Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LJ8M9

Calculation Name: 3FHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q58134

Base Structure: X-ray

Registration Date: 2023-06-20

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2833816.991885
FMO2-HF: Nuclear repulsion 2745168.731375
FMO2-HF: Total energy -88648.260509
FMO2-MP2: Total energy -88912.011058


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:-6:GLY)


Summations of interaction energy for fragment #1(A:-6:GLY)
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.
1.6682.918-0.005-0.484-0.7610.001
Interaction energy analysis for fragmet #1(A:-6:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.005
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].
3A-4HIS00.011-0.0073.6941.1682.418-0.005-0.484-0.7610.001
4A-3HIS00.0690.0416.1790.4170.4170.0000.0000.0000.000
5A-2HIS00.000-0.0045.974-0.016-0.0160.0000.0000.0000.000
6A-1HIS00.0210.0037.8890.1090.1090.0000.0000.0000.000
7A0HIS00.0060.02310.2750.0400.0400.0000.0000.0000.000
8A1MET00.011-0.00210.606-0.060-0.0600.0000.0000.0000.000
9A2MET0-0.032-0.02110.8160.0380.0380.0000.0000.0000.000
10A3LEU00.0000.02013.4650.0190.0190.0000.0000.0000.000
11A4ILE00.0160.01415.9470.0090.0090.0000.0000.0000.000
12A5LYS10.8910.93415.4200.0410.0410.0000.0000.0000.000
13A6LYS10.8700.92717.537-0.038-0.0380.0000.0000.0000.000
14A7ILE00.0320.00319.3170.0060.0060.0000.0000.0000.000
15A8GLU-1-0.790-0.87621.209-0.045-0.0450.0000.0000.0000.000
16A9GLU-1-0.842-0.89519.8150.0150.0150.0000.0000.0000.000
17A10LEU0-0.067-0.02623.3610.0040.0040.0000.0000.0000.000
18A11LYS10.7910.87725.2040.0400.0400.0000.0000.0000.000
19A12ASN0-0.080-0.04025.685-0.002-0.0020.0000.0000.0000.000
20A13SER0-0.018-0.02227.7750.0040.0040.0000.0000.0000.000
21A14GLU-1-0.868-0.94029.7130.0180.0180.0000.0000.0000.000
22A15ILE0-0.050-0.03328.5130.0010.0010.0000.0000.0000.000
23A16LYS10.8720.93830.3490.0090.0090.0000.0000.0000.000
24A17ASP-1-0.862-0.92731.6540.0010.0010.0000.0000.0000.000
25A18ILE0-0.069-0.03433.5890.0010.0010.0000.0000.0000.000
26A19ILE0-0.034-0.02429.3530.0010.0010.0000.0000.0000.000
27A20ASP-1-0.800-0.88733.632-0.004-0.0040.0000.0000.0000.000
28A21LYS10.8690.92935.730-0.012-0.0120.0000.0000.0000.000
29A22ARG10.7880.88035.880-0.023-0.0230.0000.0000.0000.000
30A23ILE00.0150.00533.6230.0000.0000.0000.0000.0000.000
31A24GLN00.0220.00037.410-0.001-0.0010.0000.0000.0000.000
32A25GLU-1-0.855-0.89840.7050.0160.0160.0000.0000.0000.000
33A26PHE00.0050.01735.6590.0010.0010.0000.0000.0000.000
34A27LYS10.8610.91738.7630.0030.0030.0000.0000.0000.000
35A28SER0-0.062-0.04342.696-0.001-0.0010.0000.0000.0000.000
36A29PHE00.001-0.01344.1450.0000.0000.0000.0000.0000.000
37A30LYS10.8640.94446.3410.0000.0000.0000.0000.0000.000
38A31ASN0-0.014-0.01447.989-0.001-0.0010.0000.0000.0000.000
39A32LYS10.8710.96847.069-0.009-0.0090.0000.0000.0000.000
40A33SER00.034-0.00951.276-0.001-0.0010.0000.0000.0000.000
41A34ASN00.0580.00251.9230.0010.0010.0000.0000.0000.000
42A35GLU-1-0.834-0.90052.1460.0100.0100.0000.0000.0000.000
43A36GLU-1-0.890-0.93949.9140.0150.0150.0000.0000.0000.000
44A37TRP00.045-0.00145.9940.0020.0020.0000.0000.0000.000
45A38PHE00.007-0.00747.5130.0010.0010.0000.0000.0000.000
46A39LYS10.9060.95348.747-0.012-0.0120.0000.0000.0000.000
47A40GLU-1-0.763-0.84842.5850.0230.0230.0000.0000.0000.000
48A41LEU0-0.0280.00143.7560.0020.0020.0000.0000.0000.000
49A42CYS0-0.043-0.02244.5870.0020.0020.0000.0000.0000.000
50A43PHE00.0110.00838.6700.0030.0030.0000.0000.0000.000
51A44CYS0-0.042-0.00239.0530.0020.0020.0000.0000.0000.000
52A45ILE0-0.0070.00940.6870.0030.0030.0000.0000.0000.000
53A46LEU00.000-0.00142.7600.0030.0030.0000.0000.0000.000
54A47THR0-0.0110.00436.5240.0030.0030.0000.0000.0000.000
55A48ALA00.0150.01837.0990.0040.0040.0000.0000.0000.000
56A49ASN0-0.056-0.03536.676-0.004-0.0040.0000.0000.0000.000
57A50PHE00.0360.02537.5710.0000.0000.0000.0000.0000.000
58A51THR00.0310.02536.0710.0030.0030.0000.0000.0000.000
59A52ALA00.0680.04936.213-0.003-0.0030.0000.0000.0000.000
60A53GLU-1-0.750-0.87636.4340.0480.0480.0000.0000.0000.000
61A54GLY00.002-0.00339.876-0.002-0.0020.0000.0000.0000.000
62A55GLY00.014-0.00741.071-0.002-0.0020.0000.0000.0000.000
63A56ILE00.006-0.01139.766-0.002-0.0020.0000.0000.0000.000
64A57ARG10.9060.95343.115-0.040-0.0400.0000.0000.0000.000
65A58ILE00.0190.01545.579-0.001-0.0010.0000.0000.0000.000
66A59GLN0-0.043-0.02744.7030.0000.0000.0000.0000.0000.000
67A60LYS10.9290.96145.644-0.026-0.0260.0000.0000.0000.000
68A61GLU-1-0.944-0.95449.9110.0250.0250.0000.0000.0000.000
69A62ILE0-0.036-0.00750.651-0.001-0.0010.0000.0000.0000.000
70A63GLY00.0340.01751.580-0.001-0.0010.0000.0000.0000.000
71A64ASP-1-0.873-0.94552.9020.0140.0140.0000.0000.0000.000
72A65GLY00.0720.03855.5730.0000.0000.0000.0000.0000.000
73A66PHE0-0.019-0.03848.4070.0010.0010.0000.0000.0000.000
74A67LEU0-0.082-0.04453.4710.0000.0000.0000.0000.0000.000
75A68THR00.004-0.00556.3130.0000.0000.0000.0000.0000.000
76A69LEU0-0.0160.02755.7060.0000.0000.0000.0000.0000.000
77A70PRO00.0250.03858.1470.0000.0000.0000.0000.0000.000
78A71ARG10.8490.88454.083-0.022-0.0220.0000.0000.0000.000
79A72GLU-1-0.845-0.93456.6720.0190.0190.0000.0000.0000.000
80A73GLU-1-0.786-0.89458.0250.0190.0190.0000.0000.0000.000
81A74LEU0-0.078-0.02451.9680.0010.0010.0000.0000.0000.000
82A75GLU-1-0.834-0.93152.9830.0270.0270.0000.0000.0000.000
83A76GLU-1-0.769-0.86853.3170.0280.0280.0000.0000.0000.000
84A77LYS10.8800.93653.673-0.019-0.0190.0000.0000.0000.000
85A78LEU0-0.007-0.00648.1050.0020.0020.0000.0000.0000.000
86A79LYS10.8310.90549.232-0.026-0.0260.0000.0000.0000.000
87A80ASN0-0.068-0.05250.3830.0020.0020.0000.0000.0000.000
88A81LEU0-0.0090.01748.5410.0010.0010.0000.0000.0000.000
89A82GLY00.0130.01146.2820.0020.0020.0000.0000.0000.000
90A83HIS0-0.060-0.02942.3670.0030.0030.0000.0000.0000.000
91A84ARG10.9770.97238.080-0.057-0.0570.0000.0000.0000.000
92A85PHE0-0.085-0.04540.8460.0000.0000.0000.0000.0000.000
93A86TYR00.0410.02445.910-0.002-0.0020.0000.0000.0000.000
94A87ARG11.0051.01448.985-0.031-0.0310.0000.0000.0000.000
95A88LYS10.9310.96344.284-0.038-0.0380.0000.0000.0000.000
96A89ARG10.8170.89440.740-0.040-0.0400.0000.0000.0000.000
97A90ALA00.0680.04547.669-0.001-0.0010.0000.0000.0000.000
98A91GLU-1-0.900-0.93351.0000.0220.0220.0000.0000.0000.000
99A92TYR0-0.042-0.03644.6370.0000.0000.0000.0000.0000.000
100A93ILE00.0310.01847.793-0.001-0.0010.0000.0000.0000.000
101A94VAL00.0400.01850.598-0.001-0.0010.0000.0000.0000.000
102A95LEU0-0.020-0.01451.837-0.001-0.0010.0000.0000.0000.000
103A96ALA0-0.014-0.00349.592-0.001-0.0010.0000.0000.0000.000
104A97ARG10.8520.91351.604-0.018-0.0180.0000.0000.0000.000
105A98ARG10.7870.90151.259-0.014-0.0140.0000.0000.0000.000
106A99PHE0-0.017-0.02150.688-0.001-0.0010.0000.0000.0000.000
107A100LYS10.9890.98952.467-0.010-0.0100.0000.0000.0000.000
108A101ASN0-0.090-0.02853.6420.0010.0010.0000.0000.0000.000
109A102ILE00.035-0.00547.921-0.001-0.0010.0000.0000.0000.000
110A103LYS10.8340.92749.319-0.004-0.0040.0000.0000.0000.000
111A104ASP-1-0.786-0.88350.3480.0040.0040.0000.0000.0000.000
112A105ILE0-0.060-0.01949.785-0.001-0.0010.0000.0000.0000.000
113A106VAL0-0.031-0.01445.026-0.001-0.0010.0000.0000.0000.000
114A107GLU-1-0.832-0.91447.2680.0000.0000.0000.0000.0000.000
115A108SER0-0.064-0.02248.964-0.001-0.0010.0000.0000.0000.000
116A109PHE0-0.043-0.02446.373-0.001-0.0010.0000.0000.0000.000
117A110GLU-1-0.872-0.92845.543-0.009-0.0090.0000.0000.0000.000
118A111ASN00.011-0.00441.5310.0000.0000.0000.0000.0000.000
119A112GLU-1-0.774-0.91237.351-0.002-0.0020.0000.0000.0000.000
120A113LYS10.8060.89934.7290.0130.0130.0000.0000.0000.000
121A114VAL00.0360.02039.5730.0020.0020.0000.0000.0000.000
122A115ALA00.0320.02843.0040.0020.0020.0000.0000.0000.000
123A116ARG10.7790.84833.709-0.006-0.0060.0000.0000.0000.000
124A117GLU-1-0.862-0.91140.6580.0030.0030.0000.0000.0000.000
125A118PHE00.0170.01542.4770.0020.0020.0000.0000.0000.000
126A119LEU0-0.027-0.01542.2750.0020.0020.0000.0000.0000.000
127A120VAL0-0.059-0.03339.3680.0020.0020.0000.0000.0000.000
128A121ARG10.9090.96542.691-0.011-0.0110.0000.0000.0000.000
129A122ASN00.0000.01045.5130.0000.0000.0000.0000.0000.000
130A123ILE0-0.0120.00545.9580.0000.0000.0000.0000.0000.000
131A124LYS10.9810.99245.496-0.017-0.0170.0000.0000.0000.000
132A125GLY00.015-0.00643.8360.0000.0000.0000.0000.0000.000
133A126ILE0-0.023-0.00841.2840.0020.0020.0000.0000.0000.000
134A127GLY00.0670.04438.597-0.001-0.0010.0000.0000.0000.000
135A128TYR00.0750.01335.012-0.002-0.0020.0000.0000.0000.000
136A129LYS10.8490.95532.471-0.042-0.0420.0000.0000.0000.000
137A130GLU-1-0.865-0.93934.8470.0370.0370.0000.0000.0000.000
138A131ALA00.0240.01638.126-0.002-0.0020.0000.0000.0000.000
139A132SER00.023-0.00234.555-0.004-0.0040.0000.0000.0000.000
140A133HIS00.0180.01235.3780.0000.0000.0000.0000.0000.000
141A134PHE00.015-0.00936.641-0.001-0.0010.0000.0000.0000.000
142A135LEU00.0060.00338.769-0.001-0.0010.0000.0000.0000.000
143A136ARG10.7970.91132.292-0.024-0.0240.0000.0000.0000.000
144A137ASN0-0.053-0.05437.422-0.001-0.0010.0000.0000.0000.000
145A138VAL0-0.068-0.01739.6740.0000.0000.0000.0000.0000.000
146A139GLY00.0050.01540.476-0.002-0.0020.0000.0000.0000.000
147A140TYR0-0.023-0.00738.888-0.002-0.0020.0000.0000.0000.000
148A141ASP-1-0.729-0.86734.849-0.002-0.0020.0000.0000.0000.000
149A142ASP-1-0.775-0.85832.370-0.016-0.0160.0000.0000.0000.000
150A143VAL0-0.022-0.01333.3620.0000.0000.0000.0000.0000.000
151A144ALA00.0540.03828.7450.0020.0020.0000.0000.0000.000
152A145ILE0-0.044-0.00330.3330.0010.0010.0000.0000.0000.000
153A146ILE00.007-0.00326.9270.0050.0050.0000.0000.0000.000
154A147ASP-1-0.825-0.92727.9370.0750.0750.0000.0000.0000.000
155A148ARG10.9300.95327.402-0.077-0.0770.0000.0000.0000.000
156A149HIS0-0.041-0.02425.2070.0160.0160.0000.0000.0000.000
157A150ILE00.0710.04421.8270.0110.0110.0000.0000.0000.000
158A151LEU0-0.033-0.01222.2680.0050.0050.0000.0000.0000.000
159A152ARG10.8560.92120.846-0.187-0.1870.0000.0000.0000.000
160A153GLU-1-0.746-0.83518.7630.1340.1340.0000.0000.0000.000
161A154LEU0-0.001-0.00617.5050.0190.0190.0000.0000.0000.000
162A155TYR0-0.079-0.03317.6470.0150.0150.0000.0000.0000.000
163A156GLU-1-0.833-0.90815.8230.2690.2690.0000.0000.0000.000
164A157ASN0-0.111-0.06313.0360.1070.1070.0000.0000.0000.000
165A158ASN0-0.048-0.02111.775-0.037-0.0370.0000.0000.0000.000
166A159TYR0-0.007-0.01714.878-0.026-0.0260.0000.0000.0000.000
167A160ILE0-0.097-0.05817.489-0.028-0.0280.0000.0000.0000.000
168A161ASP-1-0.865-0.93218.9120.1000.1000.0000.0000.0000.000
169A162GLU-1-0.863-0.94219.9970.1820.1820.0000.0000.0000.000
170A163ILE0-0.070-0.02022.466-0.019-0.0190.0000.0000.0000.000
171A164PRO00.0070.00524.567-0.005-0.0050.0000.0000.0000.000
172A165LYS10.9250.98127.784-0.102-0.1020.0000.0000.0000.000
173A166THR0-0.036-0.02830.423-0.004-0.0040.0000.0000.0000.000
174A167LEU00.0180.00628.622-0.001-0.0010.0000.0000.0000.000
175A168SER00.0170.01532.565-0.004-0.0040.0000.0000.0000.000
176A169ARG10.8900.90733.631-0.002-0.0020.0000.0000.0000.000
177A170ARG10.8490.89928.922-0.014-0.0140.0000.0000.0000.000
178A171LYS10.9110.94524.704-0.043-0.0430.0000.0000.0000.000
179A172TYR0-0.025-0.03629.1240.0030.0030.0000.0000.0000.000
180A173LEU00.037-0.00229.973-0.001-0.0010.0000.0000.0000.000
181A174GLU-1-0.771-0.83325.7050.0160.0160.0000.0000.0000.000
182A175ILE00.0370.00624.326-0.003-0.0030.0000.0000.0000.000
183A176GLU-1-0.778-0.85425.5630.0030.0030.0000.0000.0000.000
184A177ASN0-0.015-0.02227.207-0.006-0.0060.0000.0000.0000.000
185A178ILE00.0740.07320.617-0.004-0.0040.0000.0000.0000.000
186A179LEU0-0.035-0.02322.590-0.005-0.0050.0000.0000.0000.000
187A180ARG10.7680.84624.2800.0140.0140.0000.0000.0000.000
188A181ASP-1-0.851-0.91722.523-0.060-0.0600.0000.0000.0000.000
189A182ILE0-0.027-0.01819.306-0.005-0.0050.0000.0000.0000.000
190A183GLY0-0.015-0.00921.846-0.003-0.0030.0000.0000.0000.000
191A184GLU-1-0.945-0.96425.000-0.067-0.0670.0000.0000.0000.000
192A185GLU-1-0.861-0.90917.700-0.143-0.1430.0000.0000.0000.000
193A186VAL0-0.015-0.00721.296-0.004-0.0040.0000.0000.0000.000
194A187ASN0-0.086-0.03223.7660.0050.0050.0000.0000.0000.000
195A188LEU0-0.060-0.01825.5680.0080.0080.0000.0000.0000.000
196A189LYS10.8680.92328.4060.0120.0120.0000.0000.0000.000
197A190LEU00.010-0.00327.5320.0050.0050.0000.0000.0000.000
198A191SER0-0.077-0.06230.0440.0050.0050.0000.0000.0000.000
199A192GLU-1-0.769-0.88230.447-0.005-0.0050.0000.0000.0000.000
200A193LEU00.0500.02923.2550.0060.0060.0000.0000.0000.000
201A194ASP-1-0.809-0.89826.4890.0430.0430.0000.0000.0000.000
202A195LEU0-0.017-0.01328.1630.0080.0080.0000.0000.0000.000
203A196TYR00.0520.02025.0390.0050.0050.0000.0000.0000.000
204A197ILE00.0150.00922.5200.0080.0080.0000.0000.0000.000
205A198TRP0-0.039-0.02324.5120.0180.0180.0000.0000.0000.000
206A199TYR00.0040.01025.9890.0080.0080.0000.0000.0000.000
207A200LEU00.0110.00720.5110.0050.0050.0000.0000.0000.000
208A201ARG10.7570.87423.029-0.081-0.0810.0000.0000.0000.000
209A202THR0-0.095-0.07024.3710.0030.0030.0000.0000.0000.000
210A203GLY00.0230.02927.261-0.001-0.0010.0000.0000.0000.000
211A204LYS10.7720.86528.671-0.062-0.0620.0000.0000.0000.000
212A205VAL00.0870.04030.8210.0010.0010.0000.0000.0000.000
213A206LEU0-0.055-0.01233.256-0.003-0.0030.0000.0000.0000.000
214A207LYS10.8370.89735.719-0.025-0.0250.0000.0000.0000.000