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: K2MY3

Calculation Name: 4DHX-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DHX

Chain ID: B

ChEMBL ID:

UniProt ID: Q9NPA8

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -574170.137703
FMO2-HF: Nuclear repulsion 537837.321681
FMO2-HF: Total energy -36332.816022
FMO2-MP2: Total energy -36438.530965


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(B:9:ASP)


Summations of interaction energy for fragment #1(B:9:ASP)
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.
4.9347.401-0.005-1.181-1.280.001
Interaction energy analysis for fragmet #1(B:9:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.137 / q_NPA : 0.025
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].
4B10ALA0-0.0480.1274.4430.2490.4300.000-0.089-0.0920.000
5B11GLN00.032-0.1073.6500.1001.529-0.004-0.773-0.6520.001
6B11GLN0-0.0770.0763.8700.9081.1900.000-0.119-0.1630.000
7B12MET00.075-0.1163.8661.6551.914-0.001-0.136-0.1210.000
8B12MET0-0.0490.1213.9580.3350.4620.003-0.025-0.1050.000
9B13ARG00.086-0.0805.0051.0101.085-0.002-0.008-0.0650.000
10B13ARG10.8621.0514.357-0.936-0.822-0.001-0.031-0.0820.000
11B14ALA00.085-0.0996.8080.6170.6170.0000.0000.0000.000
12B14ALA0-0.0690.1158.5280.0240.0240.0000.0000.0000.000
13B15ALA00.120-0.0918.4530.4470.4470.0000.0000.0000.000
14B15ALA0-0.0690.1128.906-0.053-0.0530.0000.0000.0000.000
15B16ILE00.055-0.1089.4500.2400.2400.0000.0000.0000.000
16B16ILE0-0.0970.1049.2270.0240.0240.0000.0000.0000.000
17B17ASN00.123-0.05910.9010.1880.1880.0000.0000.0000.000
18B17ASN0-0.1050.05511.6660.1080.1080.0000.0000.0000.000
19B18GLN00.109-0.09012.7950.1520.1520.0000.0000.0000.000
20B18GLN0-0.1180.06813.608-0.074-0.0740.0000.0000.0000.000
21B19LYS00.111-0.09314.0850.1130.1130.0000.0000.0000.000
22B19LYS10.7951.04014.4450.5490.5490.0000.0000.0000.000
23B20LEU00.098-0.08115.1540.0570.0570.0000.0000.0000.000
24B20LEU0-0.1160.07413.4370.0200.0200.0000.0000.0000.000
25B21ILE00.073-0.07116.8600.0690.0690.0000.0000.0000.000
26B21ILE0-0.1200.07416.4110.0120.0120.0000.0000.0000.000
27B22GLU00.068-0.10418.7730.0520.0520.0000.0000.0000.000
28B22GLU-1-0.875-0.77818.292-0.494-0.4940.0000.0000.0000.000
29B23THR0-0.026-0.11520.0650.0260.0260.0000.0000.0000.000
30B23THR0-0.0420.05919.1870.0150.0150.0000.0000.0000.000
31B24GLY00.023-0.06721.7320.0280.0280.0000.0000.0000.000
32B25GLU00.1110.00620.2520.0410.0410.0000.0000.0000.000
33B25GLU-1-0.884-0.77219.301-0.146-0.1460.0000.0000.0000.000
34B26ARG00.050-0.11018.8890.0380.0380.0000.0000.0000.000
35B26ARG10.8581.04214.7850.0560.0560.0000.0000.0000.000
36B27GLU00.056-0.11119.6620.0400.0400.0000.0000.0000.000
37B27GLU-1-0.862-0.75623.607-0.066-0.0660.0000.0000.0000.000
38B28ARG00.174-0.08523.3770.0280.0280.0000.0000.0000.000
39B28ARG10.7761.01123.2320.1190.1190.0000.0000.0000.000
40B29LEU00.037-0.12520.9440.0180.0180.0000.0000.0000.000
41B29LEU0-0.1010.10218.6860.0060.0060.0000.0000.0000.000
42B30LYS00.098-0.08222.3720.0310.0310.0000.0000.0000.000
43B30LYS10.7070.96622.1750.0360.0360.0000.0000.0000.000
44B31GLU00.060-0.13923.3720.0260.0260.0000.0000.0000.000
45B31GLU-1-1.007-0.83126.974-0.046-0.0460.0000.0000.0000.000
46B32LEU00.070-0.11326.0470.0140.0140.0000.0000.0000.000
47B32LEU0-0.0720.10325.0660.0000.0000.0000.0000.0000.000
48B33LEU00.074-0.11023.8880.0060.0060.0000.0000.0000.000
49B33LEU0-0.0880.09720.5600.0060.0060.0000.0000.0000.000
50B34ARG00.082-0.07625.2600.0160.0160.0000.0000.0000.000
51B34ARG10.8521.04826.121-0.036-0.0360.0000.0000.0000.000
52B35ALA00.105-0.09927.9110.0100.0100.0000.0000.0000.000
53B35ALA0-0.0590.12629.915-0.002-0.0020.0000.0000.0000.000
54B36LYS00.060-0.10028.4700.0010.0010.0000.0000.0000.000
55B36LYS10.7661.00427.636-0.035-0.0350.0000.0000.0000.000
56B37LEU00.081-0.09928.3570.0040.0040.0000.0000.0000.000
57B37LEU0-0.0830.09524.9970.0020.0020.0000.0000.0000.000
58B38ILE00.106-0.08229.4510.0100.0100.0000.0000.0000.000
59B38ILE0-0.1050.07031.915-0.001-0.0010.0000.0000.0000.000
60B39GLU00.112-0.09532.6980.0030.0030.0000.0000.0000.000
61B39GLU-1-0.918-0.78732.5890.0350.0350.0000.0000.0000.000
62B40CYS0-0.003-0.12532.025-0.004-0.0040.0000.0000.0000.000
63B40CYS0-0.1970.08030.5620.0060.0060.0000.0000.0000.000
64B41GLY00.071-0.08733.3440.0070.0070.0000.0000.0000.000
65B42TRP00.1010.00630.5150.0010.0010.0000.0000.0000.000
66B42TRP0-0.1090.07426.427-0.008-0.0080.0000.0000.0000.000
67B43LYS00.116-0.08331.9840.0090.0090.0000.0000.0000.000
68B43LYS10.8991.07632.127-0.058-0.0580.0000.0000.0000.000
69B44ASP00.044-0.10832.8830.0030.0030.0000.0000.0000.000
70B44ASP-1-0.876-0.79936.9890.0630.0630.0000.0000.0000.000
71B45GLN00.079-0.11734.476-0.004-0.0040.0000.0000.0000.000
72B45GLN0-0.0630.10233.4540.0100.0100.0000.0000.0000.000
73B46LEU00.025-0.11532.7540.0080.0080.0000.0000.0000.000
74B46LEU0-0.0720.10929.4750.0000.0000.0000.0000.0000.000
75B47LYS00.114-0.05533.8630.0030.0030.0000.0000.0000.000
76B47LYS10.7540.98536.234-0.065-0.0650.0000.0000.0000.000
77B48ALA00.102-0.06637.182-0.003-0.0030.0000.0000.0000.000
78B48ALA0-0.0710.10238.4480.0000.0000.0000.0000.0000.000
79B49HIS00.103-0.05735.958-0.005-0.0050.0000.0000.0000.000
80B49HIS0-0.1190.05333.378-0.007-0.0070.0000.0000.0000.000
81B50CYS00.108-0.10636.7780.0030.0030.0000.0000.0000.000
82B50CYS0-0.1630.05035.2670.0010.0010.0000.0000.0000.000
83B51LYS00.109-0.01837.6510.0000.0000.0000.0000.0000.000
84B51LYS10.7670.98941.424-0.074-0.0740.0000.0000.0000.000
85B52GLU00.101-0.09540.799-0.005-0.0050.0000.0000.0000.000
86B52GLU-1-0.903-0.80640.6890.0830.0830.0000.0000.0000.000
87B53VAL00.113-0.08038.455-0.003-0.0030.0000.0000.0000.000
88B53VAL0-0.0870.08736.6620.0010.0010.0000.0000.0000.000
89B54ILE00.078-0.08739.9760.0020.0020.0000.0000.0000.000
90B54ILE0-0.0990.07139.969-0.001-0.0010.0000.0000.0000.000
91B55LYS00.061-0.07042.055-0.003-0.0030.0000.0000.0000.000
92B55LYS10.7010.95844.839-0.085-0.0850.0000.0000.0000.000
93B56GLU00.054-0.11843.278-0.005-0.0050.0000.0000.0000.000
94B56GLU-1-0.953-0.84342.2560.0920.0920.0000.0000.0000.000
95B57LYS00.005-0.11541.6840.0000.0000.0000.0000.0000.000
96B57LYS10.8081.03137.435-0.133-0.1330.0000.0000.0000.000
97B58GLY00.072-0.05143.072-0.002-0.0020.0000.0000.0000.000
98B59LEU00.065-0.02344.2160.0040.0040.0000.0000.0000.000
99B59LEU0-0.0900.07643.513-0.001-0.0010.0000.0000.0000.000
100B60GLU00.035-0.13745.016-0.001-0.0010.0000.0000.0000.000
101B60GLU-1-0.978-0.84647.6890.0630.0630.0000.0000.0000.000
102B61HIS00.014-0.08743.717-0.002-0.0020.0000.0000.0000.000
103B61HIS0-0.1110.08043.6540.0030.0030.0000.0000.0000.000
104B62VAL00.090-0.06040.0380.0050.0050.0000.0000.0000.000
105B62VAL0-0.1190.06838.6500.0010.0010.0000.0000.0000.000
106B63THR00.002-0.09537.143-0.008-0.0080.0000.0000.0000.000
107B63THR0-0.0510.04336.1640.0030.0030.0000.0000.0000.000
108B64VAL00.118-0.11534.8960.0040.0040.0000.0000.0000.000
109B64VAL0-0.0780.09932.895-0.001-0.0010.0000.0000.0000.000
110B65ASP00.046-0.11531.7210.0060.0060.0000.0000.0000.000
111B65ASP-1-0.920-0.82131.3080.1260.1260.0000.0000.0000.000
112B66ASP00.041-0.12832.0770.0180.0180.0000.0000.0000.000
113B66ASP-1-0.819-0.76436.2490.1250.1250.0000.0000.0000.000
114B67LEU00.081-0.07934.0250.0120.0120.0000.0000.0000.000
115B67LEU0-0.0940.10235.037-0.001-0.0010.0000.0000.0000.000
116B68VAL00.071-0.11330.1110.0050.0050.0000.0000.0000.000
117B68VAL0-0.1070.09928.1780.0010.0010.0000.0000.0000.000
118B69ALA00.097-0.08929.3270.0190.0190.0000.0000.0000.000
119B69ALA0-0.0560.12630.6470.0000.0000.0000.0000.0000.000
120B70GLU00.094-0.11330.1820.0200.0200.0000.0000.0000.000
121B70GLU-1-0.928-0.80234.3200.1550.1550.0000.0000.0000.000
122B71ILE0-0.034-0.13831.6550.0060.0060.0000.0000.0000.000
123B71ILE0-0.0680.10630.532-0.001-0.0010.0000.0000.0000.000
124B72THR00.029-0.10026.9330.0000.0000.0000.0000.0000.000
125B72THR0-0.0910.03324.9300.0050.0050.0000.0000.0000.000
126B73PRO0-0.008-0.11526.5730.0210.0210.0000.0000.0000.000
127B74LYS00.1140.02427.3690.0160.0160.0000.0000.0000.000
128B74LYS10.8461.07531.462-0.143-0.1430.0000.0000.0000.000
129B75GLY00.009-0.11428.147-0.005-0.0050.0000.0000.0000.000
130B76ARG00.1310.01924.043-0.013-0.0130.0000.0000.0000.000
131B76ARG10.8601.06821.043-0.350-0.3500.0000.0000.0000.000
132B77ALA00.056-0.12024.3980.0180.0180.0000.0000.0000.000
133B77ALA0-0.0600.11927.250-0.001-0.0010.0000.0000.0000.000
134B78LEU0-0.001-0.10126.5980.0010.0010.0000.0000.0000.000
135B78LEU0-0.0690.09829.405-0.004-0.0040.0000.0000.0000.000
136B79VAL00.085-0.10724.328-0.026-0.0260.0000.0000.0000.000
137B79VAL0-0.0910.10522.7240.0010.0010.0000.0000.0000.000
138B80PRO00.066-0.08525.0250.0180.0180.0000.0000.0000.000
139B81ASP00.075-0.01823.4910.0000.0000.0000.0000.0000.000
140B81ASP-1-0.874-0.78723.1230.2530.2530.0000.0000.0000.000
141B82SER00.040-0.07223.6170.0050.0050.0000.0000.0000.000
142B82SER0-0.0230.06827.4490.0020.0020.0000.0000.0000.000
143B83VAL00.071-0.10524.325-0.010-0.0100.0000.0000.0000.000
144B83VAL0-0.0380.12523.749-0.001-0.0010.0000.0000.0000.000
145B84LYS00.082-0.08720.356-0.023-0.0230.0000.0000.0000.000
146B84LYS10.7631.01719.808-0.255-0.2550.0000.0000.0000.000
147B85LYS00.103-0.08319.3380.0130.0130.0000.0000.0000.000
148B85LYS10.8651.06621.815-0.119-0.1190.0000.0000.0000.000
149B86GLU00.064-0.13820.504-0.008-0.0080.0000.0000.0000.000
150B86GLU-1-0.906-0.77823.5330.0180.0180.0000.0000.0000.000
151B87LEU00.087-0.10519.501-0.038-0.0380.0000.0000.0000.000
152B87LEU0-0.0840.11817.5070.0030.0030.0000.0000.0000.000
153B88LEU00.110-0.09115.963-0.046-0.0460.0000.0000.0000.000
154B88LEU0-0.1010.10313.7540.0100.0100.0000.0000.0000.000
155B89GLN00.092-0.10616.394-0.037-0.0370.0000.0000.0000.000
156B89GLN0-0.0320.12519.4700.0200.0200.0000.0000.0000.000
157B90ARG00.008-0.12319.089-0.041-0.0410.0000.0000.0000.000
158B90ARG10.8181.01319.4610.0330.0330.0000.0000.0000.000
159B91ILE00.112-0.05614.846-0.053-0.0530.0000.0000.0000.000
160B91ILE0-0.0870.09612.7760.0050.0050.0000.0000.0000.000
161B92ARG00.094-0.09414.856-0.087-0.0870.0000.0000.0000.000
162B92ARG10.8461.04814.547-0.077-0.0770.0000.0000.0000.000
163B93THR00.058-0.06715.816-0.060-0.0600.0000.0000.0000.000
164B93THR0-0.0840.03920.1920.0070.0070.0000.0000.0000.000
165B94PHE00.125-0.06917.350-0.016-0.0160.0000.0000.0000.000
166B94PHE0-0.0930.08715.0360.0100.0100.0000.0000.0000.000
167B95LEU00.056-0.09313.654-0.046-0.0460.0000.0000.0000.000
168B95LEU0-0.0930.07710.992-0.011-0.0110.0000.0000.0000.000
169B96ALA00.121-0.08014.784-0.089-0.0890.0000.0000.0000.000
170B96ALA0-0.0800.09717.7310.0140.0140.0000.0000.0000.000
171B97GLN00.008-0.09617.491-0.007-0.0070.0000.0000.0000.000
172B97GLN0-0.1350.06419.4240.0180.0180.0000.0000.0000.000
173B98HIS00.030-0.09717.0360.0290.0290.0000.0000.0000.000
174B98HIS0-0.1420.04616.2290.0100.0100.0000.0000.0000.000
175B99ALA0-0.046-0.11513.834-0.028-0.0280.0000.0000.0000.000
176B99ALA00.0400.02313.336-0.045-0.0450.0000.0000.0000.000