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: YV8N2

Calculation Name: 3K6Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K6Y

Chain ID: A

ChEMBL ID:

UniProt ID: P9WHR9

Base Structure: X-ray

Registration Date: 2023-09-23

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2403798.212425
FMO2-HF: Nuclear repulsion 2323521.660352
FMO2-HF: Total energy -80276.552074
FMO2-MP2: Total energy -80514.390444


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:171:ALA)


Summations of interaction energy for fragment #1(A:171:ALA)
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.
-0.6390.712-0.011-0.518-0.8220.002
Interaction energy analysis for fragmet #1(A:171:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.032
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].
3A173LEU0-0.031-0.0223.813-0.5080.843-0.011-0.518-0.8220.002
4A174GLU-1-0.879-0.9485.483-0.173-0.1730.0000.0000.0000.000
5A175PRO0-0.062-0.0098.2590.1550.1550.0000.0000.0000.000
6A176PHE00.0320.00911.4740.0110.0110.0000.0000.0000.000
7A177SER0-0.047-0.02814.5610.0020.0020.0000.0000.0000.000
8A178ARG10.8880.93716.7180.1560.1560.0000.0000.0000.000
9A179THR00.010-0.00220.220-0.018-0.0180.0000.0000.0000.000
10A180PRO0-0.021-0.00822.8910.0070.0070.0000.0000.0000.000
11A181VAL00.0500.03425.4430.0070.0070.0000.0000.0000.000
12A182ILE00.0120.01128.997-0.005-0.0050.0000.0000.0000.000
13A183PRO0-0.021-0.01129.6550.0050.0050.0000.0000.0000.000
14A184VAL0-0.0120.00632.6300.0040.0040.0000.0000.0000.000
15A185ALA00.0030.00236.415-0.002-0.0020.0000.0000.0000.000
16A186SER00.0450.00539.458-0.001-0.0010.0000.0000.0000.000
17A187PRO00.0080.02140.5840.0020.0020.0000.0000.0000.000
18A188ASP-1-0.818-0.90843.513-0.035-0.0350.0000.0000.0000.000
19A189PRO0-0.008-0.01147.0080.0010.0010.0000.0000.0000.000
20A190ALA0-0.009-0.01248.9230.0010.0010.0000.0000.0000.000
21A191LEU0-0.028-0.01747.1290.0020.0020.0000.0000.0000.000
22A192VAL0-0.019-0.00250.6590.0010.0010.0000.0000.0000.000
23A193ASN0-0.030-0.01252.6760.0020.0020.0000.0000.0000.000
24A194ASN0-0.0020.01152.9680.0020.0020.0000.0000.0000.000
25A195PRO00.026-0.00655.5160.0000.0000.0000.0000.0000.000
26A196VAL0-0.0050.01452.8680.0010.0010.0000.0000.0000.000
27A197VAL00.0200.02852.8690.0010.0010.0000.0000.0000.000
28A198ALA00.0330.01155.3880.0010.0010.0000.0000.0000.000
29A199ALA0-0.058-0.02858.5780.0010.0010.0000.0000.0000.000
30A200THR0-0.016-0.02553.3320.0010.0010.0000.0000.0000.000
31A201GLU-1-0.933-0.96456.088-0.020-0.0200.0000.0000.0000.000
32A202PRO0-0.028-0.00757.0950.0000.0000.0000.0000.0000.000
33A203SER0-0.041-0.04056.7040.0010.0010.0000.0000.0000.000
34A204VAL0-0.040-0.01051.9190.0000.0000.0000.0000.0000.000
35A205VAL0-0.0070.01454.0470.0000.0000.0000.0000.0000.000
36A206LYS10.8550.92353.3040.0200.0200.0000.0000.0000.000
37A207ILE0-0.062-0.03250.8620.0010.0010.0000.0000.0000.000
38A208ARG10.9070.94352.3520.0170.0170.0000.0000.0000.000
39A209SER00.019-0.01250.4870.0020.0020.0000.0000.0000.000
40A210LEU0-0.034-0.00152.278-0.001-0.0010.0000.0000.0000.000
41A211ALA00.0730.01949.5780.0010.0010.0000.0000.0000.000
42A212PRO00.0310.02250.856-0.001-0.0010.0000.0000.0000.000
43A213ARG10.8410.92748.0770.0100.0100.0000.0000.0000.000
44A214CYS0-0.048-0.02544.1830.0000.0000.0000.0000.0000.000
45A215GLN0-0.037-0.01547.528-0.002-0.0020.0000.0000.0000.000
46A216LYS10.9700.99542.7520.0240.0240.0000.0000.0000.000
47A217VAL0-0.025-0.01349.8800.0020.0020.0000.0000.0000.000
48A218LEU0-0.033-0.00445.930-0.001-0.0010.0000.0000.0000.000
49A219GLU-1-0.769-0.88348.672-0.019-0.0190.0000.0000.0000.000
50A220GLY0-0.0040.00548.065-0.002-0.0020.0000.0000.0000.000
51A221THR0-0.0060.01948.2830.0010.0010.0000.0000.0000.000
52A222GLY00.0340.02549.1320.0000.0000.0000.0000.0000.000
53A223PHE00.0180.01047.9060.0000.0000.0000.0000.0000.000
54A224VAL0-0.0050.01452.9780.0010.0010.0000.0000.0000.000
55A225ILE0-0.020-0.00851.2400.0000.0000.0000.0000.0000.000
56A226SER0-0.008-0.02554.5670.0010.0010.0000.0000.0000.000
57A227PRO00.0400.01757.9160.0000.0000.0000.0000.0000.000
58A228ASP-1-0.793-0.87760.701-0.008-0.0080.0000.0000.0000.000
59A229ARG10.8030.89955.6970.0070.0070.0000.0000.0000.000
60A230VAL00.0400.02452.908-0.001-0.0010.0000.0000.0000.000
61A231MET0-0.0240.01447.7320.0000.0000.0000.0000.0000.000
62A232THR00.046-0.00548.068-0.001-0.0010.0000.0000.0000.000
63A233ASN0-0.005-0.01242.150-0.001-0.0010.0000.0000.0000.000
64A234ALA00.0010.01242.9990.0010.0010.0000.0000.0000.000
65A235HIS10.8010.85040.7700.0290.0290.0000.0000.0000.000
66A236VAL0-0.041-0.00443.435-0.001-0.0010.0000.0000.0000.000
67A237VAL00.0040.00146.5540.0010.0010.0000.0000.0000.000
68A238ALA00.0310.04244.3200.0010.0010.0000.0000.0000.000
69A239GLY0-0.034-0.03346.270-0.001-0.0010.0000.0000.0000.000
70A240SER0-0.076-0.06347.9810.0010.0010.0000.0000.0000.000
71A241ASN0-0.047-0.04251.2270.0000.0000.0000.0000.0000.000
72A242ASN00.0000.00154.7360.0000.0000.0000.0000.0000.000
73A243VAL00.0410.02253.082-0.001-0.0010.0000.0000.0000.000
74A244THR0-0.0220.00555.7330.0010.0010.0000.0000.0000.000
75A245VAL00.0170.00655.634-0.001-0.0010.0000.0000.0000.000
76A246TYR0-0.017-0.02557.2990.0010.0010.0000.0000.0000.000
77A247ALA00.0500.01958.245-0.001-0.0010.0000.0000.0000.000
78A248GLY00.0290.01160.7000.0010.0010.0000.0000.0000.000
79A249ASP-1-0.927-0.95461.647-0.017-0.0170.0000.0000.0000.000
80A250LYS10.8620.94163.1190.0110.0110.0000.0000.0000.000
81A251PRO0-0.035-0.01161.7700.0000.0000.0000.0000.0000.000
82A252PHE0-0.005-0.00961.1510.0010.0010.0000.0000.0000.000
83A253GLU-1-0.918-0.95760.565-0.009-0.0090.0000.0000.0000.000
84A254ALA00.0140.00456.9370.0000.0000.0000.0000.0000.000
85A255THR0-0.045-0.01257.2490.0000.0000.0000.0000.0000.000
86A256VAL00.0500.02150.7620.0000.0000.0000.0000.0000.000
87A257VAL0-0.0060.00153.9020.0010.0010.0000.0000.0000.000
88A258SER0-0.018-0.02048.8710.0020.0020.0000.0000.0000.000
89A259TYR00.012-0.00844.173-0.002-0.0020.0000.0000.0000.000
90A260ASP-1-0.768-0.85741.590-0.006-0.0060.0000.0000.0000.000
91A261PRO0-0.004-0.01040.513-0.002-0.0020.0000.0000.0000.000
92A262SER00.0090.00137.428-0.002-0.0020.0000.0000.0000.000
93A263VAL00.0240.00137.455-0.003-0.0030.0000.0000.0000.000
94A264ASP-1-0.761-0.85439.312-0.027-0.0270.0000.0000.0000.000
95A265VAL00.0000.00041.214-0.002-0.0020.0000.0000.0000.000
96A266ALA0-0.016-0.00944.7270.0020.0020.0000.0000.0000.000
97A267ILE0-0.015-0.00848.192-0.001-0.0010.0000.0000.0000.000
98A268LEU0-0.015-0.01351.5120.0010.0010.0000.0000.0000.000
99A269ALA0-0.013-0.00454.6610.0000.0000.0000.0000.0000.000
100A270VAL0-0.011-0.02757.6650.0000.0000.0000.0000.0000.000
101A271PRO0-0.008-0.00760.4300.0000.0000.0000.0000.0000.000
102A272HIS0-0.050-0.02864.1050.0000.0000.0000.0000.0000.000
103A273LEU0-0.0020.00458.8130.0000.0000.0000.0000.0000.000
104A274PRO0-0.041-0.03163.4200.0000.0000.0000.0000.0000.000
105A275PRO0-0.0130.01260.2790.0000.0000.0000.0000.0000.000
106A276PRO00.0380.02460.8460.0010.0010.0000.0000.0000.000
107A277PRO0-0.033-0.00357.169-0.001-0.0010.0000.0000.0000.000
108A278LEU00.0140.01553.0070.0000.0000.0000.0000.0000.000
109A279VAL0-0.032-0.01653.3840.0010.0010.0000.0000.0000.000
110A280PHE00.012-0.00447.406-0.001-0.0010.0000.0000.0000.000
111A281ALA00.0150.00747.3640.0010.0010.0000.0000.0000.000
112A282ALA0-0.031-0.01747.7810.0000.0000.0000.0000.0000.000
113A283GLU-1-0.935-0.96545.458-0.012-0.0120.0000.0000.0000.000
114A284PRO0-0.034-0.00840.588-0.001-0.0010.0000.0000.0000.000
115A285ALA00.0000.00241.6270.0000.0000.0000.0000.0000.000
116A286LYS10.9520.96139.8010.0240.0240.0000.0000.0000.000
117A287THR00.001-0.02535.4680.0010.0010.0000.0000.0000.000
118A288GLY0-0.040-0.02838.2370.0010.0010.0000.0000.0000.000
119A289ALA0-0.0300.00440.3180.0010.0010.0000.0000.0000.000
120A290ASP-1-0.786-0.88243.047-0.039-0.0390.0000.0000.0000.000
121A291VAL0-0.035-0.02242.6540.0020.0020.0000.0000.0000.000
122A292VAL00.001-0.00145.935-0.001-0.0010.0000.0000.0000.000
123A293VAL00.0090.01542.9970.0010.0010.0000.0000.0000.000
124A294LEU0-0.0140.00546.3320.0000.0000.0000.0000.0000.000
125A295GLY00.0680.00848.8890.0010.0010.0000.0000.0000.000
126A296TYR0-0.055-0.03949.7920.0000.0000.0000.0000.0000.000
127A297PRO00.0740.04947.5300.0010.0010.0000.0000.0000.000
128A298GLY0-0.014-0.01847.9730.0010.0010.0000.0000.0000.000
129A299GLY0-0.054-0.02249.6050.0010.0010.0000.0000.0000.000
130A300GLY0-0.036-0.00452.2510.0020.0020.0000.0000.0000.000
131A301ASN00.006-0.01654.3100.0010.0010.0000.0000.0000.000
132A302PHE00.0540.02553.273-0.001-0.0010.0000.0000.0000.000
133A303THR0-0.024-0.01249.7480.0000.0000.0000.0000.0000.000
134A304ALA0-0.0080.00250.3380.0000.0000.0000.0000.0000.000
135A305THR00.0330.00144.2740.0000.0000.0000.0000.0000.000
136A306PRO0-0.031-0.00745.9060.0000.0000.0000.0000.0000.000
137A307ALA00.0130.00042.098-0.002-0.0020.0000.0000.0000.000
138A308ARG10.7430.86140.0600.0450.0450.0000.0000.0000.000
139A309ILE0-0.0150.01138.120-0.003-0.0030.0000.0000.0000.000
140A310ARG10.8680.93632.8780.0710.0710.0000.0000.0000.000
141A311GLU-1-0.883-0.96130.087-0.066-0.0660.0000.0000.0000.000
142A312ALA0-0.0240.00534.5340.0010.0010.0000.0000.0000.000
143A313ILE00.0020.00429.444-0.001-0.0010.0000.0000.0000.000
144A314ARG10.8420.92129.9230.0190.0190.0000.0000.0000.000
145A315LEU0-0.025-0.00428.669-0.005-0.0050.0000.0000.0000.000
146A316SER00.0310.00226.5410.0070.0070.0000.0000.0000.000
147A317GLY0-0.0030.00427.863-0.009-0.0090.0000.0000.0000.000
148A318PRO00.0110.02428.8360.0060.0060.0000.0000.0000.000
149A319ASH0-0.018-0.04431.465-0.003-0.0030.0000.0000.0000.000
150A320ILE0-0.013-0.01535.011-0.002-0.0020.0000.0000.0000.000
151A321TYR0-0.057-0.02837.463-0.001-0.0010.0000.0000.0000.000
152A322GLY0-0.0300.00333.1420.0000.0000.0000.0000.0000.000
153A323ASP-1-0.865-0.90133.355-0.007-0.0070.0000.0000.0000.000
154A324PRO0-0.046-0.03730.970-0.002-0.0020.0000.0000.0000.000
155A325GLU-1-0.928-0.95129.8250.0110.0110.0000.0000.0000.000
156A326PRO0-0.069-0.01927.098-0.004-0.0040.0000.0000.0000.000
157A327VAL00.007-0.00430.3340.0040.0040.0000.0000.0000.000
158A328THR0-0.023-0.03229.252-0.003-0.0030.0000.0000.0000.000
159A329ARG10.8580.93831.8260.0300.0300.0000.0000.0000.000
160A330ASP-1-0.856-0.92533.408-0.021-0.0210.0000.0000.0000.000
161A331VAL0-0.040-0.04133.2600.0010.0010.0000.0000.0000.000
162A332TYR00.0150.01335.3380.0000.0000.0000.0000.0000.000
163A333THR00.0000.00831.389-0.001-0.0010.0000.0000.0000.000
164A334ILE00.000-0.00934.8530.0020.0020.0000.0000.0000.000
165A335ARG10.7150.82936.3660.0600.0600.0000.0000.0000.000
166A336ALA00.029-0.01637.7770.0040.0040.0000.0000.0000.000
167A337ASP-1-0.901-0.93838.869-0.056-0.0560.0000.0000.0000.000
168A338VAL0-0.044-0.01839.6030.0030.0030.0000.0000.0000.000
169A339GLU-1-0.906-0.95140.889-0.039-0.0390.0000.0000.0000.000
170A340GLN0-0.041-0.03740.4540.0030.0030.0000.0000.0000.000
171A341GLY00.0280.02343.9810.0010.0010.0000.0000.0000.000
172A342ASP-1-0.771-0.88443.993-0.032-0.0320.0000.0000.0000.000
173A343SER0-0.097-0.04742.0540.0010.0010.0000.0000.0000.000
174A344GLY00.0170.00544.2420.0020.0020.0000.0000.0000.000
175A345GLY00.0430.01446.2460.0020.0020.0000.0000.0000.000
176A346PRO0-0.048-0.00446.041-0.001-0.0010.0000.0000.0000.000
177A347LEU00.0050.00341.784-0.001-0.0010.0000.0000.0000.000
178A348ILE0-0.003-0.01045.7790.0020.0020.0000.0000.0000.000
179A349ASP-1-0.747-0.88047.692-0.023-0.0230.0000.0000.0000.000
180A350LEU0-0.011-0.02148.8210.0010.0010.0000.0000.0000.000
181A351ASN0-0.109-0.05751.1480.0010.0010.0000.0000.0000.000
182A352GLY00.006-0.00152.5670.0010.0010.0000.0000.0000.000
183A353GLN0-0.057-0.02051.0930.0010.0010.0000.0000.0000.000
184A354VAL0-0.016-0.01047.423-0.002-0.0020.0000.0000.0000.000
185A355LEU00.009-0.00543.9120.0010.0010.0000.0000.0000.000
186A356GLY00.023-0.01243.0260.0000.0000.0000.0000.0000.000
187A357VAL0-0.033-0.00242.9210.0000.0000.0000.0000.0000.000
188A358VAL00.0440.02341.227-0.002-0.0020.0000.0000.0000.000
189A359PHE0-0.043-0.02534.9800.0020.0020.0000.0000.0000.000
190A360GLY0-0.006-0.01136.8980.0000.0000.0000.0000.0000.000
191A361ALA00.0340.02736.0220.0010.0010.0000.0000.0000.000
192A362ALA0-0.047-0.01630.7700.0000.0000.0000.0000.0000.000
193A363ILE0-0.047-0.02129.4570.0010.0010.0000.0000.0000.000
194A364ASP-1-0.849-0.92325.913-0.111-0.1110.0000.0000.0000.000
195A365ASP-1-0.921-0.92728.996-0.094-0.0940.0000.0000.0000.000
196A366ALA00.027-0.00330.5400.0060.0060.0000.0000.0000.000
197A367GLU-1-0.737-0.82334.023-0.058-0.0580.0000.0000.0000.000
198A368THR0-0.021-0.04932.0330.0020.0020.0000.0000.0000.000
199A369GLY00.0040.01634.9060.0010.0010.0000.0000.0000.000
200A370PHE0-0.018-0.02330.320-0.002-0.0020.0000.0000.0000.000
201A371VAL00.013-0.00136.4380.0030.0030.0000.0000.0000.000
202A372LEU0-0.0090.01137.835-0.001-0.0010.0000.0000.0000.000
203A373THR00.0220.01338.1220.0020.0020.0000.0000.0000.000
204A374ALA00.0520.01340.8360.0020.0020.0000.0000.0000.000
205A375GLY0-0.005-0.00542.0430.0020.0020.0000.0000.0000.000
206A376GLU-1-0.805-0.90037.421-0.013-0.0130.0000.0000.0000.000
207A377VAL0-0.012-0.01140.6680.0020.0020.0000.0000.0000.000
208A378ALA00.0170.01843.8450.0010.0010.0000.0000.0000.000
209A379GLY00.0060.00244.5460.0010.0010.0000.0000.0000.000
210A380GLN0-0.054-0.05143.2520.0020.0020.0000.0000.0000.000
211A381LEU00.000-0.00247.2430.0010.0010.0000.0000.0000.000
212A382ALA0-0.0050.01149.4160.0010.0010.0000.0000.0000.000
213A383LYS10.8700.94449.7990.0040.0040.0000.0000.0000.000
214A384ILE00.0290.01452.3000.0000.0000.0000.0000.0000.000
215A385GLY0-0.0050.00154.4560.0000.0000.0000.0000.0000.000
216A386ALA0-0.041-0.00954.8670.0010.0010.0000.0000.0000.000
217A387THR00.018-0.00756.836-0.001-0.0010.0000.0000.0000.000
218A388GLN0-0.041-0.01557.7360.0000.0000.0000.0000.0000.000
219A389PRO00.0360.02056.0990.0000.0000.0000.0000.0000.000
220A390VAL0-0.032-0.00450.6270.0010.0010.0000.0000.0000.000
221A391GLY0-0.016-0.01650.799-0.001-0.0010.0000.0000.0000.000
222A392THR0-0.005-0.00948.6630.0000.0000.0000.0000.0000.000
223A393GLY00.0340.02745.552-0.001-0.0010.0000.0000.0000.000
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