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: 43M6N

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 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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2114678.303187
FMO2-HF: Nuclear repulsion 2041693.320905
FMO2-HF: Total energy -72984.982281
FMO2-MP2: Total energy -73200.607447


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.
-5.374-2.4270.364-0.949-2.3640.002
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 : 0.023 / q_NPA : 0.002
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].
3A3PRO00.0550.0443.870-1.3280.112-0.005-0.551-0.8840.003
4A4TRP00.0330.0016.0940.8230.8230.0000.0000.0000.000
5A5LEU0-0.034-0.0059.161-0.183-0.1830.0000.0000.0000.000
6A6ILE00.0140.00411.8290.1240.1240.0000.0000.0000.000
7A7ALA00.0100.00115.033-0.030-0.0300.0000.0000.0000.000
8A8GLY00.0300.01618.5690.0410.0410.0000.0000.0000.000
9A9LEU0-0.054-0.04721.707-0.011-0.0110.0000.0000.0000.000
10A10GLY00.0320.00424.7780.0040.0040.0000.0000.0000.000
11A11ASN0-0.050-0.01328.143-0.001-0.0010.0000.0000.0000.000
12A12PRO00.0630.05429.578-0.002-0.0020.0000.0000.0000.000
13A13GLY00.0270.00430.7460.0090.0090.0000.0000.0000.000
14A14ASN00.015-0.01433.1610.0000.0000.0000.0000.0000.000
15A15LYS10.9190.96935.4210.0820.0820.0000.0000.0000.000
16A16TYR00.0280.01533.1440.0100.0100.0000.0000.0000.000
17A17TYR00.0340.04229.4980.0050.0050.0000.0000.0000.000
18A18GLY00.0690.03732.3100.0060.0060.0000.0000.0000.000
19A19THR0-0.098-0.06533.7850.0080.0080.0000.0000.0000.000
20A20ARG10.8560.90532.4910.0290.0290.0000.0000.0000.000
21A21HIS0-0.101-0.08431.251-0.003-0.0030.0000.0000.0000.000
22A22ASN0-0.012-0.02529.075-0.002-0.0020.0000.0000.0000.000
23A23VAL00.0520.03327.471-0.011-0.0110.0000.0000.0000.000
24A24GLY00.0170.01624.251-0.002-0.0020.0000.0000.0000.000
25A25PHE0-0.050-0.03123.258-0.018-0.0180.0000.0000.0000.000
26A26GLU-1-0.803-0.88024.100-0.095-0.0950.0000.0000.0000.000
27A27MET0-0.0070.03421.020-0.007-0.0070.0000.0000.0000.000
28A28VAL0-0.002-0.00218.705-0.008-0.0080.0000.0000.0000.000
29A29ASP-1-0.842-0.90919.877-0.232-0.2320.0000.0000.0000.000
30A30ARG10.7340.82121.9040.1130.1130.0000.0000.0000.000
31A31ILE00.0200.00116.163-0.004-0.0040.0000.0000.0000.000
32A32ALA0-0.035-0.01717.109-0.021-0.0210.0000.0000.0000.000
33A33ALA0-0.013-0.00818.194-0.021-0.0210.0000.0000.0000.000
34A34GLU-1-0.869-0.90218.132-0.129-0.1290.0000.0000.0000.000
35A35GLU-1-0.857-0.92613.671-0.292-0.2920.0000.0000.0000.000
36A36GLY00.0000.01515.107-0.047-0.0470.0000.0000.0000.000
37A37ILE0-0.077-0.02412.400-0.029-0.0290.0000.0000.0000.000
38A38THR00.009-0.00516.5150.0590.0590.0000.0000.0000.000
39A39MET0-0.071-0.02218.487-0.040-0.0400.0000.0000.0000.000
40A40ASN0-0.007-0.01020.0400.0090.0090.0000.0000.0000.000
41A41THR0-0.0090.01317.039-0.007-0.0070.0000.0000.0000.000
42A42ILE00.000-0.00319.9220.0210.0210.0000.0000.0000.000
43A43GLN00.0370.02815.625-0.040-0.0400.0000.0000.0000.000
44A44SER0-0.020-0.02119.7050.0210.0210.0000.0000.0000.000
45A45LYS10.8740.92221.5430.1680.1680.0000.0000.0000.000
46A46SER00.0140.00520.4810.0320.0320.0000.0000.0000.000
47A47LEU0-0.0180.01022.016-0.012-0.0120.0000.0000.0000.000
48A48LEU00.007-0.00914.9740.0120.0120.0000.0000.0000.000
49A49GLY00.0340.02716.3210.0260.0260.0000.0000.0000.000
50A50ILE0-0.025-0.01910.252-0.024-0.0240.0000.0000.0000.000
51A51GLY00.0390.01410.7340.1080.1080.0000.0000.0000.000
52A52SER0-0.051-0.0327.312-0.302-0.3020.0000.0000.0000.000
53A53ILE00.0460.0388.3470.1740.1740.0000.0000.0000.000
54A54GLY00.0060.0008.5960.0450.0450.0000.0000.0000.000
55A55GLU-1-0.930-0.9625.201-0.520-0.5200.0000.0000.0000.000
56A56VAL0-0.045-0.0063.968-0.978-0.5680.001-0.057-0.3550.000
57A57PRO00.0100.0032.725-0.6600.4370.368-0.341-1.125-0.001
58A58VAL0-0.023-0.0215.5180.2310.2310.0000.0000.0000.000
59A59LEU0-0.0150.0079.058-0.018-0.0180.0000.0000.0000.000
60A60VAL00.0120.01712.2220.0970.0970.0000.0000.0000.000
61A61VAL00.014-0.01615.725-0.011-0.0110.0000.0000.0000.000
62A62LYS10.8760.91118.4480.2560.2560.0000.0000.0000.000
63A63PRO00.0120.01721.655-0.008-0.0080.0000.0000.0000.000
64A64GLN0-0.067-0.05823.8960.0290.0290.0000.0000.0000.000
65A65SER00.008-0.00526.5080.0030.0030.0000.0000.0000.000
66A66TYR0-0.033-0.02928.2810.0150.0150.0000.0000.0000.000
67A67MET00.0420.05628.292-0.005-0.0050.0000.0000.0000.000
68A68ASN0-0.013-0.00828.9100.0040.0040.0000.0000.0000.000
69A69TYR00.0080.01728.7140.0090.0090.0000.0000.0000.000
70A70SER0-0.004-0.01124.470-0.017-0.0170.0000.0000.0000.000
71A71GLY0-0.006-0.00823.117-0.020-0.0200.0000.0000.0000.000
72A72GLU-1-0.873-0.92922.820-0.132-0.1320.0000.0000.0000.000
73A73ALA0-0.056-0.01422.525-0.018-0.0180.0000.0000.0000.000
74A74ILE00.0320.01217.834-0.039-0.0390.0000.0000.0000.000
75A75GLY00.0340.02617.785-0.029-0.0290.0000.0000.0000.000
76A76PRO0-0.013-0.01817.788-0.020-0.0200.0000.0000.0000.000
77A77LEU0-0.0040.00815.399-0.062-0.0620.0000.0000.0000.000
78A78ALA00.0140.00513.397-0.113-0.1130.0000.0000.0000.000
79A79ALA0-0.018-0.00412.719-0.050-0.0500.0000.0000.0000.000
80A80TYR0-0.020-0.01012.957-0.036-0.0360.0000.0000.0000.000
81A81TYR0-0.023-0.0399.534-0.139-0.1390.0000.0000.0000.000
82A82GLN0-0.038-0.0157.823-0.578-0.5780.0000.0000.0000.000
83A83VAL0-0.0150.0148.9930.1700.1700.0000.0000.0000.000
84A84PRO0-0.029-0.0038.9880.1050.1050.0000.0000.0000.000
85A85LEU00.036-0.00311.822-0.010-0.0100.0000.0000.0000.000
86A86ARG10.8970.9296.617-2.399-2.3990.0000.0000.0000.000
87A87HIS00.0000.0107.1690.7530.7530.0000.0000.0000.000
88A88ILE00.0210.02311.088-0.165-0.1650.0000.0000.0000.000
89A89LEU00.0000.00713.8110.0560.0560.0000.0000.0000.000
90A90LEU0-0.0100.00115.428-0.054-0.0540.0000.0000.0000.000
91A91ILE00.0210.01117.5280.0320.0320.0000.0000.0000.000
92A92TYR0-0.063-0.04521.289-0.017-0.0170.0000.0000.0000.000
93A93ASP-1-0.696-0.81525.063-0.036-0.0360.0000.0000.0000.000
94A94ASP-1-0.773-0.84728.0650.0300.0300.0000.0000.0000.000
95A95THR00.0340.00230.0550.0000.0000.0000.0000.0000.000
96A96SER0-0.168-0.09731.2510.0040.0040.0000.0000.0000.000
97A97LEU0-0.0020.01028.2200.0060.0060.0000.0000.0000.000
98A98PRO00.008-0.01432.686-0.007-0.0070.0000.0000.0000.000
99A99ASN0-0.043-0.02432.869-0.002-0.0020.0000.0000.0000.000
100A100GLY00.0450.03130.6360.0010.0010.0000.0000.0000.000
101A101VAL0-0.058-0.03029.5350.0030.0030.0000.0000.0000.000
102A102LEU00.0350.03223.1460.0010.0010.0000.0000.0000.000
103A103ARG10.8820.93325.017-0.068-0.0680.0000.0000.0000.000
104A104LEU00.0480.04217.441-0.008-0.0080.0000.0000.0000.000
105A105GLN0-0.087-0.04520.7060.0010.0010.0000.0000.0000.000
106A106LYN00.1120.07014.2450.0040.0040.0000.0000.0000.000
107A107LYS10.9711.00118.750-0.194-0.1940.0000.0000.0000.000
108A108GLY0-0.005-0.00521.571-0.010-0.0100.0000.0000.0000.000
109A109GLY00.0290.01925.198-0.003-0.0030.0000.0000.0000.000
110A110HIS00.1150.05526.4410.0050.0050.0000.0000.0000.000
111A111GLY00.0310.02928.548-0.008-0.0080.0000.0000.0000.000
112A112ARG10.8760.92431.672-0.012-0.0120.0000.0000.0000.000
113A113HIS00.011-0.00127.685-0.003-0.0030.0000.0000.0000.000
114A114ASN00.008-0.02029.7360.0070.0070.0000.0000.0000.000
115A115GLY00.0460.03127.532-0.003-0.0030.0000.0000.0000.000
116A116LEU00.0120.00523.370-0.003-0.0030.0000.0000.0000.000
117A117GLN0-0.022-0.02425.7650.0150.0150.0000.0000.0000.000
118A118ASN00.0270.01427.330-0.009-0.0090.0000.0000.0000.000
119A119VAL00.010-0.00221.325-0.009-0.0090.0000.0000.0000.000
120A120ILE0-0.047-0.01823.2120.0060.0060.0000.0000.0000.000
121A121GLU-1-0.905-0.93924.667-0.031-0.0310.0000.0000.0000.000
122A122HIS0-0.044-0.02422.994-0.006-0.0060.0000.0000.0000.000
123A123LEU0-0.0200.00018.504-0.017-0.0170.0000.0000.0000.000
124A124ASP-1-0.844-0.89821.8320.0430.0430.0000.0000.0000.000
125A125GLY00.0040.01024.6570.0170.0170.0000.0000.0000.000
126A126ARG10.7930.87217.619-0.072-0.0720.0000.0000.0000.000
127A127ARG10.8830.91722.361-0.142-0.1420.0000.0000.0000.000
128A128GLU-1-0.893-0.93119.0480.1670.1670.0000.0000.0000.000
129A129PHE00.0410.02416.2590.0540.0540.0000.0000.0000.000
130A130PRO0-0.0140.00113.647-0.019-0.0190.0000.0000.0000.000
131A131ARG10.7980.87816.987-0.139-0.1390.0000.0000.0000.000
132A132LEU00.0130.00519.4920.0270.0270.0000.0000.0000.000
133A133SER0-0.042-0.03921.198-0.017-0.0170.0000.0000.0000.000
134A134ILE00.0300.00923.8450.0050.0050.0000.0000.0000.000
135A135GLY00.0120.00526.915-0.004-0.0040.0000.0000.0000.000
136A136ILE0-0.028-0.00430.443-0.007-0.0070.0000.0000.0000.000
137A137GLY00.0070.00933.324-0.002-0.0020.0000.0000.0000.000
138A138SER0-0.012-0.02736.063-0.001-0.0010.0000.0000.0000.000
139A139PRO0-0.0100.00738.789-0.001-0.0010.0000.0000.0000.000
140A140PRO00.0340.03241.6250.0030.0030.0000.0000.0000.000
141A141GLY00.0590.02844.493-0.001-0.0010.0000.0000.0000.000
142A142LYS10.8510.89847.4870.0040.0040.0000.0000.0000.000
143A143MET0-0.0120.02442.866-0.001-0.0010.0000.0000.0000.000
144A144ASP-1-0.775-0.88743.441-0.025-0.0250.0000.0000.0000.000
145A145PRO00.0350.00539.481-0.002-0.0020.0000.0000.0000.000
146A146ARG10.9540.98239.0100.0410.0410.0000.0000.0000.000
147A147ALA00.002-0.01339.360-0.004-0.0040.0000.0000.0000.000
148A148PHE0-0.001-0.01936.897-0.003-0.0030.0000.0000.0000.000
149A149LEU0-0.0010.01033.779-0.002-0.0020.0000.0000.0000.000
150A150LEU0-0.035-0.02435.455-0.006-0.0060.0000.0000.0000.000
151A151GLN00.0190.02337.614-0.006-0.0060.0000.0000.0000.000
152A152LYS10.8590.92636.8980.0710.0710.0000.0000.0000.000
153A153PHE0-0.0030.00531.7500.0040.0040.0000.0000.0000.000
154A154SER0-0.021-0.03637.425-0.003-0.0030.0000.0000.0000.000
155A155SER00.0300.00438.689-0.003-0.0030.0000.0000.0000.000
156A156GLU-1-0.857-0.90738.940-0.026-0.0260.0000.0000.0000.000
157A157GLU-1-0.794-0.87336.430-0.027-0.0270.0000.0000.0000.000
158A158ARG10.7900.86930.6710.0670.0670.0000.0000.0000.000
159A159VAL00.0590.03833.669-0.002-0.0020.0000.0000.0000.000
160A160GLN0-0.0030.01433.524-0.001-0.0010.0000.0000.0000.000
161A161ILE0-0.003-0.00429.5460.0030.0030.0000.0000.0000.000
162A162ASP-1-0.805-0.91029.120-0.066-0.0660.0000.0000.0000.000
163A163THR0-0.047-0.03228.567-0.003-0.0030.0000.0000.0000.000
164A164ALA0-0.008-0.00427.2270.0040.0040.0000.0000.0000.000
165A165LEU0-0.027-0.02024.883-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.793-0.87523.564-0.095-0.0950.0000.0000.0000.000
167A167GLN0-0.045-0.01423.266-0.002-0.0020.0000.0000.0000.000
168A168GLY0-0.002-0.02621.4060.0130.0130.0000.0000.0000.000
169A169VAL00.0250.01718.834-0.001-0.0010.0000.0000.0000.000
170A170ASP-1-0.866-0.91617.6030.0170.0170.0000.0000.0000.000
171A171ALA0-0.006-0.00417.2080.0210.0210.0000.0000.0000.000
172A172VAL0-0.032-0.02514.4390.0390.0390.0000.0000.0000.000
173A173ARG10.8820.92713.1870.1900.1900.0000.0000.0000.000
174A174THR0-0.012-0.01612.4520.0420.0420.0000.0000.0000.000
175A175LEU0-0.083-0.04313.2590.0870.0870.0000.0000.0000.000
176A176VAL0-0.015-0.0168.1680.1130.1130.0000.0000.0000.000
177A177LEU0-0.016-0.0098.4840.1950.1950.0000.0000.0000.000
178A178LYS10.8090.9079.518-0.393-0.3930.0000.0000.0000.000
179A179GLY00.0130.0238.2930.1180.1180.0000.0000.0000.000
180A180PHE0-0.077-0.0535.853-0.270-0.2700.0000.0000.0000.000
181A181SER00.028-0.00610.9820.0530.0530.0000.0000.0000.000
182A182GLY0-0.011-0.02114.3080.0540.0540.0000.0000.0000.000
183A183SER0-0.023-0.01416.444-0.052-0.0520.0000.0000.0000.000
184A184THR0-0.056-0.02619.6550.0090.0090.0000.0000.0000.000
185A185GLU-1-0.836-0.88818.0390.4190.4190.0000.0000.0000.000
186A186ARG10.8820.93520.741-0.184-0.1840.0000.0000.0000.000
187A187PHE00.0510.02217.2560.0030.0030.0000.0000.0000.000
188A188ASN0-0.011-0.00421.286-0.016-0.0160.0000.0000.0000.000
189A189LEU00.0160.01220.6490.0070.0070.0000.0000.0000.000
190A190VAL00.001-0.00324.382-0.004-0.0040.0000.0000.0000.000
191A191GLN00.0240.02025.449-0.005-0.0050.0000.0000.0000.000