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: KK3N3

Calculation Name: 5H8A-D-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5H8A

Chain ID: D

ChEMBL ID:

UniProt ID: O74958

Base Structure: X-ray

Registration Date: 2025-07-11

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 330
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1810239.366317
FMO2-HF: Nuclear repulsion 1740720.152672
FMO2-HF: Total energy -69519.213645
FMO2-MP2: Total energy -69716.743203


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(D:314:PRO)


Summations of interaction energy for fragment #1(D:314:PRO)
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.
-0.471.337-0.015-0.853-0.9390
Interaction energy analysis for fragmet #1(D:314:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.026
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].
3D316LEU00.1100.0053.892-1.817-0.467-0.015-0.625-0.7100.000
4D316LEU0-0.0990.1067.2130.0170.0170.0000.0000.0000.000
5D317ASN00.114-0.0696.6240.4570.4570.0000.0000.0000.000
6D317ASN0-0.0960.0887.8100.1040.1040.0000.0000.0000.000
7D318PHE00.057-0.1108.768-0.003-0.0030.0000.0000.0000.000
8D318PHE0-0.0590.0979.967-0.012-0.0120.0000.0000.0000.000
9D319SER00.114-0.04512.1280.0780.0780.0000.0000.0000.000
10D319SER0-0.0670.04412.4930.0220.0220.0000.0000.0000.000
11D320ARG00.036-0.09414.099-0.048-0.0480.0000.0000.0000.000
12D320ARG10.8211.03114.6380.3130.3130.0000.0000.0000.000
13D321ALA00.161-0.11515.592-0.007-0.0070.0000.0000.0000.000
14D321ALA0-0.0690.11615.1010.0020.0020.0000.0000.0000.000
15D322SER0-0.027-0.08716.345-0.009-0.0090.0000.0000.0000.000
16D322SER0-0.0160.07121.011-0.001-0.0010.0000.0000.0000.000
17D323GLU00.127-0.09518.8190.0310.0310.0000.0000.0000.000
18D323GLU-1-0.894-0.79618.292-0.257-0.2570.0000.0000.0000.000
19D324HIS00.029-0.09417.1740.0140.0140.0000.0000.0000.000
20D324HIS0-0.0940.10212.928-0.003-0.0030.0000.0000.0000.000
21D325ARG00.045-0.12818.3170.0060.0060.0000.0000.0000.000
22D325ARG10.6790.92621.7840.2060.2060.0000.0000.0000.000
23D326ASN00.100-0.03021.367-0.022-0.0220.0000.0000.0000.000
24D326ASN0-0.1040.02523.0580.0120.0120.0000.0000.0000.000
25D327GLU00.031-0.11323.8500.0060.0060.0000.0000.0000.000
26D327GLU-1-0.919-0.83424.991-0.217-0.2170.0000.0000.0000.000
27D328LYS00.032-0.11727.2980.0120.0120.0000.0000.0000.000
28D328LYS10.7410.97728.4200.1560.1560.0000.0000.0000.000
29D329GLY0-0.005-0.08826.5910.0110.0110.0000.0000.0000.000
30D330GLU00.0970.02426.1160.0010.0010.0000.0000.0000.000
31D330GLU-1-0.856-0.76925.270-0.169-0.1690.0000.0000.0000.000
32D331ARG00.161-0.09022.178-0.013-0.0130.0000.0000.0000.000
33D331ARG10.7001.00018.0490.2560.2560.0000.0000.0000.000
34D332ILE0-0.025-0.12020.0290.0220.0220.0000.0000.0000.000
35D332ILE0-0.0910.09118.363-0.003-0.0030.0000.0000.0000.000
36D333SER00.119-0.05216.783-0.010-0.0100.0000.0000.0000.000
37D333SER0-0.167-0.01015.225-0.009-0.0090.0000.0000.0000.000
38D334MET00.061-0.11912.7220.0330.0330.0000.0000.0000.000
39D334MET0-0.1020.11011.868-0.019-0.0190.0000.0000.0000.000
40D335ILE00.058-0.08111.363-0.111-0.1110.0000.0000.0000.000
41D335ILE0-0.1470.07910.290-0.004-0.0040.0000.0000.0000.000
42D336ASN00.123-0.08512.328-0.024-0.0240.0000.0000.0000.000
43D336ASN0-0.1300.06515.8190.0170.0170.0000.0000.0000.000
44D337PRO00.118-0.04714.7400.0580.0580.0000.0000.0000.000
45D338ARG0-0.046-0.01917.8480.0350.0350.0000.0000.0000.000
46D338ARG10.8791.04119.8860.2980.2980.0000.0000.0000.000
47D339VAL00.105-0.08719.5490.0380.0380.0000.0000.0000.000
48D339VAL0-0.1310.08219.090-0.001-0.0010.0000.0000.0000.000
49D340VAL00.124-0.08520.423-0.030-0.0300.0000.0000.0000.000
50D340VAL0-0.0740.10524.4310.0030.0030.0000.0000.0000.000
51D341LEU0-0.006-0.14521.6410.0080.0080.0000.0000.0000.000
52D341LEU0-0.1290.09418.308-0.005-0.0050.0000.0000.0000.000
53D342ASP00.071-0.04122.9870.0030.0030.0000.0000.0000.000
54D342ASP-1-0.847-0.80824.940-0.149-0.1490.0000.0000.0000.000
55D343GLU00.124-0.11723.668-0.022-0.0220.0000.0000.0000.000
56D343GLU-1-0.868-0.74525.203-0.173-0.1730.0000.0000.0000.000
57D344ASN00.073-0.07423.867-0.008-0.0080.0000.0000.0000.000
58D344ASN0-0.1580.02624.6500.0090.0090.0000.0000.0000.000
59D345GLY00.065-0.08720.497-0.011-0.0110.0000.0000.0000.000
60D346ILE00.043-0.01720.314-0.036-0.0360.0000.0000.0000.000
61D346ILE0-0.0850.11722.8690.0040.0040.0000.0000.0000.000
62D347SER00.139-0.07722.4790.0040.0040.0000.0000.0000.000
63D347SER0-0.0500.07921.7520.0010.0010.0000.0000.0000.000
64D348HIS00.020-0.09123.5530.0110.0110.0000.0000.0000.000
65D348HIS0-0.0510.09226.189-0.004-0.0040.0000.0000.0000.000
66D349ARG00.072-0.07725.5310.0160.0160.0000.0000.0000.000
67D349ARG10.8701.05525.5530.1440.1440.0000.0000.0000.000
68D350SER00.002-0.07622.2070.0140.0140.0000.0000.0000.000
69D350SER0-0.0410.04421.4080.0030.0030.0000.0000.0000.000
70D351ARG00.135-0.06022.404-0.025-0.0250.0000.0000.0000.000
71D351ARG10.7260.97725.2460.1050.1050.0000.0000.0000.000
72D352TYR00.062-0.10919.8870.0160.0160.0000.0000.0000.000
73D352TYR0-0.0290.10417.7100.0010.0010.0000.0000.0000.000
74D353PHE00.080-0.07321.409-0.008-0.0080.0000.0000.0000.000
75D353PHE0-0.0890.07724.365-0.001-0.0010.0000.0000.0000.000
76D354ILE00.096-0.09220.921-0.005-0.0050.0000.0000.0000.000
77D354ILE0-0.0380.12119.1020.0000.0000.0000.0000.0000.000
78D355MET00.064-0.10021.679-0.003-0.0030.0000.0000.0000.000
79D355MET0-0.1580.09123.4750.0030.0030.0000.0000.0000.000
80D356LEU00.129-0.10622.7880.0110.0110.0000.0000.0000.000
81D356LEU0-0.1120.11520.8520.0000.0000.0000.0000.0000.000
82D357CYS00.144-0.09823.735-0.004-0.0040.0000.0000.0000.000
83D357CYS0-0.2140.08724.4690.0000.0000.0000.0000.0000.000
84D358ASP00.046-0.13825.0400.0190.0190.0000.0000.0000.000
85D358ASP-1-0.881-0.80428.1080.0600.0600.0000.0000.0000.000
86D359ASN00.148-0.06527.8930.0050.0050.0000.0000.0000.000
87D359ASN0-0.0990.08430.5880.0020.0020.0000.0000.0000.000
88D360GLU00.110-0.12628.009-0.008-0.0080.0000.0000.0000.000
89D360GLU-1-0.967-0.83027.2890.1180.1180.0000.0000.0000.000
90D361THR0-0.057-0.11629.051-0.001-0.0010.0000.0000.0000.000
91D361THR00.0190.08133.5040.0000.0000.0000.0000.0000.000
92D362ALA00.148-0.07030.695-0.004-0.0040.0000.0000.0000.000
93D362ALA0-0.0750.11029.8300.0000.0000.0000.0000.0000.000
94D363ILE00.097-0.08726.243-0.010-0.0100.0000.0000.0000.000
95D363ILE0-0.1020.09023.7470.0010.0010.0000.0000.0000.000
96D364ALA00.095-0.12227.539-0.004-0.0040.0000.0000.0000.000
97D364ALA0-0.0630.11329.2650.0010.0010.0000.0000.0000.000
98D365HIS00.033-0.09129.189-0.003-0.0030.0000.0000.0000.000
99D365HIS0-0.0330.09533.157-0.005-0.0050.0000.0000.0000.000
100D366ALA00.108-0.07729.137-0.005-0.0050.0000.0000.0000.000
101D366ALA0-0.0340.12728.3250.0000.0000.0000.0000.0000.000
102D367LYS00.038-0.09527.062-0.011-0.0110.0000.0000.0000.000
103D367LYS10.7571.01421.943-0.091-0.0910.0000.0000.0000.000
104D368LYS00.109-0.08427.899-0.005-0.0050.0000.0000.0000.000
105D368LYS10.7621.03131.849-0.033-0.0330.0000.0000.0000.000
106D369THR0-0.067-0.12331.391-0.003-0.0030.0000.0000.0000.000
107D369THR0-0.0420.04132.894-0.001-0.0010.0000.0000.0000.000
108D370SER00.008-0.05329.483-0.003-0.0030.0000.0000.0000.000
109D370SER0-0.0380.08529.776-0.002-0.0020.0000.0000.0000.000
110D371ILE00.058-0.12430.502-0.009-0.0090.0000.0000.0000.000
111D371ILE0-0.0490.11433.8420.0000.0000.0000.0000.0000.000
112D372TRP00.078-0.08129.7250.0080.0080.0000.0000.0000.000
113D372TRP0-0.0630.06227.4250.0020.0020.0000.0000.0000.000
114D373ALA00.103-0.10431.130-0.005-0.0050.0000.0000.0000.000
115D373ALA0-0.0510.10833.3440.0010.0010.0000.0000.0000.000
116D374VAL00.031-0.10631.2420.0050.0050.0000.0000.0000.000
117D374VAL0-0.0740.10930.490-0.001-0.0010.0000.0000.0000.000
118D375LYS00.120-0.11331.619-0.001-0.0010.0000.0000.0000.000
119D375LYS10.8771.10731.169-0.024-0.0240.0000.0000.0000.000
120D376LYS00.107-0.09033.467-0.006-0.0060.0000.0000.0000.000
121D376LYS10.7310.98237.364-0.002-0.0020.0000.0000.0000.000
122D377ASP00.013-0.10833.337-0.006-0.0060.0000.0000.0000.000
123D377ASP-1-0.834-0.78931.7980.0010.0010.0000.0000.0000.000
124D378SER0-0.013-0.10930.243-0.005-0.0050.0000.0000.0000.000
125D378SER00.0140.10229.6090.0000.0000.0000.0000.0000.000
126D379SER0-0.030-0.12131.490-0.009-0.0090.0000.0000.0000.000
127D379SER0-0.0560.04834.9690.0000.0000.0000.0000.0000.000
128D380LYS00.130-0.07133.842-0.004-0.0040.0000.0000.0000.000
129D380LYS10.8721.07435.3800.0360.0360.0000.0000.0000.000
130D381ARG00.090-0.09430.960-0.003-0.0030.0000.0000.0000.000
131D381ARG10.7721.00827.0080.0830.0830.0000.0000.0000.000
132D382ILE00.115-0.08229.638-0.011-0.0110.0000.0000.0000.000
133D382ILE0-0.0860.10727.8920.0010.0010.0000.0000.0000.000
134D383SER00.085-0.07130.533-0.006-0.0060.0000.0000.0000.000
135D383SER0-0.0660.03035.1290.0010.0010.0000.0000.0000.000
136D384ASP00.016-0.07633.7860.0000.0000.0000.0000.0000.000
137D384ASP-1-0.890-0.82532.530-0.073-0.0730.0000.0000.0000.000
138D385ALA00.120-0.07729.244-0.002-0.0020.0000.0000.0000.000
139D385ALA0-0.0830.08128.398-0.001-0.0010.0000.0000.0000.000
140D386TYR00.105-0.10030.553-0.009-0.0090.0000.0000.0000.000
141D386TYR0-0.0980.09230.6020.0030.0030.0000.0000.0000.000
142D387LYS00.027-0.11031.690-0.002-0.0020.0000.0000.0000.000
143D387LYS10.7060.95335.4710.0470.0470.0000.0000.0000.000
144D388LYS00.012-0.09132.4240.0020.0020.0000.0000.0000.000
145D388LYS10.7370.96932.1400.0780.0780.0000.0000.0000.000
146D389ALA00.125-0.09728.232-0.004-0.0040.0000.0000.0000.000
147D389ALA0-0.0930.09827.240-0.002-0.0020.0000.0000.0000.000
148D390SER0-0.002-0.07925.9020.0120.0120.0000.0000.0000.000
149D390SER0-0.0780.05825.2830.0030.0030.0000.0000.0000.000
150D391VAL00.134-0.08925.036-0.018-0.0180.0000.0000.0000.000
151D391VAL0-0.0930.13226.2700.0020.0020.0000.0000.0000.000
152D392TYR00.015-0.11721.7620.0110.0110.0000.0000.0000.000
153D392TYR0-0.0910.09121.095-0.001-0.0010.0000.0000.0000.000
154D393PHE00.064-0.10922.684-0.008-0.0080.0000.0000.0000.000
155D393PHE0-0.0380.10523.7280.0020.0020.0000.0000.0000.000
156D394ILE00.105-0.08118.3710.0000.0000.0000.0000.0000.000
157D394ILE0-0.0880.09716.158-0.005-0.0050.0000.0000.0000.000
158D395PHE00.100-0.06419.5480.0010.0010.0000.0000.0000.000
159D395PHE0-0.1340.05621.0700.0000.0000.0000.0000.0000.000
160D396VAL00.053-0.11519.0070.0150.0150.0000.0000.0000.000
161D396VAL0-0.0290.12217.1760.0000.0000.0000.0000.0000.000
162D397ALA00.174-0.07319.725-0.025-0.0250.0000.0000.0000.000
163D397ALA0-0.1260.08920.7140.0040.0040.0000.0000.0000.000
164D398GLN00.093-0.10221.1360.0260.0260.0000.0000.0000.000
165D398GLN0-0.0830.09824.031-0.015-0.0150.0000.0000.0000.000
166D399GLN00.099-0.09023.4760.0010.0010.0000.0000.0000.000
167D399GLN0-0.1140.08724.3930.0000.0000.0000.0000.0000.000
168D400THR0-0.063-0.10720.4390.0030.0030.0000.0000.0000.000
169D400THR0-0.0170.03619.665-0.013-0.0130.0000.0000.0000.000
170D401TYR00.038-0.06617.3070.0470.0470.0000.0000.0000.000
171D401TYR0-0.0970.07316.5930.0070.0070.0000.0000.0000.000
172D402ASN00.132-0.11415.9790.0420.0420.0000.0000.0000.000
173D402ASN0-0.0840.07618.3690.0250.0250.0000.0000.0000.000
174D403ALA00.159-0.05415.194-0.048-0.0480.0000.0000.0000.000
175D403ALA0-0.0620.11614.479-0.001-0.0010.0000.0000.0000.000
176D404LEU0-0.009-0.13016.4870.0270.0270.0000.0000.0000.000
177D404LEU0-0.0850.12120.263-0.005-0.0050.0000.0000.0000.000
178D405GLY00.071-0.11018.505-0.005-0.0050.0000.0000.0000.000
179D406TYR00.0210.01718.4320.0070.0070.0000.0000.0000.000
180D406TYR0-0.0630.06315.129-0.016-0.0160.0000.0000.0000.000
181D407ALA00.127-0.10719.628-0.002-0.0020.0000.0000.0000.000
182D407ALA0-0.0500.12023.6390.0030.0030.0000.0000.0000.000
183D408GLN00.108-0.07022.804-0.010-0.0100.0000.0000.0000.000
184D408GLN0-0.0890.10024.3350.0000.0000.0000.0000.0000.000
185D409VAL00.077-0.12025.0780.0110.0110.0000.0000.0000.000
186D409VAL0-0.0670.13526.8140.0000.0000.0000.0000.0000.000
187D410VAL0-0.012-0.11128.446-0.009-0.0090.0000.0000.0000.000
188D410VAL0-0.1080.09929.2300.0000.0000.0000.0000.0000.000
189D411SER00.060-0.10731.5860.0020.0020.0000.0000.0000.000
190D411SER0-0.0410.05635.0140.0020.0020.0000.0000.0000.000
191D412ASP00.151-0.02833.293-0.002-0.0020.0000.0000.0000.000
192D412ASP-1-0.835-0.75336.066-0.042-0.0420.0000.0000.0000.000
193D413LEU00.062-0.11235.4940.0030.0030.0000.0000.0000.000
194D413LEU0-0.1110.09632.8700.0000.0000.0000.0000.0000.000
195D414ASN00.106-0.07636.335-0.001-0.0010.0000.0000.0000.000
196D414ASN0-0.0720.12039.0250.0010.0010.0000.0000.0000.000
197D415SER00.087-0.06939.3340.0020.0020.0000.0000.0000.000
198D415SER0-0.0410.07241.767-0.001-0.0010.0000.0000.0000.000
199D416THR0-0.027-0.09141.3500.0030.0030.0000.0000.0000.000
200D416THR0-0.0610.03743.3180.0000.0000.0000.0000.0000.000
201D417GLU00.085-0.05539.8090.0020.0020.0000.0000.0000.000
202D417GLU-1-1.039-0.89039.068-0.007-0.0070.0000.0000.0000.000
203D418LEU00.099-0.12837.754-0.001-0.0010.0000.0000.0000.000
204D418LEU0-0.0910.12336.9940.0000.0000.0000.0000.0000.000
205D419PRO0-0.006-0.09034.1220.0010.0010.0000.0000.0000.000
206D420PHE00.1100.03037.2940.0000.0000.0000.0000.0000.000
207D420PHE0-0.0650.07336.4350.0010.0010.0000.0000.0000.000
208D421TRP00.070-0.06035.4210.0000.0000.0000.0000.0000.000
209D421TRP0-0.1200.07431.0600.0010.0010.0000.0000.0000.000
210D422SER0-0.027-0.08535.8340.0050.0050.0000.0000.0000.000
211D422SER0-0.0530.04036.176-0.002-0.0020.0000.0000.0000.000
212D423ASP00.085-0.07736.8020.0010.0010.0000.0000.0000.000
213D423ASP-1-0.835-0.76935.7080.0250.0250.0000.0000.0000.000
214D424SER00.083-0.07438.691-0.004-0.0040.0000.0000.0000.000
215D424SER0-0.0010.09640.9330.0010.0010.0000.0000.0000.000
216D425SER0-0.005-0.10936.754-0.004-0.0040.0000.0000.0000.000
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