FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 98VJ2

Calculation Name: 3B5O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B5O

Chain ID: A

ChEMBL ID:

UniProt ID: D0VWS1

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2802302.123687
FMO2-HF: Nuclear repulsion 2713164.043973
FMO2-HF: Total energy -89138.079714
FMO2-MP2: Total energy -89399.087479


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
2.9747.991.259-2.616-3.658-0.007
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.123 / q_NPA : 0.066
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].
3A2GLU-1-0.855-0.9382.661-5.222-1.9990.908-1.974-2.157-0.007
4A3PHE00.0720.0412.9250.4921.1370.049-0.199-0.4950.000
5A4ASN0-0.036-0.0073.3852.5433.1080.007-0.211-0.3610.000
6A5HIS00.001-0.0026.1580.7780.7780.0000.0000.0000.000
7A6LEU0-0.0110.0167.8420.4150.4150.0000.0000.0000.000
8A7THR00.031-0.0057.3870.3270.3270.0000.0000.0000.000
9A8LYS10.8850.9559.8691.0011.0010.0000.0000.0000.000
10A9GLN0-0.025-0.02611.8750.1910.1910.0000.0000.0000.000
11A10LEU00.0060.00711.6790.1250.1250.0000.0000.0000.000
12A11ASN0-0.002-0.01613.0020.1640.1640.0000.0000.0000.000
13A12GLN0-0.057-0.02415.8350.0410.0410.0000.0000.0000.000
14A13LEU0-0.027-0.00417.3520.0520.0520.0000.0000.0000.000
15A14LEU00.0140.01218.6490.0460.0460.0000.0000.0000.000
16A15ALA0-0.021-0.00920.1680.0350.0350.0000.0000.0000.000
17A16GLN0-0.068-0.02920.931-0.010-0.0100.0000.0000.0000.000
18A17ASP-1-0.815-0.91523.195-0.272-0.2720.0000.0000.0000.000
19A18TYR0-0.099-0.07622.3500.0120.0120.0000.0000.0000.000
20A19VAL00.0450.01925.9370.0000.0000.0000.0000.0000.000
21A20ALA0-0.014-0.00628.0050.0070.0070.0000.0000.0000.000
22A21PHE00.0110.00324.8780.0050.0050.0000.0000.0000.000
23A22SER0-0.029-0.02426.993-0.010-0.0100.0000.0000.0000.000
24A23ILE00.017-0.00328.9400.0130.0130.0000.0000.0000.000
25A24THR0-0.041-0.04431.2970.0120.0120.0000.0000.0000.000
26A25GLU-1-0.859-0.88831.768-0.167-0.1670.0000.0000.0000.000
27A26ASN00.0430.03430.7680.0140.0140.0000.0000.0000.000
28A27PRO0-0.019-0.01532.5120.0080.0080.0000.0000.0000.000
29A28VAL00.0460.01235.1530.0080.0080.0000.0000.0000.000
30A29VAL0-0.015-0.01134.2540.0070.0070.0000.0000.0000.000
31A30GLN0-0.091-0.05736.4530.0090.0090.0000.0000.0000.000
32A31MET0-0.052-0.00938.9250.0050.0050.0000.0000.0000.000
33A32LEU00.0110.00838.0760.0050.0050.0000.0000.0000.000
34A33SER0-0.051-0.02342.1530.0020.0020.0000.0000.0000.000
35A34GLN0-0.050-0.02843.7480.0030.0030.0000.0000.0000.000
36A35ALA0-0.0110.02043.6220.0030.0030.0000.0000.0000.000
37A36SER00.011-0.00145.7080.0010.0010.0000.0000.0000.000
38A37PHE00.0510.00945.735-0.002-0.0020.0000.0000.0000.000
39A38ALA00.0250.00545.111-0.002-0.0020.0000.0000.0000.000
40A39GLN00.0020.02243.961-0.003-0.0030.0000.0000.0000.000
41A40ILE00.0600.02339.445-0.003-0.0030.0000.0000.0000.000
42A41ALA00.0200.01840.259-0.003-0.0030.0000.0000.0000.000
43A42TYR0-0.030-0.03440.6820.0010.0010.0000.0000.0000.000
44A43VAL0-0.015-0.01436.196-0.001-0.0010.0000.0000.0000.000
45A44MET00.0100.01134.555-0.006-0.0060.0000.0000.0000.000
46A45GLN0-0.038-0.02636.977-0.001-0.0010.0000.0000.0000.000
47A46GLN00.0340.02336.591-0.001-0.0010.0000.0000.0000.000
48A47TYR0-0.042-0.04328.0180.0030.0030.0000.0000.0000.000
49A48SER0-0.040-0.03632.519-0.002-0.0020.0000.0000.0000.000
50A49ILE0-0.041-0.02133.2420.0020.0020.0000.0000.0000.000
51A50PHE00.0240.00824.9920.0050.0050.0000.0000.0000.000
52A51PRO00.0350.01927.4490.0000.0000.0000.0000.0000.000
53A52LYS10.8700.93528.0800.0580.0580.0000.0000.0000.000
54A53GLU-1-0.847-0.92729.546-0.050-0.0500.0000.0000.0000.000
55A54LEU0-0.0140.00123.5730.0040.0040.0000.0000.0000.000
56A55VAL00.0310.04524.3320.0000.0000.0000.0000.0000.000
57A56GLY00.0100.00625.3400.0100.0100.0000.0000.0000.000
58A57PHE0-0.011-0.02223.4050.0100.0100.0000.0000.0000.000
59A58THR00.0360.00519.799-0.005-0.0050.0000.0000.0000.000
60A59GLU-1-0.733-0.82521.1660.0380.0380.0000.0000.0000.000
61A60LEU0-0.078-0.03523.2230.0180.0180.0000.0000.0000.000
62A61ALA00.0310.01317.9180.0170.0170.0000.0000.0000.000
63A62ARG10.8380.90518.542-0.014-0.0140.0000.0000.0000.000
64A63ARG10.8170.88719.8370.0020.0020.0000.0000.0000.000
65A64LYS10.7690.88419.0070.0240.0240.0000.0000.0000.000
66A65ALA00.0270.00915.6920.0250.0250.0000.0000.0000.000
67A66LEU0-0.031-0.02216.9540.0490.0490.0000.0000.0000.000
68A67GLY0-0.050-0.01619.5490.0240.0240.0000.0000.0000.000
69A68ALA0-0.0180.00215.8240.0050.0050.0000.0000.0000.000
70A69GLY0-0.012-0.00316.1250.0580.0580.0000.0000.0000.000
71A70TRP00.0170.00510.9650.0630.0630.0000.0000.0000.000
72A71ASN0-0.014-0.03214.121-0.074-0.0740.0000.0000.0000.000
73A72GLY00.0190.00912.922-0.045-0.0450.0000.0000.0000.000
74A73VAL00.0200.00710.800-0.057-0.0570.0000.0000.0000.000
75A74ALA0-0.013-0.01113.445-0.059-0.0590.0000.0000.0000.000
76A75GLN0-0.085-0.05316.322-0.015-0.0150.0000.0000.0000.000
77A76GLU-1-0.820-0.90813.516-0.166-0.1660.0000.0000.0000.000
78A77LEU0-0.018-0.01115.875-0.032-0.0320.0000.0000.0000.000
79A78GLN0-0.064-0.03718.167-0.003-0.0030.0000.0000.0000.000
80A79GLU-1-0.853-0.91019.0590.0300.0300.0000.0000.0000.000
81A80ASN0-0.060-0.04316.866-0.034-0.0340.0000.0000.0000.000
82A81ILE0-0.029-0.01120.796-0.006-0.0060.0000.0000.0000.000
83A82ASP-1-0.856-0.93323.8310.0060.0060.0000.0000.0000.000
84A83GLU-1-0.840-0.88222.664-0.083-0.0830.0000.0000.0000.000
85A84GLU-1-0.860-0.92223.873-0.116-0.1160.0000.0000.0000.000
86A85MET0-0.069-0.05126.4960.0050.0050.0000.0000.0000.000
87A86GLY00.0430.02928.2790.0040.0040.0000.0000.0000.000
88A87SER0-0.070-0.02725.2390.0010.0010.0000.0000.0000.000
89A88THR0-0.043-0.04525.1810.0070.0070.0000.0000.0000.000
90A89THR0-0.048-0.03828.442-0.002-0.0020.0000.0000.0000.000
91A90GLY0-0.017-0.01131.6290.0020.0020.0000.0000.0000.000
92A91GLY0-0.030-0.01332.4760.0050.0050.0000.0000.0000.000
93A92ILE0-0.045-0.01733.6450.0010.0010.0000.0000.0000.000
94A93SER00.0240.02431.173-0.007-0.0070.0000.0000.0000.000
95A94HIS00.0840.01925.3880.0060.0060.0000.0000.0000.000
96A95TYR0-0.012-0.00130.5620.0010.0010.0000.0000.0000.000
97A96THR0-0.017-0.00432.7260.0010.0010.0000.0000.0000.000
98A97LEU0-0.015-0.00231.6200.0010.0010.0000.0000.0000.000
99A98LEU00.0170.01432.120-0.001-0.0010.0000.0000.0000.000
100A99ALA0-0.010-0.01834.9550.0010.0010.0000.0000.0000.000
101A100ASP-1-0.838-0.92137.897-0.044-0.0440.0000.0000.0000.000
102A101GLY00.0100.01638.4820.0020.0020.0000.0000.0000.000
103A102LEU00.012-0.00936.9080.0000.0000.0000.0000.0000.000
104A103GLU-1-0.813-0.90140.587-0.045-0.0450.0000.0000.0000.000
105A104GLU-1-0.978-0.99842.999-0.048-0.0480.0000.0000.0000.000
106A105GLY0-0.009-0.01043.0850.0010.0010.0000.0000.0000.000
107A106LEU0-0.054-0.01841.7290.0000.0000.0000.0000.0000.000
108A107GLY0-0.0190.00345.6230.0020.0020.0000.0000.0000.000
109A108VAL0-0.057-0.02742.3040.0020.0020.0000.0000.0000.000
110A109ALA0-0.016-0.00842.918-0.002-0.0020.0000.0000.0000.000
111A110VAL00.0260.02338.140-0.002-0.0020.0000.0000.0000.000
112A111LYS10.7990.89839.4470.0450.0450.0000.0000.0000.000
113A112ASN0-0.084-0.05040.5770.0010.0010.0000.0000.0000.000
114A113THR0-0.0010.00139.0810.0020.0020.0000.0000.0000.000
115A114MET0-0.038-0.01639.4630.0000.0000.0000.0000.0000.000
116A115PRO00.000-0.00636.468-0.003-0.0030.0000.0000.0000.000
117A116SER0-0.018-0.02038.3410.0030.0030.0000.0000.0000.000
118A117VAL0-0.022-0.01638.5260.0010.0010.0000.0000.0000.000
119A118ALA00.0310.01435.699-0.001-0.0010.0000.0000.0000.000
120A119THR00.0230.00633.548-0.007-0.0070.0000.0000.0000.000
121A120SER0-0.027-0.01533.6680.0000.0000.0000.0000.0000.000
122A121LYS10.8190.88333.0130.0980.0980.0000.0000.0000.000
123A122LEU00.0180.03927.539-0.001-0.0010.0000.0000.0000.000
124A123LEU00.0260.01029.530-0.003-0.0030.0000.0000.0000.000
125A124ARG10.9050.95029.7630.0510.0510.0000.0000.0000.000
126A125THR0-0.025-0.01727.1800.0030.0030.0000.0000.0000.000
127A126VAL00.0440.03024.206-0.003-0.0030.0000.0000.0000.000
128A127LEU00.0100.01025.037-0.001-0.0010.0000.0000.0000.000
129A128SER0-0.105-0.07026.0580.0040.0040.0000.0000.0000.000
130A129LEU0-0.025-0.00521.8770.0020.0020.0000.0000.0000.000
131A130PHE00.025-0.02120.2440.0020.0020.0000.0000.0000.000
132A131ASP-1-0.843-0.91322.5480.0000.0000.0000.0000.0000.000
133A132ARG10.7620.88320.3970.1190.1190.0000.0000.0000.000
134A133GLN0-0.065-0.05215.6900.0100.0100.0000.0000.0000.000
135A134VAL00.0390.01714.158-0.035-0.0350.0000.0000.0000.000
136A135ASP-1-0.757-0.88812.1790.0110.0110.0000.0000.0000.000
137A136TYR0-0.0170.01013.748-0.072-0.0720.0000.0000.0000.000
138A137VAL0-0.0260.00516.533-0.033-0.0330.0000.0000.0000.000
139A138LEU00.0180.01212.475-0.019-0.0190.0000.0000.0000.000
140A139GLY00.0140.01613.493-0.070-0.0700.0000.0000.0000.000
141A140ALA0-0.019-0.01714.383-0.032-0.0320.0000.0000.0000.000
142A141THR0-0.005-0.03815.7820.0120.0120.0000.0000.0000.000
143A142TYR0-0.092-0.07111.711-0.112-0.1120.0000.0000.0000.000
144A143ALA00.0120.00714.582-0.030-0.0300.0000.0000.0000.000
145A144ILE00.0280.03817.5730.0130.0130.0000.0000.0000.000
146A145GLU-1-0.815-0.88213.500-0.582-0.5820.0000.0000.0000.000
147A146ALA0-0.007-0.00915.9130.0040.0040.0000.0000.0000.000
148A147THR0-0.039-0.05017.6690.0250.0250.0000.0000.0000.000
149A148SER0-0.009-0.00920.8300.0300.0300.0000.0000.0000.000
150A149ILE00.0330.02819.6920.0170.0170.0000.0000.0000.000
151A150PRO0-0.0080.00922.1550.0220.0220.0000.0000.0000.000
152A151GLU-1-0.762-0.87624.830-0.147-0.1470.0000.0000.0000.000
153A152LEU00.0170.01426.2100.0170.0170.0000.0000.0000.000
154A153THR0-0.011-0.02226.7450.0120.0120.0000.0000.0000.000
155A154LEU0-0.048-0.02428.5490.0120.0120.0000.0000.0000.000
156A155ILE0-0.024-0.01230.3100.0120.0120.0000.0000.0000.000
157A156VAL0-0.0130.00931.5420.0090.0090.0000.0000.0000.000
158A157LYS10.9460.99233.5710.1330.1330.0000.0000.0000.000
159A158LEU0-0.037-0.02934.4830.0080.0080.0000.0000.0000.000
160A159VAL00.007-0.00236.2470.0080.0080.0000.0000.0000.000
161A160GLU-1-0.930-0.97036.826-0.103-0.1030.0000.0000.0000.000
162A161TRP0-0.071-0.03239.6010.0050.0050.0000.0000.0000.000
163A162LEU0-0.037-0.01440.1640.0040.0040.0000.0000.0000.000
164A163HIS0-0.030-0.02840.6880.0080.0080.0000.0000.0000.000
165A164GLU-1-0.934-0.95844.303-0.059-0.0590.0000.0000.0000.000
166A165GLY0-0.063-0.04345.7060.0020.0020.0000.0000.0000.000
167A166ALA0-0.061-0.02842.930-0.003-0.0030.0000.0000.0000.000
168A167ILE00.0430.03436.7290.0030.0030.0000.0000.0000.000
169A168PRO00.0150.01940.0780.0000.0000.0000.0000.0000.000
170A169LYS10.8160.88238.7820.0460.0460.0000.0000.0000.000
171A170ASP-1-0.810-0.89136.603-0.057-0.0570.0000.0000.0000.000
172A171LEU00.0290.03534.939-0.004-0.0040.0000.0000.0000.000
173A172GLN00.0030.00333.740-0.004-0.0040.0000.0000.0000.000
174A173TYR0-0.033-0.01830.008-0.008-0.0080.0000.0000.0000.000
175A174PHE00.010-0.00228.883-0.007-0.0070.0000.0000.0000.000
176A175PHE00.0480.01529.460-0.009-0.0090.0000.0000.0000.000
177A176SER00.026-0.02428.701-0.008-0.0080.0000.0000.0000.000
178A177LYS10.7100.84425.8160.0890.0890.0000.0000.0000.000
179A178HIS0-0.058-0.03023.775-0.005-0.0050.0000.0000.0000.000
180A179LEU0-0.060-0.02224.215-0.022-0.0220.0000.0000.0000.000
181A180ASP-1-0.953-0.93325.613-0.145-0.1450.0000.0000.0000.000
182A188ALA00.010-0.01311.1880.0070.0070.0000.0000.0000.000
183A189GLY00.0770.06310.171-0.094-0.0940.0000.0000.0000.000
184A190LEU00.0630.05610.9030.0370.0370.0000.0000.0000.000
185A191ARG10.8910.9456.9751.5211.5210.0000.0000.0000.000
186A192THR0-0.075-0.0646.047-0.261-0.2610.0000.0000.0000.000
187A193SER00.005-0.0096.6240.3840.3840.0000.0000.0000.000
188A194VAL00.018-0.0027.5140.2840.2840.0000.0000.0000.000
189A195ALA0-0.046-0.0172.607-0.379-0.0690.294-0.184-0.4190.000
190A196ALA0-0.043-0.0094.0422.1172.3900.001-0.048-0.2260.000
191A197TYR0-0.032-0.0086.594-0.030-0.0300.0000.0000.0000.000
192A198ILE0-0.0360.0105.858-0.068-0.0680.0000.0000.0000.000
193A199GLN0-0.028-0.0196.5300.4280.4280.0000.0000.0000.000
194A200PRO0-0.005-0.0236.344-0.255-0.2550.0000.0000.0000.000
195A201GLU-1-0.911-0.9568.6240.1830.1830.0000.0000.0000.000
196A202GLU-1-0.844-0.91211.327-0.013-0.0130.0000.0000.0000.000
197A203PHE0-0.042-0.0345.022-0.230-0.2300.0000.0000.0000.000
198A204GLY00.0000.00810.926-0.048-0.0480.0000.0000.0000.000
199A205GLU-1-0.758-0.86214.718-0.134-0.1340.0000.0000.0000.000
200A206PHE0-0.0110.00610.678-0.048-0.0480.0000.0000.0000.000
201A207ALA00.010-0.00813.308-0.016-0.0160.0000.0000.0000.000
202A208ALA0-0.021-0.00814.6480.0240.0240.0000.0000.0000.000
203A209GLY00.0220.00616.9090.0260.0260.0000.0000.0000.000
204A210PHE0-0.022-0.00414.6260.0080.0080.0000.0000.0000.000
205A211ARG10.8100.89217.0930.3100.3100.0000.0000.0000.000
206A212ALA00.0220.01119.8510.0200.0200.0000.0000.0000.000
207A213MET0-0.0080.01020.0880.0310.0310.0000.0000.0000.000
208A214ILE00.0220.01119.5180.0140.0140.0000.0000.0000.000
209A215ASP-1-0.836-0.89022.607-0.202-0.2020.0000.0000.0000.000
210A216ALA0-0.036-0.01425.1510.0160.0160.0000.0000.0000.000
211A217MET00.0040.00723.7520.0090.0090.0000.0000.0000.000
212A218GLN00.0340.02226.6290.0070.0070.0000.0000.0000.000
213A219VAL0-0.010-0.01128.3700.0120.0120.0000.0000.0000.000
214A220TRP0-0.023-0.00629.5870.0080.0080.0000.0000.0000.000
215A221TRP00.012-0.00328.3780.0150.0150.0000.0000.0000.000
216A222GLN0-0.043-0.03131.9150.0030.0030.0000.0000.0000.000
217A223GLU-1-0.843-0.90334.577-0.088-0.0880.0000.0000.0000.000
218A224LEU0-0.0050.00634.6690.0070.0070.0000.0000.0000.000
219A225ALA00.0300.01836.6070.0050.0050.0000.0000.0000.000
220A226GLN0-0.043-0.03138.4030.0040.0040.0000.0000.0000.000
221A227GLU-1-0.762-0.85139.539-0.068-0.0680.0000.0000.0000.000
222A228ALA00.0110.02740.5970.0050.0050.0000.0000.0000.000
223A229ILE0-0.013-0.01642.4460.0040.0040.0000.0000.0000.000
224A230SER0-0.092-0.06644.6020.0040.0040.0000.0000.0000.000
225A231SER0-0.021-0.03946.5850.0020.0020.0000.0000.0000.000
226A232GLU-1-0.876-0.90148.766-0.051-0.0510.0000.0000.0000.000
227A233VAL0-0.075-0.02848.6050.0010.0010.0000.0000.0000.000
228A234VAL0-0.004-0.00251.7320.0020.0020.0000.0000.0000.000
229A235LEU00.0030.00853.114-0.001-0.0010.0000.0000.0000.000
230A236SER0-0.057-0.02954.6380.0010.0010.0000.0000.0000.000