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: 6YRRZ

Calculation Name: 1YB2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YB2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HJW1

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2689215.792248
FMO2-HF: Nuclear repulsion 2597574.820092
FMO2-HF: Total energy -91640.972156
FMO2-MP2: Total energy -91903.377472


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:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-30.489-18.39311.244-9.394-13.946-0.069
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / 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].
3A8ILE0-0.063-0.0283.644-3.493-0.593-0.027-1.594-1.2790.003
4A9LEU0-0.032-0.0035.1370.0370.115-0.001-0.004-0.0730.000
5A10VAL00.0160.0047.946-0.117-0.1170.0000.0000.0000.000
6A11SER0-0.023-0.03410.429-0.099-0.0990.0000.0000.0000.000
7A12GLU-1-0.808-0.88413.9170.2440.2440.0000.0000.0000.000
8A13ASP-1-0.805-0.88917.3110.2120.2120.0000.0000.0000.000
9A14GLU-1-0.818-0.90916.2300.2530.2530.0000.0000.0000.000
10A15TYR0-0.036-0.00811.2840.0800.0800.0000.0000.0000.000
11A16GLY0-0.031-0.02910.872-0.099-0.0990.0000.0000.0000.000
12A17LYS10.8380.9277.899-0.185-0.1850.0000.0000.0000.000
13A18PHE0-0.019-0.0152.959-0.7310.2510.153-0.297-0.8380.000
14A19ASP-1-0.797-0.8875.580-1.353-1.3530.0000.0000.0000.000
15A20GLU-1-0.846-0.9341.980-18.652-16.8076.892-4.261-4.477-0.050
16A21SER0-0.071-0.0454.5530.3280.449-0.001-0.017-0.1030.000
17A22THR0-0.095-0.0578.0150.3210.3210.0000.0000.0000.000
18A23ASN0-0.0180.0036.379-0.055-0.0550.0000.0000.0000.000
19A24SER0-0.0130.0147.8060.2980.2980.0000.0000.0000.000
20A25ILE00.0330.0068.055-0.024-0.0240.0000.0000.0000.000
21A26LEU0-0.025-0.01610.122-0.005-0.0050.0000.0000.0000.000
22A27VAL00.0600.03712.2900.0870.0870.0000.0000.0000.000
23A28LYS10.8460.90814.150-0.271-0.2710.0000.0000.0000.000
24A29GLY0-0.010-0.01515.7760.0200.0200.0000.0000.0000.000
25A30LYS10.8900.94217.155-0.074-0.0740.0000.0000.0000.000
26A31MET0-0.0030.00112.4830.0270.0270.0000.0000.0000.000
27A32HIS0-0.022-0.01013.379-0.005-0.0050.0000.0000.0000.000
28A33HIS00.0690.01911.800-0.073-0.0730.0000.0000.0000.000
29A34LEU0-0.0030.0167.9200.0750.0750.0000.0000.0000.000
30A35GLY00.0270.01011.911-0.016-0.0160.0000.0000.0000.000
31A36ILE0-0.036-0.02213.164-0.060-0.0600.0000.0000.0000.000
32A37SER0-0.004-0.00711.5090.0070.0070.0000.0000.0000.000
33A38ARG10.8600.92410.2600.4410.4410.0000.0000.0000.000
34A39VAL00.0490.0295.0830.0440.0440.0000.0000.0000.000
35A40ILE0-0.066-0.0374.4430.3290.488-0.001-0.021-0.1370.000
36A41GLU-1-0.873-0.9333.135-4.245-2.8520.188-0.526-1.055-0.004
37A42PRO00.0180.0052.439-0.7870.4761.127-0.510-1.8790.001
38A43GLY00.0320.0013.967-0.301-0.2120.003-0.027-0.0650.000
39A44ASP-1-0.783-0.8485.971-0.544-0.5440.0000.0000.0000.000
40A45GLU-1-0.807-0.8827.6590.2840.2840.0000.0000.0000.000
41A46LEU0-0.006-0.0096.344-0.109-0.1090.0000.0000.0000.000
42A47ILE0-0.016-0.01810.5030.0400.0400.0000.0000.0000.000
43A48VAL00.0210.01313.115-0.041-0.0410.0000.0000.0000.000
44A49SER0-0.049-0.04215.0090.0200.0200.0000.0000.0000.000
45A50GLY0-0.0180.00018.1300.0060.0060.0000.0000.0000.000
46A51LYS10.8140.91615.778-0.211-0.2110.0000.0000.0000.000
47A52SER0-0.043-0.04413.877-0.021-0.0210.0000.0000.0000.000
48A53PHE0-0.005-0.00210.2520.0040.0040.0000.0000.0000.000
49A54ILE0-0.040-0.0138.302-0.094-0.0940.0000.0000.0000.000
50A55VAL00.0280.0162.438-0.177-0.2271.736-0.431-1.2540.001
51A56SER0-0.003-0.0164.109-0.777-0.5040.000-0.052-0.2210.000
52A57ASP-1-0.789-0.8882.5871.8224.7681.175-1.647-2.475-0.020
53A58PHE0-0.034-0.0284.102-1.907-1.8100.000-0.007-0.0900.000
54A59SER00.0530.0227.076-0.299-0.2990.0000.0000.0000.000
55A60PRO00.0040.00010.341-0.067-0.0670.0000.0000.0000.000
56A61MET0-0.0190.00312.946-0.059-0.0590.0000.0000.0000.000
57A62TYR00.0990.0368.493-0.143-0.1430.0000.0000.0000.000
58A63PHE0-0.012-0.00312.262-0.053-0.0530.0000.0000.0000.000
59A64GLY00.0180.00013.585-0.055-0.0550.0000.0000.0000.000
60A65ARG10.7730.88613.537-0.447-0.4470.0000.0000.0000.000
61A66VAL00.0010.0089.905-0.047-0.0470.0000.0000.0000.000
62A67ILE0-0.091-0.02113.258-0.118-0.1180.0000.0000.0000.000
63A86CYS00.0410.01916.312-0.017-0.0170.0000.0000.0000.000
64A87GLY0-0.065-0.04213.925-0.027-0.0270.0000.0000.0000.000
65A88LEU00.0180.01014.0580.0570.0570.0000.0000.0000.000
66A89ARG10.9260.96010.953-0.936-0.9360.0000.0000.0000.000
67A90PRO00.0230.01116.515-0.017-0.0170.0000.0000.0000.000
68A91GLY0-0.064-0.03815.7810.0550.0550.0000.0000.0000.000
69A92MET0-0.063-0.00712.7800.0040.0040.0000.0000.0000.000
70A93ASP-1-0.782-0.85215.0060.1250.1250.0000.0000.0000.000
71A94ILE0-0.055-0.03816.1320.0300.0300.0000.0000.0000.000
72A95LEU00.0010.01118.401-0.032-0.0320.0000.0000.0000.000
73A96GLU-1-0.793-0.88920.7260.2020.2020.0000.0000.0000.000
74A97VAL0-0.023-0.01623.314-0.019-0.0190.0000.0000.0000.000
75A98GLY00.0310.02425.9800.0050.0050.0000.0000.0000.000
76A99VAL0-0.005-0.01328.0470.0100.0100.0000.0000.0000.000
77A100GLY00.0230.00730.2510.0040.0040.0000.0000.0000.000
78A101SER0-0.032-0.02432.787-0.005-0.0050.0000.0000.0000.000
79A102GLY00.0850.04630.924-0.005-0.0050.0000.0000.0000.000
80A103ASN0-0.045-0.02330.4570.0070.0070.0000.0000.0000.000
81A104MET00.0030.00622.9980.0080.0080.0000.0000.0000.000
82A105SER00.041-0.02925.9800.0110.0110.0000.0000.0000.000
83A106SER00.0070.03326.3870.0060.0060.0000.0000.0000.000
84A107TYR0-0.030-0.01524.8110.0060.0060.0000.0000.0000.000
85A108ILE0-0.021-0.00120.8740.0240.0240.0000.0000.0000.000
86A109LEU00.0260.01122.4590.0160.0160.0000.0000.0000.000
87A110TYR0-0.029-0.01324.6060.0050.0050.0000.0000.0000.000
88A111ALA0-0.051-0.02720.1480.0080.0080.0000.0000.0000.000
89A112LEU0-0.022-0.01218.5080.0260.0260.0000.0000.0000.000
90A113ASN0-0.047-0.01920.941-0.021-0.0210.0000.0000.0000.000
91A114GLY00.0310.02023.727-0.008-0.0080.0000.0000.0000.000
92A115LYS10.8910.94419.740-0.205-0.2050.0000.0000.0000.000
93A116GLY00.0660.05118.4280.0330.0330.0000.0000.0000.000
94A117THR0-0.064-0.06019.120-0.027-0.0270.0000.0000.0000.000
95A118LEU00.0280.02020.1780.0280.0280.0000.0000.0000.000
96A119THR0-0.027-0.00522.213-0.023-0.0230.0000.0000.0000.000
97A120VAL00.0200.00923.8150.0110.0110.0000.0000.0000.000
98A121VAL0-0.021-0.01525.589-0.014-0.0140.0000.0000.0000.000
99A122GLU-1-0.821-0.91328.1870.1110.1110.0000.0000.0000.000
100A123ARG10.8040.87231.506-0.094-0.0940.0000.0000.0000.000
101A124ASP-1-0.838-0.92134.3130.0650.0650.0000.0000.0000.000
102A125GLU-1-0.848-0.91236.2570.0570.0570.0000.0000.0000.000
103A126ASP-1-0.807-0.89138.3300.0660.0660.0000.0000.0000.000
104A127ASN0-0.050-0.03236.3940.0020.0020.0000.0000.0000.000
105A128LEU00.0360.03031.7560.0050.0050.0000.0000.0000.000
106A129LYS10.8350.89834.988-0.062-0.0620.0000.0000.0000.000
107A130LYS10.8100.87437.396-0.072-0.0720.0000.0000.0000.000
108A131ALA0-0.0030.01332.5280.0030.0030.0000.0000.0000.000
109A132MET0-0.013-0.01829.9990.0060.0060.0000.0000.0000.000
110A133ASP-1-0.834-0.88734.2700.0720.0720.0000.0000.0000.000
111A134ASN0-0.025-0.01535.509-0.004-0.0040.0000.0000.0000.000
112A135LEU0-0.042-0.01529.6710.0050.0050.0000.0000.0000.000
113A136SER0-0.054-0.04033.4970.0000.0000.0000.0000.0000.000
114A137GLU-1-0.970-0.97135.6250.0800.0800.0000.0000.0000.000
115A138PHE0-0.085-0.04734.0620.0000.0000.0000.0000.0000.000
116A139TYR0-0.062-0.04328.5380.0110.0110.0000.0000.0000.000
117A140ASP-1-0.876-0.92930.3600.0920.0920.0000.0000.0000.000
118A141ILE00.006-0.01229.4020.0100.0100.0000.0000.0000.000
119A142GLY00.0100.01229.588-0.003-0.0030.0000.0000.0000.000
120A143ASN0-0.096-0.05822.759-0.014-0.0140.0000.0000.0000.000
121A144VAL00.0170.01024.6070.0130.0130.0000.0000.0000.000
122A145ARG10.9150.95724.740-0.087-0.0870.0000.0000.0000.000
123A146THR00.0310.01427.3400.0090.0090.0000.0000.0000.000
124A147SER0-0.059-0.02429.024-0.012-0.0120.0000.0000.0000.000
125A148ARG10.8080.88330.568-0.053-0.0530.0000.0000.0000.000
126A149SER0-0.014-0.00430.892-0.006-0.0060.0000.0000.0000.000
127A150ASP-1-0.746-0.85931.5210.0890.0890.0000.0000.0000.000
128A151ILE00.0120.00324.354-0.003-0.0030.0000.0000.0000.000
129A152ALA0-0.038-0.03027.545-0.001-0.0010.0000.0000.0000.000
130A153ASP-1-0.847-0.90729.7630.0480.0480.0000.0000.0000.000
131A154PHE0-0.034-0.02423.404-0.006-0.0060.0000.0000.0000.000
132A155ILE0-0.016-0.00526.698-0.002-0.0020.0000.0000.0000.000
133A156SER0-0.006-0.01322.1880.0000.0000.0000.0000.0000.000
134A157ASP-1-0.900-0.94222.6040.0130.0130.0000.0000.0000.000
135A158GLN0-0.088-0.02618.569-0.018-0.0180.0000.0000.0000.000
136A159MET0-0.0230.00114.6400.0040.0040.0000.0000.0000.000
137A160TYR0-0.001-0.02715.4950.0040.0040.0000.0000.0000.000
138A161ASP-1-0.815-0.89711.2140.4090.4090.0000.0000.0000.000
139A162ALA0-0.021-0.01812.2830.1030.1030.0000.0000.0000.000
140A163VAL0-0.011-0.00115.056-0.055-0.0550.0000.0000.0000.000
141A164ILE0-0.0030.00118.4110.0270.0270.0000.0000.0000.000
142A165ALA0-0.009-0.00821.454-0.022-0.0220.0000.0000.0000.000
143A166ASP-1-0.909-0.94824.4650.1570.1570.0000.0000.0000.000
144A167ILE00.0070.00127.374-0.013-0.0130.0000.0000.0000.000
145A168PRO0-0.011-0.02030.2770.0030.0030.0000.0000.0000.000
146A169ASP-1-0.727-0.83531.4010.0870.0870.0000.0000.0000.000
147A170PRO00.0500.03225.744-0.006-0.0060.0000.0000.0000.000
148A171TRP00.0700.03126.4340.0000.0000.0000.0000.0000.000
149A172ASN0-0.101-0.05727.572-0.008-0.0080.0000.0000.0000.000
150A173HIS10.7850.87126.445-0.097-0.0970.0000.0000.0000.000
151A174VAL00.0340.03722.0250.0010.0010.0000.0000.0000.000
152A175GLN00.010-0.01321.3440.0150.0150.0000.0000.0000.000
153A176LYS10.7950.90121.486-0.062-0.0620.0000.0000.0000.000
154A177ILE00.0430.02519.452-0.002-0.0020.0000.0000.0000.000
155A178ALA00.0600.02417.3370.0120.0120.0000.0000.0000.000
156A179SER0-0.120-0.06616.793-0.007-0.0070.0000.0000.0000.000
157A180MET00.0440.02417.981-0.020-0.0200.0000.0000.0000.000
158A181MET0-0.0120.01813.9650.0000.0000.0000.0000.0000.000
159A182LYS10.8800.93010.236-0.303-0.3030.0000.0000.0000.000
160A183PRO0-0.0030.0027.7990.0850.0850.0000.0000.0000.000
161A184GLY00.0460.0286.9540.0380.0380.0000.0000.0000.000
162A185SER0-0.065-0.0357.9300.1760.1760.0000.0000.0000.000
163A186VAL0-0.009-0.02010.664-0.027-0.0270.0000.0000.0000.000
164A187ALA0-0.018-0.00613.452-0.041-0.0410.0000.0000.0000.000
165A188THR0-0.006-0.01917.2110.0280.0280.0000.0000.0000.000
166A189PHE0-0.008-0.00919.990-0.025-0.0250.0000.0000.0000.000
167A190TYR00.0230.01023.4100.0090.0090.0000.0000.0000.000
168A191LEU00.006-0.00726.463-0.013-0.0130.0000.0000.0000.000
169A192PRO0-0.008-0.00129.4750.0030.0030.0000.0000.0000.000
170A193ASN0-0.041-0.03732.256-0.006-0.0060.0000.0000.0000.000
171A194PHE00.0720.04530.2660.0070.0070.0000.0000.0000.000
172A195ASP-1-0.879-0.93331.1000.0980.0980.0000.0000.0000.000
173A196GLN0-0.008-0.01631.5090.0040.0040.0000.0000.0000.000
174A197SER0-0.0030.02926.3280.0060.0060.0000.0000.0000.000
175A198GLU-1-0.871-0.94526.9900.1130.1130.0000.0000.0000.000
176A199LYS10.9080.95527.952-0.083-0.0830.0000.0000.0000.000
177A200THR0-0.019-0.02624.110-0.005-0.0050.0000.0000.0000.000
178A201VAL00.0380.02522.7730.0020.0020.0000.0000.0000.000
179A202LEU0-0.042-0.02723.7660.0000.0000.0000.0000.0000.000
180A203SER0-0.076-0.04225.226-0.011-0.0110.0000.0000.0000.000
181A204LEU00.0140.01119.614-0.004-0.0040.0000.0000.0000.000
182A205SER00.0210.02119.637-0.001-0.0010.0000.0000.0000.000
183A206ALA00.0030.00220.261-0.011-0.0110.0000.0000.0000.000
184A207SER0-0.042-0.02319.934-0.008-0.0080.0000.0000.0000.000
185A208GLY00.0020.00616.970-0.006-0.0060.0000.0000.0000.000
186A209MET0-0.039-0.01415.0280.0310.0310.0000.0000.0000.000
187A210HIS0-0.046-0.02913.700-0.020-0.0200.0000.0000.0000.000
188A211HIS00.0010.00815.3150.0570.0570.0000.0000.0000.000
189A212LEU0-0.034-0.00912.0500.0110.0110.0000.0000.0000.000
190A213GLU-1-0.823-0.90716.0290.3750.3750.0000.0000.0000.000
191A214THR00.002-0.01219.4780.0050.0050.0000.0000.0000.000
192A215VAL0-0.035-0.00622.514-0.009-0.0090.0000.0000.0000.000
193A216GLU-1-0.873-0.93625.0640.1300.1300.0000.0000.0000.000
194A217LEU0-0.030-0.01725.1910.0050.0050.0000.0000.0000.000
195A218MET0-0.011-0.00929.341-0.012-0.0120.0000.0000.0000.000
196A219LYS10.9020.96632.582-0.119-0.1190.0000.0000.0000.000
197A220ARG10.9930.99234.543-0.105-0.1050.0000.0000.0000.000
198A221ARG10.8690.94737.897-0.094-0.0940.0000.0000.0000.000
199A222ILE00.008-0.00838.982-0.004-0.0040.0000.0000.0000.000
200A223LEU00.006-0.01041.8850.0010.0010.0000.0000.0000.000
201A224VAL00.0020.01443.913-0.001-0.0010.0000.0000.0000.000
202A225ARG10.9470.97746.156-0.066-0.0660.0000.0000.0000.000
203A226GLU-1-0.818-0.91649.5710.0680.0680.0000.0000.0000.000
204A227GLY0-0.001-0.00852.184-0.002-0.0020.0000.0000.0000.000
205A228ALA0-0.082-0.02450.656-0.002-0.0020.0000.0000.0000.000
206A229THR00.0350.00551.6580.0020.0020.0000.0000.0000.000
207A230ARG10.7670.87647.485-0.073-0.0730.0000.0000.0000.000
208A231PRO00.0370.01745.073-0.003-0.0030.0000.0000.0000.000
209A232ALA00.0350.01346.3710.0020.0020.0000.0000.0000.000
210A233SER00.014-0.00441.5690.0000.0000.0000.0000.0000.000
211A234ASP-1-0.891-0.92341.7870.0990.0990.0000.0000.0000.000
212A235ASP-1-0.813-0.90442.2220.0820.0820.0000.0000.0000.000
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