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: 4LGNN

Calculation Name: 3DA5-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3DA5

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWU1

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 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1144880.572712
FMO2-HF: Nuclear repulsion 1095339.621362
FMO2-HF: Total energy -49540.95135
FMO2-MP2: Total energy -49690.303409


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:8:LYS)


Summations of interaction energy for fragment #1(A:8:LYS)
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.
-0.7230.948-0.002-0.735-0.9340.006
Interaction energy analysis for fragmet #1(A:8:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.176 / q_NPA : 0.057
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].
4A9LYS10.7120.9994.2020.8791.2310.002-0.176-0.1780.000
5A10THR00.013-0.0693.886-1.660-0.184-0.006-0.836-0.6350.005
6A10THR0-0.0170.0755.9310.0660.0660.0000.0000.0000.000
7A11LEU00.165-0.0796.4080.3780.3780.0000.0000.0000.000
8A11LEU0-0.1090.0999.7930.0110.0110.0000.0000.0000.000
9A12TRP00.071-0.1129.5440.1890.1890.0000.0000.0000.000
10A12TRP0-0.0790.07711.658-0.021-0.0210.0000.0000.0000.000
11A13GLU00.089-0.0908.5960.2640.2640.0000.0000.0000.000
12A13GLU-1-0.897-0.7847.868-0.951-0.9510.0000.0000.0000.000
13A14LEU00.050-0.0829.0660.1520.1520.0000.0000.0000.000
14A14LEU0-0.0950.0816.2700.0340.0340.0000.0000.0000.000
15A15VAL00.007-0.1159.6610.1490.1490.0000.0000.0000.000
16A15VAL0-0.1030.11512.5240.0020.0020.0000.0000.0000.000
17A16GLY00.062-0.10512.7490.0620.0620.0000.0000.0000.000
18A17ARG00.0340.00113.9210.0540.0540.0000.0000.0000.000
19A17ARG10.7200.97611.8380.7420.7420.0000.0000.0000.000
20A18ASN00.170-0.05815.6240.0360.0360.0000.0000.0000.000
21A18ASN0-0.0840.08918.1590.0050.0050.0000.0000.0000.000
22A19LYS00.129-0.09117.865-0.038-0.0380.0000.0000.0000.000
23A19LYS10.8211.04720.5190.2980.2980.0000.0000.0000.000
24A20ASP00.079-0.10920.044-0.018-0.0180.0000.0000.0000.000
25A20ASP-1-0.887-0.79622.440-0.213-0.2130.0000.0000.0000.000
26A21ALA00.131-0.07917.9140.0150.0150.0000.0000.0000.000
27A21ALA0-0.0660.11517.156-0.001-0.0010.0000.0000.0000.000
28A22LEU00.074-0.10716.112-0.002-0.0020.0000.0000.0000.000
29A22LEU0-0.0940.09114.536-0.015-0.0150.0000.0000.0000.000
30A23ARG00.062-0.10517.113-0.022-0.0220.0000.0000.0000.000
31A23ARG10.6530.93621.7680.2170.2170.0000.0000.0000.000
32A24ASP00.126-0.10820.319-0.001-0.0010.0000.0000.0000.000
33A24ASP-1-0.910-0.75720.677-0.198-0.1980.0000.0000.0000.000
34A25PHE00.148-0.07415.6580.0400.0400.0000.0000.0000.000
35A25PHE0-0.0760.07811.355-0.021-0.0210.0000.0000.0000.000
36A26LEU00.028-0.10116.5490.0030.0030.0000.0000.0000.000
37A26LEU0-0.0890.08614.912-0.009-0.0090.0000.0000.0000.000
38A27LYS00.082-0.09617.5100.0110.0110.0000.0000.0000.000
39A27LYS10.7671.01921.6930.1690.1690.0000.0000.0000.000
40A28GLU00.036-0.16318.8560.0190.0190.0000.0000.0000.000
41A28GLU-1-0.947-0.83217.435-0.188-0.1880.0000.0000.0000.000
42A29HIS00.033-0.04116.3410.0390.0390.0000.0000.0000.000
43A29HIS10.7370.97915.5510.2190.2190.0000.0000.0000.000
44A30ARG00.137-0.11317.878-0.025-0.0250.0000.0000.0000.000
45A30ARG10.7191.02621.4910.1660.1660.0000.0000.0000.000
46A31GLY0-0.061-0.13219.4540.0260.0260.0000.0000.0000.000
47A32THR00.0110.03817.8520.0080.0080.0000.0000.0000.000
48A32THR0-0.0130.07117.344-0.008-0.0080.0000.0000.0000.000
49A33ILE00.057-0.08514.1090.0300.0300.0000.0000.0000.000
50A33ILE0-0.0620.09111.937-0.011-0.0110.0000.0000.0000.000
51A34LEU0-0.003-0.11913.2600.0370.0370.0000.0000.0000.000
52A34LEU0-0.0630.09913.4510.0000.0000.0000.0000.0000.000
53A35LEU00.088-0.11610.798-0.069-0.0690.0000.0000.0000.000
54A35LEU0-0.0430.12610.925-0.003-0.0030.0000.0000.0000.000
55A36ARG00.143-0.0809.2850.2180.2180.0000.0000.0000.000
56A36ARG10.7511.0247.6430.7910.7910.0000.0000.0000.000
57A37ASP00.144-0.0718.822-0.423-0.4230.0000.0000.0000.000
58A37ASP-1-0.866-0.77612.215-0.872-0.8720.0000.0000.0000.000
59A38ILE0-0.017-0.1087.2200.2420.2420.0000.0000.0000.000
60A38ILE0-0.1070.0704.669-0.317-0.285-0.001-0.008-0.0220.000
61A39ALA00.175-0.0898.754-0.026-0.0260.0000.0000.0000.000
62A39ALA0-0.0370.12111.5580.0170.0170.0000.0000.0000.000
63A40SER00.038-0.06411.8230.1500.1500.0000.0000.0000.000
64A40SER0-0.0660.04213.457-0.039-0.0390.0000.0000.0000.000
65A41GLU00.105-0.09912.877-0.096-0.0960.0000.0000.0000.000
66A41GLU-1-0.919-0.80414.902-0.337-0.3370.0000.0000.0000.000
67A42HIS00.120-0.07513.958-0.027-0.0270.0000.0000.0000.000
68A42HIS0-0.1020.09716.733-0.011-0.0110.0000.0000.0000.000
69A43LYS00.109-0.05910.7050.0120.0120.0000.0000.0000.000
70A43LYS10.7161.0129.6390.5810.5810.0000.0000.0000.000
71A44VAL00.075-0.13711.718-0.027-0.0270.0000.0000.0000.000
72A44VAL0-0.0770.11415.3710.0130.0130.0000.0000.0000.000
73A45VAL00.078-0.10312.683-0.147-0.1470.0000.0000.0000.000
74A45VAL0-0.0750.09011.6270.0040.0040.0000.0000.0000.000
75A46TYR00.006-0.11713.8000.0940.0940.0000.0000.0000.000
76A46TYR0-0.0140.11314.0710.0300.0300.0000.0000.0000.000
77A47LYS00.137-0.07515.237-0.062-0.0620.0000.0000.0000.000
78A47LYS10.8041.04418.8310.2740.2740.0000.0000.0000.000
79A48PRO00.024-0.09715.7600.0160.0160.0000.0000.0000.000
80A49ILE00.0830.01018.4750.0350.0350.0000.0000.0000.000
81A49ILE0-0.0570.12021.8760.0030.0030.0000.0000.0000.000
82A50PHE00.058-0.09721.954-0.024-0.0240.0000.0000.0000.000
83A50PHE0-0.1240.06720.0550.0040.0040.0000.0000.0000.000
84A51LYS00.156-0.06124.4630.0080.0080.0000.0000.0000.000
85A51LYS10.7791.05525.0250.2400.2400.0000.0000.0000.000
86A52ARG00.068-0.09227.7030.0060.0060.0000.0000.0000.000
87A52ARG10.8621.05031.4180.1280.1280.0000.0000.0000.000
88A53TYR00.057-0.08830.7190.0030.0030.0000.0000.0000.000
89A53TYR0-0.0760.10733.7180.0000.0000.0000.0000.0000.000
90A54ASN00.067-0.08227.8770.0050.0050.0000.0000.0000.000
91A54ASN0-0.1020.06827.1550.0050.0050.0000.0000.0000.000
92A55GLY00.107-0.05128.3250.0090.0090.0000.0000.0000.000
93A56ASP00.094-0.03224.981-0.003-0.0030.0000.0000.0000.000
94A56ASP-1-0.895-0.77525.459-0.183-0.1830.0000.0000.0000.000
95A57PRO0-0.017-0.10020.6640.0090.0090.0000.0000.0000.000
96A58ASP00.109-0.00622.5660.0130.0130.0000.0000.0000.000
97A58ASP-1-0.946-0.84323.998-0.227-0.2270.0000.0000.0000.000
98A59LEU00.013-0.14021.883-0.033-0.0330.0000.0000.0000.000
99A59LEU0-0.0720.08519.520-0.006-0.0060.0000.0000.0000.000
100A60ILE00.117-0.05422.6540.0310.0310.0000.0000.0000.000
101A60ILE0-0.0940.10423.786-0.002-0.0020.0000.0000.0000.000
102A61GLU00.010-0.14123.007-0.041-0.0410.0000.0000.0000.000
103A61GLU-1-0.942-0.84023.379-0.266-0.2660.0000.0000.0000.000
104A62ASP00.028-0.12624.775-0.008-0.0080.0000.0000.0000.000
105A62ASP-1-0.865-0.81227.844-0.223-0.2230.0000.0000.0000.000
106A63ASN00.114-0.07426.0960.0170.0170.0000.0000.0000.000
107A63ASN0-0.1310.06626.772-0.001-0.0010.0000.0000.0000.000
108A64SER00.067-0.09724.098-0.027-0.0270.0000.0000.0000.000
109A64SER0-0.0240.08424.4840.0080.0080.0000.0000.0000.000
110A65ASN00.096-0.06924.297-0.029-0.0290.0000.0000.0000.000
111A65ASN0-0.1320.06528.0230.0130.0130.0000.0000.0000.000
112A66ASP00.144-0.09224.708-0.003-0.0030.0000.0000.0000.000
113A66ASP-1-0.945-0.82223.887-0.276-0.2760.0000.0000.0000.000
114A67VAL00.019-0.12120.708-0.023-0.0230.0000.0000.0000.000
115A67VAL0-0.0790.10519.089-0.007-0.0070.0000.0000.0000.000
116A68GLU00.066-0.11220.395-0.059-0.0590.0000.0000.0000.000
117A68GLU-1-0.847-0.77323.420-0.261-0.2610.0000.0000.0000.000
118A69HIS00.112-0.06722.039-0.019-0.0190.0000.0000.0000.000
119A69HIS0-0.0870.08024.0400.0140.0140.0000.0000.0000.000
120A70TRP00.066-0.10519.9880.0050.0050.0000.0000.0000.000
121A70TRP0-0.1360.06719.065-0.015-0.0150.0000.0000.0000.000
122A71TYR00.170-0.06717.465-0.061-0.0610.0000.0000.0000.000
123A71TYR0-0.1180.06815.1060.0130.0130.0000.0000.0000.000
124A72ASP00.064-0.13718.265-0.047-0.0470.0000.0000.0000.000
125A72ASP-1-0.934-0.80621.012-0.340-0.3400.0000.0000.0000.000
126A73TYR00.068-0.11620.8240.0210.0210.0000.0000.0000.000
127A73TYR0-0.0670.09519.5490.0200.0200.0000.0000.0000.000
128A74HIS0-0.005-0.09516.4600.0330.0330.0000.0000.0000.000
129A74HIS10.6980.91214.8530.6280.6280.0000.0000.0000.000
130A75LEU00.120-0.07517.513-0.013-0.0130.0000.0000.0000.000
131A75LEU0-0.0900.10017.8840.0040.0040.0000.0000.0000.000
132A76GLU00.075-0.16718.4040.0100.0100.0000.0000.0000.000
133A76GLU-1-0.894-0.77522.864-0.243-0.2430.0000.0000.0000.000
134A77ARG00.014-0.09320.5830.0390.0390.0000.0000.0000.000
135A77ARG10.7171.00420.6210.2720.2720.0000.0000.0000.000
136A78TYR00.032-0.09116.8080.0440.0440.0000.0000.0000.000
137A78TYR0-0.0880.07516.1690.0100.0100.0000.0000.0000.000
138A79TRP00.086-0.07316.2010.0030.0030.0000.0000.0000.000
139A79TRP0-0.1490.04111.340-0.047-0.0470.0000.0000.0000.000
140A80ASN00.145-0.06317.2850.0080.0080.0000.0000.0000.000
141A80ASN0-0.1350.07721.5100.0060.0060.0000.0000.0000.000
142A81THR0-0.023-0.10819.9140.0230.0230.0000.0000.0000.000
143A81THR0-0.0060.04220.133-0.009-0.0090.0000.0000.0000.000
144A82PRO00.055-0.07519.859-0.028-0.0280.0000.0000.0000.000
145A83GLU0-0.015-0.05418.591-0.018-0.0180.0000.0000.0000.000
146A83GLU-1-0.831-0.76418.214-0.114-0.1140.0000.0000.0000.000
147A84LEU00.088-0.09815.3740.0020.0020.0000.0000.0000.000
148A84LEU0-0.0350.14515.038-0.004-0.0040.0000.0000.0000.000
149A85LYS00.155-0.06914.940-0.080-0.0800.0000.0000.0000.000
150A85LYS10.8621.08018.3690.3070.3070.0000.0000.0000.000
151A86LYS00.082-0.08816.013-0.054-0.0540.0000.0000.0000.000
152A86LYS10.7721.01515.4380.1370.1370.0000.0000.0000.000
153A87GLU00.049-0.12412.2610.0070.0070.0000.0000.0000.000
154A87GLU-1-0.933-0.8219.971-0.493-0.4930.0000.0000.0000.000
155A88PHE00.117-0.07411.392-0.110-0.1100.0000.0000.0000.000
156A88PHE0-0.0940.08913.412-0.004-0.0040.0000.0000.0000.000
157A89TYR00.098-0.10011.979-0.138-0.1380.0000.0000.0000.000
158A89TYR0-0.0860.09715.5660.0080.0080.0000.0000.0000.000
159A90LYS00.033-0.10111.942-0.041-0.0410.0000.0000.0000.000
160A90LYS10.8751.05111.4590.2060.2060.0000.0000.0000.000
161A91LYS00.106-0.0927.8930.0290.0290.0000.0000.0000.000
162A91LYS10.6671.0176.6971.1051.1050.0000.0000.0000.000
163A92PHE0-0.006-0.1237.825-0.417-0.4170.0000.0000.0000.000
164A92PHE0-0.0620.1028.215-0.046-0.0460.0000.0000.0000.000
165A93GLY00.042-0.05510.4810.0270.0270.0000.0000.0000.000
166A94PRO00.0220.00613.623-0.022-0.0220.0000.0000.0000.000
167A95VAL00.081-0.00116.265-0.073-0.0730.0000.0000.0000.000
168A95VAL0-0.0290.13718.4530.0000.0000.0000.0000.0000.000
169A96ASP00.132-0.08516.9260.0620.0620.0000.0000.0000.000
170A96ASP-1-0.875-0.76516.277-0.512-0.5120.0000.0000.0000.000
171A97LEU00.020-0.12818.188-0.040-0.0400.0000.0000.0000.000
172A97LEU0-0.0180.11221.8640.0030.0030.0000.0000.0000.000
173A98ASN00.076-0.07520.3090.0230.0230.0000.0000.0000.000
174A98ASN0-0.1260.05219.8410.0290.0290.0000.0000.0000.000
175A99GLN00.053-0.09317.3070.0390.0390.0000.0000.0000.000
176A99GLN0-0.1110.06315.360-0.103-0.1030.0000.0000.0000.000
177A100PRO0-0.027-0.10118.0590.0220.0220.0000.0000.0000.000
178A101ILE00.067-0.01818.368-0.077-0.0770.0000.0000.0000.000
179A101ILE0-0.0670.11619.5000.0020.0020.0000.0000.0000.000
180A102ILE00.138-0.08517.2580.0620.0620.0000.0000.0000.000
181A102ILE0-0.1190.07914.633-0.014-0.0140.0000.0000.0000.000
182A103LEU00.099-0.08918.656-0.031-0.0310.0000.0000.0000.000
183A103LEU0-0.0830.12222.3540.0060.0060.0000.0000.0000.000
184A104ALA00.104-0.08818.0660.0110.0110.0000.0000.0000.000
185A104ALA0-0.0720.08817.604-0.015-0.0150.0000.0000.0000.000
186A105LYS00.030-0.10619.5860.0090.0090.0000.0000.0000.000
187A105LYS10.9281.09721.9150.2110.2110.0000.0000.0000.000
188A106PRO00.021-0.09218.842-0.030-0.0300.0000.0000.0000.000
189A107LEU00.072-0.01519.0350.0210.0210.0000.0000.0000.000
190A107LEU0-0.0850.10116.4540.0010.0010.0000.0000.0000.000
191A108ARG00.040-0.08220.4820.0250.0250.0000.0000.0000.000
192A108ARG10.8241.02821.6350.1920.1920.0000.0000.0000.000
193A109GLN00.191-0.06822.983-0.025-0.0250.0000.0000.0000.000
194A109GLN0-0.0900.09527.191-0.007-0.0070.0000.0000.0000.000
195A110HIS00.067-0.13822.9220.0090.0090.0000.0000.0000.000
196A110HIS0-0.1060.10319.704-0.017-0.0170.0000.0000.0000.000
197A111ASN00.096-0.04423.8210.0070.0070.0000.0000.0000.000
198A111ASN0-0.0950.06623.912-0.008-0.0080.0000.0000.0000.000
199A112ARG0-0.003-0.12023.5980.0160.0160.0000.0000.0000.000
200A112ARG10.9051.07322.4030.2550.2550.0000.0000.0000.000
201A113GLY00.064-0.06424.8310.0010.0010.0000.0000.0000.000
202A114ASP00.029-0.01824.005-0.030-0.0300.0000.0000.0000.000
203A114ASP-1-0.947-0.83425.932-0.183-0.1830.0000.0000.0000.000
204A115LEU00.109-0.12823.321-0.001-0.0010.0000.0000.0000.000
205A115LEU0-0.1020.10023.2260.0040.0040.0000.0000.0000.000
206A116VAL0-0.017-0.09719.8640.0220.0220.0000.0000.0000.000
207A116VAL0-0.0730.07918.093-0.006-0.0060.0000.0000.0000.000
208A117HIS00.128-0.07920.045-0.006-0.0060.0000.0000.0000.000
209A117HIS0-0.0620.11320.958-0.002-0.0020.0000.0000.0000.000
210A118LEU00.036-0.11615.583-0.003-0.0030.0000.0000.0000.000
211A118LEU0-0.0850.09214.127-0.018-0.0180.0000.0000.0000.000
212A119LEU00.145-0.11315.1840.0510.0510.0000.0000.0000.000
213A119LEU0-0.0980.14014.662-0.011-0.0110.0000.0000.0000.000
214A120PRO00.036-0.09112.652-0.175-0.1750.0000.0000.0000.000
215A121GLN00.1500.00510.883-0.270-0.2700.0000.0000.0000.000
216A121GLN0-0.1210.08712.0920.0820.0820.0000.0000.0000.000
217A122PHE0-0.005-0.14510.122-0.282-0.2820.0000.0000.0000.000
218A122PHE0-0.0810.11211.6960.0280.0280.0000.0000.0000.000
219A123VAL00.029-0.0898.954-0.175-0.1750.0000.0000.0000.000
220A123VAL0-0.0520.11310.1690.0410.0410.0000.0000.0000.000
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222A124VAL0-0.0800.0783.385-0.364-0.5470.0050.288-0.1090.001
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225A126VAL0-0.1260.0748.7550.0030.0030.0000.0000.0000.000
226A127TYR00.098-0.09910.1360.0040.0040.0000.0000.0000.000
227A127TYR0-0.0360.1148.340-0.042-0.0420.0000.0000.0000.000
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229A128ASN00.005-0.00114.5110.0150.0150.0000.0000.0000.000