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: M94JZ

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 OptHSide
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 -776011.248892
FMO2-HF: Nuclear repulsion 735523.455223
FMO2-HF: Total energy -40487.793669
FMO2-MP2: Total energy -40606.612193


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.
-8.196-0.4481.142-4.585-4.308-0.011
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 : 0.189 / q_NPA : 0.039
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].
4A43LYS10.8641.0654.3340.2690.6410.000-0.200-0.1710.000
5A44GLU00.161-0.1103.766-4.073-1.038-0.043-1.700-1.2920.003
6A44GLU-1-0.902-0.7954.9991.6351.6350.0000.0000.0000.000
7A45MET00.093-0.0865.619-0.609-0.6090.0000.0000.0000.000
8A45MET0-0.1360.1198.912-0.082-0.0820.0000.0000.0000.000
9A46GLN00.080-0.1068.3520.2250.2250.0000.0000.0000.000
10A46GLN0-0.0880.0968.822-0.020-0.0200.0000.0000.0000.000
11A47ASN00.098-0.07910.458-0.096-0.0960.0000.0000.0000.000
12A47ASN0-0.1240.06214.951-0.024-0.0240.0000.0000.0000.000
13A48VAL00.121-0.11914.2000.0420.0420.0000.0000.0000.000
14A48VAL0-0.1250.10512.546-0.011-0.0110.0000.0000.0000.000
15A49PRO00.022-0.08715.295-0.012-0.0120.0000.0000.0000.000
16A50TYR00.0440.00719.067-0.015-0.0150.0000.0000.0000.000
17A50TYR0-0.1160.03719.014-0.008-0.0080.0000.0000.0000.000
18A51THR00.007-0.09421.1300.0120.0120.0000.0000.0000.000
19A51THR0-0.0330.05924.3910.0010.0010.0000.0000.0000.000
20A52ILE00.169-0.08824.860-0.012-0.0120.0000.0000.0000.000
21A52ILE0-0.1130.10624.064-0.001-0.0010.0000.0000.0000.000
22A53ALA00.177-0.09526.9820.0090.0090.0000.0000.0000.000
23A53ALA0-0.1210.09330.1110.0010.0010.0000.0000.0000.000
24A54VAL00.066-0.11030.384-0.007-0.0070.0000.0000.0000.000
25A54VAL0-0.1070.10230.619-0.001-0.0010.0000.0000.0000.000
26A55ASP00.052-0.09832.7070.0050.0050.0000.0000.0000.000
27A55ASP-1-0.881-0.78236.437-0.072-0.0720.0000.0000.0000.000
28A56GLY0-0.024-0.13834.4840.0050.0050.0000.0000.0000.000
29A57ILE00.0910.00434.7400.0040.0040.0000.0000.0000.000
30A57ILE0-0.0720.11533.9910.0000.0000.0000.0000.0000.000
31A58MET00.059-0.09730.990-0.009-0.0090.0000.0000.0000.000
32A58MET0-0.0870.10928.7470.0010.0010.0000.0000.0000.000
33A59ALA00.112-0.11328.4470.0050.0050.0000.0000.0000.000
34A59ALA0-0.0170.10427.958-0.002-0.0020.0000.0000.0000.000
35A60PHE00.115-0.01629.9660.0020.0020.0000.0000.0000.000
36A60PHE0-0.1140.08131.2030.0000.0000.0000.0000.0000.000
37A61ASN00.038-0.05228.7830.0020.0020.0000.0000.0000.000
38A61ASN0-0.1720.02528.2530.0040.0040.0000.0000.0000.000
39A62GLN00.217-0.25924.892-0.006-0.0060.0000.0000.0000.000
40A62GLN0-0.0020.15822.939-0.003-0.0030.0000.0000.0000.000
41A63SER0-0.1580.01622.5260.0170.0170.0000.0000.0000.000
42A63SER0-0.0390.07021.9700.0020.0020.0000.0000.0000.000
43A64TYR00.064-0.12018.267-0.006-0.0060.0000.0000.0000.000
44A64TYR0-0.0670.10117.2070.0060.0060.0000.0000.0000.000
45A65LEU00.141-0.07715.9930.0070.0070.0000.0000.0000.000
46A65LEU0-0.0860.09713.745-0.010-0.0100.0000.0000.0000.000
47A66ASN00.103-0.07112.3410.0170.0170.0000.0000.0000.000
48A66ASN0-0.1250.04611.7190.0270.0270.0000.0000.0000.000
49A67LEU00.046-0.1859.356-0.067-0.0670.0000.0000.0000.000
50A67LEU0-0.0020.1398.984-0.002-0.0020.0000.0000.0000.000
51A68PRO0-0.040-0.0864.3290.2750.359-0.001-0.033-0.0500.000
52A69LYS00.1450.0555.027-0.262-0.138-0.002-0.012-0.1110.000
53A69LYS10.7651.0183.693-1.546-1.3970.001-0.030-0.1200.000
54A70ASP0-0.025-0.1412.862-2.479-1.0610.481-0.924-0.976-0.009
55A70ASP-1-0.914-0.8072.5500.1340.7850.332-0.516-0.4670.002
56A71SER00.078-0.0903.189-1.394-0.0890.101-0.696-0.710-0.006
57A71SER0-0.0460.0762.560-1.102-0.4770.275-0.461-0.440-0.001
58A72GLN00.134-0.0574.6540.3540.339-0.002-0.0130.0290.000
59A72GLN0-0.0910.0976.7790.1030.1030.0000.0000.0000.000
60A73LEU00.105-0.0948.255-0.138-0.1380.0000.0000.0000.000
61A73LEU0-0.0650.1056.9520.0200.0200.0000.0000.0000.000
62A74SER00.145-0.0429.8580.1100.1100.0000.0000.0000.000
63A74SER0-0.0300.09613.5300.0290.0290.0000.0000.0000.000
64A75TYR00.055-0.09413.500-0.010-0.0100.0000.0000.0000.000
65A75TYR0-0.0790.08516.5120.0260.0260.0000.0000.0000.000
66A76LEU00.062-0.09216.4010.0370.0370.0000.0000.0000.000
67A76LEU0-0.0650.11417.4670.0000.0000.0000.0000.0000.000
68A77ASP00.128-0.12414.2180.0690.0690.0000.0000.0000.000
69A77ASP-1-0.989-0.82213.149-0.703-0.7030.0000.0000.0000.000
70A78LEU00.048-0.11915.1920.0230.0230.0000.0000.0000.000
71A78LEU0-0.0820.11313.911-0.004-0.0040.0000.0000.0000.000
72A79GLY0-0.020-0.11115.8100.0430.0430.0000.0000.0000.000
73A80ASN00.0970.03118.4640.0450.0450.0000.0000.0000.000
74A80ASN0-0.0680.07918.1300.0230.0230.0000.0000.0000.000
75A81LYS00.053-0.08117.0310.0330.0330.0000.0000.0000.000
76A81LYS10.8631.04211.9760.5580.5580.0000.0000.0000.000
77A82VAL00.098-0.07618.3700.0260.0260.0000.0000.0000.000
78A82VAL0-0.1010.09219.0400.0010.0010.0000.0000.0000.000
79A83LYS00.135-0.08720.9170.0260.0260.0000.0000.0000.000
80A83LYS10.7330.97522.6060.2420.2420.0000.0000.0000.000
81A84ALA00.095-0.08621.4840.0260.0260.0000.0000.0000.000
82A84ALA0-0.0990.09820.691-0.006-0.0060.0000.0000.0000.000
83A85LEU00.084-0.08221.9020.0170.0170.0000.0000.0000.000
84A85LEU0-0.0960.08219.455-0.002-0.0020.0000.0000.0000.000
85A86LEU00.070-0.07423.2660.0180.0180.0000.0000.0000.000
86A86LEU0-0.1230.06225.4460.0020.0020.0000.0000.0000.000
87A87TYR00.122-0.06726.1960.0160.0160.0000.0000.0000.000
88A87TYR0-0.1170.07226.5720.0020.0020.0000.0000.0000.000
89A88ASP00.090-0.11925.4350.0150.0150.0000.0000.0000.000
90A88ASP-1-1.019-0.85624.030-0.158-0.1580.0000.0000.0000.000
91A89GLU00.104-0.12826.4600.0110.0110.0000.0000.0000.000
92A89GLU-1-0.860-0.79524.777-0.098-0.0980.0000.0000.0000.000
93A90ARG0-0.122-0.10327.9600.0110.0110.0000.0000.0000.000
94A90ARG10.7090.99128.1810.0810.0810.0000.0000.0000.000
95A91GLY00.078-0.06730.1350.0060.0060.0000.0000.0000.000
96A92VAL00.044-0.03230.3720.0050.0050.0000.0000.0000.000
97A92VAL0-0.1400.10029.6130.0000.0000.0000.0000.0000.000
98A93THR00.043-0.07429.737-0.011-0.0110.0000.0000.0000.000
99A93THR00.0050.07732.7590.0000.0000.0000.0000.0000.000
100A94PRO00.093-0.08128.8710.0020.0020.0000.0000.0000.000
101A95GLU00.112-0.02230.890-0.002-0.0020.0000.0000.0000.000
102A95GLU-1-0.918-0.78635.333-0.094-0.0940.0000.0000.0000.000
103A96LYS00.078-0.10733.5200.0070.0070.0000.0000.0000.000
104A96LYS10.8391.05733.1120.0800.0800.0000.0000.0000.000
105A97ILE00.119-0.09030.5160.0080.0080.0000.0000.0000.000
106A97ILE0-0.0720.10827.6870.0000.0000.0000.0000.0000.000
107A98ARG00.031-0.12931.9410.0000.0000.0000.0000.0000.000
108A98ARG10.8251.02633.0090.1150.1150.0000.0000.0000.000
109A99ASN00.049-0.05334.0950.0010.0010.0000.0000.0000.000
110A99ASN0-0.1130.06137.7060.0020.0020.0000.0000.0000.000
111A100ALA00.091-0.09834.1700.0080.0080.0000.0000.0000.000
112A100ALA0-0.0830.10233.566-0.001-0.0010.0000.0000.0000.000
113A101LYS00.099-0.05335.649-0.002-0.0020.0000.0000.0000.000
114A101LYS10.8391.04837.0880.0720.0720.0000.0000.0000.000
115A102SER0-0.009-0.11933.404-0.001-0.0010.0000.0000.0000.000
116A102SER0-0.0390.05732.6790.0030.0030.0000.0000.0000.000
117A103ALA00.118-0.05930.0370.0070.0070.0000.0000.0000.000
118A103ALA0-0.0710.10429.193-0.001-0.0010.0000.0000.0000.000
119A104VAL00.021-0.13126.648-0.007-0.0070.0000.0000.0000.000
120A104VAL0-0.0600.12426.4360.0010.0010.0000.0000.0000.000
121A105TYR00.110-0.03222.8960.0110.0110.0000.0000.0000.000
122A105TYR0-0.0400.08118.725-0.013-0.0130.0000.0000.0000.000
123A106THR00.009-0.07723.373-0.014-0.0140.0000.0000.0000.000
124A106THR0-0.0720.06624.083-0.001-0.0010.0000.0000.0000.000
125A107ILE00.107-0.10819.1590.0100.0100.0000.0000.0000.000
126A107ILE0-0.0690.10117.123-0.006-0.0060.0000.0000.0000.000
127A108THR00.050-0.07219.6370.0050.0050.0000.0000.0000.000
128A108THR0-0.0700.06820.6840.0090.0090.0000.0000.0000.000
129A109TRP00.158-0.05717.122-0.007-0.0070.0000.0000.0000.000
130A109TRP0-0.1010.10214.178-0.021-0.0210.0000.0000.0000.000
131A110LYS00.046-0.15416.6000.0170.0170.0000.0000.0000.000
132A110LYS10.7661.00212.2690.0890.0890.0000.0000.0000.000
133A111ASP0-0.014-0.12117.8630.0240.0240.0000.0000.0000.000
134A111ASP-1-0.825-0.74719.826-0.095-0.0950.0000.0000.0000.000
135A112GLY0-0.026-0.10220.6790.0090.0090.0000.0000.0000.000
136A113SER00.0370.00822.1350.0040.0040.0000.0000.0000.000
137A113SER0-0.0350.05521.190-0.008-0.0080.0000.0000.0000.000
138A114LYS00.020-0.14021.907-0.008-0.0080.0000.0000.0000.000
139A114LYS10.8361.03523.5360.0830.0830.0000.0000.0000.000
140A115LYS00.084-0.07421.5950.0090.0090.0000.0000.0000.000
141A115LYS10.8221.05819.3040.2420.2420.0000.0000.0000.000
142A116GLU00.113-0.11122.583-0.012-0.0120.0000.0000.0000.000
143A116GLU-1-1.008-0.83226.373-0.109-0.1090.0000.0000.0000.000
144A117VAL00.040-0.13722.5940.0040.0040.0000.0000.0000.000
145A117VAL0-0.0990.09720.570-0.005-0.0050.0000.0000.0000.000
146A118ASP00.180-0.08024.0250.0020.0020.0000.0000.0000.000
147A118ASP-1-0.938-0.81127.849-0.132-0.1320.0000.0000.0000.000
148A119LEU00.064-0.11025.885-0.012-0.0120.0000.0000.0000.000
149A119LEU0-0.0910.08023.294-0.001-0.0010.0000.0000.0000.000
150A120LYS00.033-0.10526.751-0.005-0.0050.0000.0000.0000.000
151A120LYS10.7411.00031.2840.1050.1050.0000.0000.0000.000
152A121LYS00.005-0.08428.4460.0080.0080.0000.0000.0000.000
153A121LYS10.7691.00528.4270.1290.1290.0000.0000.0000.000
154A122ASP00.205-0.04325.634-0.011-0.0110.0000.0000.0000.000
155A122ASP-1-0.953-0.81324.478-0.223-0.2230.0000.0000.0000.000
156A123SER0-0.005-0.13324.9330.0130.0130.0000.0000.0000.000
157A123SER00.0000.08626.7600.0020.0020.0000.0000.0000.000
158A124TYR00.034-0.08322.831-0.012-0.0120.0000.0000.0000.000
159A124TYR0-0.0490.09719.7150.0080.0080.0000.0000.0000.000
160A125THR00.003-0.06121.1990.0220.0220.0000.0000.0000.000
161A125THR0-0.0180.06319.051-0.005-0.0050.0000.0000.0000.000
162A126ALA00.158-0.09918.269-0.024-0.0240.0000.0000.0000.000
163A126ALA0-0.0580.12418.6630.0040.0040.0000.0000.0000.000
164A127ASN00.039-0.06916.626-0.049-0.0490.0000.0000.0000.000
165A127ASN0-0.1480.03217.9250.0080.0080.0000.0000.0000.000
166A128LEU00.101-0.12212.7780.0160.0160.0000.0000.0000.000
167A128LEU0-0.0400.12111.255-0.011-0.0110.0000.0000.0000.000
168A129PHE00.045-0.07412.1460.0710.0710.0000.0000.0000.000
169A129PHE0-0.1110.05111.3210.0020.0020.0000.0000.0000.000
170A130ASP00.101-0.1029.580-0.150-0.1500.0000.0000.0000.000
171A130ASP-1-0.869-0.7629.131-0.369-0.3690.0000.0000.0000.000
172A131SER00.083-0.1167.3230.1780.1780.0000.0000.0000.000
173A131SER0-0.0900.0706.594-0.107-0.1070.0000.0000.0000.000
174A132ASN00.068-0.0988.6020.0660.0660.0000.0000.0000.000
175A132ASN0-0.1200.0806.719-0.041-0.0410.0000.0000.0000.000
176A133SER00.047-0.0959.7410.1010.1010.0000.0000.0000.000
177A133SER0-0.1040.05212.6640.0160.0160.0000.0000.0000.000
178A134ILE00.045-0.11912.1640.0520.0520.0000.0000.0000.000
179A134ILE0-0.0710.11912.272-0.007-0.0070.0000.0000.0000.000
180A135LYS00.095-0.07413.9550.0240.0240.0000.0000.0000.000
181A135LYS10.8481.05917.5380.0330.0330.0000.0000.0000.000
182A136GLN00.084-0.10516.7970.0110.0110.0000.0000.0000.000
183A136GLN0-0.1410.05720.0990.0130.0130.0000.0000.0000.000
184A137ILE00.055-0.10018.892-0.009-0.0090.0000.0000.0000.000
185A137ILE0-0.0990.08815.729-0.007-0.0070.0000.0000.0000.000
186A138ASP00.137-0.06820.0470.0060.0060.0000.0000.0000.000
187A138ASP-1-0.943-0.78024.193-0.091-0.0910.0000.0000.0000.000
188A139ILE00.152-0.10423.803-0.007-0.0070.0000.0000.0000.000
189A139ILE0-0.1240.09921.523-0.002-0.0020.0000.0000.0000.000
190A140ASN00.084-0.06925.1420.0110.0110.0000.0000.0000.000
191A140ASN0-0.1400.05128.6140.0020.0020.0000.0000.0000.000
192A141VAL00.120-0.10828.785-0.005-0.0050.0000.0000.0000.000
193A141VAL0-0.0810.12128.739-0.001-0.0010.0000.0000.0000.000
194A142LYS00.123-0.05931.2300.0060.0060.0000.0000.0000.000
195A142LYS10.8021.04033.1200.0790.0790.0000.0000.0000.000
196A143THR00.105-0.08334.956-0.004-0.0040.0000.0000.0000.000
197A143THR0-0.0500.04936.394-0.001-0.0010.0000.0000.0000.000
198A144LYS0-0.060-0.07437.1200.0030.0030.0000.0000.0000.000
199A144LYS10.9810.97638.5980.0600.0600.0000.0000.0000.000