FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 3JVYL

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:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2792522.26051
FMO2-HF: Nuclear repulsion 2703384.919901
FMO2-HF: Total energy -89137.340609
FMO2-MP2: Total energy -89398.356349


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.
1.1544.7051.061-1.744-2.8690.001
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 : 0.059 / q_NPA : 0.019
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-1-0.852-0.9293.819-0.7250.5250.001-0.518-0.7340.000
4A3PHE00.0700.0362.884-0.8520.0460.115-0.357-0.6560.002
5A4ASN0-0.030-0.0263.616-0.905-0.1070.010-0.292-0.517-0.001
6A5HIS0-0.006-0.0065.1490.4640.570-0.001-0.008-0.0960.000
7A6LEU0-0.0010.0197.6120.1910.1910.0000.0000.0000.000
8A7THR00.0250.0026.9530.0240.0240.0000.0000.0000.000
9A8LYS10.9040.9759.1170.5710.5710.0000.0000.0000.000
10A9GLN00.010-0.00711.1290.0740.0740.0000.0000.0000.000
11A10LEU0-0.023-0.00811.4740.0540.0540.0000.0000.0000.000
12A11ASN0-0.008-0.02912.1220.0710.0710.0000.0000.0000.000
13A12GLN0-0.014-0.00815.1940.0130.0130.0000.0000.0000.000
14A13LEU0-0.022-0.00216.8880.0280.0280.0000.0000.0000.000
15A14LEU0-0.010-0.00118.1870.0210.0210.0000.0000.0000.000
16A15ALA0-0.029-0.02219.5250.0140.0140.0000.0000.0000.000
17A16GLN0-0.102-0.04220.821-0.006-0.0060.0000.0000.0000.000
18A17ASP-1-0.893-0.94622.864-0.092-0.0920.0000.0000.0000.000
19A18TYR0-0.105-0.06622.1260.0110.0110.0000.0000.0000.000
20A19VAL00.0570.02425.540-0.005-0.0050.0000.0000.0000.000
21A20ALA0-0.035-0.01127.2350.0000.0000.0000.0000.0000.000
22A21PHE00.0390.01423.9310.0010.0010.0000.0000.0000.000
23A22SER00.0170.03425.810-0.010-0.0100.0000.0000.0000.000
24A23ILE00.0270.00027.9990.0080.0080.0000.0000.0000.000
25A24THR0-0.032-0.02730.2000.0050.0050.0000.0000.0000.000
26A25GLU-1-0.943-0.97430.930-0.070-0.0700.0000.0000.0000.000
27A26ASN00.0150.01629.9660.0090.0090.0000.0000.0000.000
28A27PRO0-0.004-0.01431.9360.0020.0020.0000.0000.0000.000
29A28VAL00.0390.01234.4650.0030.0030.0000.0000.0000.000
30A29VAL0-0.022-0.01533.2940.0020.0020.0000.0000.0000.000
31A30GLN0-0.082-0.05335.7940.0050.0050.0000.0000.0000.000
32A31MET0-0.0710.00038.0740.0030.0030.0000.0000.0000.000
33A32LEU00.000-0.01137.5200.0020.0020.0000.0000.0000.000
34A33SER0-0.059-0.02641.4090.0010.0010.0000.0000.0000.000
35A34GLN0-0.021-0.01443.7160.0000.0000.0000.0000.0000.000
36A35ALA0-0.0220.01942.8980.0020.0020.0000.0000.0000.000
37A36SER00.0440.01544.948-0.001-0.0010.0000.0000.0000.000
38A37PHE00.0620.01544.854-0.001-0.0010.0000.0000.0000.000
39A38ALA00.011-0.00344.311-0.001-0.0010.0000.0000.0000.000
40A39GLN00.0060.01043.481-0.001-0.0010.0000.0000.0000.000
41A40ILE00.0580.02538.767-0.001-0.0010.0000.0000.0000.000
42A41ALA00.0150.01139.617-0.002-0.0020.0000.0000.0000.000
43A42TYR0-0.040-0.03839.9790.0010.0010.0000.0000.0000.000
44A43VAL00.001-0.00535.6170.0000.0000.0000.0000.0000.000
45A44MET00.0080.01333.728-0.002-0.0020.0000.0000.0000.000
46A45GLN0-0.027-0.02136.1760.0000.0000.0000.0000.0000.000
47A46GLN00.0430.03735.9970.0020.0020.0000.0000.0000.000
48A47TYR0-0.048-0.06027.4620.0030.0030.0000.0000.0000.000
49A48SER0-0.029-0.02931.7550.0000.0000.0000.0000.0000.000
50A49ILE0-0.032-0.02332.5970.0010.0010.0000.0000.0000.000
51A50PHE00.0170.00124.9080.0040.0040.0000.0000.0000.000
52A51PRO00.0610.02827.1260.0020.0020.0000.0000.0000.000
53A52LYS10.8990.97027.8830.0220.0220.0000.0000.0000.000
54A53GLU-1-0.943-0.98929.109-0.009-0.0090.0000.0000.0000.000
55A54LEU00.0000.00523.2280.0060.0060.0000.0000.0000.000
56A55VAL00.0280.03824.1150.0020.0020.0000.0000.0000.000
57A56GLY00.0070.00425.0050.0060.0060.0000.0000.0000.000
58A57PHE00.011-0.01323.4380.0090.0090.0000.0000.0000.000
59A58THR00.0410.01419.4950.0060.0060.0000.0000.0000.000
60A59GLU-1-0.732-0.82221.0280.0320.0320.0000.0000.0000.000
61A60LEU0-0.058-0.03023.1640.0120.0120.0000.0000.0000.000
62A61ALA00.0190.01317.8880.0160.0160.0000.0000.0000.000
63A62ARG10.8430.91218.656-0.007-0.0070.0000.0000.0000.000
64A63ARG10.8180.88419.747-0.021-0.0210.0000.0000.0000.000
65A64LYS10.8590.94119.123-0.078-0.0780.0000.0000.0000.000
66A65ALA00.0280.01315.5210.0240.0240.0000.0000.0000.000
67A66LEU0-0.021-0.01916.9930.0230.0230.0000.0000.0000.000
68A67GLY0-0.058-0.01819.2950.0110.0110.0000.0000.0000.000
69A68ALA0-0.029-0.00316.2970.0020.0020.0000.0000.0000.000
70A69GLY0-0.009-0.00416.4060.0370.0370.0000.0000.0000.000
71A70TRP00.001-0.00211.8140.0210.0210.0000.0000.0000.000
72A71ASN0-0.020-0.03413.980-0.048-0.0480.0000.0000.0000.000
73A72GLY00.0210.00312.263-0.029-0.0290.0000.0000.0000.000
74A73VAL00.0130.01910.835-0.033-0.0330.0000.0000.0000.000
75A74ALA0-0.020-0.01613.231-0.029-0.0290.0000.0000.0000.000
76A75GLN0-0.066-0.03015.8550.0010.0010.0000.0000.0000.000
77A76GLU-1-0.843-0.92913.122-0.172-0.1720.0000.0000.0000.000
78A77LEU0-0.045-0.02815.720-0.007-0.0070.0000.0000.0000.000
79A78GLN0-0.078-0.04617.8470.0080.0080.0000.0000.0000.000
80A79GLU-1-0.874-0.92818.363-0.074-0.0740.0000.0000.0000.000
81A80ASN00.0250.01616.409-0.010-0.0100.0000.0000.0000.000
82A81ILE0-0.047-0.01920.3010.0020.0020.0000.0000.0000.000
83A82ASP-1-0.868-0.94223.394-0.023-0.0230.0000.0000.0000.000
84A83GLU-1-0.822-0.88022.641-0.093-0.0930.0000.0000.0000.000
85A84GLU-1-0.867-0.93323.160-0.075-0.0750.0000.0000.0000.000
86A85MET0-0.084-0.05725.8320.0060.0060.0000.0000.0000.000
87A86GLY00.0370.02027.9480.0040.0040.0000.0000.0000.000
88A87SER0-0.088-0.03025.013-0.001-0.0010.0000.0000.0000.000
89A88THR0-0.052-0.05024.5470.0030.0030.0000.0000.0000.000
90A89THR0-0.048-0.03627.886-0.004-0.0040.0000.0000.0000.000
91A90GLY0-0.019-0.01430.9110.0030.0030.0000.0000.0000.000
92A91GLY0-0.026-0.01132.0150.0040.0040.0000.0000.0000.000
93A92ILE0-0.042-0.00933.2670.0030.0030.0000.0000.0000.000
94A93SER00.0290.02830.494-0.004-0.0040.0000.0000.0000.000
95A94HIS00.0960.01724.7000.0020.0020.0000.0000.0000.000
96A95TYR0-0.0040.00029.8090.0020.0020.0000.0000.0000.000
97A96THR0-0.016-0.01631.8580.0010.0010.0000.0000.0000.000
98A97LEU00.0090.01631.0670.0010.0010.0000.0000.0000.000
99A98LEU00.0210.02331.5370.0000.0000.0000.0000.0000.000
100A99ALA0-0.036-0.03134.2750.0020.0020.0000.0000.0000.000
101A100ASP-1-0.874-0.95437.180-0.029-0.0290.0000.0000.0000.000
102A101GLY00.0070.00837.5970.0010.0010.0000.0000.0000.000
103A102LEU0-0.010-0.02136.1990.0000.0000.0000.0000.0000.000
104A103GLU-1-0.838-0.91639.769-0.024-0.0240.0000.0000.0000.000
105A104GLU-1-0.993-0.99842.150-0.035-0.0350.0000.0000.0000.000
106A105GLY0-0.018-0.01342.2150.0010.0010.0000.0000.0000.000
107A106LEU0-0.062-0.02940.6500.0010.0010.0000.0000.0000.000
108A107GLY0-0.0220.00444.5920.0010.0010.0000.0000.0000.000
109A108VAL0-0.071-0.02841.4810.0020.0020.0000.0000.0000.000
110A109ALA00.0140.00642.392-0.001-0.0010.0000.0000.0000.000
111A110VAL00.0570.02837.2350.0000.0000.0000.0000.0000.000
112A111LYS10.8160.96538.9530.0280.0280.0000.0000.0000.000
113A112ASN0-0.089-0.05540.2730.0010.0010.0000.0000.0000.000
114A113THR00.002-0.03038.7240.0010.0010.0000.0000.0000.000
115A114MET0-0.043-0.02339.2370.0010.0010.0000.0000.0000.000
116A115PRO00.009-0.00436.109-0.002-0.0020.0000.0000.0000.000
117A116SER0-0.013-0.01038.1180.0020.0020.0000.0000.0000.000
118A117VAL0-0.008-0.01438.2940.0010.0010.0000.0000.0000.000
119A118ALA00.0270.01835.5130.0020.0020.0000.0000.0000.000
120A119THR00.0260.00133.202-0.001-0.0010.0000.0000.0000.000
121A120SER0-0.021-0.00633.4840.0020.0020.0000.0000.0000.000
122A121LYS10.8370.90633.0130.0180.0180.0000.0000.0000.000
123A122LEU00.0250.02627.5230.0040.0040.0000.0000.0000.000
124A123LEU00.0330.01229.4910.0030.0030.0000.0000.0000.000
125A124ARG10.9160.95329.993-0.001-0.0010.0000.0000.0000.000
126A125THR0-0.040-0.01927.2590.0050.0050.0000.0000.0000.000
127A126VAL00.0420.02624.2790.0050.0050.0000.0000.0000.000
128A127LEU00.0120.01325.3200.0050.0050.0000.0000.0000.000
129A128SER0-0.102-0.05926.5510.0080.0080.0000.0000.0000.000
130A129LEU0-0.032-0.01722.1380.0100.0100.0000.0000.0000.000
131A130PHE0-0.002-0.02120.2150.0140.0140.0000.0000.0000.000
132A131ASP-1-0.882-0.93023.0400.0510.0510.0000.0000.0000.000
133A132ARG10.8100.92721.393-0.072-0.0720.0000.0000.0000.000
134A133GLN0-0.071-0.04716.639-0.030-0.0300.0000.0000.0000.000
135A134VAL00.0560.02114.903-0.016-0.0160.0000.0000.0000.000
136A135ASP-1-0.758-0.89612.8360.4000.4000.0000.0000.0000.000
137A136TYR0-0.0060.01114.348-0.031-0.0310.0000.0000.0000.000
138A137VAL0-0.022-0.00717.021-0.029-0.0290.0000.0000.0000.000
139A138LEU00.0230.00312.599-0.030-0.0300.0000.0000.0000.000
140A139GLY00.0160.02713.522-0.039-0.0390.0000.0000.0000.000
141A140ALA00.001-0.00814.464-0.042-0.0420.0000.0000.0000.000
142A141THR0-0.015-0.03215.690-0.017-0.0170.0000.0000.0000.000
143A142TYR0-0.025-0.01111.012-0.062-0.0620.0000.0000.0000.000
144A143ALA00.0110.00614.262-0.035-0.0350.0000.0000.0000.000
145A144ILE00.0120.02417.128-0.008-0.0080.0000.0000.0000.000
146A145GLU-1-0.868-0.92813.071-0.315-0.3150.0000.0000.0000.000
147A146ALA0-0.051-0.03315.008-0.013-0.0130.0000.0000.0000.000
148A147THR0-0.045-0.04116.6580.0010.0010.0000.0000.0000.000
149A148SER00.0190.01019.6700.0110.0110.0000.0000.0000.000
150A149ILE00.0430.02519.0720.0090.0090.0000.0000.0000.000
151A150PRO0-0.004-0.00420.9740.0130.0130.0000.0000.0000.000
152A151GLU-1-0.848-0.88823.768-0.067-0.0670.0000.0000.0000.000
153A152LEU00.0140.01025.0670.0090.0090.0000.0000.0000.000
154A153THR0-0.013-0.02125.5980.0050.0050.0000.0000.0000.000
155A154LEU0-0.041-0.02327.6710.0070.0070.0000.0000.0000.000
156A155ILE0-0.016-0.00329.4140.0070.0070.0000.0000.0000.000
157A156VAL00.0220.02130.3850.0050.0050.0000.0000.0000.000
158A157LYS10.9470.98732.4810.0700.0700.0000.0000.0000.000
159A158LEU0-0.032-0.02333.9510.0050.0050.0000.0000.0000.000
160A159VAL00.009-0.00535.1630.0040.0040.0000.0000.0000.000
161A160GLU-1-0.947-0.97935.889-0.063-0.0630.0000.0000.0000.000
162A161TRP0-0.082-0.03438.4670.0030.0030.0000.0000.0000.000
163A162LEU0-0.052-0.02839.1780.0030.0030.0000.0000.0000.000
164A163HIS0-0.041-0.02139.8100.0040.0040.0000.0000.0000.000
165A164GLU-1-0.903-0.93843.153-0.034-0.0340.0000.0000.0000.000
166A165GLY0-0.054-0.03445.5610.0000.0000.0000.0000.0000.000
167A166ALA0-0.057-0.03042.104-0.002-0.0020.0000.0000.0000.000
168A167ILE00.0400.02935.7530.0020.0020.0000.0000.0000.000
169A168PRO00.0200.01939.597-0.001-0.0010.0000.0000.0000.000
170A169LYS10.8940.93537.4190.0430.0430.0000.0000.0000.000
171A170ASP-1-0.854-0.92636.316-0.047-0.0470.0000.0000.0000.000
172A171LEU00.0060.01633.863-0.003-0.0030.0000.0000.0000.000
173A172GLN00.0120.00533.2860.0000.0000.0000.0000.0000.000
174A173TYR0-0.027-0.00929.467-0.006-0.0060.0000.0000.0000.000
175A174PHE00.011-0.00228.050-0.006-0.0060.0000.0000.0000.000
176A175PHE00.0560.01828.660-0.006-0.0060.0000.0000.0000.000
177A176SER00.020-0.00228.125-0.006-0.0060.0000.0000.0000.000
178A177LYS10.7210.86625.2390.0790.0790.0000.0000.0000.000
179A178HIS0-0.063-0.03122.993-0.009-0.0090.0000.0000.0000.000
180A179LEU0-0.062-0.02823.277-0.015-0.0150.0000.0000.0000.000
181A180ASP-1-0.973-0.96724.442-0.113-0.1130.0000.0000.0000.000
182A188ALA00.011-0.00810.091-0.002-0.0020.0000.0000.0000.000
183A189GLY00.0740.0539.308-0.112-0.1120.0000.0000.0000.000
184A190LEU00.0770.04810.5460.0110.0110.0000.0000.0000.000
185A191ARG10.9120.9595.0971.6061.6060.0000.0000.0000.000
186A192THR0-0.080-0.0615.468-0.032-0.0320.0000.0000.0000.000
187A193SER00.0400.0286.1930.0970.0970.0000.0000.0000.000
188A194VAL00.032-0.0017.6540.1470.1470.0000.0000.0000.000
189A195ALA0-0.057-0.0232.503-0.325-0.0100.937-0.539-0.7130.000
190A196ALA0-0.048-0.0154.2070.9401.124-0.001-0.030-0.1530.000
191A197TYR0-0.0240.0006.0330.0170.0170.0000.0000.0000.000
192A198ILE0-0.0410.0096.422-0.024-0.0240.0000.0000.0000.000
193A199GLN0-0.011-0.0127.3770.5120.5120.0000.0000.0000.000
194A200PRO00.006-0.0167.619-0.126-0.1260.0000.0000.0000.000
195A201GLU-1-0.935-0.9709.8860.4610.4610.0000.0000.0000.000
196A202GLU-1-0.849-0.91512.2140.2340.2340.0000.0000.0000.000
197A203PHE0-0.041-0.0325.941-0.129-0.1290.0000.0000.0000.000
198A204GLY0-0.010-0.00611.549-0.096-0.0960.0000.0000.0000.000
199A205GLU-1-0.830-0.92115.1180.0820.0820.0000.0000.0000.000
200A206PHE0-0.0140.00410.539-0.043-0.0430.0000.0000.0000.000
201A207ALA0-0.009-0.02113.596-0.060-0.0600.0000.0000.0000.000
202A208ALA0-0.0060.00114.792-0.031-0.0310.0000.0000.0000.000
203A209GLY00.0270.01617.115-0.016-0.0160.0000.0000.0000.000
204A210PHE0-0.013-0.00414.489-0.020-0.0200.0000.0000.0000.000
205A211ARG10.9110.94417.0630.0440.0440.0000.0000.0000.000
206A212ALA00.0060.01019.789-0.005-0.0050.0000.0000.0000.000
207A213MET0-0.023-0.00319.9110.0030.0030.0000.0000.0000.000
208A214ILE00.0190.00719.315-0.004-0.0040.0000.0000.0000.000
209A215ASP-1-0.832-0.89422.291-0.041-0.0410.0000.0000.0000.000
210A216ALA0-0.039-0.01724.9760.0010.0010.0000.0000.0000.000
211A217MET0-0.012-0.00223.3140.0020.0020.0000.0000.0000.000
212A218GLN00.0500.02026.346-0.007-0.0070.0000.0000.0000.000
213A219VAL0-0.024-0.01328.0300.0020.0020.0000.0000.0000.000
214A220TRP0-0.0120.00428.9210.0010.0010.0000.0000.0000.000
215A221TRP00.0450.01927.8570.0030.0030.0000.0000.0000.000
216A222GLN0-0.028-0.02431.9820.0040.0040.0000.0000.0000.000
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