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: 2N55R

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2681716.248324
FMO2-HF: Nuclear repulsion 2590075.759803
FMO2-HF: Total energy -91640.488521
FMO2-MP2: Total energy -91902.888483


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.
-26.286-14.25113.612-10.123-15.523-0.067
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 : 0.021 / q_NPA : -0.003
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].
3A8ILE0-0.061-0.0193.694-2.868-0.178-0.036-1.403-1.2520.003
4A9LEU0-0.0340.0025.3940.4060.4060.0000.0000.0000.000
5A10VAL00.0250.0047.675-0.158-0.1580.0000.0000.0000.000
6A11SER0-0.022-0.03910.368-0.088-0.0880.0000.0000.0000.000
7A12GLU-1-0.829-0.90213.6010.2510.2510.0000.0000.0000.000
8A13ASP-1-0.847-0.90716.7060.1730.1730.0000.0000.0000.000
9A14GLU-1-0.817-0.88915.6420.1890.1890.0000.0000.0000.000
10A15TYR0-0.019-0.00410.9080.0800.0800.0000.0000.0000.000
11A16GLY0-0.034-0.02710.497-0.095-0.0950.0000.0000.0000.000
12A17LYS10.8310.9167.9290.0130.0130.0000.0000.0000.000
13A18PHE0-0.012-0.0102.693-0.4710.5020.196-0.287-0.881-0.001
14A19ASP-1-0.839-0.9045.507-2.076-2.0760.0000.0000.0000.000
15A20GLU-1-0.846-0.9482.046-18.769-15.8445.235-3.903-4.257-0.048
16A21SER0-0.055-0.0324.9690.3910.509-0.001-0.005-0.1110.000
17A22THR0-0.076-0.0458.3370.3430.3430.0000.0000.0000.000
18A23ASN0-0.0060.0147.010-0.035-0.0350.0000.0000.0000.000
19A24SER0-0.0220.0038.5750.3330.3330.0000.0000.0000.000
20A25ILE00.0370.0058.214-0.076-0.0760.0000.0000.0000.000
21A26LEU0-0.024-0.01010.0090.0450.0450.0000.0000.0000.000
22A27VAL00.0630.02511.7110.0750.0750.0000.0000.0000.000
23A28LYS10.8260.90413.842-0.183-0.1830.0000.0000.0000.000
24A29GLY0-0.008-0.00615.6310.0090.0090.0000.0000.0000.000
25A30LYS10.9180.96017.424-0.013-0.0130.0000.0000.0000.000
26A31MET0-0.002-0.01012.4820.0240.0240.0000.0000.0000.000
27A32HIS0-0.023-0.00913.3030.0130.0130.0000.0000.0000.000
28A33HIS00.0580.02312.161-0.099-0.0990.0000.0000.0000.000
29A34LEU0-0.0050.0088.1680.0980.0980.0000.0000.0000.000
30A35GLY00.007-0.01512.247-0.034-0.0340.0000.0000.0000.000
31A36ILE0-0.046-0.01912.722-0.084-0.0840.0000.0000.0000.000
32A37SER00.0230.00611.768-0.003-0.0030.0000.0000.0000.000
33A38ARG10.8570.93510.0590.4240.4240.0000.0000.0000.000
34A39VAL00.0510.0265.5170.0350.0350.0000.0000.0000.000
35A40ILE0-0.074-0.0334.1930.0880.3220.000-0.039-0.1940.000
36A41GLU-1-0.870-0.9352.747-4.748-3.2220.382-0.712-1.196-0.006
37A42PRO00.0270.0072.344-0.5360.8011.393-0.423-2.3070.000
38A43GLY00.008-0.0163.846-0.528-0.4140.006-0.027-0.0920.000
39A44ASP-1-0.795-0.8616.017-0.528-0.5280.0000.0000.0000.000
40A45GLU-1-0.835-0.8907.6530.3570.3570.0000.0000.0000.000
41A46LEU0-0.014-0.0156.288-0.138-0.1380.0000.0000.0000.000
42A47ILE0-0.025-0.02110.4930.0430.0430.0000.0000.0000.000
43A48VAL00.0230.01112.765-0.047-0.0470.0000.0000.0000.000
44A49SER0-0.041-0.03415.1020.0210.0210.0000.0000.0000.000
45A50GLY0-0.019-0.00518.2970.0100.0100.0000.0000.0000.000
46A51LYS10.8220.92015.541-0.188-0.1880.0000.0000.0000.000
47A52SER0-0.033-0.04313.974-0.033-0.0330.0000.0000.0000.000
48A53PHE0-0.027-0.0129.6210.0030.0030.0000.0000.0000.000
49A54ILE0-0.0090.0027.531-0.094-0.0940.0000.0000.0000.000
50A55VAL00.0080.0122.1510.894-0.7284.415-0.995-1.7980.005
51A56SER00.0210.0074.253-0.809-0.5120.001-0.082-0.2170.000
52A57ASP-1-0.804-0.8992.4474.7068.3142.002-2.518-3.092-0.020
53A58PHE0-0.036-0.0373.294-1.811-1.9760.0190.271-0.1260.000
54A59SER00.0580.0276.256-0.097-0.0970.0000.0000.0000.000
55A60PRO00.0070.0009.525-0.097-0.0970.0000.0000.0000.000
56A61MET0-0.0180.00312.173-0.072-0.0720.0000.0000.0000.000
57A62TYR00.0640.0187.821-0.173-0.1730.0000.0000.0000.000
58A63PHE0-0.018-0.00311.855-0.075-0.0750.0000.0000.0000.000
59A64GLY00.0330.00013.272-0.059-0.0590.0000.0000.0000.000
60A65ARG10.8180.91013.432-0.425-0.4250.0000.0000.0000.000
61A66VAL00.0050.0109.753-0.053-0.0530.0000.0000.0000.000
62A67ILE0-0.090-0.01613.096-0.126-0.1260.0000.0000.0000.000
63A86CYS00.0350.01815.807-0.009-0.0090.0000.0000.0000.000
64A87GLY0-0.050-0.03713.772-0.027-0.0270.0000.0000.0000.000
65A88LEU00.0070.01214.3480.0550.0550.0000.0000.0000.000
66A89ARG10.9390.96211.228-0.996-0.9960.0000.0000.0000.000
67A90PRO00.019-0.00116.6410.0040.0040.0000.0000.0000.000
68A91GLY0-0.069-0.03916.1700.0610.0610.0000.0000.0000.000
69A92MET0-0.059-0.00413.2580.0030.0030.0000.0000.0000.000
70A93ASP-1-0.796-0.86715.4840.2110.2110.0000.0000.0000.000
71A94ILE0-0.038-0.02116.7560.0330.0330.0000.0000.0000.000
72A95LEU00.0170.01318.976-0.038-0.0380.0000.0000.0000.000
73A96GLU-1-0.811-0.90121.1960.2400.2400.0000.0000.0000.000
74A97VAL0-0.023-0.01823.643-0.022-0.0220.0000.0000.0000.000
75A98GLY00.0260.01926.2580.0040.0040.0000.0000.0000.000
76A99VAL0-0.004-0.00728.3310.0110.0110.0000.0000.0000.000
77A100GLY00.0280.01630.4260.0050.0050.0000.0000.0000.000
78A101SER0-0.043-0.04032.884-0.003-0.0030.0000.0000.0000.000
79A102GLY00.0940.04731.075-0.006-0.0060.0000.0000.0000.000
80A103ASN0-0.039-0.02130.4560.0060.0060.0000.0000.0000.000
81A104MET00.0090.00722.4480.0060.0060.0000.0000.0000.000
82A105SER00.042-0.02225.8230.0120.0120.0000.0000.0000.000
83A106SER00.0020.02626.8520.0060.0060.0000.0000.0000.000
84A107TYR0-0.035-0.02424.5990.0020.0020.0000.0000.0000.000
85A108ILE0-0.0180.00021.5310.0240.0240.0000.0000.0000.000
86A109LEU00.0250.00722.9740.0190.0190.0000.0000.0000.000
87A110TYR0-0.035-0.01025.3950.0030.0030.0000.0000.0000.000
88A111ALA0-0.043-0.02220.4530.0050.0050.0000.0000.0000.000
89A112LEU0-0.026-0.01619.0560.0230.0230.0000.0000.0000.000
90A113ASN0-0.035-0.01021.640-0.017-0.0170.0000.0000.0000.000
91A114GLY00.0220.01524.442-0.011-0.0110.0000.0000.0000.000
92A115LYS10.8990.94920.062-0.244-0.2440.0000.0000.0000.000
93A116GLY00.0640.04819.2010.0380.0380.0000.0000.0000.000
94A117THR0-0.081-0.05819.812-0.036-0.0360.0000.0000.0000.000
95A118LEU00.0190.01720.7630.0320.0320.0000.0000.0000.000
96A119THR0-0.021-0.00422.872-0.031-0.0310.0000.0000.0000.000
97A120VAL00.0220.01324.4410.0130.0130.0000.0000.0000.000
98A121VAL0-0.022-0.00525.998-0.015-0.0150.0000.0000.0000.000
99A122GLU-1-0.817-0.91428.5740.1350.1350.0000.0000.0000.000
100A123ARG10.8480.91331.910-0.118-0.1180.0000.0000.0000.000
101A124ASP-1-0.894-0.94834.7210.0820.0820.0000.0000.0000.000
102A125GLU-1-0.829-0.91836.9460.0780.0780.0000.0000.0000.000
103A126ASP-1-0.855-0.92138.7850.0770.0770.0000.0000.0000.000
104A127ASN0-0.061-0.05036.2650.0000.0000.0000.0000.0000.000
105A128LEU00.0350.02432.4040.0050.0050.0000.0000.0000.000
106A129LYS10.8550.90535.544-0.078-0.0780.0000.0000.0000.000
107A130LYS10.8870.93438.145-0.095-0.0950.0000.0000.0000.000
108A131ALA00.0060.02233.2390.0020.0020.0000.0000.0000.000
109A132MET0-0.005-0.01130.5180.0070.0070.0000.0000.0000.000
110A133ASP-1-0.829-0.88634.7790.0890.0890.0000.0000.0000.000
111A134ASN0-0.023-0.01336.148-0.005-0.0050.0000.0000.0000.000
112A135LEU0-0.028-0.01230.1710.0030.0030.0000.0000.0000.000
113A136SER0-0.061-0.03834.0190.0000.0000.0000.0000.0000.000
114A137GLU-1-0.976-0.97235.6760.0930.0930.0000.0000.0000.000
115A138PHE0-0.085-0.04534.308-0.002-0.0020.0000.0000.0000.000
116A139TYR0-0.060-0.04229.0150.0100.0100.0000.0000.0000.000
117A140ASP-1-0.874-0.92630.9150.1170.1170.0000.0000.0000.000
118A141ILE00.000-0.01629.9680.0110.0110.0000.0000.0000.000
119A142GLY00.0070.01030.216-0.002-0.0020.0000.0000.0000.000
120A143ASN0-0.106-0.06223.443-0.014-0.0140.0000.0000.0000.000
121A144VAL00.0240.01225.1650.0190.0190.0000.0000.0000.000
122A145ARG10.9220.96725.201-0.133-0.1330.0000.0000.0000.000
123A146THR00.0400.01827.7200.0090.0090.0000.0000.0000.000
124A147SER0-0.044-0.02129.328-0.011-0.0110.0000.0000.0000.000
125A148ARG10.8290.91130.926-0.076-0.0760.0000.0000.0000.000
126A149SER0-0.029-0.02131.368-0.006-0.0060.0000.0000.0000.000
127A150ASP-1-0.751-0.86631.6740.1170.1170.0000.0000.0000.000
128A151ILE00.0200.00324.806-0.003-0.0030.0000.0000.0000.000
129A152ALA0-0.051-0.03427.9730.0010.0010.0000.0000.0000.000
130A153ASP-1-0.888-0.93929.8150.0740.0740.0000.0000.0000.000
131A154PHE0-0.051-0.01023.704-0.006-0.0060.0000.0000.0000.000
132A155ILE0-0.020-0.01226.7330.0010.0010.0000.0000.0000.000
133A156SER0-0.0050.00021.4810.0020.0020.0000.0000.0000.000
134A157ASP-1-0.903-0.95122.6730.0700.0700.0000.0000.0000.000
135A158GLN0-0.103-0.03918.434-0.020-0.0200.0000.0000.0000.000
136A159MET0-0.030-0.01114.632-0.002-0.0020.0000.0000.0000.000
137A160TYR00.011-0.01315.3730.0150.0150.0000.0000.0000.000
138A161ASP-1-0.815-0.90411.6450.6250.6250.0000.0000.0000.000
139A162ALA0-0.023-0.01412.9170.1100.1100.0000.0000.0000.000
140A163VAL0-0.0050.00515.647-0.059-0.0590.0000.0000.0000.000
141A164ILE0-0.010-0.00318.8040.0270.0270.0000.0000.0000.000
142A165ALA0-0.010-0.01021.415-0.023-0.0230.0000.0000.0000.000
143A166ASP-1-0.917-0.95124.2890.1780.1780.0000.0000.0000.000
144A167ILE0-0.004-0.00826.906-0.014-0.0140.0000.0000.0000.000
145A168PRO0-0.005-0.01629.7010.0020.0020.0000.0000.0000.000
146A169ASP-1-0.775-0.88330.7630.1140.1140.0000.0000.0000.000
147A170PRO00.0540.03425.063-0.004-0.0040.0000.0000.0000.000
148A171TRP00.0520.02625.8970.0010.0010.0000.0000.0000.000
149A172ASN0-0.094-0.05527.113-0.008-0.0080.0000.0000.0000.000
150A173HIS10.7910.87826.183-0.128-0.1280.0000.0000.0000.000
151A174VAL00.0680.05221.6390.0080.0080.0000.0000.0000.000
152A175GLN00.015-0.00221.1090.0190.0190.0000.0000.0000.000
153A176LYS10.8200.90321.461-0.099-0.0990.0000.0000.0000.000
154A177ILE00.0530.03219.3550.0010.0010.0000.0000.0000.000
155A178ALA00.0490.02317.3840.0210.0210.0000.0000.0000.000
156A179SER0-0.111-0.05416.9110.0090.0090.0000.0000.0000.000
157A180MET00.0380.02018.219-0.019-0.0190.0000.0000.0000.000
158A181MET0-0.0150.02013.7000.0020.0020.0000.0000.0000.000
159A182LYS10.8650.91910.122-0.503-0.5030.0000.0000.0000.000
160A183PRO0-0.0010.0038.2980.0850.0850.0000.0000.0000.000
161A184GLY00.0500.0216.6360.0960.0960.0000.0000.0000.000
162A185SER0-0.071-0.0357.5920.1970.1970.0000.0000.0000.000
163A186VAL0-0.004-0.02310.660-0.063-0.0630.0000.0000.0000.000
164A187ALA0-0.018-0.00713.326-0.037-0.0370.0000.0000.0000.000
165A188THR0-0.021-0.02117.0360.0170.0170.0000.0000.0000.000
166A189PHE0-0.025-0.02019.173-0.025-0.0250.0000.0000.0000.000
167A190TYR00.0210.01323.0560.0030.0030.0000.0000.0000.000
168A191LEU00.0130.00026.147-0.013-0.0130.0000.0000.0000.000
169A192PRO0-0.0010.00129.1180.0020.0020.0000.0000.0000.000
170A193ASN0-0.031-0.03632.151-0.005-0.0050.0000.0000.0000.000
171A194PHE00.0740.03730.3240.0080.0080.0000.0000.0000.000
172A195ASP-1-0.857-0.93031.0190.1060.1060.0000.0000.0000.000
173A196GLN0-0.030-0.02031.0090.0050.0050.0000.0000.0000.000
174A197SER00.0100.02626.4010.0070.0070.0000.0000.0000.000
175A198GLU-1-0.884-0.94226.6370.1240.1240.0000.0000.0000.000
176A199LYS10.9180.96327.577-0.100-0.1000.0000.0000.0000.000
177A200THR0-0.017-0.03223.588-0.002-0.0020.0000.0000.0000.000
178A201VAL00.0240.02822.3000.0070.0070.0000.0000.0000.000
179A202LEU0-0.035-0.01923.0390.0030.0030.0000.0000.0000.000
180A203SER0-0.089-0.04924.477-0.006-0.0060.0000.0000.0000.000
181A204LEU00.0380.02418.9810.0000.0000.0000.0000.0000.000
182A205SER00.0170.02019.0740.0040.0040.0000.0000.0000.000
183A206ALA0-0.005-0.00419.762-0.006-0.0060.0000.0000.0000.000
184A207SER0-0.034-0.02719.712-0.006-0.0060.0000.0000.0000.000
185A208GLY0-0.0060.00316.677-0.002-0.0020.0000.0000.0000.000
186A209MET0-0.032-0.00514.7590.0470.0470.0000.0000.0000.000
187A210HIS0-0.030-0.02913.004-0.030-0.0300.0000.0000.0000.000
188A211HIS00.0130.01714.8640.0660.0660.0000.0000.0000.000
189A212LEU0-0.045-0.00712.0170.0090.0090.0000.0000.0000.000
190A213GLU-1-0.838-0.93116.1250.3430.3430.0000.0000.0000.000
191A214THR00.0140.00519.4210.0130.0130.0000.0000.0000.000
192A215VAL0-0.038-0.00622.141-0.013-0.0130.0000.0000.0000.000
193A216GLU-1-0.864-0.93724.7190.1360.1360.0000.0000.0000.000
194A217LEU0-0.029-0.01524.9580.0010.0010.0000.0000.0000.000
195A218MET0-0.0100.00128.795-0.010-0.0100.0000.0000.0000.000
196A219LYS10.9130.96731.961-0.130-0.1300.0000.0000.0000.000
197A220ARG10.9980.98333.730-0.106-0.1060.0000.0000.0000.000
198A221ARG10.8690.93937.241-0.098-0.0980.0000.0000.0000.000
199A222ILE00.000-0.00538.678-0.006-0.0060.0000.0000.0000.000
200A223LEU0-0.007-0.01441.0700.0010.0010.0000.0000.0000.000
201A224VAL00.0050.01843.5580.0000.0000.0000.0000.0000.000
202A225ARG10.9670.98645.561-0.067-0.0670.0000.0000.0000.000
203A226GLU-1-0.842-0.93749.0190.0690.0690.0000.0000.0000.000
204A227GLY0-0.027-0.01751.208-0.002-0.0020.0000.0000.0000.000
205A228ALA0-0.080-0.02750.143-0.002-0.0020.0000.0000.0000.000
206A229THR00.0240.00351.4190.0010.0010.0000.0000.0000.000
207A230ARG10.8000.90046.646-0.075-0.0750.0000.0000.0000.000
208A231PRO00.0370.01644.677-0.003-0.0030.0000.0000.0000.000
209A232ALA00.0580.01946.0080.0020.0020.0000.0000.0000.000
210A233SER00.0230.00641.0690.0000.0000.0000.0000.0000.000
211A234ASP-1-0.883-0.93141.5830.1020.1020.0000.0000.0000.000
212A235ASP-1-0.823-0.89042.0590.0830.0830.0000.0000.0000.000
213A236LEU0-0.053-0.02340.662-0.001-0.0010.0000.0000.0000.000
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