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

tag_button

FMODB ID: K2QR3

Calculation Name: 3DA5-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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 OptHSide
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 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1143581.559198
FMO2-HF: Nuclear repulsion 1094041.228171
FMO2-HF: Total energy -49540.331026
FMO2-MP2: Total energy -49689.700822


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: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.
0.2161.934-0.008-0.74-0.970.004
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 : 0.177 / q_NPA : 0.068
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].
4A9LYS10.7891.0374.0970.8591.2030.002-0.170-0.1760.000
5A10THR00.044-0.0683.891-1.662-0.056-0.005-0.944-0.6560.004
6A10THR0-0.0070.0805.8040.0700.0700.0000.0000.0000.000
7A11LEU00.167-0.0756.4630.3490.3490.0000.0000.0000.000
8A11LEU0-0.1180.1019.9040.0050.0050.0000.0000.0000.000
9A12TRP00.097-0.1179.6910.1750.1750.0000.0000.0000.000
10A12TRP0-0.0960.07811.429-0.020-0.0200.0000.0000.0000.000
11A13GLU00.079-0.0858.8230.2390.2390.0000.0000.0000.000
12A13GLU-1-0.950-0.8228.011-0.890-0.8900.0000.0000.0000.000
13A14LEU00.039-0.1049.1950.1860.1860.0000.0000.0000.000
14A14LEU0-0.1000.0726.4220.0220.0220.0000.0000.0000.000
15A15VAL0-0.016-0.1059.9480.1360.1360.0000.0000.0000.000
16A15VAL0-0.0780.10912.7030.0030.0030.0000.0000.0000.000
17A16GLY00.047-0.09413.0540.0740.0740.0000.0000.0000.000
18A17ARG00.016-0.01614.1650.0510.0510.0000.0000.0000.000
19A17ARG10.7441.00011.7750.7170.7170.0000.0000.0000.000
20A18ASN00.193-0.05415.8070.0390.0390.0000.0000.0000.000
21A18ASN0-0.0810.09718.4910.0040.0040.0000.0000.0000.000
22A19LYS00.104-0.10118.223-0.037-0.0370.0000.0000.0000.000
23A19LYS10.8551.06920.6160.2980.2980.0000.0000.0000.000
24A20ASP00.087-0.12220.177-0.019-0.0190.0000.0000.0000.000
25A20ASP-1-0.878-0.80122.848-0.218-0.2180.0000.0000.0000.000
26A21ALA00.097-0.06918.3670.0150.0150.0000.0000.0000.000
27A21ALA0-0.0640.11717.647-0.001-0.0010.0000.0000.0000.000
28A22LEU00.068-0.11816.370-0.001-0.0010.0000.0000.0000.000
29A22LEU0-0.0830.09314.655-0.016-0.0160.0000.0000.0000.000
30A23ARG00.080-0.10617.347-0.027-0.0270.0000.0000.0000.000
31A23ARG10.6750.96921.8330.2290.2290.0000.0000.0000.000
32A24ASP00.153-0.10120.3930.0010.0010.0000.0000.0000.000
33A24ASP-1-0.923-0.77820.644-0.212-0.2120.0000.0000.0000.000
34A25PHE00.099-0.07715.8840.0380.0380.0000.0000.0000.000
35A25PHE0-0.1050.08411.559-0.027-0.0270.0000.0000.0000.000
36A26LEU00.071-0.09417.0470.0090.0090.0000.0000.0000.000
37A26LEU0-0.0680.08614.914-0.007-0.0070.0000.0000.0000.000
38A27LYS00.048-0.09717.8600.0110.0110.0000.0000.0000.000
39A27LYS10.8171.02522.0210.1760.1760.0000.0000.0000.000
40A28GLU00.030-0.17219.3700.0190.0190.0000.0000.0000.000
41A28GLU-1-0.968-0.83118.155-0.210-0.2100.0000.0000.0000.000
42A29HIS00.049-0.02816.4020.0380.0380.0000.0000.0000.000
43A29HIS10.7150.97615.6490.2480.2480.0000.0000.0000.000
44A30ARG00.193-0.09917.936-0.021-0.0210.0000.0000.0000.000
45A30ARG10.7231.02721.3540.1830.1830.0000.0000.0000.000
46A31GLY0-0.089-0.15119.6540.0270.0270.0000.0000.0000.000
47A32THR0-0.0040.00217.7460.0140.0140.0000.0000.0000.000
48A32THR0-0.0110.09117.313-0.002-0.0020.0000.0000.0000.000
49A33ILE00.082-0.07513.8680.0270.0270.0000.0000.0000.000
50A33ILE0-0.0790.09912.142-0.014-0.0140.0000.0000.0000.000
51A34LEU00.001-0.12213.0480.0380.0380.0000.0000.0000.000
52A34LEU0-0.0970.08413.3090.0010.0010.0000.0000.0000.000
53A35LEU00.084-0.11310.655-0.082-0.0820.0000.0000.0000.000
54A35LEU0-0.0480.12111.100-0.002-0.0020.0000.0000.0000.000
55A36ARG00.179-0.0678.6960.2120.2120.0000.0000.0000.000
56A36ARG10.7641.0227.1260.8390.8390.0000.0000.0000.000
57A37ASP00.113-0.0768.645-0.419-0.4190.0000.0000.0000.000
58A37ASP-1-0.852-0.77811.936-0.868-0.8680.0000.0000.0000.000
59A38ILE00.004-0.1086.8030.3110.3110.0000.0000.0000.000
60A38ILE0-0.1320.0594.486-0.295-0.255-0.001-0.009-0.0300.000
61A39ALA00.179-0.0858.320-0.020-0.0200.0000.0000.0000.000
62A39ALA0-0.0280.12911.2520.0150.0150.0000.0000.0000.000
63A40SER00.032-0.06411.3840.1480.1480.0000.0000.0000.000
64A40SER0-0.0410.05413.472-0.028-0.0280.0000.0000.0000.000
65A41GLU00.126-0.09412.492-0.098-0.0980.0000.0000.0000.000
66A41GLU-1-0.971-0.82215.169-0.258-0.2580.0000.0000.0000.000
67A42HIS00.009-0.10413.562-0.006-0.0060.0000.0000.0000.000
68A42HIS0-0.0780.09315.887-0.009-0.0090.0000.0000.0000.000
69A43LYS00.261-0.02210.1170.0070.0070.0000.0000.0000.000
70A43LYS10.7081.0098.4420.5800.5800.0000.0000.0000.000
71A44VAL00.002-0.15811.443-0.013-0.0130.0000.0000.0000.000
72A44VAL0-0.0760.11315.0390.0130.0130.0000.0000.0000.000
73A45VAL00.101-0.08712.540-0.145-0.1450.0000.0000.0000.000
74A45VAL0-0.0950.08911.1410.0000.0000.0000.0000.0000.000
75A46TYR00.004-0.12413.4500.1000.1000.0000.0000.0000.000
76A46TYR0-0.0080.13213.9280.0310.0310.0000.0000.0000.000
77A47LYS00.142-0.08815.103-0.067-0.0670.0000.0000.0000.000
78A47LYS10.8061.04918.6220.2840.2840.0000.0000.0000.000
79A48PRO00.024-0.09715.8690.0210.0210.0000.0000.0000.000
80A49ILE00.0720.00118.4880.0320.0320.0000.0000.0000.000
81A49ILE0-0.0510.13921.6340.0040.0040.0000.0000.0000.000
82A50PHE00.098-0.07322.257-0.020-0.0200.0000.0000.0000.000
83A50PHE0-0.1430.05420.0310.0060.0060.0000.0000.0000.000
84A51LYS00.152-0.07924.4610.0040.0040.0000.0000.0000.000
85A51LYS10.8221.07826.0220.2240.2240.0000.0000.0000.000
86A52ARG00.075-0.07327.6470.0060.0060.0000.0000.0000.000
87A52ARG10.8671.06131.1360.1320.1320.0000.0000.0000.000
88A53TYR0-0.010-0.10930.5260.0030.0030.0000.0000.0000.000
89A53TYR0-0.0490.10633.7500.0000.0000.0000.0000.0000.000
90A54ASN00.000-0.08728.0100.0080.0080.0000.0000.0000.000
91A54ASN0-0.0310.03627.2590.0030.0030.0000.0000.0000.000
92A55GLY00.139-0.02227.9040.0040.0040.0000.0000.0000.000
93A56ASP00.081-0.02925.176-0.007-0.0070.0000.0000.0000.000
94A56ASP-1-0.939-0.78625.920-0.187-0.1870.0000.0000.0000.000
95A57PRO0-0.021-0.12520.8380.0090.0090.0000.0000.0000.000
96A58ASP00.1670.03322.8280.0090.0090.0000.0000.0000.000
97A58ASP-1-0.985-0.85824.242-0.223-0.2230.0000.0000.0000.000
98A59LEU00.018-0.13221.827-0.025-0.0250.0000.0000.0000.000
99A59LEU0-0.0740.08519.321-0.008-0.0080.0000.0000.0000.000
100A60ILE00.100-0.07122.4020.0300.0300.0000.0000.0000.000
101A60ILE0-0.0830.10323.583-0.002-0.0020.0000.0000.0000.000
102A61GLU00.021-0.13822.956-0.038-0.0380.0000.0000.0000.000
103A61GLU-1-0.989-0.85723.272-0.267-0.2670.0000.0000.0000.000
104A62ASP00.069-0.13724.794-0.008-0.0080.0000.0000.0000.000
105A62ASP-1-0.929-0.82028.183-0.216-0.2160.0000.0000.0000.000
106A63ASN00.067-0.08025.8130.0150.0150.0000.0000.0000.000
107A63ASN0-0.1230.08026.2720.0020.0020.0000.0000.0000.000
108A64SER00.120-0.10223.916-0.025-0.0250.0000.0000.0000.000
109A64SER00.0180.11224.5260.0070.0070.0000.0000.0000.000
110A65ASN00.135-0.05024.410-0.020-0.0200.0000.0000.0000.000
111A65ASN0-0.0920.07228.0950.0010.0010.0000.0000.0000.000
112A66ASP00.152-0.09024.576-0.003-0.0030.0000.0000.0000.000
113A66ASP-1-1.003-0.85123.927-0.261-0.2610.0000.0000.0000.000
114A67VAL00.002-0.12820.601-0.024-0.0240.0000.0000.0000.000
115A67VAL0-0.0930.10419.080-0.006-0.0060.0000.0000.0000.000
116A68GLU00.068-0.14920.223-0.057-0.0570.0000.0000.0000.000
117A68GLU-1-0.942-0.80922.835-0.259-0.2590.0000.0000.0000.000
118A69HIS00.063-0.06321.754-0.013-0.0130.0000.0000.0000.000
119A69HIS0-0.0880.08423.7910.0150.0150.0000.0000.0000.000
120A70TRP00.071-0.10619.5070.0130.0130.0000.0000.0000.000
121A70TRP0-0.0930.08918.574-0.012-0.0120.0000.0000.0000.000
122A71TYR00.199-0.06917.082-0.051-0.0510.0000.0000.0000.000
123A71TYR0-0.1280.06214.6280.0110.0110.0000.0000.0000.000
124A72ASP00.039-0.14317.865-0.041-0.0410.0000.0000.0000.000
125A72ASP-1-0.925-0.79420.900-0.316-0.3160.0000.0000.0000.000
126A73TYR00.084-0.10620.5630.0220.0220.0000.0000.0000.000
127A73TYR0-0.0940.08019.2130.0160.0160.0000.0000.0000.000
128A74HIS0-0.013-0.08816.2340.0320.0320.0000.0000.0000.000
129A74HIS10.7170.91414.5400.6100.6100.0000.0000.0000.000
130A75LEU00.129-0.05916.726-0.002-0.0020.0000.0000.0000.000
131A75LEU0-0.1160.09317.2090.0060.0060.0000.0000.0000.000
132A76GLU00.079-0.15617.6400.0110.0110.0000.0000.0000.000
133A76GLU-1-0.888-0.78322.170-0.233-0.2330.0000.0000.0000.000
134A77ARG00.033-0.07720.2720.0360.0360.0000.0000.0000.000
135A77ARG10.6820.99120.1090.2590.2590.0000.0000.0000.000
136A78TYR00.043-0.08516.6400.0450.0450.0000.0000.0000.000
137A78TYR0-0.0990.05416.0040.0040.0040.0000.0000.0000.000
138A79TRP00.073-0.06615.7700.0170.0170.0000.0000.0000.000
139A79TRP0-0.1790.02410.138-0.063-0.0630.0000.0000.0000.000
140A80ASN00.134-0.08616.8750.0030.0030.0000.0000.0000.000
141A80ASN0-0.1010.10120.823-0.005-0.0050.0000.0000.0000.000
142A81THR0-0.019-0.10419.3810.0190.0190.0000.0000.0000.000
143A81THR0-0.0040.04619.775-0.006-0.0060.0000.0000.0000.000
144A82PRO00.081-0.06319.519-0.023-0.0230.0000.0000.0000.000
145A83GLU0-0.024-0.05518.312-0.022-0.0220.0000.0000.0000.000
146A83GLU-1-0.835-0.77217.761-0.071-0.0710.0000.0000.0000.000
147A84LEU00.102-0.10715.0990.0020.0020.0000.0000.0000.000
148A84LEU0-0.0260.15514.578-0.005-0.0050.0000.0000.0000.000
149A85LYS00.161-0.06914.741-0.072-0.0720.0000.0000.0000.000
150A85LYS10.8691.09318.1390.2710.2710.0000.0000.0000.000
151A86LYS00.099-0.07615.826-0.053-0.0530.0000.0000.0000.000
152A86LYS10.7571.01414.9800.0890.0890.0000.0000.0000.000
153A87GLU00.048-0.15712.090-0.024-0.0240.0000.0000.0000.000
154A87GLU-1-0.984-0.8389.989-0.196-0.1960.0000.0000.0000.000
155A88PHE00.102-0.07810.861-0.108-0.1080.0000.0000.0000.000
156A88PHE0-0.0820.10112.910-0.011-0.0110.0000.0000.0000.000
157A89TYR00.104-0.09811.397-0.156-0.1560.0000.0000.0000.000
158A89TYR0-0.0810.10015.0940.0060.0060.0000.0000.0000.000
159A90LYS00.037-0.08511.610-0.070-0.0700.0000.0000.0000.000
160A90LYS10.8561.04011.1300.1510.1510.0000.0000.0000.000
161A91LYS00.105-0.0757.5440.0300.0300.0000.0000.0000.000
162A91LYS10.6731.0115.9971.3361.3360.0000.0000.0000.000
163A92PHE00.016-0.1357.846-0.313-0.3130.0000.0000.0000.000
164A92PHE0-0.0700.0998.253-0.094-0.0940.0000.0000.0000.000
165A93GLY00.010-0.07510.1000.0050.0050.0000.0000.0000.000
166A94PRO00.0170.00913.245-0.023-0.0230.0000.0000.0000.000
167A95VAL00.0840.00815.819-0.073-0.0730.0000.0000.0000.000
168A95VAL0-0.0220.13017.792-0.001-0.0010.0000.0000.0000.000
169A96ASP00.145-0.08216.8520.0590.0590.0000.0000.0000.000
170A96ASP-1-0.903-0.76816.325-0.495-0.4950.0000.0000.0000.000
171A97LEU00.049-0.13318.178-0.045-0.0450.0000.0000.0000.000
172A97LEU0-0.0110.12821.5040.0010.0010.0000.0000.0000.000
173A98ASN00.052-0.08120.4730.0200.0200.0000.0000.0000.000
174A98ASN0-0.1140.05920.1350.0270.0270.0000.0000.0000.000
175A99GLN00.055-0.09917.3500.0330.0330.0000.0000.0000.000
176A99GLN0-0.1280.06615.236-0.101-0.1010.0000.0000.0000.000
177A100PRO0-0.024-0.10517.8190.0230.0230.0000.0000.0000.000
178A101ILE00.080-0.00418.257-0.078-0.0780.0000.0000.0000.000
179A101ILE0-0.0770.11719.6420.0010.0010.0000.0000.0000.000
180A102ILE00.104-0.10117.1250.0600.0600.0000.0000.0000.000
181A102ILE0-0.1100.06814.506-0.014-0.0140.0000.0000.0000.000
182A103LEU00.108-0.08518.539-0.036-0.0360.0000.0000.0000.000
183A103LEU0-0.0720.12222.0740.0060.0060.0000.0000.0000.000
184A104ALA00.112-0.07317.8390.0160.0160.0000.0000.0000.000
185A104ALA0-0.0870.08117.433-0.016-0.0160.0000.0000.0000.000
186A105LYS00.033-0.11519.3630.0100.0100.0000.0000.0000.000
187A105LYS10.9151.09721.7150.2180.2180.0000.0000.0000.000
188A106PRO00.032-0.08218.908-0.035-0.0350.0000.0000.0000.000
189A107LEU00.074-0.03219.0410.0210.0210.0000.0000.0000.000
190A107LEU0-0.0620.10816.2960.0000.0000.0000.0000.0000.000
191A108ARG00.015-0.06920.4810.0240.0240.0000.0000.0000.000
192A108ARG10.8181.02120.7690.1920.1920.0000.0000.0000.000
193A109GLN00.180-0.06822.874-0.024-0.0240.0000.0000.0000.000
194A109GLN0-0.0980.09726.831-0.006-0.0060.0000.0000.0000.000
195A110HIS00.104-0.12022.5460.0090.0090.0000.0000.0000.000
196A110HIS0-0.1110.10818.946-0.017-0.0170.0000.0000.0000.000
197A111ASN00.118-0.06423.5720.0080.0080.0000.0000.0000.000
198A111ASN0-0.1190.05723.909-0.004-0.0040.0000.0000.0000.000
199A112ARG0-0.010-0.09723.1340.0200.0200.0000.0000.0000.000
200A112ARG10.8971.07722.0810.2420.2420.0000.0000.0000.000
201A113GLY00.066-0.07924.396-0.006-0.0060.0000.0000.0000.000
202A114ASP00.0970.00023.881-0.024-0.0240.0000.0000.0000.000
203A114ASP-1-0.965-0.83125.302-0.190-0.1900.0000.0000.0000.000
204A115LEU00.124-0.14222.938-0.003-0.0030.0000.0000.0000.000
205A115LEU0-0.1180.10422.8100.0050.0050.0000.0000.0000.000
206A116VAL00.002-0.09119.4290.0240.0240.0000.0000.0000.000
207A116VAL0-0.0740.08917.645-0.006-0.0060.0000.0000.0000.000
208A117HIS00.092-0.09719.735-0.003-0.0030.0000.0000.0000.000
209A117HIS0-0.0470.11420.668-0.005-0.0050.0000.0000.0000.000
210A118LEU00.063-0.10715.3360.0010.0010.0000.0000.0000.000
211A118LEU0-0.0880.09513.870-0.021-0.0210.0000.0000.0000.000
212A119LEU00.144-0.12714.8650.0590.0590.0000.0000.0000.000
213A119LEU0-0.1040.14114.371-0.010-0.0100.0000.0000.0000.000
214A120PRO00.029-0.09612.630-0.169-0.1690.0000.0000.0000.000
215A121GLN00.1550.00510.805-0.272-0.2720.0000.0000.0000.000
216A121GLN0-0.1140.10011.7420.0800.0800.0000.0000.0000.000
217A122PHE0-0.031-0.1409.891-0.286-0.2860.0000.0000.0000.000
218A122PHE0-0.0810.11111.4150.0310.0310.0000.0000.0000.000
219A123VAL00.050-0.1008.705-0.173-0.1730.0000.0000.0000.000
220A123VAL0-0.0330.12810.0560.0410.0410.0000.0000.0000.000
221A124VAL00.069-0.0864.9980.0670.070-0.002-0.0040.0020.000
222A124VAL0-0.0840.0693.332-0.240-0.515-0.0020.387-0.1100.000
223A125PRO00.021-0.0766.4120.3450.3450.0000.0000.0000.000
224A126VAL00.050-0.0177.547-0.167-0.1670.0000.0000.0000.000
225A126VAL0-0.1230.0778.4250.0020.0020.0000.0000.0000.000
226A127TYR00.062-0.1199.9730.0020.0020.0000.0000.0000.000
227A127TYR0-0.0530.1218.590-0.022-0.0220.0000.0000.0000.000
228A128ASN00.001-0.09212.6380.0410.0410.0000.0000.0000.000
229A128ASN00.0280.01514.7820.0330.0330.0000.0000.0000.000