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: K9NZ3

Calculation Name: 1YO6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YO6

Chain ID: A

ChEMBL ID:

UniProt ID: P90780

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 237
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2840880.502524
FMO2-HF: Nuclear repulsion 2751907.534575
FMO2-HF: Total energy -88972.96795
FMO2-MP2: Total energy -89233.738643


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.
-2.8751.9311.205-1.928-4.0830.003
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 : 0.048 / q_NPA : 0.052
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].
3A3PRO0-0.021-0.0073.762-0.3102.6320.205-1.114-2.0320.006
4A4GLY00.013-0.0026.3030.4650.4650.0000.0000.0000.000
5A5SER00.012-0.0117.214-0.260-0.2600.0000.0000.0000.000
6A6VAL00.016-0.00310.422-0.091-0.0910.0000.0000.0000.000
7A7VAL00.0020.00812.9040.0170.0170.0000.0000.0000.000
8A8VAL0-0.0010.00516.212-0.040-0.0400.0000.0000.0000.000
9A9THR00.0460.01718.5630.0100.0100.0000.0000.0000.000
10A10GLY00.0050.00622.151-0.015-0.0150.0000.0000.0000.000
11A11ALA0-0.012-0.00721.241-0.011-0.0110.0000.0000.0000.000
12A12ASN00.024-0.00323.217-0.001-0.0010.0000.0000.0000.000
13A13ARG10.9670.97826.3040.0870.0870.0000.0000.0000.000
14A14GLY0-0.0050.00526.023-0.002-0.0020.0000.0000.0000.000
15A15ILE00.0440.01720.661-0.004-0.0040.0000.0000.0000.000
16A16GLY00.0880.03620.687-0.019-0.0190.0000.0000.0000.000
17A17LEU0-0.0230.00720.299-0.005-0.0050.0000.0000.0000.000
18A18GLY00.0680.02920.464-0.004-0.0040.0000.0000.0000.000
19A19LEU0-0.018-0.01015.824-0.031-0.0310.0000.0000.0000.000
20A20VAL00.0250.01215.918-0.027-0.0270.0000.0000.0000.000
21A21GLN0-0.024-0.02216.000-0.010-0.0100.0000.0000.0000.000
22A22GLN0-0.059-0.02413.686-0.026-0.0260.0000.0000.0000.000
23A23LEU00.001-0.01011.742-0.047-0.0470.0000.0000.0000.000
24A24VAL0-0.0030.00111.0920.0230.0230.0000.0000.0000.000
25A25LYS10.7820.88712.5880.2920.2920.0000.0000.0000.000
26A26ASP-1-0.743-0.8346.027-0.787-0.7870.0000.0000.0000.000
27A27LYS10.8320.8997.2540.2910.2910.0000.0000.0000.000
28A28ASN0-0.041-0.0192.335-1.368-0.4520.777-0.526-1.168-0.003
29A29ILE0-0.0640.0004.4220.5110.655-0.001-0.006-0.1360.000
30A30ARG10.8900.9396.600-1.611-1.6110.0000.0000.0000.000
31A31HIS00.0100.0079.244-0.081-0.0810.0000.0000.0000.000
32A32ILE00.001-0.00211.188-0.002-0.0020.0000.0000.0000.000
33A33ILE00.0180.01713.943-0.027-0.0270.0000.0000.0000.000
34A34ALA00.0070.01117.324-0.031-0.0310.0000.0000.0000.000
35A35THR00.0130.00820.0150.0070.0070.0000.0000.0000.000
36A36ALA00.0100.00223.730-0.013-0.0130.0000.0000.0000.000
37A37ARG10.9380.97727.2320.0390.0390.0000.0000.0000.000
38A38ASP-1-0.778-0.87230.671-0.018-0.0180.0000.0000.0000.000
39A39VAL00.0440.00626.850-0.004-0.0040.0000.0000.0000.000
40A40GLU-1-0.901-0.93329.318-0.014-0.0140.0000.0000.0000.000
41A41LYS10.8410.88231.9600.0210.0210.0000.0000.0000.000
42A42ALA0-0.0020.01826.917-0.005-0.0050.0000.0000.0000.000
43A43THR0-0.021-0.02227.362-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.848-0.92525.460-0.087-0.0870.0000.0000.0000.000
45A45LEU00.0070.01521.357-0.003-0.0030.0000.0000.0000.000
46A46LYS10.8660.92722.8000.0190.0190.0000.0000.0000.000
47A47SER0-0.069-0.03624.5570.0040.0040.0000.0000.0000.000
48A48ILE00.0430.02418.3100.0000.0000.0000.0000.0000.000
49A49LYS10.8180.89619.9810.0390.0390.0000.0000.0000.000
50A50ASP-1-0.781-0.87113.414-0.024-0.0240.0000.0000.0000.000
51A51SER00.0430.02316.285-0.001-0.0010.0000.0000.0000.000
52A52ARG10.7440.8598.681-0.019-0.0190.0000.0000.0000.000
53A53VAL0-0.036-0.00914.5580.0160.0160.0000.0000.0000.000
54A54HIS00.0130.00715.978-0.011-0.0110.0000.0000.0000.000
55A55VAL0-0.007-0.00519.159-0.009-0.0090.0000.0000.0000.000
56A56LEU00.0090.00021.8080.0040.0040.0000.0000.0000.000
57A57PRO0-0.039-0.02424.602-0.010-0.0100.0000.0000.0000.000
58A58LEU0-0.013-0.02024.6460.0040.0040.0000.0000.0000.000
59A59THR0-0.010-0.00328.227-0.009-0.0090.0000.0000.0000.000
60A60VAL00.014-0.01326.4740.0040.0040.0000.0000.0000.000
61A61THR00.0400.03029.1280.0000.0000.0000.0000.0000.000
62A62CYM-1-0.823-0.80231.752-0.007-0.0070.0000.0000.0000.000
63A63ASP-1-0.772-0.90231.311-0.011-0.0110.0000.0000.0000.000
64A64LYS10.8540.89931.326-0.001-0.0010.0000.0000.0000.000
65A65SER0-0.013-0.04929.7450.0040.0040.0000.0000.0000.000
66A66LEU0-0.026-0.01426.2800.0040.0040.0000.0000.0000.000
67A67ASP-1-0.787-0.87526.8400.0130.0130.0000.0000.0000.000
68A68THR0-0.051-0.02727.6650.0100.0100.0000.0000.0000.000
69A69PHE0-0.005-0.01020.5510.0080.0080.0000.0000.0000.000
70A70VAL00.0150.00122.8710.0100.0100.0000.0000.0000.000
71A71SER0-0.029-0.02522.7680.0140.0140.0000.0000.0000.000
72A72LYS10.9440.97823.377-0.022-0.0220.0000.0000.0000.000
73A73VAL0-0.007-0.00618.4690.0140.0140.0000.0000.0000.000
74A74GLY00.0210.00618.3690.0280.0280.0000.0000.0000.000
75A75GLU-1-0.985-0.99319.6100.1280.1280.0000.0000.0000.000
76A76ILE0-0.0050.00016.4360.0190.0190.0000.0000.0000.000
77A77VAL0-0.063-0.02914.1940.0350.0350.0000.0000.0000.000
78A78GLY00.0330.02315.1950.0490.0490.0000.0000.0000.000
79A79SER0-0.057-0.04614.657-0.015-0.0150.0000.0000.0000.000
80A80ASP-1-0.814-0.87811.3070.6030.6030.0000.0000.0000.000
81A81GLY00.0150.01612.4850.0150.0150.0000.0000.0000.000
82A82LEU0-0.056-0.02813.2100.0580.0580.0000.0000.0000.000
83A83SER00.0180.0257.8700.0800.0800.0000.0000.0000.000
84A84LEU0-0.020-0.0089.625-0.176-0.1760.0000.0000.0000.000
85A85LEU00.0050.01611.6040.0430.0430.0000.0000.0000.000
86A86ILE0-0.022-0.01315.156-0.050-0.0500.0000.0000.0000.000
87A87ASN00.021-0.00516.8740.0370.0370.0000.0000.0000.000
88A88ASN0-0.022-0.03820.608-0.027-0.0270.0000.0000.0000.000
89A89ALA0-0.069-0.02122.3160.0050.0050.0000.0000.0000.000
90A90GLY00.0510.01925.469-0.003-0.0030.0000.0000.0000.000
91A91VAL0-0.050-0.02328.4800.0030.0030.0000.0000.0000.000
92A92LEU0-0.0010.00331.862-0.004-0.0040.0000.0000.0000.000
93A93LEU0-0.008-0.00533.9780.0030.0030.0000.0000.0000.000
94A94SER0-0.009-0.00737.575-0.001-0.0010.0000.0000.0000.000
95A95TYR0-0.002-0.01840.1740.0030.0030.0000.0000.0000.000
96A96GLY00.002-0.01840.589-0.004-0.0040.0000.0000.0000.000
97A97THR0-0.006-0.02042.9230.0010.0010.0000.0000.0000.000
98A98ASN0-0.0060.01645.5850.0010.0010.0000.0000.0000.000
99A99THR0-0.0240.00145.1300.0000.0000.0000.0000.0000.000
100A100GLU-1-0.847-0.92647.535-0.029-0.0290.0000.0000.0000.000
101A101PRO0-0.007-0.01048.302-0.001-0.0010.0000.0000.0000.000
102A102ASN00.0430.03545.7190.0020.0020.0000.0000.0000.000
103A103ARG10.9850.97644.5580.0270.0270.0000.0000.0000.000
104A104ALA00.0270.02543.142-0.001-0.0010.0000.0000.0000.000
105A105VAL00.0490.02641.025-0.001-0.0010.0000.0000.0000.000
106A106ILE0-0.021-0.01239.705-0.003-0.0030.0000.0000.0000.000
107A107ALA0-0.022-0.01138.589-0.003-0.0030.0000.0000.0000.000
108A108GLU-1-0.875-0.93936.828-0.042-0.0420.0000.0000.0000.000
109A109GLN0-0.028-0.02833.143-0.004-0.0040.0000.0000.0000.000
110A110LEU0-0.001-0.01333.724-0.006-0.0060.0000.0000.0000.000
111A111ASP-1-0.863-0.91232.941-0.041-0.0410.0000.0000.0000.000
112A112VAL0-0.018-0.00330.861-0.002-0.0020.0000.0000.0000.000
113A113ASN0-0.051-0.03628.962-0.008-0.0080.0000.0000.0000.000
114A114THR0-0.043-0.02128.312-0.007-0.0070.0000.0000.0000.000
115A115THR00.003-0.00928.758-0.002-0.0020.0000.0000.0000.000
116A116SER00.0490.01528.9450.0030.0030.0000.0000.0000.000
117A117VAL0-0.0180.00023.6060.0020.0020.0000.0000.0000.000
118A118VAL0-0.0040.01624.409-0.002-0.0020.0000.0000.0000.000
119A119LEU00.0280.00925.6010.0040.0040.0000.0000.0000.000
120A120LEU0-0.039-0.01721.9360.0080.0080.0000.0000.0000.000
121A121THR0-0.005-0.02220.1680.0020.0020.0000.0000.0000.000
122A122GLN0-0.013-0.02121.6050.0100.0100.0000.0000.0000.000
123A123LYS10.8000.88323.8730.0130.0130.0000.0000.0000.000
124A124LEU00.0060.00818.8790.0140.0140.0000.0000.0000.000
125A125LEU00.0100.01818.7820.0110.0110.0000.0000.0000.000
126A126PRO0-0.008-0.00618.8060.0060.0060.0000.0000.0000.000
127A127LEU00.0100.00816.6590.0170.0170.0000.0000.0000.000
128A128LEU00.0060.01513.7890.0370.0370.0000.0000.0000.000
129A129LYS10.8350.89614.0390.0080.0080.0000.0000.0000.000
130A130ASN0-0.034-0.01315.4120.0190.0190.0000.0000.0000.000
131A131ALA00.0300.03110.4560.0270.0270.0000.0000.0000.000
132A132ALA00.0160.00410.8220.0250.0250.0000.0000.0000.000
133A133SER0-0.075-0.04512.089-0.009-0.0090.0000.0000.0000.000
134A134LYS10.8280.92110.403-0.307-0.3070.0000.0000.0000.000
135A135GLU-1-0.906-0.9556.054-0.219-0.2190.0000.0000.0000.000
136A136SER0-0.022-0.0069.961-0.047-0.0470.0000.0000.0000.000
137A137GLY00.0190.01111.997-0.007-0.0070.0000.0000.0000.000
138A138ASP-1-0.873-0.92513.861-0.145-0.1450.0000.0000.0000.000
139A139GLN0-0.060-0.0469.396-0.010-0.0100.0000.0000.0000.000
140A140LEU00.0040.02610.568-0.010-0.0100.0000.0000.0000.000
141A141SER00.0330.0025.4800.0340.0340.0000.0000.0000.000
142A142VAL00.005-0.0156.4940.2150.2150.0000.0000.0000.000
143A143SER0-0.008-0.0012.770-0.823-0.1550.225-0.276-0.6180.000
144A144ARG10.8090.9194.7330.7630.899-0.001-0.006-0.1290.000
145A145ALA00.0420.0057.2210.2280.2280.0000.0000.0000.000
146A146ALA0-0.0230.00010.551-0.085-0.0850.0000.0000.0000.000
147A147VAL0-0.004-0.00112.4220.0590.0590.0000.0000.0000.000
148A148ILE0-0.0140.00212.340-0.012-0.0120.0000.0000.0000.000
149A149THR0-0.019-0.01216.6580.0430.0430.0000.0000.0000.000
150A150ILE0-0.0250.00519.009-0.013-0.0130.0000.0000.0000.000
151A151SER00.016-0.02721.8770.0290.0290.0000.0000.0000.000
152A152SER00.020-0.01524.736-0.001-0.0010.0000.0000.0000.000
153A153GLY00.0690.02526.9900.0030.0030.0000.0000.0000.000
154A154LEU0-0.060-0.02428.2010.0070.0070.0000.0000.0000.000
155A155GLY00.0370.00929.7700.0090.0090.0000.0000.0000.000
156A156SER0-0.076-0.05828.347-0.002-0.0020.0000.0000.0000.000
157A157ILE00.003-0.02330.0630.0050.0050.0000.0000.0000.000
158A158THR00.0160.00231.4110.0060.0060.0000.0000.0000.000
159A159ASP-1-0.827-0.87630.058-0.112-0.1120.0000.0000.0000.000
160A160ASN0-0.048-0.01433.0770.0020.0020.0000.0000.0000.000
161A161THR00.001-0.01135.7890.0050.0050.0000.0000.0000.000
162A162SER00.0080.00736.8000.0020.0020.0000.0000.0000.000
163A163GLY0-0.0020.01739.0260.0030.0030.0000.0000.0000.000
164A164SER0-0.014-0.01739.180-0.003-0.0030.0000.0000.0000.000
165A165ALA00.0000.01141.5250.0020.0020.0000.0000.0000.000
166A166GLN00.0170.01142.2780.0030.0030.0000.0000.0000.000
167A167PHE00.0460.01439.027-0.001-0.0010.0000.0000.0000.000
168A168PRO00.0230.02740.682-0.001-0.0010.0000.0000.0000.000
169A169VAL00.0350.00135.958-0.001-0.0010.0000.0000.0000.000
170A170LEU00.0120.01336.676-0.004-0.0040.0000.0000.0000.000
171A171ALA00.0380.01637.315-0.002-0.0020.0000.0000.0000.000
172A172TYR00.0080.01429.151-0.004-0.0040.0000.0000.0000.000
173A173ARG10.8320.91032.6680.0720.0720.0000.0000.0000.000
174A174MET00.0030.00332.721-0.003-0.0030.0000.0000.0000.000
175A175SER0-0.018-0.00132.195-0.003-0.0030.0000.0000.0000.000
176A176LYS10.8900.93925.8210.1120.1120.0000.0000.0000.000
177A177ALA00.0370.01928.236-0.008-0.0080.0000.0000.0000.000
178A178ALA0-0.0170.00029.659-0.003-0.0030.0000.0000.0000.000
179A179ILE00.0120.00824.836-0.001-0.0010.0000.0000.0000.000
180A180ASN00.0010.03024.940-0.021-0.0210.0000.0000.0000.000
181A181MET00.0190.01425.462-0.008-0.0080.0000.0000.0000.000
182A182PHE00.0160.01023.0270.0000.0000.0000.0000.0000.000
183A183GLY00.0500.02422.0570.0000.0000.0000.0000.0000.000
184A184ARG10.8460.91122.0650.1190.1190.0000.0000.0000.000
185A185THR0-0.019-0.02024.2550.0020.0020.0000.0000.0000.000
186A186LEU00.0360.02120.0050.0030.0030.0000.0000.0000.000
187A187ALA00.0060.01119.6350.0000.0000.0000.0000.0000.000
188A188VAL0-0.086-0.04520.632-0.004-0.0040.0000.0000.0000.000
189A189ASP-1-0.875-0.94623.206-0.058-0.0580.0000.0000.0000.000
190A190LEU0-0.049-0.02218.5210.0130.0130.0000.0000.0000.000
191A191LYS10.8590.93818.4020.1280.1280.0000.0000.0000.000
192A192ASP-1-0.864-0.93818.257-0.055-0.0550.0000.0000.0000.000
193A193ASP-1-0.822-0.88717.706-0.008-0.0080.0000.0000.0000.000
194A194ASN0-0.036-0.03313.449-0.007-0.0070.0000.0000.0000.000
195A195VAL0-0.0020.01512.917-0.040-0.0400.0000.0000.0000.000
196A196LEU0-0.031-0.00910.7920.0030.0030.0000.0000.0000.000
197A197VAL00.0110.00813.9080.0180.0180.0000.0000.0000.000
198A198VAL0-0.0240.00114.597-0.001-0.0010.0000.0000.0000.000
199A199ASN00.007-0.00117.507-0.003-0.0030.0000.0000.0000.000
200A200PHE00.0470.00414.637-0.014-0.0140.0000.0000.0000.000
201A201CYS0-0.100-0.01220.0830.0300.0300.0000.0000.0000.000
202A202PRO00.0080.00921.701-0.021-0.0210.0000.0000.0000.000
203A203GLY00.0170.00722.6830.0090.0090.0000.0000.0000.000
204A204TRP00.0070.00725.2060.0020.0020.0000.0000.0000.000
205A218VAL00.0420.00824.442-0.003-0.0030.0000.0000.0000.000
206A219GLU-1-0.781-0.88519.120-0.235-0.2350.0000.0000.0000.000
207A220GLN00.0160.01319.280-0.023-0.0230.0000.0000.0000.000
208A221SER00.0400.01219.197-0.020-0.0200.0000.0000.0000.000
209A222THR0-0.042-0.02717.653-0.020-0.0200.0000.0000.0000.000
210A223ALA00.0490.02915.008-0.055-0.0550.0000.0000.0000.000
211A224GLU-1-0.822-0.89814.210-0.321-0.3210.0000.0000.0000.000
212A225LEU0-0.026-0.00214.653-0.047-0.0470.0000.0000.0000.000
213A226ILE00.0250.01310.193-0.060-0.0600.0000.0000.0000.000
214A227SER0-0.0010.00710.073-0.195-0.1950.0000.0000.0000.000
215A228SER0-0.058-0.05610.254-0.114-0.1140.0000.0000.0000.000
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