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: J2JL9

Calculation Name: 2DX5-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2DX5

Chain ID: A

ChEMBL ID:

UniProt ID: P0CH28

Base Structure: X-ray

Registration Date: 2025-07-10

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -834489.382214
FMO2-HF: Nuclear repulsion 792130.320785
FMO2-HF: Total energy -42359.06143
FMO2-MP2: Total energy -42481.863362


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
-7.371-3.7560.304-1.873-2.0490.002
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.011
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].
4A11LEU0-0.0880.0872.714-0.3280.6010.327-0.433-0.8240.001
5A12GLU00.109-0.0693.826-1.1660.693-0.022-1.043-0.794-0.001
6A12GLU-1-0.937-0.8486.240-2.695-2.6950.0000.0000.0000.000
7A13ILE00.140-0.0706.8270.3180.3180.0000.0000.0000.000
8A13ILE0-0.0790.0959.6410.0070.0070.0000.0000.0000.000
9A14ASN0-0.001-0.0749.982-0.062-0.0620.0000.0000.0000.000
10A14ASN0-0.1100.04413.2910.0450.0450.0000.0000.0000.000
11A15GLU00.148-0.1028.9170.0810.0810.0000.0000.0000.000
12A15GLU-1-0.805-0.7216.653-0.918-0.9180.0000.0000.0000.000
13A16THR0-0.074-0.1088.5390.0700.0700.0000.0000.0000.000
14A16THR00.0010.08510.241-0.022-0.0220.0000.0000.0000.000
15A17LEU00.172-0.0718.331-0.103-0.1030.0000.0000.0000.000
16A17LEU0-0.1140.0856.6230.0990.0990.0000.0000.0000.000
17A18VAL00.065-0.1038.991-0.104-0.1040.0000.0000.0000.000
18A18VAL0-0.1060.11311.925-0.005-0.0050.0000.0000.0000.000
19A19ILE00.007-0.14811.760-0.019-0.0190.0000.0000.0000.000
20A19ILE0-0.0160.11113.852-0.018-0.0180.0000.0000.0000.000
21A20GLN00.150-0.07510.8090.0480.0480.0000.0000.0000.000
22A20GLN0-0.0920.1047.713-0.206-0.2060.0000.0000.0000.000
23A21GLN00.082-0.09411.646-0.065-0.0650.0000.0000.0000.000
24A21GLN0-0.0910.10815.455-0.011-0.0110.0000.0000.0000.000
25A22ARG00.031-0.09113.9240.0450.0450.0000.0000.0000.000
26A22ARG10.7790.98214.050-0.490-0.4900.0000.0000.0000.000
27A23GLY00.041-0.08515.735-0.053-0.0530.0000.0000.0000.000
28A24VAL00.0480.00316.732-0.051-0.0510.0000.0000.0000.000
29A24VAL0-0.0730.12015.7860.0020.0020.0000.0000.0000.000
30A25ARG00.134-0.09717.842-0.003-0.0030.0000.0000.0000.000
31A25ARG10.7901.01820.984-0.108-0.1080.0000.0000.0000.000
32A26VAL00.062-0.11017.6470.0230.0230.0000.0000.0000.000
33A26VAL0-0.0330.13915.517-0.001-0.0010.0000.0000.0000.000
34A27TYR00.047-0.09019.012-0.020-0.0200.0000.0000.0000.000
35A27TYR0-0.1260.04422.3780.0140.0140.0000.0000.0000.000
36A28ASP00.131-0.02121.8270.0010.0010.0000.0000.0000.000
37A28ASP-1-0.962-0.85121.861-0.109-0.1090.0000.0000.0000.000
38A29GLY00.068-0.07623.3460.0040.0040.0000.0000.0000.000
39A30GLU00.035-0.04926.5400.0100.0100.0000.0000.0000.000
40A30GLU-1-0.820-0.76729.7320.0100.0100.0000.0000.0000.000
41A31GLU0-0.024-0.14026.387-0.007-0.0070.0000.0000.0000.000
42A31GLU-1-0.865-0.77924.631-0.050-0.0500.0000.0000.0000.000
43A32LYS00.146-0.02827.8570.0120.0120.0000.0000.0000.000
44A32LYS10.8891.04330.4360.0090.0090.0000.0000.0000.000
45A33ILE0-0.061-0.14027.1300.0010.0010.0000.0000.0000.000
46A33ILE0-0.0540.08226.6380.0010.0010.0000.0000.0000.000
47A34LYS00.117-0.08624.463-0.001-0.0010.0000.0000.0000.000
48A34LYS10.7360.96823.1500.0700.0700.0000.0000.0000.000
49A35PHE00.1220.01521.582-0.023-0.0230.0000.0000.0000.000
50A35PHE0-0.1530.00121.2610.0070.0070.0000.0000.0000.000
51A36ASP00.122-0.12517.659-0.003-0.0030.0000.0000.0000.000
52A36ASP-1-0.919-0.76716.736-0.064-0.0640.0000.0000.0000.000
53A37ALA00.101-0.09018.0850.0200.0200.0000.0000.0000.000
54A37ALA0-0.1240.07519.1990.0010.0010.0000.0000.0000.000
55A38GLY00.004-0.11514.409-0.031-0.0310.0000.0000.0000.000
56A39THR0-0.0330.01712.425-0.052-0.0520.0000.0000.0000.000
57A39THR0-0.0760.05110.305-0.026-0.0260.0000.0000.0000.000
58A40LEU00.213-0.08110.9110.1420.1420.0000.0000.0000.000
59A40LEU0-0.1180.10012.086-0.029-0.0290.0000.0000.0000.000
60A41LEU00.070-0.1138.350-0.120-0.1200.0000.0000.0000.000
61A41LEU0-0.1870.0715.4440.3230.3230.0000.0000.0000.000
62A42LEU00.164-0.0889.382-0.048-0.0480.0000.0000.0000.000
63A42LEU0-0.1000.10212.733-0.012-0.0120.0000.0000.0000.000
64A43SER0-0.038-0.0878.8800.2870.2870.0000.0000.0000.000
65A43SER0-0.0690.0098.216-0.047-0.0470.0000.0000.0000.000
66A44THR00.086-0.08410.221-0.085-0.0850.0000.0000.0000.000
67A44THR0-0.0710.07111.7360.0310.0310.0000.0000.0000.000
68A45HIS00.096-0.07110.974-0.010-0.0100.0000.0000.0000.000
69A45HIS0-0.0610.09810.556-0.001-0.0010.0000.0000.0000.000
70A46ARG00.100-0.0648.957-0.021-0.0210.0000.0000.0000.000
71A46ARG10.7110.9603.8013.2833.597-0.001-0.197-0.1170.001
72A47LEU00.153-0.06510.3980.2240.2240.0000.0000.0000.000
73A47LEU0-0.1260.06912.531-0.002-0.0020.0000.0000.0000.000
74A48ILE00.070-0.0716.919-0.410-0.4100.0000.0000.0000.000
75A48ILE0-0.0890.0704.7010.0970.176-0.001-0.014-0.0640.000
76A49TRP00.082-0.0958.0320.3320.3320.0000.0000.0000.000
77A49TRP0-0.0880.08610.3870.0480.0480.0000.0000.0000.000
78A50ARG00.093-0.0508.085-0.418-0.4180.0000.0000.0000.000
79A50ARG10.8721.0343.659-4.979-4.6250.004-0.175-0.1830.001
80A51ASP00.056-0.1178.9360.1550.1550.0000.0000.0000.000
81A51ASP-1-0.819-0.76412.027-0.030-0.0300.0000.0000.0000.000
82A52GLN00.176-0.06812.1570.0930.0930.0000.0000.0000.000
83A52GLN0-0.1410.05316.342-0.011-0.0110.0000.0000.0000.000
84A53LYS0-0.055-0.12314.8990.0440.0440.0000.0000.0000.000
85A53LYS10.7670.98715.9360.0530.0530.0000.0000.0000.000
86A54ASN00.137-0.03111.745-0.066-0.0660.0000.0000.0000.000
87A54ASN0-0.0810.05511.644-0.029-0.0290.0000.0000.0000.000
88A55ASN00.095-0.04211.540-0.095-0.0950.0000.0000.0000.000
89A55ASN0-0.0960.03615.4880.0190.0190.0000.0000.0000.000
90A56GLU00.134-0.06511.760-0.063-0.0630.0000.0000.0000.000
91A56GLU-1-1.016-0.86612.906-0.247-0.2470.0000.0000.0000.000
92A57CYS00.115-0.1639.275-0.068-0.0680.0000.0000.0000.000
93A57CYS0-0.1460.0708.3720.1480.1480.0000.0000.0000.000
94A58CYS0-0.042-0.0785.514-0.057-0.031-0.002-0.001-0.0230.000
95A58CYS0-0.1720.0784.8150.2690.323-0.001-0.010-0.0440.000
96A59MET00.160-0.0166.939-0.528-0.5280.0000.0000.0000.000
97A59MET0-0.1450.05510.2350.0030.0030.0000.0000.0000.000
98A60ALA00.210-0.0608.271-0.333-0.3330.0000.0000.0000.000
99A60ALA0-0.0940.07611.5540.0430.0430.0000.0000.0000.000
100A61ILE0-0.028-0.1548.5070.1010.1010.0000.0000.0000.000
101A61ILE0-0.0350.1136.417-0.012-0.0120.0000.0000.0000.000
102A62PRO00.009-0.1009.761-0.002-0.0020.0000.0000.0000.000
103A63LEU0-0.002-0.02613.051-0.067-0.0670.0000.0000.0000.000
104A63LEU0-0.0900.11512.8340.0050.0050.0000.0000.0000.000
105A64SER00.177-0.06014.603-0.022-0.0220.0000.0000.0000.000
106A64SER0-0.0180.07214.912-0.012-0.0120.0000.0000.0000.000
107A65GLN00.006-0.11016.8710.0250.0250.0000.0000.0000.000
108A65GLN0-0.0700.09416.382-0.019-0.0190.0000.0000.0000.000
109A66ILE00.077-0.05817.7410.0090.0090.0000.0000.0000.000
110A66ILE0-0.1470.08016.558-0.004-0.0040.0000.0000.0000.000
111A67VAL00.073-0.09219.3910.0120.0120.0000.0000.0000.000
112A67VAL0-0.0940.11123.2140.0020.0020.0000.0000.0000.000
113A68PHE00.130-0.12323.1100.0080.0080.0000.0000.0000.000
114A68PHE0-0.0690.11125.7850.0000.0000.0000.0000.0000.000
115A69ILE0-0.029-0.10222.220-0.015-0.0150.0000.0000.0000.000
116A69ILE0-0.0360.09420.0860.0020.0020.0000.0000.0000.000
117A70GLU00.108-0.09123.5020.0030.0030.0000.0000.0000.000
118A70GLU-1-0.933-0.83126.3090.0030.0030.0000.0000.0000.000
119A71GLU00.087-0.10525.0120.0070.0070.0000.0000.0000.000
120A71GLU-1-0.943-0.83125.7290.1070.1070.0000.0000.0000.000
121A72GLN00.082-0.07027.262-0.009-0.0090.0000.0000.0000.000
122A72GLN0-0.1200.05827.918-0.004-0.0040.0000.0000.0000.000
123A73ALA0-0.050-0.13028.8480.0000.0000.0000.0000.0000.000
124A73ALA00.0440.03030.743-0.001-0.0010.0000.0000.0000.000
125A81LYS00.1150.05524.0630.0060.0060.0000.0000.0000.000
126A81LYS10.7840.99424.319-0.069-0.0690.0000.0000.0000.000
127A82ILE00.118-0.10122.090-0.017-0.0170.0000.0000.0000.000
128A82ILE0-0.1280.10520.0320.0070.0070.0000.0000.0000.000
129A83VAL00.051-0.12221.8820.0040.0040.0000.0000.0000.000
130A83VAL0-0.0360.11824.472-0.001-0.0010.0000.0000.0000.000
131A84VAL00.048-0.10219.7360.0130.0130.0000.0000.0000.000
132A84VAL0-0.0790.09217.9200.0000.0000.0000.0000.0000.000
133A85HIS00.085-0.08021.272-0.018-0.0180.0000.0000.0000.000
134A85HIS0-0.1230.07924.267-0.013-0.0130.0000.0000.0000.000
135A86LEU00.113-0.12718.8260.0070.0070.0000.0000.0000.000
136A86LEU0-0.0750.10017.073-0.005-0.0050.0000.0000.0000.000
137A87HIS0-0.017-0.09219.956-0.006-0.0060.0000.0000.0000.000
138A87HIS00.0290.01621.456-0.016-0.0160.0000.0000.0000.000
139A101SER00.0930.04832.3010.0000.0000.0000.0000.0000.000
140A101SER0-0.0410.04631.724-0.004-0.0040.0000.0000.0000.000
141A102LYS00.027-0.10927.6270.0040.0040.0000.0000.0000.000
142A102LYS10.8941.07126.2450.1500.1500.0000.0000.0000.000
143A103ASN00.023-0.07726.3330.0050.0050.0000.0000.0000.000
144A103ASN0-0.0690.07223.251-0.006-0.0060.0000.0000.0000.000
145A104SER00.076-0.08825.271-0.017-0.0170.0000.0000.0000.000
146A104SER0-0.0100.08626.9110.0060.0060.0000.0000.0000.000
147A105TYR00.018-0.07022.656-0.015-0.0150.0000.0000.0000.000
148A105TYR0-0.0730.05223.4990.0050.0050.0000.0000.0000.000
149A106ILE00.036-0.06319.946-0.007-0.0070.0000.0000.0000.000
150A106ILE0-0.0480.09816.965-0.002-0.0020.0000.0000.0000.000
151A107ARG00.073-0.10521.4180.0050.0050.0000.0000.0000.000
152A107ARG10.6900.98823.532-0.008-0.0080.0000.0000.0000.000
153A108LEU00.067-0.15319.215-0.015-0.0150.0000.0000.0000.000
154A108LEU0-0.0440.12916.8080.0080.0080.0000.0000.0000.000
155A109SER00.080-0.03420.3830.0040.0040.0000.0000.0000.000
156A109SER0-0.0630.02922.893-0.009-0.0090.0000.0000.0000.000
157A110PHE00.016-0.11220.6070.0120.0120.0000.0000.0000.000
158A110PHE0-0.0520.12717.215-0.009-0.0090.0000.0000.0000.000
159A111LYS00.211-0.03721.652-0.014-0.0140.0000.0000.0000.000
160A111LYS10.8021.02322.279-0.174-0.1740.0000.0000.0000.000
161A112GLU00.066-0.11020.920-0.027-0.0270.0000.0000.0000.000
162A112GLU-1-0.946-0.80919.0860.3800.3800.0000.0000.0000.000
163A113HIS00.057-0.10221.0810.0220.0220.0000.0000.0000.000
164A113HIS0-0.0760.10723.026-0.018-0.0180.0000.0000.0000.000
165A114GLY00.089-0.10119.8260.0340.0340.0000.0000.0000.000
166A115GLN00.1400.03220.0270.0280.0280.0000.0000.0000.000
167A115GLN0-0.0770.09022.6160.0180.0180.0000.0000.0000.000
168A116ILE0-0.091-0.13222.4620.0060.0060.0000.0000.0000.000
169A116ILE0-0.0340.11724.886-0.003-0.0030.0000.0000.0000.000
170A117GLU00.088-0.14920.980-0.026-0.0260.0000.0000.0000.000
171A117GLU-1-0.937-0.81920.2940.3080.3080.0000.0000.0000.000
172A118PHE00.094-0.11318.0430.0140.0140.0000.0000.0000.000
173A118PHE0-0.0830.11513.329-0.017-0.0170.0000.0000.0000.000
174A119TYR00.100-0.09518.899-0.002-0.0020.0000.0000.0000.000
175A119TYR0-0.0310.12122.6290.0000.0000.0000.0000.0000.000
176A120ARG00.082-0.08621.606-0.022-0.0220.0000.0000.0000.000
177A120ARG10.7321.00322.200-0.159-0.1590.0000.0000.0000.000
178A121ARG00.079-0.10717.675-0.037-0.0370.0000.0000.0000.000
179A121ARG10.8381.02216.754-0.254-0.2540.0000.0000.0000.000
180A122LEU00.080-0.08317.2210.0110.0110.0000.0000.0000.000
181A122LEU0-0.1080.08516.402-0.002-0.0020.0000.0000.0000.000
182A123SER00.073-0.04018.207-0.033-0.0330.0000.0000.0000.000
183A123SER0-0.0160.06122.892-0.005-0.0050.0000.0000.0000.000
184A124GLU0-0.033-0.10921.162-0.029-0.0290.0000.0000.0000.000
185A124GLU-1-0.858-0.79620.2930.1810.1810.0000.0000.0000.000
186A125GLU00.118-0.08716.640-0.028-0.0280.0000.0000.0000.000
187A125GLU-1-0.998-0.84814.5990.2000.2000.0000.0000.0000.000
188A126MET00.120-0.12817.890-0.037-0.0370.0000.0000.0000.000
189A126MET0-0.1560.09318.3240.0020.0020.0000.0000.0000.000
190A127THR0-0.013-0.08218.774-0.041-0.0410.0000.0000.0000.000
191A127THR0-0.0180.07723.0910.0050.0050.0000.0000.0000.000
192A128GLN00.002-0.10220.952-0.021-0.0210.0000.0000.0000.000
193A128GLN0-0.0310.12620.8450.0090.0090.0000.0000.0000.000
194A129ARG00.094-0.11517.833-0.005-0.0050.0000.0000.0000.000
195A129ARG10.8311.09114.7490.2250.2250.0000.0000.0000.000
196A130ARG0-0.083-0.14318.970-0.033-0.0330.0000.0000.0000.000
197A130ARG10.9180.97120.2430.0880.0880.0000.0000.0000.000