FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: Q19MY

Calculation Name: 1RYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RYB

Chain ID: A

ChEMBL ID:

UniProt ID: Q9M5P4

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2111292.928533
FMO2-HF: Nuclear repulsion 2038309.861768
FMO2-HF: Total energy -72983.066765
FMO2-MP2: Total energy -73198.943129


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:TYR)


Summations of interaction energy for fragment #1(A:1:TYR)
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.
-4.448-1.4480.163-1.031-2.1330.004
Interaction energy analysis for fragmet #1(A:1:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.006
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].
3A3PRO00.0590.0383.842-1.3120.449-0.011-0.769-0.9810.004
4A4TRP00.0550.0066.1320.6960.6960.0000.0000.0000.000
5A5LEU0-0.0280.0009.081-0.161-0.1610.0000.0000.0000.000
6A6ILE00.0190.00911.9820.1150.1150.0000.0000.0000.000
7A7ALA0-0.007-0.00714.911-0.029-0.0290.0000.0000.0000.000
8A8GLY00.0500.03318.4550.0360.0360.0000.0000.0000.000
9A9LEU0-0.054-0.04621.718-0.014-0.0140.0000.0000.0000.000
10A10GLY00.0440.00624.9350.0080.0080.0000.0000.0000.000
11A11ASN0-0.077-0.02928.236-0.009-0.0090.0000.0000.0000.000
12A12PRO00.0680.04729.5360.0000.0000.0000.0000.0000.000
13A13GLY00.0450.00730.7290.0080.0080.0000.0000.0000.000
14A14ASN00.026-0.01033.1520.0000.0000.0000.0000.0000.000
15A15LYS10.9290.96435.2780.0800.0800.0000.0000.0000.000
16A16TYR0-0.0080.01432.9580.0070.0070.0000.0000.0000.000
17A17TYR00.0360.04430.1080.0060.0060.0000.0000.0000.000
18A18GLY00.0220.00232.1580.0060.0060.0000.0000.0000.000
19A19THR0-0.100-0.06633.7430.0070.0070.0000.0000.0000.000
20A20ARG10.9240.95032.4820.0290.0290.0000.0000.0000.000
21A21HIS0-0.093-0.07431.291-0.003-0.0030.0000.0000.0000.000
22A22ASN00.0020.00829.006-0.004-0.0040.0000.0000.0000.000
23A23VAL00.0620.03527.613-0.009-0.0090.0000.0000.0000.000
24A24GLY00.0280.01624.321-0.001-0.0010.0000.0000.0000.000
25A25PHE0-0.059-0.04523.230-0.017-0.0170.0000.0000.0000.000
26A26GLU-1-0.781-0.85424.176-0.086-0.0860.0000.0000.0000.000
27A27MET0-0.0130.02520.787-0.003-0.0030.0000.0000.0000.000
28A28VAL00.003-0.00318.907-0.007-0.0070.0000.0000.0000.000
29A29ASP-1-0.863-0.90320.010-0.194-0.1940.0000.0000.0000.000
30A30ARG10.7280.80821.9370.0890.0890.0000.0000.0000.000
31A31ILE00.018-0.00315.831-0.003-0.0030.0000.0000.0000.000
32A32ALA0-0.026-0.01617.161-0.018-0.0180.0000.0000.0000.000
33A33ALA0-0.016-0.01118.243-0.014-0.0140.0000.0000.0000.000
34A34GLU-1-0.887-0.92518.326-0.105-0.1050.0000.0000.0000.000
35A35GLU-1-0.862-0.91413.904-0.217-0.2170.0000.0000.0000.000
36A36GLY0-0.049-0.00915.057-0.043-0.0430.0000.0000.0000.000
37A37ILE0-0.048-0.01812.791-0.038-0.0380.0000.0000.0000.000
38A38THR00.0250.00416.6790.0340.0340.0000.0000.0000.000
39A39MET0-0.072-0.03618.152-0.038-0.0380.0000.0000.0000.000
40A40ASN0-0.034-0.02219.9630.0010.0010.0000.0000.0000.000
41A41THR00.0160.02917.407-0.005-0.0050.0000.0000.0000.000
42A42ILE00.0130.00720.0940.0130.0130.0000.0000.0000.000
43A43GLN00.0380.02715.554-0.027-0.0270.0000.0000.0000.000
44A44SER0-0.009-0.00519.6450.0160.0160.0000.0000.0000.000
45A45LYS10.9220.96521.5580.1970.1970.0000.0000.0000.000
46A46SER00.0090.01020.4950.0300.0300.0000.0000.0000.000
47A47LEU0-0.0180.00722.062-0.007-0.0070.0000.0000.0000.000
48A48LEU0-0.011-0.01815.0440.0080.0080.0000.0000.0000.000
49A49GLY00.0230.01616.1760.0230.0230.0000.0000.0000.000
50A50ILE00.008-0.00410.351-0.030-0.0300.0000.0000.0000.000
51A51GLY00.0250.00710.7580.0920.0920.0000.0000.0000.000
52A52SER0-0.001-0.0027.502-0.254-0.2540.0000.0000.0000.000
53A53ILE00.0490.0468.6330.1420.1420.0000.0000.0000.000
54A54GLY0-0.020-0.0048.4210.0030.0030.0000.0000.0000.000
55A55GLU-1-0.959-0.9885.080-0.375-0.3750.0000.0000.0000.000
56A56VAL0-0.060-0.0224.090-0.874-0.4500.000-0.051-0.3730.000
57A57PRO00.0320.0163.026-0.4510.3640.174-0.211-0.7790.000
58A58VAL0-0.020-0.0145.7040.0430.0430.0000.0000.0000.000
59A59LEU0-0.013-0.0048.9870.0070.0070.0000.0000.0000.000
60A60VAL0-0.025-0.00312.1110.0820.0820.0000.0000.0000.000
61A61VAL00.046-0.00515.455-0.007-0.0070.0000.0000.0000.000
62A62LYS10.8590.91318.3160.2240.2240.0000.0000.0000.000
63A63PRO00.0280.01321.708-0.010-0.0100.0000.0000.0000.000
64A64GLN0-0.092-0.06623.7980.0330.0330.0000.0000.0000.000
65A65SER00.0160.00326.5690.0000.0000.0000.0000.0000.000
66A66TYR0-0.020-0.01028.3830.0140.0140.0000.0000.0000.000
67A67MET00.0360.03728.328-0.007-0.0070.0000.0000.0000.000
68A68ASN00.0170.01228.9920.0030.0030.0000.0000.0000.000
69A69TYR0-0.016-0.00428.8860.0080.0080.0000.0000.0000.000
70A70SER0-0.001-0.01024.559-0.017-0.0170.0000.0000.0000.000
71A71GLY0-0.006-0.01223.266-0.020-0.0200.0000.0000.0000.000
72A72GLU-1-0.914-0.95922.847-0.149-0.1490.0000.0000.0000.000
73A73ALA0-0.038-0.00321.946-0.018-0.0180.0000.0000.0000.000
74A74ILE0-0.004-0.02117.892-0.037-0.0370.0000.0000.0000.000
75A75GLY00.0100.01717.889-0.031-0.0310.0000.0000.0000.000
76A76PRO00.005-0.01517.806-0.033-0.0330.0000.0000.0000.000
77A77LEU00.0060.01915.453-0.061-0.0610.0000.0000.0000.000
78A78ALA00.0120.00713.405-0.114-0.1140.0000.0000.0000.000
79A79ALA0-0.046-0.00912.778-0.064-0.0640.0000.0000.0000.000
80A80TYR0-0.021-0.01312.764-0.038-0.0380.0000.0000.0000.000
81A81TYR0-0.013-0.0389.661-0.116-0.1160.0000.0000.0000.000
82A82GLN0-0.057-0.0137.988-0.531-0.5310.0000.0000.0000.000
83A83VAL0-0.0190.0018.657-0.006-0.0060.0000.0000.0000.000
84A84PRO0-0.012-0.0048.8920.1430.1430.0000.0000.0000.000
85A85LEU00.0270.00111.729-0.010-0.0100.0000.0000.0000.000
86A86ARG10.9780.9788.118-1.381-1.3810.0000.0000.0000.000
87A87HIS0-0.069-0.0316.9910.5140.5140.0000.0000.0000.000
88A88ILE00.0280.02811.096-0.148-0.1480.0000.0000.0000.000
89A89LEU0-0.007-0.00714.1580.0610.0610.0000.0000.0000.000
90A90LEU0-0.027-0.00415.706-0.043-0.0430.0000.0000.0000.000
91A91ILE00.0180.00717.9470.0310.0310.0000.0000.0000.000
92A92TYR0-0.062-0.04221.466-0.017-0.0170.0000.0000.0000.000
93A93ASP-1-0.709-0.82325.264-0.040-0.0400.0000.0000.0000.000
94A94ASP-1-0.782-0.90128.3050.0140.0140.0000.0000.0000.000
95A95THR0-0.035-0.03230.2130.0030.0030.0000.0000.0000.000
96A96SER0-0.120-0.06731.6130.0050.0050.0000.0000.0000.000
97A97LEU00.0020.01328.5030.0070.0070.0000.0000.0000.000
98A98PRO00.022-0.01532.883-0.006-0.0060.0000.0000.0000.000
99A99ASN0-0.022-0.01332.875-0.003-0.0030.0000.0000.0000.000
100A100GLY00.0320.01830.7890.0020.0020.0000.0000.0000.000
101A101VAL0-0.043-0.01329.6020.0040.0040.0000.0000.0000.000
102A102LEU00.0230.04023.459-0.002-0.0020.0000.0000.0000.000
103A103ARG10.9390.95225.085-0.057-0.0570.0000.0000.0000.000
104A104LEU00.0380.03917.768-0.007-0.0070.0000.0000.0000.000
105A105GLN0-0.094-0.04321.2960.0070.0070.0000.0000.0000.000
106A106LYN00.0780.03915.212-0.001-0.0010.0000.0000.0000.000
107A107LYS10.9820.99219.286-0.147-0.1470.0000.0000.0000.000
108A108GLY0-0.014-0.00221.822-0.006-0.0060.0000.0000.0000.000
109A109GLY00.0170.01825.234-0.006-0.0060.0000.0000.0000.000
110A110HIS00.1340.07626.8560.0020.0020.0000.0000.0000.000
111A111GLY00.0160.01628.475-0.005-0.0050.0000.0000.0000.000
112A112ARG10.8850.91931.386-0.001-0.0010.0000.0000.0000.000
113A113HIS00.0130.01328.121-0.004-0.0040.0000.0000.0000.000
114A114ASN00.0510.00129.9520.0040.0040.0000.0000.0000.000
115A115GLY00.0200.01827.798-0.005-0.0050.0000.0000.0000.000
116A116LEU0-0.002-0.00923.173-0.006-0.0060.0000.0000.0000.000
117A117GLN0-0.048-0.03025.9470.0030.0030.0000.0000.0000.000
118A118ASN00.0660.04127.373-0.012-0.0120.0000.0000.0000.000
119A119VAL0-0.002-0.01021.088-0.009-0.0090.0000.0000.0000.000
120A120ILE0-0.024-0.01623.3130.0020.0020.0000.0000.0000.000
121A121GLU-1-0.953-0.95624.548-0.051-0.0510.0000.0000.0000.000
122A122HIS0-0.011-0.01323.149-0.007-0.0070.0000.0000.0000.000
123A123LEU0-0.061-0.01918.645-0.022-0.0220.0000.0000.0000.000
124A124ASP-1-0.909-0.96021.847-0.011-0.0110.0000.0000.0000.000
125A125GLY0-0.026-0.00324.2450.0180.0180.0000.0000.0000.000
126A126ARG10.8920.94717.574-0.011-0.0110.0000.0000.0000.000
127A127ARG10.9670.96922.426-0.080-0.0800.0000.0000.0000.000
128A128GLU-1-0.972-0.98619.1850.1310.1310.0000.0000.0000.000
129A129PHE00.0190.01916.7240.0400.0400.0000.0000.0000.000
130A130PRO00.0030.00514.205-0.009-0.0090.0000.0000.0000.000
131A131ARG10.8110.89417.484-0.097-0.0970.0000.0000.0000.000
132A132LEU00.0300.00719.6500.0240.0240.0000.0000.0000.000
133A133SER0-0.054-0.01521.336-0.016-0.0160.0000.0000.0000.000
134A134ILE00.0460.00324.0700.0070.0070.0000.0000.0000.000
135A135GLY0-0.011-0.00327.103-0.004-0.0040.0000.0000.0000.000
136A136ILE0-0.024-0.01030.702-0.005-0.0050.0000.0000.0000.000
137A137GLY00.0020.01433.501-0.001-0.0010.0000.0000.0000.000
138A138SER0-0.005-0.02036.342-0.001-0.0010.0000.0000.0000.000
139A139PRO0-0.012-0.00238.951-0.001-0.0010.0000.0000.0000.000
140A140PRO00.0440.04941.5090.0030.0030.0000.0000.0000.000
141A141GLY00.011-0.01344.382-0.001-0.0010.0000.0000.0000.000
142A142LYS10.9260.94446.7050.0060.0060.0000.0000.0000.000
143A143MET0-0.0250.02742.838-0.001-0.0010.0000.0000.0000.000
144A144ASP-1-0.804-0.92143.741-0.028-0.0280.0000.0000.0000.000
145A145PRO00.0310.00140.022-0.002-0.0020.0000.0000.0000.000
146A146ARG10.9710.98639.1280.0470.0470.0000.0000.0000.000
147A147ALA0-0.001-0.00239.478-0.004-0.0040.0000.0000.0000.000
148A148PHE0-0.001-0.01136.978-0.003-0.0030.0000.0000.0000.000
149A149LEU00.0020.00233.979-0.002-0.0020.0000.0000.0000.000
150A150LEU0-0.070-0.03335.583-0.006-0.0060.0000.0000.0000.000
151A151GLN00.0290.02137.767-0.004-0.0040.0000.0000.0000.000
152A152LYS10.9470.97936.8380.0640.0640.0000.0000.0000.000
153A153PHE00.0030.01531.7980.0040.0040.0000.0000.0000.000
154A154SER00.0070.00137.354-0.002-0.0020.0000.0000.0000.000
155A155SER00.0550.01138.843-0.003-0.0030.0000.0000.0000.000
156A156GLU-1-0.905-0.96739.216-0.022-0.0220.0000.0000.0000.000
157A157GLU-1-0.860-0.89636.364-0.024-0.0240.0000.0000.0000.000
158A158ARG10.7980.85430.7840.0600.0600.0000.0000.0000.000
159A159VAL00.0540.04833.938-0.002-0.0020.0000.0000.0000.000
160A160GLN00.007-0.00233.673-0.001-0.0010.0000.0000.0000.000
161A161ILE0-0.017-0.01229.5440.0020.0020.0000.0000.0000.000
162A162ASP-1-0.836-0.92629.264-0.056-0.0560.0000.0000.0000.000
163A163THR0-0.040-0.00828.804-0.001-0.0010.0000.0000.0000.000
164A164ALA0-0.005-0.01127.3360.0040.0040.0000.0000.0000.000
165A165LEU0-0.007-0.01424.8650.0000.0000.0000.0000.0000.000
166A166GLU-1-0.779-0.84323.686-0.072-0.0720.0000.0000.0000.000
167A167GLN0-0.036-0.01323.310-0.003-0.0030.0000.0000.0000.000
168A168GLY0-0.002-0.03321.6650.0120.0120.0000.0000.0000.000
169A169VAL00.0230.01218.5890.0010.0010.0000.0000.0000.000
170A170ASP-1-0.875-0.92717.7000.0320.0320.0000.0000.0000.000
171A171ALA0-0.003-0.00517.5510.0240.0240.0000.0000.0000.000
172A172VAL0-0.051-0.03214.4260.0320.0320.0000.0000.0000.000
173A173ARG10.9160.95513.2230.1340.1340.0000.0000.0000.000
174A174THR0-0.0050.01012.5690.0420.0420.0000.0000.0000.000
175A175LEU0-0.094-0.05412.9490.0810.0810.0000.0000.0000.000
176A176VAL0-0.022-0.0238.3330.0990.0990.0000.0000.0000.000
177A177LEU0-0.020-0.0088.4770.1410.1410.0000.0000.0000.000
178A178LYS10.8170.9319.368-0.282-0.2820.0000.0000.0000.000
179A179GLY00.0190.0258.7250.1210.1210.0000.0000.0000.000
180A180PHE0-0.054-0.0396.360-0.273-0.2730.0000.0000.0000.000
181A181SER00.000-0.01811.2800.0010.0010.0000.0000.0000.000
182A182GLY0-0.001-0.01514.6700.0360.0360.0000.0000.0000.000
183A183SER0-0.019-0.01616.652-0.039-0.0390.0000.0000.0000.000
184A184THR0-0.051-0.02819.9550.0000.0000.0000.0000.0000.000
185A185GLU-1-0.856-0.90519.1700.3470.3470.0000.0000.0000.000
186A186ARG10.8720.94120.175-0.150-0.1500.0000.0000.0000.000
187A187PHE00.0660.03617.6620.0090.0090.0000.0000.0000.000
188A188ASN0-0.005-0.00621.907-0.014-0.0140.0000.0000.0000.000
189A189LEU0-0.0100.00020.9230.0070.0070.0000.0000.0000.000
190A190VAL00.0220.00024.485-0.004-0.0040.0000.0000.0000.000
191A191GLN00.0040.01625.689-0.001-0.0010.0000.0000.0000.000