FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: RYLL8

Calculation Name: 2D1H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2D1H

Chain ID: A

ChEMBL ID:

UniProt ID: F9VNN8

Base Structure: X-ray

Registration Date: 2025-07-08

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -788849.865508
FMO2-HF: Nuclear repulsion 746698.454058
FMO2-HF: Total energy -42151.41145
FMO2-MP2: Total energy -42270.293157


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-3.4120.9660.002-2.133-2.2460.008
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.192 / q_NPA : 0.045
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].
4A2MET0-0.0370.0993.718-0.0210.5080.013-0.195-0.3470.000
5A3LYS00.169-0.0573.873-2.7450.111-0.018-1.742-1.0960.006
6A3LYS10.7261.0138.1301.1561.1560.0000.0000.0000.000
7A4GLU00.042-0.1317.187-0.024-0.0240.0000.0000.0000.000
8A4GLU-1-0.860-0.7907.970-0.925-0.9250.0000.0000.0000.000
9A5LYS00.077-0.1455.9430.3500.3500.0000.0000.0000.000
10A5LYS10.8631.0475.0320.4420.4420.0000.0000.0000.000
11A6LEU00.009-0.0596.6770.3020.3020.0000.0000.0000.000
12A6LEU0-0.0840.1084.615-0.148-0.104-0.001-0.009-0.0330.000
13A7GLU00.148-0.0897.3400.1820.1820.0000.0000.0000.000
14A7GLU-1-0.880-0.78411.497-0.490-0.4900.0000.0000.0000.000
15A8SER00.026-0.0799.8080.0840.0840.0000.0000.0000.000
16A8SER0-0.0850.0308.6890.1260.1260.0000.0000.0000.000
17A9LYS00.098-0.0568.3250.1970.1970.0000.0000.0000.000
18A9LYS10.7260.9583.6951.3461.4680.011-0.022-0.1110.001
19A10LYS00.091-0.1099.732-0.036-0.0360.0000.0000.0000.000
20A10LYS10.7701.00612.6960.4010.4010.0000.0000.0000.000
21A11ASP00.119-0.09912.328-0.026-0.0260.0000.0000.0000.000
22A11ASP-1-0.911-0.78814.803-0.135-0.1350.0000.0000.0000.000
23A12GLU00.049-0.13611.5200.0100.0100.0000.0000.0000.000
24A12GLU-1-0.905-0.81710.5630.0160.0160.0000.0000.0000.000
25A13ILE00.091-0.07011.0740.0790.0790.0000.0000.0000.000
26A13ILE0-0.1180.0697.773-0.063-0.0630.0000.0000.0000.000
27A14ARG00.108-0.10911.8180.0050.0050.0000.0000.0000.000
28A14ARG10.7450.98515.7310.1890.1890.0000.0000.0000.000
29A15CYS00.084-0.10315.4670.0050.0050.0000.0000.0000.000
30A15CYS0-0.1280.11316.2670.0150.0150.0000.0000.0000.000
31A16CYS00.063-0.14413.9160.0310.0310.0000.0000.0000.000
32A16CYS0-0.2910.18513.0960.0160.0160.0000.0000.0000.000
33A17TYR00.013-0.11814.9760.0450.0450.0000.0000.0000.000
34A17TYR0-0.0980.02510.763-0.070-0.0700.0000.0000.0000.000
35A18LYS00.026-0.06616.1150.0030.0030.0000.0000.0000.000
36A18LYS10.8571.05319.2150.0520.0520.0000.0000.0000.000
37A19ILE00.079-0.08218.1520.0210.0210.0000.0000.0000.000
38A19ILE0-0.1240.07514.960-0.012-0.0120.0000.0000.0000.000
39A20THR00.032-0.10819.3010.0140.0140.0000.0000.0000.000
40A20THR0-0.0750.02621.899-0.001-0.0010.0000.0000.0000.000
41A21ASP00.202-0.07419.121-0.046-0.0460.0000.0000.0000.000
42A21ASP-1-0.913-0.79619.748-0.205-0.2050.0000.0000.0000.000
43A22THR0-0.038-0.10619.484-0.037-0.0370.0000.0000.0000.000
44A22THR0-0.0370.05222.5830.0060.0060.0000.0000.0000.000
45A23ASP00.118-0.06819.199-0.033-0.0330.0000.0000.0000.000
46A23ASP-1-0.848-0.75018.558-0.271-0.2710.0000.0000.0000.000
47A24VAL00.068-0.10715.310-0.059-0.0590.0000.0000.0000.000
48A24VAL0-0.0830.12513.611-0.004-0.0040.0000.0000.0000.000
49A25ALA00.118-0.08915.200-0.108-0.1080.0000.0000.0000.000
50A25ALA0-0.0400.11118.9340.0120.0120.0000.0000.0000.000
51A26VAL00.043-0.09617.359-0.036-0.0360.0000.0000.0000.000
52A26VAL0-0.0780.09318.5560.0050.0050.0000.0000.0000.000
53A27LEU00.129-0.09714.127-0.010-0.0100.0000.0000.0000.000
54A27LEU0-0.1030.09811.303-0.002-0.0020.0000.0000.0000.000
55A28LEU00.059-0.12712.433-0.125-0.1250.0000.0000.0000.000
56A28LEU0-0.1020.12010.568-0.015-0.0150.0000.0000.0000.000
57A29LYS00.120-0.08513.434-0.075-0.0750.0000.0000.0000.000
58A29LYS10.7160.99517.9920.4640.4640.0000.0000.0000.000
59A30MET00.086-0.11016.1460.0190.0190.0000.0000.0000.000
60A30MET0-0.1070.07315.7070.0240.0240.0000.0000.0000.000
61A31VAL00.053-0.09111.4290.0540.0540.0000.0000.0000.000
62A31VAL0-0.1070.0789.392-0.049-0.0490.0000.0000.0000.000
63A32GLU00.005-0.10712.717-0.085-0.0850.0000.0000.0000.000
64A32GLU-1-0.880-0.78813.868-0.500-0.5000.0000.0000.0000.000
65A33ILE00.113-0.09414.394-0.002-0.0020.0000.0000.0000.000
66A33ILE0-0.1380.06317.4610.0230.0230.0000.0000.0000.000
67A34GLU0-0.005-0.10315.5210.0580.0580.0000.0000.0000.000
68A34GLU-1-0.920-0.80613.023-1.003-1.0030.0000.0000.0000.000
69A35LYS00.080-0.10116.2670.0260.0260.0000.0000.0000.000
70A35LYS10.8281.03320.3680.3810.3810.0000.0000.0000.000
71A36PRO00.003-0.10319.481-0.011-0.0110.0000.0000.0000.000
72A37ILE00.042-0.02321.2730.0260.0260.0000.0000.0000.000
73A37ILE0-0.0700.13620.445-0.001-0.0010.0000.0000.0000.000
74A38THR00.021-0.11023.018-0.014-0.0140.0000.0000.0000.000
75A38THR0-0.0820.04127.2040.0100.0100.0000.0000.0000.000
76A39SER00.056-0.06625.155-0.018-0.0180.0000.0000.0000.000
77A39SER0-0.0470.04326.2810.0080.0080.0000.0000.0000.000
78A40GLU0-0.008-0.13026.224-0.001-0.0010.0000.0000.0000.000
79A40GLU-1-0.823-0.80929.347-0.223-0.2230.0000.0000.0000.000
80A41GLU00.090-0.06726.2160.0160.0160.0000.0000.0000.000
81A41GLU-1-0.820-0.79325.531-0.308-0.3080.0000.0000.0000.000
82A42LEU00.105-0.07923.6600.0030.0030.0000.0000.0000.000
83A42LEU0-0.0860.07920.449-0.001-0.0010.0000.0000.0000.000
84A43ALA00.088-0.07924.524-0.006-0.0060.0000.0000.0000.000
85A43ALA0-0.0890.09128.4480.0030.0030.0000.0000.0000.000
86A44ASP00.047-0.09827.6220.0100.0100.0000.0000.0000.000
87A44ASP-1-0.891-0.80128.643-0.196-0.1960.0000.0000.0000.000
88A45ILE00.055-0.08124.3880.0220.0220.0000.0000.0000.000
89A45ILE0-0.0970.07222.352-0.009-0.0090.0000.0000.0000.000
90A46PHE00.024-0.09224.8550.0060.0060.0000.0000.0000.000
91A46PHE0-0.1290.04819.600-0.005-0.0050.0000.0000.0000.000
92A47LYS00.140-0.05625.7750.0080.0080.0000.0000.0000.000
93A47LYS10.7290.99129.4730.1920.1920.0000.0000.0000.000
94A48LEU00.054-0.11327.8010.0160.0160.0000.0000.0000.000
95A48LEU0-0.0850.08725.156-0.002-0.0020.0000.0000.0000.000
96A49SER00.114-0.04829.154-0.003-0.0030.0000.0000.0000.000
97A49SER0-0.0290.07331.617-0.002-0.0020.0000.0000.0000.000
98A50LYS00.186-0.06729.130-0.014-0.0140.0000.0000.0000.000
99A50LYS10.7651.02229.7320.1920.1920.0000.0000.0000.000
100A51THR00.007-0.11028.762-0.017-0.0170.0000.0000.0000.000
101A51THR0-0.0230.08131.1850.0030.0030.0000.0000.0000.000
102A52THR00.001-0.08828.190-0.004-0.0040.0000.0000.0000.000
103A52THR0-0.0230.07426.4600.0050.0050.0000.0000.0000.000
104A53VAL00.125-0.06624.661-0.009-0.0090.0000.0000.0000.000
105A53VAL0-0.1060.11823.752-0.002-0.0020.0000.0000.0000.000
106A54GLU00.145-0.09624.069-0.031-0.0310.0000.0000.0000.000
107A54GLU-1-0.933-0.80926.942-0.198-0.1980.0000.0000.0000.000
108A55ASN00.016-0.09425.167-0.011-0.0110.0000.0000.0000.000
109A55ASN0-0.0530.09026.5140.0020.0020.0000.0000.0000.000
110A56SER00.074-0.06921.9610.0090.0090.0000.0000.0000.000
111A56SER0-0.0440.05420.8790.0020.0020.0000.0000.0000.000
112A57LEU00.057-0.10220.524-0.032-0.0320.0000.0000.0000.000
113A57LEU0-0.0990.08320.0200.0000.0000.0000.0000.0000.000
114A58LYS00.122-0.08920.876-0.029-0.0290.0000.0000.0000.000
115A58LYS10.7311.01424.6660.2050.2050.0000.0000.0000.000
116A59LYS00.116-0.09421.0610.0050.0050.0000.0000.0000.000
117A59LYS10.7731.03419.4830.2100.2100.0000.0000.0000.000
118A60LEU00.085-0.09517.0160.0100.0100.0000.0000.0000.000
119A60LEU0-0.0770.09515.190-0.015-0.0150.0000.0000.0000.000
120A61ILE00.061-0.07016.877-0.064-0.0640.0000.0000.0000.000
121A61ILE0-0.1040.06120.1060.0090.0090.0000.0000.0000.000
122A62GLU00.036-0.09819.065-0.019-0.0190.0000.0000.0000.000
123A62GLU-1-0.893-0.80820.268-0.194-0.1940.0000.0000.0000.000
124A63LEU0-0.008-0.11416.2530.0420.0420.0000.0000.0000.000
125A63LEU0-0.0880.09915.169-0.006-0.0060.0000.0000.0000.000
126A64GLY00.003-0.11915.100-0.029-0.0290.0000.0000.0000.000
127A65LEU00.0590.00612.913-0.070-0.0700.0000.0000.0000.000
128A65LEU0-0.0970.09310.782-0.017-0.0170.0000.0000.0000.000
129A66VAL00.056-0.08113.791-0.123-0.1230.0000.0000.0000.000
130A66VAL0-0.0780.08015.5560.0070.0070.0000.0000.0000.000
131A67VAL00.115-0.11716.6530.0530.0530.0000.0000.0000.000
132A67VAL0-0.0570.13517.0950.0050.0050.0000.0000.0000.000
133A68ARG00.163-0.07919.455-0.013-0.0130.0000.0000.0000.000
134A68ARG10.7991.05023.2110.2330.2330.0000.0000.0000.000
135A69THR0-0.015-0.12823.0560.0170.0170.0000.0000.0000.000
136A69THR0-0.0140.10422.8910.0000.0000.0000.0000.0000.000
137A70LYS00.137-0.06625.355-0.003-0.0030.0000.0000.0000.000
138A70LYS10.8441.07029.6400.1660.1660.0000.0000.0000.000
139A71THR0-0.099-0.16429.1200.0100.0100.0000.0000.0000.000
140A71THR00.0640.05927.682-0.001-0.0010.0000.0000.0000.000
141A79PRO00.019-0.02234.982-0.001-0.0010.0000.0000.0000.000
142A80LYS00.0510.01531.0090.0040.0040.0000.0000.0000.000
143A80LYS10.8561.07329.7670.2170.2170.0000.0000.0000.000
144A81TYR00.101-0.08928.1050.0030.0030.0000.0000.0000.000
145A81TYR0-0.1020.08627.4920.0010.0010.0000.0000.0000.000
146A82TYR00.104-0.08624.9940.0040.0040.0000.0000.0000.000
147A82TYR0-0.0970.09023.9900.0120.0120.0000.0000.0000.000
148A83TYR00.084-0.08021.5310.0120.0120.0000.0000.0000.000
149A83TYR0-0.0700.08420.6610.0130.0130.0000.0000.0000.000
150A84SER00.067-0.07218.1710.0020.0020.0000.0000.0000.000
151A84SER00.0070.08217.9210.0240.0240.0000.0000.0000.000
152A85ILE00.094-0.09613.5550.0830.0830.0000.0000.0000.000
153A85ILE0-0.0840.13111.466-0.010-0.0100.0000.0000.0000.000
154A86SER00.012-0.10013.7010.0430.0430.0000.0000.0000.000
155A86SER0-0.0350.06112.7310.0230.0230.0000.0000.0000.000
156A87SER00.109-0.05412.137-0.203-0.2030.0000.0000.0000.000
157A87SER0-0.0190.08412.5240.0700.0700.0000.0000.0000.000
158A88ASN00.004-0.0779.316-0.186-0.1860.0000.0000.0000.000
159A88ASN0-0.0760.0649.7920.0080.0080.0000.0000.0000.000
160A89ILE00.124-0.1059.0670.0540.0540.0000.0000.0000.000
161A89ILE0-0.0510.1237.909-0.016-0.0160.0000.0000.0000.000
162A90LEU00.064-0.1204.8190.4280.447-0.002-0.006-0.0110.000
163A90LEU0-0.0450.1153.668-0.125-0.001-0.0010.040-0.1630.000
164A91GLU00.074-0.0984.488-0.834-0.723-0.001-0.026-0.0840.000
165A91GLU-1-0.941-0.8304.3660.7160.859-0.001-0.012-0.1300.000
166A92LYS00.109-0.0896.1670.6160.6160.0000.0000.0000.000
167A92LYS10.7611.0259.5730.4490.4490.0000.0000.0000.000
168A93ILE00.117-0.0786.9110.4680.4680.0000.0000.0000.000
169A93ILE0-0.0720.0935.970-0.108-0.1080.0000.0000.0000.000
170A94ARG00.096-0.0975.1150.0270.063-0.002-0.005-0.0290.000
171A94ARG10.8651.0613.846-4.073-3.7180.006-0.156-0.2050.001
172A95ASN00.091-0.0665.7900.4510.490-0.0020.000-0.0370.000
173A95ASN0-0.1460.0508.2010.1910.1910.0000.0000.0000.000
174A96ASP00.066-0.1099.4290.1740.1740.0000.0000.0000.000
175A96ASP-1-0.844-0.74910.275-0.442-0.4420.0000.0000.0000.000
176A97LEU00.062-0.0988.8840.0330.0330.0000.0000.0000.000
177A97LEU0-0.0590.1066.5930.0040.0040.0000.0000.0000.000
178A98LEU00.081-0.0829.5790.0100.0100.0000.0000.0000.000
179A98LEU0-0.0610.1028.5380.0580.0580.0000.0000.0000.000
180A99ASN00.125-0.05311.1840.0080.0080.0000.0000.0000.000
181A99ASN0-0.1660.02312.937-0.008-0.0080.0000.0000.0000.000
182A100CYS00.098-0.12213.190-0.016-0.0160.0000.0000.0000.000
183A101ALA00.138-0.10013.368-0.069-0.0690.0000.0000.0000.000
184A101ALA0-0.0880.10812.9630.0310.0310.0000.0000.0000.000
185A102LYS00.078-0.09714.814-0.007-0.0070.0000.0000.0000.000
186A102LYS10.7060.99115.982-0.399-0.3990.0000.0000.0000.000
187A103ARG00.059-0.09117.100-0.008-0.0080.0000.0000.0000.000
188A103ARG10.8691.04315.739-0.060-0.0600.0000.0000.0000.000
189A104MET00.114-0.07118.200-0.031-0.0310.0000.0000.0000.000
190A104MET0-0.1040.09017.1230.0110.0110.0000.0000.0000.000
191A105GLU00.113-0.08818.936-0.028-0.0280.0000.0000.0000.000
192A105GLU-1-0.909-0.79818.7690.4180.4180.0000.0000.0000.000
193A106LEU00.049-0.11020.583-0.010-0.0100.0000.0000.0000.000
194A106LEU0-0.1130.08420.876-0.001-0.0010.0000.0000.0000.000
195A107ALA00.125-0.08022.520-0.018-0.0180.0000.0000.0000.000
196A107ALA0-0.1070.08722.958-0.004-0.0040.0000.0000.0000.000
197A108ALA00.040-0.11623.821-0.025-0.0250.0000.0000.0000.000
198A108ALA0-0.0920.10523.5660.0050.0050.0000.0000.0000.000
199A109THR0-0.124-0.17025.355-0.008-0.0080.0000.0000.0000.000
200A109THR00.0010.03226.1850.0050.0050.0000.0000.0000.000