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: GY481

Calculation Name: 2ES9-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ES9

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZRJ2

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 OptAll
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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -737645.55816
FMO2-HF: Nuclear repulsion 698909.53769
FMO2-HF: Total energy -38736.02047
FMO2-MP2: Total energy -38848.83451


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:11:THR)


Summations of interaction energy for fragment #1(A:11:THR)
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.
-5.972-8.71811.876-3.229-5.895-0.05
Interaction energy analysis for fragmet #1(A:11:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.125 / q_NPA : 0.076
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].
4A12ALA0-0.0510.1224.5490.0020.169-0.001-0.074-0.0920.000
5A13ILE00.054-0.0983.7110.7691.944-0.003-0.587-0.5850.002
6A13ILE0-0.0500.0994.499-0.172-0.089-0.001-0.016-0.0650.000
7A14GLU00.069-0.1273.3380.9951.0770.0170.148-0.2460.000
8A14GLU-1-0.916-0.8011.875-7.792-11.76411.541-4.420-3.148-0.045
9A15LYS00.105-0.0974.1410.3400.650-0.001-0.129-0.1780.000
10A15LYS10.7581.0304.835-2.338-2.293-0.001-0.016-0.0280.000
11A16ALA00.079-0.1186.0380.1490.1490.0000.0000.0000.000
12A16ALA0-0.0650.0968.048-0.059-0.0590.0000.0000.0000.000
13A17LEU00.056-0.1187.7520.1840.1840.0000.0000.0000.000
14A17LEU0-0.0880.0927.231-0.001-0.0010.0000.0000.0000.000
15A18ASP00.103-0.1028.032-0.099-0.0990.0000.0000.0000.000
16A18ASP-1-0.850-0.7737.1821.7281.7280.0000.0000.0000.000
17A19PHE0-0.034-0.0969.7000.0070.0070.0000.0000.0000.000
18A19PHE0-0.0550.07210.6910.0250.0250.0000.0000.0000.000
19A20ILE00.026-0.10912.0200.0160.0160.0000.0000.0000.000
20A20ILE0-0.0870.10212.646-0.017-0.0170.0000.0000.0000.000
21A21GLY00.063-0.08612.607-0.014-0.0140.0000.0000.0000.000
22A22GLY0-0.034-0.00914.1280.0110.0110.0000.0000.0000.000
23A23MET00.0620.01815.9100.0170.0170.0000.0000.0000.000
24A23MET0-0.1720.06616.418-0.016-0.0160.0000.0000.0000.000
25A24ASN00.149-0.02818.5410.0090.0090.0000.0000.0000.000
26A24ASN0-0.1400.03323.148-0.002-0.0020.0000.0000.0000.000
27A25THR0-0.004-0.16219.009-0.028-0.0280.0000.0000.0000.000
28A25THR0-0.0100.11816.916-0.002-0.0020.0000.0000.0000.000
29A26SER00.107-0.05620.144-0.029-0.0290.0000.0000.0000.000
30A26SER0-0.0140.09522.5390.0050.0050.0000.0000.0000.000
31A27ALA00.077-0.10023.647-0.010-0.0100.0000.0000.0000.000
32A27ALA0-0.1030.11124.9070.0020.0020.0000.0000.0000.000
33A28SER0-0.024-0.09624.726-0.011-0.0110.0000.0000.0000.000
34A28SER0-0.0110.06728.3350.0020.0020.0000.0000.0000.000
35A29VAL00.062-0.10226.755-0.017-0.0170.0000.0000.0000.000
36A29VAL0-0.1130.10128.142-0.001-0.0010.0000.0000.0000.000
37A30PRO00.035-0.08622.2640.0150.0150.0000.0000.0000.000
38A31HIS00.0780.00924.326-0.011-0.0110.0000.0000.0000.000
39A31HIS0-0.0480.12425.0780.0110.0110.0000.0000.0000.000
40A32SER00.102-0.07124.661-0.009-0.0090.0000.0000.0000.000
41A32SER0-0.0110.06527.8590.0030.0030.0000.0000.0000.000
42A33MET00.025-0.09324.033-0.018-0.0180.0000.0000.0000.000
43A33MET0-0.0620.10923.4660.0040.0040.0000.0000.0000.000
44A34ASP00.108-0.07020.4960.0030.0030.0000.0000.0000.000
45A34ASP-1-0.850-0.80820.8400.0530.0530.0000.0000.0000.000
46A35GLU00.162-0.06020.019-0.017-0.0170.0000.0000.0000.000
47A35GLU-1-0.918-0.81322.957-0.097-0.0970.0000.0000.0000.000
48A36SER0-0.021-0.12821.024-0.035-0.0350.0000.0000.0000.000
49A36SER0-0.0650.05123.020-0.001-0.0010.0000.0000.0000.000
50A37THR00.008-0.09418.689-0.028-0.0280.0000.0000.0000.000
51A37THR0-0.0440.06116.5680.0150.0150.0000.0000.0000.000
52A38ALA00.121-0.07316.026-0.006-0.0060.0000.0000.0000.000
53A38ALA0-0.0500.10117.201-0.003-0.0030.0000.0000.0000.000
54A39LYS00.029-0.10916.244-0.069-0.0690.0000.0000.0000.000
55A39LYS10.7030.96920.3310.1260.1260.0000.0000.0000.000
56A40GLY0-0.003-0.10417.546-0.041-0.0410.0000.0000.0000.000
57A41ILE00.1140.03913.336-0.029-0.0290.0000.0000.0000.000
58A41ILE0-0.0990.08711.2270.0070.0070.0000.0000.0000.000
59A42LEU00.062-0.09612.714-0.112-0.1120.0000.0000.0000.000
60A42LEU0-0.1090.08412.9830.0020.0020.0000.0000.0000.000
61A43LYS00.145-0.05814.035-0.109-0.1090.0000.0000.0000.000
62A43LYS10.6920.94617.8060.2670.2670.0000.0000.0000.000
63A44TYR00.073-0.08414.562-0.051-0.0510.0000.0000.0000.000
64A44TYR0-0.0540.08812.3380.0270.0270.0000.0000.0000.000
65A45LEU00.051-0.10910.4190.0770.0770.0000.0000.0000.000
66A45LEU0-0.0690.1137.8340.0060.0060.0000.0000.0000.000
67A46HIS00.127-0.06611.378-0.143-0.1430.0000.0000.0000.000
68A46HIS0-0.0860.07914.438-0.045-0.0450.0000.0000.0000.000
69A47ASP00.053-0.10613.816-0.026-0.0260.0000.0000.0000.000
70A47ASP-1-0.918-0.82215.874-0.275-0.2750.0000.0000.0000.000
71A48LEU0-0.026-0.12611.9170.0760.0760.0000.0000.0000.000
72A48LEU0-0.0880.10110.3520.0050.0050.0000.0000.0000.000
73A49GLY00.018-0.09112.074-0.046-0.0460.0000.0000.0000.000
74A50VAL0-0.021-0.0208.3550.0210.0210.0000.0000.0000.000
75A50VAL0-0.0770.1006.198-0.106-0.1060.0000.0000.0000.000
76A51PRO00.040-0.0999.171-0.119-0.1190.0000.0000.0000.000
77A52VAL00.054-0.01610.208-0.274-0.2740.0000.0000.0000.000
78A52VAL0-0.0830.1078.6800.0090.0090.0000.0000.0000.000
79A53SER00.046-0.09311.0140.2090.2090.0000.0000.0000.000
80A53SER0-0.0460.05113.244-0.062-0.0620.0000.0000.0000.000
81A54PRO00.004-0.12013.894-0.016-0.0160.0000.0000.0000.000
82A55GLU00.088-0.00116.3220.0450.0450.0000.0000.0000.000
83A55GLU-1-0.846-0.75414.914-0.740-0.7400.0000.0000.0000.000
84A56VAL00.053-0.11011.4320.1050.1050.0000.0000.0000.000
85A56VAL0-0.0680.1109.316-0.040-0.0400.0000.0000.0000.000
86A57VAL00.053-0.09612.240-0.011-0.0110.0000.0000.0000.000
87A57VAL0-0.1000.07513.2700.0150.0150.0000.0000.0000.000
88A58VAL00.094-0.08613.9120.0710.0710.0000.0000.0000.000
89A58VAL0-0.1160.07717.5440.0070.0070.0000.0000.0000.000
90A59ALA00.177-0.07714.3410.0940.0940.0000.0000.0000.000
91A59ALA0-0.0980.10913.433-0.021-0.0210.0000.0000.0000.000
92A60ARG00.057-0.10911.9400.0590.0590.0000.0000.0000.000
93A60ARG10.6580.9667.409-0.155-0.1550.0000.0000.0000.000
94A61GLY00.010-0.11912.9520.0930.0930.0000.0000.0000.000
95A62GLU00.063-0.01516.4250.0630.0630.0000.0000.0000.000
96A62GLU-1-1.002-0.86817.671-0.287-0.2870.0000.0000.0000.000
97A63GLN00.061-0.09914.4730.0450.0450.0000.0000.0000.000
98A63GLN0-0.1260.07711.093-0.110-0.1100.0000.0000.0000.000
99A64GLU0-0.002-0.14515.4290.0350.0350.0000.0000.0000.000
100A64GLU-1-0.875-0.76612.0630.1320.1320.0000.0000.0000.000
101A65GLY0-0.012-0.09916.3680.0380.0380.0000.0000.0000.000
102A66TRP00.058-0.01718.5630.0330.0330.0000.0000.0000.000
103A66TRP0-0.0890.08113.020-0.037-0.0370.0000.0000.0000.000
104A67ASN00.176-0.03519.738-0.016-0.0160.0000.0000.0000.000
105A67ASN0-0.1890.03923.239-0.015-0.0150.0000.0000.0000.000
106A68PRO00.024-0.09021.969-0.019-0.0190.0000.0000.0000.000
107A69GLU00.1150.01623.311-0.028-0.0280.0000.0000.0000.000
108A69GLU-1-0.900-0.79326.459-0.113-0.1130.0000.0000.0000.000
109A70PHE00.096-0.11621.896-0.015-0.0150.0000.0000.0000.000
110A70PHE0-0.1110.11417.3310.0020.0020.0000.0000.0000.000
111A71THR00.014-0.10118.910-0.012-0.0120.0000.0000.0000.000
112A71THR0-0.0230.09217.721-0.001-0.0010.0000.0000.0000.000
113A72LYS00.151-0.07119.589-0.048-0.0480.0000.0000.0000.000
114A72LYS10.6720.97923.8280.1360.1360.0000.0000.0000.000
115A73LYS0-0.030-0.11122.292-0.027-0.0270.0000.0000.0000.000
116A73LYS10.8131.02322.6680.1090.1090.0000.0000.0000.000
117A74VAL00.104-0.11317.825-0.002-0.0020.0000.0000.0000.000
118A74VAL0-0.0600.11315.778-0.001-0.0010.0000.0000.0000.000
119A75ALA00.112-0.10617.928-0.048-0.0480.0000.0000.0000.000
120A75ALA0-0.0500.13218.6710.0010.0010.0000.0000.0000.000
121A76GLY0-0.005-0.09718.958-0.027-0.0270.0000.0000.0000.000
122A77TRP0-0.019-0.03220.1600.0060.0060.0000.0000.0000.000
123A77TRP0-0.0480.09218.9000.0110.0110.0000.0000.0000.000
124A78ALA00.136-0.07916.4390.0200.0200.0000.0000.0000.000
125A78ALA0-0.0470.12515.658-0.009-0.0090.0000.0000.0000.000
126A79GLU00.092-0.11117.362-0.056-0.0560.0000.0000.0000.000
127A79GLU-1-1.044-0.86520.793-0.277-0.2770.0000.0000.0000.000
128A80LYS00.121-0.04420.035-0.012-0.0120.0000.0000.0000.000
129A80LYS10.8391.02922.3460.2000.2000.0000.0000.0000.000
130A81VAL00.053-0.09017.9080.0320.0320.0000.0000.0000.000
131A81VAL0-0.1130.09716.0650.0080.0080.0000.0000.0000.000
132A82ALA00.162-0.07617.4460.0080.0080.0000.0000.0000.000
133A82ALA0-0.0640.11316.672-0.010-0.0100.0000.0000.0000.000
134A83SER0-0.092-0.12718.142-0.013-0.0130.0000.0000.0000.000
135A83SER0-0.1000.04322.6470.0210.0210.0000.0000.0000.000
136A84GLY00.004-0.09220.7780.0230.0230.0000.0000.0000.000
137A85ASN00.0430.01722.0800.0230.0230.0000.0000.0000.000
138A85ASN0-0.1190.04324.8350.0210.0210.0000.0000.0000.000
139A86ARG00.117-0.05623.237-0.017-0.0170.0000.0000.0000.000
140A86ARG10.8591.03825.7680.1370.1370.0000.0000.0000.000
141A87ILE00.055-0.12523.3250.0060.0060.0000.0000.0000.000
142A87ILE0-0.0350.13821.1950.0020.0020.0000.0000.0000.000
143A88LEU00.106-0.11224.6750.0030.0030.0000.0000.0000.000
144A88LEU0-0.0950.11027.8120.0000.0000.0000.0000.0000.000
145A89ILE00.028-0.13423.350-0.006-0.0060.0000.0000.0000.000
146A89ILE0-0.0450.14921.3410.0000.0000.0000.0000.0000.000
147A90LYS00.099-0.06724.5660.0060.0060.0000.0000.0000.000
148A90LYS10.8211.02727.3460.0090.0090.0000.0000.0000.000
149A91ASN00.043-0.08125.5820.0010.0010.0000.0000.0000.000
150A91ASN0-0.1350.03226.281-0.006-0.0060.0000.0000.0000.000
151A92PRO00.061-0.10722.2630.0070.0070.0000.0000.0000.000
152A93GLU00.0730.01021.3320.0030.0030.0000.0000.0000.000
153A93GLU-1-0.847-0.77824.7650.0230.0230.0000.0000.0000.000
154A94TYR00.056-0.09021.8280.0280.0280.0000.0000.0000.000
155A94TYR0-0.0730.07721.715-0.009-0.0090.0000.0000.0000.000
156A95PHE00.067-0.07417.7390.0450.0450.0000.0000.0000.000
157A95PHE0-0.0810.10213.380-0.008-0.0080.0000.0000.0000.000
158A96SER00.080-0.05918.428-0.022-0.0220.0000.0000.0000.000
159A96SER0-0.0480.05218.1640.0170.0170.0000.0000.0000.000
160A97THR00.082-0.08116.7470.0190.0190.0000.0000.0000.000
161A97THR0-0.0100.08617.995-0.003-0.0030.0000.0000.0000.000
162A98TYR00.080-0.04815.7430.0050.0050.0000.0000.0000.000
163A98TYR0-0.0780.07714.1400.0220.0220.0000.0000.0000.000
164A99MET00.089-0.09312.6720.1380.1380.0000.0000.0000.000
165A99MET0-0.1100.08513.260-0.018-0.0180.0000.0000.0000.000
166A100GLN00.120-0.07611.7200.0250.0250.0000.0000.0000.000
167A100GLN0-0.1510.05314.611-0.028-0.0280.0000.0000.0000.000
168A101GLU00.053-0.11412.072-0.060-0.0600.0000.0000.0000.000
169A101GLU-1-0.908-0.78914.1160.2040.2040.0000.0000.0000.000
170A102GLN00.183-0.03910.087-0.030-0.0300.0000.0000.0000.000
171A102GLN0-0.0930.0778.4400.2140.2140.0000.0000.0000.000
172A103LEU00.089-0.0897.4110.4060.4060.0000.0000.0000.000
173A103LEU0-0.1070.0797.199-0.057-0.0570.0000.0000.0000.000
174A104LYS00.155-0.0787.572-0.224-0.2240.0000.0000.0000.000
175A104LYS10.7210.98211.647-0.202-0.2020.0000.0000.0000.000
176A105GLU00.049-0.1129.212-0.233-0.2330.0000.0000.0000.000
177A105GLU-1-1.042-0.8628.7851.1481.1480.0000.0000.0000.000
178A106LEU00.054-0.1054.499-0.221-0.168-0.001-0.005-0.0460.000
179A106LEU0-0.0860.0963.215-0.2790.0860.076-0.128-0.3130.001
180A107VAL00.123-0.0804.803-0.395-0.288-0.002-0.005-0.1000.000
181A107VAL0-0.0900.0906.871-0.073-0.0730.0000.0000.0000.000
182A108LEU00.035-0.1006.899-0.204-0.2040.0000.0000.0000.000
183A108LEU0-0.1140.07510.3020.0030.0030.0000.0000.0000.000
184A109GLU00.058-0.0947.627-0.277-0.2770.0000.0000.0000.000
185A109GLU-1-1.020-0.8596.5461.8631.8630.0000.0000.0000.000
186A110HIS0-0.151-0.1696.2070.1960.1960.0000.0000.0000.000
187A110HIS00.0210.0073.030-0.277-1.4380.2522.003-1.094-0.008