A105GLU-1-0.933-0.95858.4240.0540.0540.0000.0000.0000.000
92A106LYS10.8200.89858.254-0.055-0.0550.0000.0000.0000.000
93A107ALA0-0.0010.00754.3350.0020.0020.0000.0000.0000.000
94A108ARG10.9220.95954.081-0.061-0.0610.0000.0000.0000.000
95A109ALA00.0200.00955.0680.0010.0010.0000.0000.0000.000
96A110LEU0-0.015-0.01550.9340.0010.0010.0000.0000.0000.000
97A111LYS10.8430.92950.320-0.076-0.0760.0000.0000.0000.000
98A112GLN0-0.009-0.00450.8130.0010.0010.0000.0000.0000.000
99A113ILE0-0.0090.00452.1260.0010.0010.0000.0000.0000.000
100A114LEU0-0.014-0.02046.9550.0020.0020.0000.0000.0000.000
101A115SER0-0.023-0.02047.3480.0020.0020.0000.0000.0000.000
102A116LYS10.9420.97047.701-0.065-0.0650.0000.0000.0000.000
103A117ILE0-0.0120.01044.762-0.001-0.0010.0000.0000.0000.000
104A118PRO0-0.028-0.02543.6710.0000.0000.0000.0000.0000.000
105A119ASP-1-0.817-0.87745.3750.0760.0760.0000.0000.0000.000
106A120GLU-1-0.838-0.88948.3490.0620.0620.0000.0000.0000.000
107A121ILE0-0.083-0.04242.605-0.001-0.0010.0000.0000.0000.000
108A122ASN0-0.025-0.02043.7920.0040.0040.0000.0000.0000.000
109A123ASP-1-0.788-0.87946.5010.0580.0580.0000.0000.0000.000
110A124ARG10.9070.94442.650-0.085-0.0850.0000.0000.0000.000
111A125VAL0-0.007-0.00649.7460.0010.0010.0000.0000.0000.000
112A126ARG10.9040.94452.641-0.057-0.0570.0000.0000.0000.000
113A127PHE00.0370.02745.3890.0020.0020.0000.0000.0000.000
114A128LEU0-0.011-0.02149.5910.0020.0020.0000.0000.0000.000
115A129GLN0-0.060-0.01852.212-0.002-0.0020.0000.0000.0000.000
116A130THR00.053-0.01250.4060.0000.0000.0000.0000.0000.000
117A131ILE0-0.015-0.01247.5450.0020.0020.0000.0000.0000.000
118A132LYS10.8330.92251.196-0.058-0.0580.0000.0000.0000.000
119A133ASP-1-0.809-0.88754.7560.0610.0610.0000.0000.0000.000
120A134ILE0-0.013-0.01048.6520.0010.0010.0000.0000.0000.000
121A135ALA0-0.017-0.00952.4280.0010.0010.0000.0000.0000.000
122A136SER0-0.015-0.01153.394-0.001-0.0010.0000.0000.0000.000
123A137ALA00.0790.04554.410-0.001-0.0010.0000.0000.0000.000
124A138ILE0-0.044-0.02349.3400.0010.0010.0000.0000.0000.000
125A139LYS10.7920.90853.565-0.061-0.0610.0000.0000.0000.000
126A140GLU-1-0.815-0.91756.5030.0580.0580.0000.0000.0000.000
127A141LEU0-0.0070.00552.744-0.001-0.0010.0000.0000.0000.000
128A142LEU0-0.020-0.02052.8210.0000.0000.0000.0000.0000.000
129A143ASP-1-0.877-0.94056.6500.0600.0600.0000.0000.0000.000
130A144THR0-0.048-0.04859.009-0.002-0.0020.0000.0000.0000.000
131A145VAL0-0.012-0.00655.239-0.001-0.0010.0000.0000.0000.000
132A146ASN0-0.026-0.04657.1790.0010.0010.0000.0000.0000.000
133A147ASN00.0030.01160.125-0.003-0.0030.0000.0000.0000.000
134A148VAL00.0290.02860.044-0.002-0.0020.0000.0000.0000.000
135A149PHE00.0080.00056.236-0.001-0.0010.0000.0000.0000.000
136A150LYS10.7390.85162.062-0.052-0.0520.0000.0000.0000.000
137A151LYS10.8400.92764.573-0.051-0.0510.0000.0000.0000.000
138A152TYR0-0.022-0.00559.3310.0000.0000.0000.0000.0000.000
139A153GLN00.0670.03563.9260.0000.0000.0000.0000.0000.000
140A154TYR00.0620.01462.8280.0030.0030.0000.0000.0000.000
141A155GLN0-0.043-0.02661.6150.0020.0020.0000.0000.0000.000
142A156ASN0-0.036-0.02259.3050.0010.0010.0000.0000.0000.000
143A157ARG10.9350.97158.489-0.057-0.0570.0000.0000.0000.000
144A158ARG10.9450.97951.879-0.079-0.0790.0000.0000.0000.000
145A159ALA00.0550.02652.0230.0030.0030.0000.0000.0000.000
146A160LEU00.0330.03752.1770.0030.0030.0000.0000.0000.000
147A161GLU-1-0.815-0.90853.6390.0790.0790.0000.0000.0000.000
148A162HIS0-0.081-0.04645.484-0.001-0.0010.0000.0000.0000.000
149A163GLN00.0280.00247.4000.0070.0070.0000.0000.0000.000
150A164LYS10.8340.92949.483-0.073-0.0730.0000.0000.0000.000
151A165LYS10.9120.95248.525-0.091-0.0910.0000.0000.0000.000
152A166GLU-1-0.770-0.86143.5400.1260.1260.0000.0000.0000.000
153A167PHE00.0840.03545.5380.0040.0040.0000.0000.0000.000
154A168VAL0-0.008-0.01247.3760.0010.0010.0000.0000.0000.000
155A169LYS10.7840.87942.156-0.124-0.1240.0000.0000.0000.000
156A170TYR00.0190.00740.0640.0050.0050.0000.0000.0000.000
157A171SER00.0210.02843.7410.0010.0010.0000.0000.0000.000
158A172LYS10.9280.97144.364-0.098-0.0980.0000.0000.0000.000
159A173SER00.0640.03039.5310.0040.0040.0000.0000.0000.000
160A174PHE00.0200.03041.0250.0040.0040.0000.0000.0000.000
161A175SER0-0.009-0.01943.164-0.003-0.0030.0000.0000.0000.000
162A176ASP-1-0.841-0.91840.2480.1150.1150.0000.0000.0000.000
163A177THR0-0.030-0.02038.3710.0070.0070.0000.0000.0000.000
164A178LEU00.0080.01540.2370.0000.0000.0000.0000.0000.000
165A179LYS10.8040.89141.924-0.108-0.1080.0000.0000.0000.000
166A180THR0-0.023-0.01036.6990.0000.0000.0000.0000.0000.000
167A181TYR00.0330.02938.871-0.001-0.0010.0000.0000.0000.000
168A182PHE0-0.027-0.02540.067-0.002-0.0020.0000.0000.0000.000
169A183LYS10.9050.95438.708-0.112-0.1120.0000.0000.0000.000
170A184ASP-1-0.816-0.88533.9200.1630.1630.0000.0000.0000.000
171A185GLY0-0.0080.00636.0830.0030.0030.0000.0000.0000.000
172A186LYS10.8370.88730.788-0.180-0.1800.0000.0000.0000.000
173A187ALA00.0320.01736.2790.0040.0040.0000.0000.0000.000
174A188ILE00.0400.01332.501-0.001-0.0010.0000.0000.0000.000
175A189ASN0-0.0170.00134.4470.0070.0070.0000.0000.0000.000
176A190VAL00.0430.00536.6650.0000.0000.0000.0000.0000.000
177A191PHE00.0430.02739.025-0.002-0.0020.0000.0000.0000.000
178A192VAL00.0460.02034.884-0.002-0.0020.0000.0000.0000.000
179A193SER0-0.072-0.04638.217-0.002-0.0020.0000.0000.0000.000
180A194ALA00.0340.01440.086-0.003-0.0030.0000.0000.0000.000
181A195ASN00.0360.02139.783-0.008-0.0080.0000.0000.0000.000
182A196ARG10.9330.96433.577-0.174-0.1740.0000.0000.0000.000
183A197LEU0-0.021-0.01241.556-0.002-0.0020.0000.0000.0000.000
184A198ILE00.0290.01244.921-0.004-0.0040.0000.0000.0000.000
185A199HIS0-0.0050.00643.123-0.004-0.0040.0000.0000.0000.000
186A200GLN00.001-0.00642.801-0.006-0.0060.0000.0000.0000.000
187A201THR0-0.018-0.00646.715-0.003-0.0030.0000.0000.0000.000
188A202ASN00.0810.04947.278-0.008-0.0080.0000.0000.0000.000
189A203LEU00.0250.02444.407-0.002-0.0020.0000.0000.0000.000
190A204ILE0-0.058-0.00949.051-0.003-0.0030.0000.0000.0000.000
191A205LEU00.0130.01152.108-0.003-0.0030.0000.0000.0000.000
192A206GLN00.0520.03348.8500.0000.0000.0000.0000.0000.000
193A207THR0-0.051-0.03350.958-0.001-0.0010.0000.0000.0000.000
194A208PHE0-0.001-0.02753.252-0.002-0.0020.0000.0000.0000.000
195A209LYS10.8840.94356.053-0.067-0.0670.0000.0000.0000.000
196A210THR0-0.049-0.02353.839-0.002-0.0020.0000.0000.0000.000
197A211VAL0-0.075-0.02955.716-0.001-0.0010.0000.0000.0000.000
198A212ALA0-0.0200.00858.467-0.003-0.0030.0000.0000.0000.000