FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 2L98R

Calculation Name: 1YN5-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YN5

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2025-07-09

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -775968.142853
FMO2-HF: Nuclear repulsion 735483.061233
FMO2-HF: Total energy -40485.08162
FMO2-MP2: Total energy -40603.981095


3D Structure Molmil
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:42:ALA)


Summations of interaction energy for fragment #1(A:42:ALA)
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.
-8.234-0.3941.057-4.501-4.398-0.011
Interaction energy analysis for fragmet #1(A:42:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.183 / q_NPA : 0.046
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].
4A43LYS10.8341.0994.1570.6041.0640.000-0.256-0.2040.000
5A44GLU00.142-0.1173.766-4.113-1.010-0.045-1.739-1.3190.003
6A44GLU-1-0.929-0.8105.3431.6771.6770.0000.0000.0000.000
7A45MET00.062-0.0825.666-0.610-0.6100.0000.0000.0000.000
8A45MET0-0.1330.1068.756-0.095-0.0950.0000.0000.0000.000
9A46GLN00.107-0.0988.4000.2150.2150.0000.0000.0000.000
10A46GLN0-0.0590.1178.8770.0580.0580.0000.0000.0000.000
11A47ASN00.111-0.09010.489-0.103-0.1030.0000.0000.0000.000
12A47ASN0-0.1250.06315.333-0.022-0.0220.0000.0000.0000.000
13A48VAL00.073-0.15114.2290.0450.0450.0000.0000.0000.000
14A48VAL0-0.1070.10612.595-0.012-0.0120.0000.0000.0000.000
15A49PRO0-0.016-0.08415.316-0.014-0.0140.0000.0000.0000.000
16A50TYR00.0720.00219.087-0.014-0.0140.0000.0000.0000.000
17A50TYR0-0.1250.01818.969-0.006-0.0060.0000.0000.0000.000
18A51THR00.021-0.09321.1430.0120.0120.0000.0000.0000.000
19A51THR0-0.0120.05624.5140.0000.0000.0000.0000.0000.000
20A52ILE00.137-0.12324.866-0.013-0.0130.0000.0000.0000.000
21A52ILE0-0.0800.13324.489-0.001-0.0010.0000.0000.0000.000
22A53ALA00.149-0.10326.9860.0090.0090.0000.0000.0000.000
23A53ALA0-0.1290.10930.1460.0010.0010.0000.0000.0000.000
24A54VAL00.051-0.12730.387-0.007-0.0070.0000.0000.0000.000
25A54VAL0-0.1000.10830.724-0.001-0.0010.0000.0000.0000.000
26A55ASP0-0.003-0.13432.7060.0050.0050.0000.0000.0000.000
27A55ASP-1-0.855-0.79036.876-0.072-0.0720.0000.0000.0000.000
28A56GLY0-0.006-0.11934.4800.0050.0050.0000.0000.0000.000
29A57ILE00.0920.00234.7450.0040.0040.0000.0000.0000.000
30A57ILE0-0.0710.11934.0090.0000.0000.0000.0000.0000.000
31A58MET00.074-0.11930.988-0.009-0.0090.0000.0000.0000.000
32A58MET0-0.0590.14728.3830.0020.0020.0000.0000.0000.000
33A59ALA00.108-0.11228.4930.0050.0050.0000.0000.0000.000
34A59ALA0-0.0290.12327.961-0.002-0.0020.0000.0000.0000.000
35A60PHE00.143-0.01029.9760.0020.0020.0000.0000.0000.000
36A60PHE0-0.1130.08431.5470.0010.0010.0000.0000.0000.000
37A61ASN0-0.019-0.11028.8020.0030.0030.0000.0000.0000.000
38A61ASN0-0.1750.02327.9390.0010.0010.0000.0000.0000.000
39A62GLN00.237-0.16025.108-0.005-0.0050.0000.0000.0000.000
40A62GLN0-0.1380.13323.192-0.003-0.0030.0000.0000.0000.000
41A63SER0-0.014-0.04322.5410.0170.0170.0000.0000.0000.000
42A63SER0-0.0330.09321.9350.0020.0020.0000.0000.0000.000
43A64TYR00.090-0.12518.247-0.005-0.0050.0000.0000.0000.000
44A64TYR0-0.0700.10617.1880.0080.0080.0000.0000.0000.000
45A65LEU00.118-0.08816.0010.0050.0050.0000.0000.0000.000
46A65LEU0-0.1050.12713.649-0.009-0.0090.0000.0000.0000.000
47A66ASN00.148-0.07512.3460.0220.0220.0000.0000.0000.000
48A66ASN0-0.1060.05411.5640.0220.0220.0000.0000.0000.000
49A67LEU00.013-0.1889.360-0.073-0.0730.0000.0000.0000.000
50A67LEU0-0.0390.1439.125-0.005-0.0050.0000.0000.0000.000
51A68PRO0-0.019-0.0944.3030.3000.404-0.001-0.046-0.0570.000
52A69LYS00.1350.0425.055-0.285-0.159-0.002-0.011-0.1130.000
53A69LYS10.8291.0563.456-2.071-1.8480.005-0.052-0.1760.000
54A70ASP00.029-0.1542.898-2.475-1.1920.428-0.757-0.954-0.007
55A70ASP-1-0.966-0.8072.4380.4231.0040.453-0.558-0.4760.001
56A71SER00.026-0.0833.198-1.2450.0110.092-0.640-0.709-0.005
57A71SER0-0.0300.0543.013-1.420-0.6940.129-0.430-0.425-0.003
58A72GLN00.176-0.0254.6430.3620.340-0.002-0.0120.0350.000
59A72GLN0-0.0790.1086.6590.1410.1410.0000.0000.0000.000
60A73LEU00.098-0.1078.233-0.142-0.1420.0000.0000.0000.000
61A73LEU0-0.0850.1146.6080.0120.0120.0000.0000.0000.000
62A74SER00.135-0.0349.8300.1160.1160.0000.0000.0000.000
63A74SER0-0.0370.09713.5660.0300.0300.0000.0000.0000.000
64A75TYR00.084-0.09913.468-0.014-0.0140.0000.0000.0000.000
65A75TYR0-0.0940.08716.5110.0130.0130.0000.0000.0000.000
66A76LEU00.071-0.10516.3770.0390.0390.0000.0000.0000.000
67A76LEU0-0.0580.12017.305-0.002-0.0020.0000.0000.0000.000
68A77ASP00.137-0.11114.1950.0690.0690.0000.0000.0000.000
69A77ASP-1-1.013-0.82513.364-0.712-0.7120.0000.0000.0000.000
70A78LEU00.062-0.14315.1610.0200.0200.0000.0000.0000.000
71A78LEU0-0.0950.12714.299-0.004-0.0040.0000.0000.0000.000
72A79GLY0-0.022-0.10715.7900.0440.0440.0000.0000.0000.000
73A80ASN00.1090.02618.4630.0460.0460.0000.0000.0000.000
74A80ASN0-0.0840.08018.0120.0210.0210.0000.0000.0000.000
75A81LYS00.049-0.09717.0430.0330.0330.0000.0000.0000.000
76A81LYS10.8841.07412.2320.5990.5990.0000.0000.0000.000
77A82VAL00.098-0.09618.3510.0260.0260.0000.0000.0000.000
78A82VAL0-0.0790.10019.1970.0020.0020.0000.0000.0000.000
79A83LYS00.141-0.07320.9030.0270.0270.0000.0000.0000.000
80A83LYS10.7300.98822.4890.2460.2460.0000.0000.0000.000
81A84ALA00.105-0.10721.4300.0260.0260.0000.0000.0000.000
82A84ALA0-0.1130.10020.726-0.006-0.0060.0000.0000.0000.000
83A85LEU00.093-0.08221.8850.0170.0170.0000.0000.0000.000
84A85LEU0-0.0990.09019.599-0.002-0.0020.0000.0000.0000.000
85A86LEU00.063-0.07623.2550.0190.0190.0000.0000.0000.000
86A86LEU0-0.1250.06725.3680.0020.0020.0000.0000.0000.000
87A87TYR00.128-0.07826.1730.0170.0170.0000.0000.0000.000
88A87TYR0-0.1010.07226.5430.0020.0020.0000.0000.0000.000
89A88ASP00.058-0.11625.4010.0160.0160.0000.0000.0000.000
90A88ASP-1-1.006-0.85324.493-0.168-0.1680.0000.0000.0000.000
91A89GLU00.075-0.10226.4400.0110.0110.0000.0000.0000.000
92A89GLU-1-0.940-0.79224.270-0.108-0.1080.0000.0000.0000.000
93A90ARG0-0.055-0.14927.9540.0120.0120.0000.0000.0000.000
94A90ARG10.7491.02629.0130.0810.0810.0000.0000.0000.000
95A91GLY00.073-0.06530.1250.0070.0070.0000.0000.0000.000
96A92VAL00.040-0.04130.3540.0050.0050.0000.0000.0000.000
97A92VAL0-0.1210.11329.5180.0000.0000.0000.0000.0000.000
98A93THR00.018-0.07029.718-0.012-0.0120.0000.0000.0000.000
99A93THR00.0110.08032.6860.0000.0000.0000.0000.0000.000
100A94PRO00.088-0.09328.8060.0020.0020.0000.0000.0000.000
101A95GLU00.102-0.04430.864-0.003-0.0030.0000.0000.0000.000
102A95GLU-1-0.985-0.83035.353-0.092-0.0920.0000.0000.0000.000
103A96LYS00.047-0.12933.5100.0070.0070.0000.0000.0000.000
104A96LYS10.8881.10933.0350.0820.0820.0000.0000.0000.000
105A97ILE00.077-0.08630.4800.0090.0090.0000.0000.0000.000
106A97ILE0-0.0500.09927.610-0.001-0.0010.0000.0000.0000.000
107A98ARG00.031-0.12131.9220.0000.0000.0000.0000.0000.000
108A98ARG10.8681.07532.6800.1220.1220.0000.0000.0000.000
109A99ASN00.076-0.08234.0720.0010.0010.0000.0000.0000.000
110A99ASN0-0.0930.08037.704-0.001-0.0010.0000.0000.0000.000
111A100ALA00.076-0.09134.1600.0080.0080.0000.0000.0000.000
112A100ALA0-0.0990.11033.558-0.001-0.0010.0000.0000.0000.000
113A101LYS00.114-0.05335.634-0.002-0.0020.0000.0000.0000.000
114A101LYS10.8091.03136.9230.0710.0710.0000.0000.0000.000
115A102SER0-0.006-0.12333.3930.0000.0000.0000.0000.0000.000
116A102SER0-0.0420.06732.6930.0040.0040.0000.0000.0000.000
117A103ALA00.093-0.07729.9650.0080.0080.0000.0000.0000.000
118A103ALA0-0.0620.10929.163-0.001-0.0010.0000.0000.0000.000
119A104VAL0-0.008-0.12226.604-0.007-0.0070.0000.0000.0000.000
120A104VAL0-0.0570.13926.4800.0010.0010.0000.0000.0000.000
121A105TYR00.127-0.03422.8750.0110.0110.0000.0000.0000.000
122A105TYR0-0.0370.07719.100-0.013-0.0130.0000.0000.0000.000
123A106THR00.000-0.12223.370-0.015-0.0150.0000.0000.0000.000
124A106THR0-0.0190.09323.8090.0040.0040.0000.0000.0000.000
125A107ILE00.069-0.10619.1900.0090.0090.0000.0000.0000.000
126A107ILE0-0.0480.10516.939-0.006-0.0060.0000.0000.0000.000
127A108THR00.029-0.07019.6480.0050.0050.0000.0000.0000.000
128A108THR0-0.0760.06120.7450.0080.0080.0000.0000.0000.000
129A109TRP00.133-0.08117.131-0.009-0.0090.0000.0000.0000.000
130A109TRP0-0.1000.11914.167-0.019-0.0190.0000.0000.0000.000
131A110LYS00.074-0.12016.6240.0150.0150.0000.0000.0000.000
132A110LYS10.7691.03912.6920.0480.0480.0000.0000.0000.000
133A111ASP0-0.018-0.14917.8940.0230.0230.0000.0000.0000.000
134A111ASP-1-0.817-0.71619.962-0.084-0.0840.0000.0000.0000.000
135A112GLY0-0.041-0.10920.7020.0080.0080.0000.0000.0000.000
136A113SER00.028-0.00322.1460.0030.0030.0000.0000.0000.000
137A113SER0-0.0560.03621.327-0.008-0.0080.0000.0000.0000.000
138A114LYS0-0.004-0.14421.926-0.007-0.0070.0000.0000.0000.000
139A114LYS10.8841.07523.7710.0750.0750.0000.0000.0000.000
140A115LYS00.114-0.08621.5830.0090.0090.0000.0000.0000.000
141A115LYS10.8431.07519.6820.2300.2300.0000.0000.0000.000
142A116GLU00.092-0.14522.585-0.012-0.0120.0000.0000.0000.000
143A116GLU-1-0.985-0.80426.368-0.111-0.1110.0000.0000.0000.000
144A117VAL00.042-0.13922.6040.0040.0040.0000.0000.0000.000
145A117VAL0-0.1210.11520.706-0.005-0.0050.0000.0000.0000.000
146A118ASP00.197-0.11524.0150.0010.0010.0000.0000.0000.000
147A118ASP-1-0.967-0.81827.857-0.135-0.1350.0000.0000.0000.000
148A119LEU00.056-0.10425.892-0.012-0.0120.0000.0000.0000.000
149A119LEU0-0.0980.08223.185-0.001-0.0010.0000.0000.0000.000
150A120LYS00.056-0.10326.733-0.005-0.0050.0000.0000.0000.000
151A120LYS10.7401.01731.0830.1060.1060.0000.0000.0000.000
152A121LYS00.036-0.09028.4300.0080.0080.0000.0000.0000.000
153A121LYS10.8251.05128.4630.1270.1270.0000.0000.0000.000
154A122ASP00.200-0.02725.612-0.009-0.0090.0000.0000.0000.000
155A122ASP-1-0.948-0.82624.401-0.230-0.2300.0000.0000.0000.000
156A123SER0-0.017-0.12624.9050.0130.0130.0000.0000.0000.000
157A123SER0-0.0350.06026.8520.0030.0030.0000.0000.0000.000
158A124TYR00.042-0.10422.794-0.012-0.0120.0000.0000.0000.000
159A124TYR0-0.0410.10619.6920.0060.0060.0000.0000.0000.000
160A125THR00.011-0.09021.0600.0250.0250.0000.0000.0000.000
161A125THR0-0.0300.07318.953-0.006-0.0060.0000.0000.0000.000
162A126ALA00.142-0.09618.234-0.025-0.0250.0000.0000.0000.000
163A126ALA0-0.0530.12918.5750.0040.0040.0000.0000.0000.000
164A127ASN00.071-0.07516.591-0.047-0.0470.0000.0000.0000.000
165A127ASN0-0.1420.04917.8860.0010.0010.0000.0000.0000.000
166A128LEU00.098-0.13412.7390.0120.0120.0000.0000.0000.000
167A128LEU0-0.0520.13011.396-0.012-0.0120.0000.0000.0000.000
168A129PHE00.034-0.07112.1290.0720.0720.0000.0000.0000.000
169A129PHE0-0.0970.05511.3470.0000.0000.0000.0000.0000.000
170A130ASP00.178-0.1149.601-0.152-0.1520.0000.0000.0000.000
171A130ASP-1-1.036-0.8208.999-0.392-0.3920.0000.0000.0000.000
172A131SER00.061-0.1247.3140.1780.1780.0000.0000.0000.000
173A131SER0-0.1390.0366.732-0.147-0.1470.0000.0000.0000.000
174A132ASN00.044-0.1008.5450.0660.0660.0000.0000.0000.000
175A132ASN0-0.0700.1076.8030.0270.0270.0000.0000.0000.000
176A133SER00.043-0.1249.7730.1000.1000.0000.0000.0000.000
177A133SER0-0.0180.09112.6370.0180.0180.0000.0000.0000.000
178A134ILE00.056-0.11012.1840.0500.0500.0000.0000.0000.000
179A134ILE0-0.0490.14012.243-0.006-0.0060.0000.0000.0000.000
180A135LYS00.069-0.10713.9750.0280.0280.0000.0000.0000.000
181A135LYS10.8501.06517.6870.0260.0260.0000.0000.0000.000
182A136GLN00.083-0.12316.8240.0110.0110.0000.0000.0000.000
183A136GLN0-0.1270.07820.1850.0140.0140.0000.0000.0000.000
184A137ILE00.040-0.12818.912-0.008-0.0080.0000.0000.0000.000
185A137ILE0-0.0860.10915.872-0.006-0.0060.0000.0000.0000.000
186A138ASP00.111-0.07620.0560.0050.0050.0000.0000.0000.000
187A138ASP-1-0.948-0.78224.323-0.089-0.0890.0000.0000.0000.000
188A139ILE00.175-0.11223.811-0.007-0.0070.0000.0000.0000.000
189A139ILE0-0.1280.11821.560-0.002-0.0020.0000.0000.0000.000
190A140ASN00.088-0.09225.1420.0110.0110.0000.0000.0000.000
191A140ASN0-0.1550.05928.6990.0020.0020.0000.0000.0000.000
192A141VAL00.105-0.10428.784-0.005-0.0050.0000.0000.0000.000
193A141VAL0-0.0650.12128.807-0.001-0.0010.0000.0000.0000.000
194A142LYS00.119-0.05131.2240.0070.0070.0000.0000.0000.000
195A142LYS10.7991.03533.7110.0740.0740.0000.0000.0000.000
196A143THR00.069-0.07334.950-0.004-0.0040.0000.0000.0000.000
197A143THR0-0.0620.05236.335-0.002-0.0020.0000.0000.0000.000
198A144LYS00.020-0.05337.1110.0010.0010.0000.0000.0000.000
199A144LYS10.9690.95838.1800.0660.0660.0000.0000.0000.000