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

tag_button

FMODB ID: K3183

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 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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2111611.959534
FMO2-HF: Nuclear repulsion 2038627.681461
FMO2-HF: Total energy -72984.278072
FMO2-MP2: Total energy -73199.947824


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.
-4.595-1.5940.169-1.017-2.1520.004
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 : 0.028 / q_NPA : 0.004
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].
3A3PRO00.0350.0303.842-1.2940.435-0.012-0.741-0.9760.004
4A4TRP00.0470.0016.1500.7130.7130.0000.0000.0000.000
5A5LEU0-0.0180.0109.094-0.165-0.1650.0000.0000.0000.000
6A6ILE00.0190.00811.9890.1190.1190.0000.0000.0000.000
7A7ALA0-0.007-0.00914.928-0.030-0.0300.0000.0000.0000.000
8A8GLY00.0490.03618.4720.0370.0370.0000.0000.0000.000
9A9LEU0-0.062-0.04921.735-0.014-0.0140.0000.0000.0000.000
10A10GLY00.0470.01224.9510.0080.0080.0000.0000.0000.000
11A11ASN0-0.090-0.03928.254-0.007-0.0070.0000.0000.0000.000
12A12PRO00.0820.05629.2500.0000.0000.0000.0000.0000.000
13A13GLY00.0520.01430.7560.0090.0090.0000.0000.0000.000
14A14ASN00.025-0.01133.176-0.001-0.0010.0000.0000.0000.000
15A15LYS10.9340.96835.2900.0850.0850.0000.0000.0000.000
16A16TYR0-0.0100.01232.9930.0090.0090.0000.0000.0000.000
17A17TYR00.0490.04729.7200.0050.0050.0000.0000.0000.000
18A18GLY00.0490.02632.1450.0060.0060.0000.0000.0000.000
19A19THR0-0.096-0.05733.7420.0070.0070.0000.0000.0000.000
20A20ARG10.8990.93232.4990.0320.0320.0000.0000.0000.000
21A21HIS0-0.089-0.07631.305-0.003-0.0030.0000.0000.0000.000
22A22ASN0-0.026-0.01729.015-0.003-0.0030.0000.0000.0000.000
23A23VAL00.0660.03927.410-0.009-0.0090.0000.0000.0000.000
24A24GLY00.0240.01724.335-0.002-0.0020.0000.0000.0000.000
25A25PHE0-0.048-0.03523.249-0.017-0.0170.0000.0000.0000.000
26A26GLU-1-0.813-0.87724.159-0.092-0.0920.0000.0000.0000.000
27A27MET0-0.0080.02420.904-0.004-0.0040.0000.0000.0000.000
28A28VAL00.0050.00018.720-0.007-0.0070.0000.0000.0000.000
29A29ASP-1-0.871-0.91119.983-0.214-0.2140.0000.0000.0000.000
30A30ARG10.7240.82121.9600.0990.0990.0000.0000.0000.000
31A31ILE00.027-0.00115.871-0.004-0.0040.0000.0000.0000.000
32A32ALA0-0.025-0.01517.125-0.020-0.0200.0000.0000.0000.000
33A33ALA0-0.013-0.00918.207-0.016-0.0160.0000.0000.0000.000
34A34GLU-1-0.858-0.89818.475-0.115-0.1150.0000.0000.0000.000
35A35GLU-1-0.851-0.91213.893-0.233-0.2330.0000.0000.0000.000
36A36GLY0-0.040-0.00414.997-0.045-0.0450.0000.0000.0000.000
37A37ILE0-0.053-0.01912.808-0.040-0.0400.0000.0000.0000.000
38A38THR00.0200.00416.6530.0420.0420.0000.0000.0000.000
39A39MET0-0.070-0.03318.397-0.043-0.0430.0000.0000.0000.000
40A40ASN0-0.028-0.01919.9900.0060.0060.0000.0000.0000.000
41A41THR0-0.0010.01917.020-0.006-0.0060.0000.0000.0000.000
42A42ILE00.0110.00419.8740.0140.0140.0000.0000.0000.000
43A43GLN00.0420.03215.462-0.033-0.0330.0000.0000.0000.000
44A44SER0-0.007-0.00319.5900.0150.0150.0000.0000.0000.000
45A45LYS10.8570.90921.4480.1900.1900.0000.0000.0000.000
46A46SER00.0100.00720.3250.0300.0300.0000.0000.0000.000
47A47LEU0-0.0170.00821.870-0.008-0.0080.0000.0000.0000.000
48A48LEU00.001-0.01014.8970.0070.0070.0000.0000.0000.000
49A49GLY00.0310.01916.1960.0230.0230.0000.0000.0000.000
50A50ILE0-0.003-0.00710.184-0.032-0.0320.0000.0000.0000.000
51A51GLY00.0290.00610.7670.0950.0950.0000.0000.0000.000
52A52SER0-0.040-0.0167.477-0.254-0.2540.0000.0000.0000.000
53A53ILE00.0710.0558.5620.1450.1450.0000.0000.0000.000
54A54GLY0-0.0090.0018.4420.0040.0040.0000.0000.0000.000
55A55GLU-1-0.960-0.9945.082-0.414-0.4140.0000.0000.0000.000
56A56VAL0-0.066-0.0214.117-0.871-0.4380.000-0.052-0.3810.000
57A57PRO00.0310.0192.927-0.4810.3580.181-0.224-0.7950.000
58A58VAL0-0.014-0.0185.6850.0630.0630.0000.0000.0000.000
59A59LEU0-0.020-0.0048.9860.0000.0000.0000.0000.0000.000
60A60VAL0-0.0090.00612.1350.0870.0870.0000.0000.0000.000
61A61VAL00.033-0.01215.462-0.008-0.0080.0000.0000.0000.000
62A62LYS10.8720.91518.3410.2410.2410.0000.0000.0000.000
63A63PRO00.0190.01321.665-0.010-0.0100.0000.0000.0000.000
64A64GLN0-0.095-0.07223.6420.0320.0320.0000.0000.0000.000
65A65SER00.0320.01126.4930.0000.0000.0000.0000.0000.000
66A66TYR0-0.041-0.02128.2510.0140.0140.0000.0000.0000.000
67A67MET00.0390.03928.401-0.007-0.0070.0000.0000.0000.000
68A68ASN00.0080.01329.0050.0040.0040.0000.0000.0000.000
69A69TYR00.0040.00328.8000.0080.0080.0000.0000.0000.000
70A70SER00.005-0.00424.559-0.017-0.0170.0000.0000.0000.000
71A71GLY0-0.013-0.01423.207-0.021-0.0210.0000.0000.0000.000
72A72GLU-1-0.871-0.91622.799-0.156-0.1560.0000.0000.0000.000
73A73ALA0-0.041-0.00222.132-0.018-0.0180.0000.0000.0000.000
74A74ILE00.013-0.01517.880-0.037-0.0370.0000.0000.0000.000
75A75GLY00.0070.01717.833-0.031-0.0310.0000.0000.0000.000
76A76PRO00.003-0.01417.796-0.031-0.0310.0000.0000.0000.000
77A77LEU00.0120.01615.370-0.063-0.0630.0000.0000.0000.000
78A78ALA00.0070.00513.356-0.117-0.1170.0000.0000.0000.000
79A79ALA0-0.042-0.00712.790-0.059-0.0590.0000.0000.0000.000
80A80TYR0-0.021-0.01212.804-0.038-0.0380.0000.0000.0000.000
81A81TYR0-0.011-0.0389.517-0.122-0.1220.0000.0000.0000.000
82A82GLN0-0.056-0.0148.187-0.534-0.5340.0000.0000.0000.000
83A83VAL0-0.0240.0008.7240.0140.0140.0000.0000.0000.000
84A84PRO0-0.021-0.0028.9050.1410.1410.0000.0000.0000.000
85A85LEU00.0380.00411.729-0.014-0.0140.0000.0000.0000.000
86A86ARG10.9270.9527.507-1.593-1.5930.0000.0000.0000.000
87A87HIS0-0.023-0.0097.2810.5730.5730.0000.0000.0000.000
88A88ILE00.0310.03011.093-0.151-0.1510.0000.0000.0000.000
89A89LEU0-0.016-0.00914.1610.0630.0630.0000.0000.0000.000
90A90LEU0-0.025-0.00415.712-0.045-0.0450.0000.0000.0000.000
91A91ILE00.0260.01117.8650.0310.0310.0000.0000.0000.000
92A92TYR0-0.059-0.04521.476-0.017-0.0170.0000.0000.0000.000
93A93ASP-1-0.702-0.81825.274-0.044-0.0440.0000.0000.0000.000
94A94ASP-1-0.749-0.84028.2280.0130.0130.0000.0000.0000.000
95A95THR00.014-0.01430.2170.0010.0010.0000.0000.0000.000
96A96SER0-0.167-0.10031.5310.0050.0050.0000.0000.0000.000
97A97LEU0-0.0060.00928.4480.0070.0070.0000.0000.0000.000
98A98PRO00.032-0.00932.884-0.006-0.0060.0000.0000.0000.000
99A99ASN0-0.029-0.01932.879-0.003-0.0030.0000.0000.0000.000
100A100GLY00.0360.02230.7980.0020.0020.0000.0000.0000.000
101A101VAL0-0.046-0.01729.5700.0030.0030.0000.0000.0000.000
102A102LEU00.0220.03723.379-0.002-0.0020.0000.0000.0000.000
103A103ARG10.9110.95025.093-0.051-0.0510.0000.0000.0000.000
104A104LEU00.0360.03017.687-0.009-0.0090.0000.0000.0000.000
105A105GLN0-0.086-0.03821.2790.0080.0080.0000.0000.0000.000
106A106LYN00.0980.06314.9200.0010.0010.0000.0000.0000.000
107A107LYS10.9941.00119.272-0.150-0.1500.0000.0000.0000.000
108A108GLY0-0.010-0.00921.809-0.007-0.0070.0000.0000.0000.000
109A109GLY00.0210.01225.225-0.006-0.0060.0000.0000.0000.000
110A110HIS00.1260.06026.8510.0030.0030.0000.0000.0000.000
111A111GLY00.0120.01828.473-0.006-0.0060.0000.0000.0000.000
112A112ARG10.8970.93531.3840.0000.0000.0000.0000.0000.000
113A113HIS00.0250.01528.007-0.004-0.0040.0000.0000.0000.000
114A114ASN00.019-0.01929.9560.0050.0050.0000.0000.0000.000
115A115GLY00.0330.02327.809-0.004-0.0040.0000.0000.0000.000
116A116LEU0-0.015-0.01123.343-0.006-0.0060.0000.0000.0000.000
117A117GLN0-0.038-0.02825.9490.0080.0080.0000.0000.0000.000
118A118ASN00.0190.00927.498-0.012-0.0120.0000.0000.0000.000
119A119VAL00.004-0.00621.189-0.009-0.0090.0000.0000.0000.000
120A120ILE0-0.018-0.01223.3150.0030.0030.0000.0000.0000.000
121A121GLU-1-0.917-0.94024.547-0.054-0.0540.0000.0000.0000.000
122A122HIS0-0.018-0.01523.055-0.007-0.0070.0000.0000.0000.000
123A123LEU0-0.0330.00018.529-0.021-0.0210.0000.0000.0000.000
124A124ASP-1-0.848-0.90021.621-0.019-0.0190.0000.0000.0000.000
125A125GLY0-0.0070.00024.3110.0190.0190.0000.0000.0000.000
126A126ARG10.8000.87917.749-0.001-0.0010.0000.0000.0000.000
127A127ARG10.9370.94922.419-0.089-0.0890.0000.0000.0000.000
128A128GLU-1-0.951-0.97119.1850.1250.1250.0000.0000.0000.000
129A129PHE00.0250.01916.7040.0410.0410.0000.0000.0000.000
130A130PRO00.0110.00714.152-0.010-0.0100.0000.0000.0000.000
131A131ARG10.8120.90217.477-0.094-0.0940.0000.0000.0000.000
132A132LEU00.0250.01419.5860.0240.0240.0000.0000.0000.000
133A133SER0-0.071-0.05321.339-0.017-0.0170.0000.0000.0000.000
134A134ILE00.0330.00023.9310.0070.0070.0000.0000.0000.000
135A135GLY0-0.0030.00327.110-0.004-0.0040.0000.0000.0000.000
136A136ILE0-0.021-0.00530.707-0.005-0.0050.0000.0000.0000.000
137A137GLY0-0.0100.00633.508-0.001-0.0010.0000.0000.0000.000
138A138SER0-0.013-0.01836.347-0.002-0.0020.0000.0000.0000.000
139A139PRO0-0.0190.00238.956-0.001-0.0010.0000.0000.0000.000
140A140PRO00.0490.03541.5160.0030.0030.0000.0000.0000.000
141A141GLY00.019-0.00244.390-0.001-0.0010.0000.0000.0000.000
142A142LYS10.9210.94246.7110.0070.0070.0000.0000.0000.000
143A143MET0-0.0250.02742.833-0.001-0.0010.0000.0000.0000.000
144A144ASP-1-0.785-0.91343.869-0.031-0.0310.0000.0000.0000.000
145A145PRO00.0310.00039.970-0.002-0.0020.0000.0000.0000.000
146A146ARG10.9650.98639.1410.0480.0480.0000.0000.0000.000
147A147ALA00.007-0.00239.491-0.004-0.0040.0000.0000.0000.000
148A148PHE0-0.008-0.01736.925-0.003-0.0030.0000.0000.0000.000
149A149LEU0-0.011-0.00234.025-0.002-0.0020.0000.0000.0000.000
150A150LEU0-0.059-0.03235.585-0.006-0.0060.0000.0000.0000.000
151A151GLN00.0150.01937.784-0.004-0.0040.0000.0000.0000.000
152A152LYS10.8940.94136.6100.0710.0710.0000.0000.0000.000
153A153PHE00.0130.01431.7420.0040.0040.0000.0000.0000.000
154A154SER0-0.035-0.02937.370-0.002-0.0020.0000.0000.0000.000
155A155SER00.0550.00938.859-0.003-0.0030.0000.0000.0000.000
156A156GLU-1-0.865-0.92539.232-0.026-0.0260.0000.0000.0000.000
157A157GLU-1-0.835-0.89036.382-0.030-0.0300.0000.0000.0000.000
158A158ARG10.8180.86330.7960.0650.0650.0000.0000.0000.000
159A159VAL00.0550.04733.953-0.002-0.0020.0000.0000.0000.000
160A160GLN00.0000.00833.686-0.001-0.0010.0000.0000.0000.000
161A161ILE0-0.018-0.01429.6040.0020.0020.0000.0000.0000.000
162A162ASP-1-0.816-0.91429.278-0.062-0.0620.0000.0000.0000.000
163A163THR0-0.042-0.01628.819-0.001-0.0010.0000.0000.0000.000
164A164ALA0-0.005-0.01227.5050.0040.0040.0000.0000.0000.000
165A165LEU0-0.014-0.01024.886-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.783-0.85723.701-0.082-0.0820.0000.0000.0000.000
167A167GLN0-0.039-0.01123.322-0.002-0.0020.0000.0000.0000.000
168A168GLY00.009-0.02921.6740.0120.0120.0000.0000.0000.000
169A169VAL00.0190.01418.7390.0010.0010.0000.0000.0000.000
170A170ASP-1-0.885-0.93317.7130.0200.0200.0000.0000.0000.000
171A171ALA0-0.014-0.01317.5560.0250.0250.0000.0000.0000.000
172A172VAL0-0.041-0.02514.4110.0320.0320.0000.0000.0000.000
173A173ARG10.8840.93313.2330.1500.1500.0000.0000.0000.000
174A174THR00.0010.00612.5730.0450.0450.0000.0000.0000.000
175A175LEU0-0.092-0.05213.1230.0840.0840.0000.0000.0000.000
176A176VAL0-0.014-0.0228.3970.1000.1000.0000.0000.0000.000
177A177LEU0-0.011-0.0038.4750.1460.1460.0000.0000.0000.000
178A178LYS10.8010.9109.355-0.283-0.2830.0000.0000.0000.000
179A179GLY00.0110.0238.7040.1220.1220.0000.0000.0000.000
180A180PHE0-0.057-0.0456.307-0.269-0.2690.0000.0000.0000.000
181A181SER00.022-0.00211.3190.0260.0260.0000.0000.0000.000
182A182GLY0-0.009-0.02214.4630.0500.0500.0000.0000.0000.000
183A183SER0-0.014-0.01016.746-0.039-0.0390.0000.0000.0000.000
184A184THR0-0.062-0.03319.9350.0040.0040.0000.0000.0000.000
185A185GLU-1-0.885-0.91218.7610.3570.3570.0000.0000.0000.000
186A186ARG10.9140.95520.154-0.145-0.1450.0000.0000.0000.000
187A187PHE00.0610.03017.5800.0070.0070.0000.0000.0000.000
188A188ASN0-0.035-0.01521.893-0.016-0.0160.0000.0000.0000.000
189A189LEU00.0020.00620.7430.0070.0070.0000.0000.0000.000
190A190VAL00.021-0.00124.480-0.004-0.0040.0000.0000.0000.000
191A191GLN00.0060.01325.688-0.001-0.0010.0000.0000.0000.000