Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: MV69Z

Calculation Name: 3OSY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OSY

Chain ID: A

ChEMBL ID:

UniProt ID: B8YLV9

Base Structure: X-ray

Registration Date: 2023-06-21

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 187
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004390.197978
FMO2-HF: Nuclear repulsion 1931787.769139
FMO2-HF: Total energy -72602.428839
FMO2-MP2: Total energy -72812.468795


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:-5:PRO)


Summations of interaction energy for fragment #1(A:-5: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.
-10.251-3.9093.608-3.475-6.474-0.011
Interaction energy analysis for fragmet #1(A:-5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.022
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].
3A-3GLY00.0380.0363.428-2.3230.422-0.016-1.434-1.2960.001
4A-2SER00.0390.0025.413-0.566-0.5660.0000.0000.0000.000
5A-1HIS0-0.021-0.0173.1090.4090.8320.062-0.129-0.3560.000
6A0MET0-0.0050.0122.408-0.6560.5331.137-0.595-1.730-0.007
7A1GLY00.0070.0145.4610.2590.2590.0000.0000.0000.000
8A2PRO00.009-0.0098.8770.0890.0890.0000.0000.0000.000
9A3SER00.001-0.0047.0170.2900.2900.0000.0000.0000.000
10A4LEU00.0300.0125.2020.1440.1440.0000.0000.0000.000
11A5ASP-1-0.909-0.9469.149-0.130-0.1300.0000.0000.0000.000
12A6PHE0-0.0160.00112.2910.1060.1060.0000.0000.0000.000
13A7ALA00.0550.03210.2310.1080.1080.0000.0000.0000.000
14A8LEU00.0350.01311.1970.1250.1250.0000.0000.0000.000
15A9SER0-0.063-0.02513.8380.1010.1010.0000.0000.0000.000
16A10LEU0-0.041-0.03114.9180.0550.0550.0000.0000.0000.000
17A11LEU00.0180.01213.9450.0330.0330.0000.0000.0000.000
18A12ARG10.9530.97716.5730.1670.1670.0000.0000.0000.000
19A13ARG10.8330.90919.5360.2120.2120.0000.0000.0000.000
20A14ASN0-0.011-0.01019.7850.0020.0020.0000.0000.0000.000
21A15VAL0-0.0150.01416.1170.0050.0050.0000.0000.0000.000
22A16ARG10.8810.93519.4680.1220.1220.0000.0000.0000.000
23A17GLN0-0.012-0.00120.274-0.009-0.0090.0000.0000.0000.000
24A18VAL0-0.014-0.02422.8270.0000.0000.0000.0000.0000.000
25A19GLN0-0.0050.01225.3930.0090.0090.0000.0000.0000.000
26A20THR0-0.025-0.03328.1860.0000.0000.0000.0000.0000.000
27A21ASP-1-0.902-0.95830.872-0.028-0.0280.0000.0000.0000.000
28A22GLN0-0.0430.00429.7230.0020.0020.0000.0000.0000.000
29A23GLY00.002-0.00427.5970.0030.0030.0000.0000.0000.000
30A24HIS0-0.040-0.02623.641-0.017-0.0170.0000.0000.0000.000
31A25PHE00.0040.00022.400-0.007-0.0070.0000.0000.0000.000
32A26THR0-0.037-0.00617.3700.0110.0110.0000.0000.0000.000
33A27MET00.0050.02020.587-0.011-0.0110.0000.0000.0000.000
34A28LEU0-0.004-0.00218.418-0.011-0.0110.0000.0000.0000.000
35A29GLY00.0400.01421.4320.0080.0080.0000.0000.0000.000
36A30VAL0-0.047-0.03123.110-0.023-0.0230.0000.0000.0000.000
37A31ARG10.9050.92524.9090.1470.1470.0000.0000.0000.000
38A32ASP-1-0.864-0.91227.863-0.118-0.1180.0000.0000.0000.000
39A33ARG10.8420.92130.4730.0710.0710.0000.0000.0000.000
40A34LEU00.0070.02629.0150.0040.0040.0000.0000.0000.000
41A35ALA0-0.003-0.00325.673-0.010-0.0100.0000.0000.0000.000
42A36VAL0-0.005-0.00122.4020.0020.0020.0000.0000.0000.000
43A37LEU00.0410.01923.747-0.004-0.0040.0000.0000.0000.000
44A38PRO00.0330.02122.021-0.009-0.0090.0000.0000.0000.000
45A39ARG00.0420.07224.6980.0140.0140.0000.0000.0000.000
46A40HIS0-0.047-0.06223.0040.0080.0080.0000.0000.0000.000
47A41SER0-0.037-0.04026.1750.0130.0130.0000.0000.0000.000
48A42GLN0-0.067-0.03728.1700.0080.0080.0000.0000.0000.000
49A43PRO0-0.0040.01129.8120.0090.0090.0000.0000.0000.000
50A44GLY00.0880.04632.122-0.002-0.0020.0000.0000.0000.000
51A45LYS10.9210.93535.3510.0320.0320.0000.0000.0000.000
52A46THR0-0.030-0.00836.0620.0020.0020.0000.0000.0000.000
53A47ILE0-0.0020.01830.1050.0010.0010.0000.0000.0000.000
54A48TRP00.0050.00330.0330.0040.0040.0000.0000.0000.000
55A49ILE00.030-0.00726.639-0.009-0.0090.0000.0000.0000.000
56A50GLU-1-0.829-0.91223.100-0.029-0.0290.0000.0000.0000.000
57A51HIS0-0.042-0.03326.2560.0020.0020.0000.0000.0000.000
58A52LYS10.9230.97930.0280.0180.0180.0000.0000.0000.000
59A53LEU0-0.0020.01031.834-0.006-0.0060.0000.0000.0000.000
60A54VAL0-0.041-0.02332.0240.0000.0000.0000.0000.0000.000
61A55ASN0-0.044-0.04134.6970.0020.0020.0000.0000.0000.000
62A56VAL0-0.020-0.01133.342-0.005-0.0050.0000.0000.0000.000
63A57LEU0-0.057-0.03135.9570.0040.0040.0000.0000.0000.000
64A58ASP-1-0.881-0.95136.224-0.097-0.0970.0000.0000.0000.000
65A59ALA0-0.023-0.01333.619-0.004-0.0040.0000.0000.0000.000
66A60VAL00.0080.01732.8960.0030.0030.0000.0000.0000.000
67A61GLU-1-0.865-0.93931.018-0.123-0.1230.0000.0000.0000.000
68A62LEU0-0.040-0.01426.580-0.001-0.0010.0000.0000.0000.000
69A63VAL00.0260.00530.008-0.001-0.0010.0000.0000.0000.000
70A64ASP-1-0.773-0.87628.371-0.202-0.2020.0000.0000.0000.000
71A65GLU-1-0.819-0.88929.973-0.211-0.2110.0000.0000.0000.000
72A66GLN0-0.102-0.07030.0100.0060.0060.0000.0000.0000.000
73A67GLY00.0160.02633.4480.0080.0080.0000.0000.0000.000
74A68VAL0-0.055-0.02329.2690.0070.0070.0000.0000.0000.000
75A69ASN00.011-0.00330.153-0.017-0.0170.0000.0000.0000.000
76A70LEU0-0.020-0.01425.042-0.009-0.0090.0000.0000.0000.000
77A71GLH0-0.058-0.04824.891-0.013-0.0130.0000.0000.0000.000
78A72LEU0-0.021-0.00622.233-0.006-0.0060.0000.0000.0000.000
79A73THR00.0360.01626.3360.0070.0070.0000.0000.0000.000
80A74LEU0-0.030-0.01027.816-0.008-0.0080.0000.0000.0000.000
81A75ILE0-0.014-0.00228.6920.0110.0110.0000.0000.0000.000
82A76THR00.0130.00030.597-0.011-0.0110.0000.0000.0000.000
83A77LEU00.003-0.00528.8050.0090.0090.0000.0000.0000.000
84A78ASP-1-0.792-0.90433.362-0.055-0.0550.0000.0000.0000.000
85A79THR00.014-0.01532.5860.0050.0050.0000.0000.0000.000
86A80ASN0-0.043-0.03535.579-0.003-0.0030.0000.0000.0000.000
87A81GLU-1-0.894-0.90330.265-0.061-0.0610.0000.0000.0000.000
88A82LYS10.8770.92931.0620.0960.0960.0000.0000.0000.000
89A83PHE00.0290.03124.440-0.004-0.0040.0000.0000.0000.000
90A84ARG10.8520.92418.7390.2720.2720.0000.0000.0000.000
91A85ASP-1-0.724-0.83224.499-0.241-0.2410.0000.0000.0000.000
92A86ILE0-0.055-0.01220.116-0.011-0.0110.0000.0000.0000.000
93A87THR00.036-0.00921.703-0.033-0.0330.0000.0000.0000.000
94A88LYS10.8220.90422.9190.2210.2210.0000.0000.0000.000
95A89PHE0-0.012-0.00418.075-0.001-0.0010.0000.0000.0000.000
96A90ILE0-0.0150.01818.429-0.061-0.0610.0000.0000.0000.000
97A91PRO0-0.003-0.00218.4570.0240.0240.0000.0000.0000.000
98A92GLU-1-0.760-0.84121.201-0.286-0.2860.0000.0000.0000.000
99A93ASN0-0.040-0.03623.1280.0040.0040.0000.0000.0000.000
100A94ILE00.0170.02619.888-0.033-0.0330.0000.0000.0000.000
101A95SER00.0010.00917.2140.0070.0070.0000.0000.0000.000
102A96THR00.0400.02115.1160.0220.0220.0000.0000.0000.000
103A97ALA0-0.059-0.03610.5450.0060.0060.0000.0000.0000.000
104A98SER00.044-0.0039.6080.1380.1380.0000.0000.0000.000
105A99ASP-1-0.875-0.9293.520-8.860-7.3070.059-0.725-0.887-0.005
106A100ALA0-0.033-0.0016.031-0.014-0.0140.0000.0000.0000.000
107A101THR0-0.053-0.0344.435-0.633-0.523-0.001-0.010-0.0980.000
108A102LEU00.0090.0177.0110.2220.2220.0000.0000.0000.000
109A103VAL0-0.020-0.00910.1030.0920.0920.0000.0000.0000.000
110A104ILE00.009-0.00912.2250.0050.0050.0000.0000.0000.000
111A105ASN0-0.021-0.01814.7680.0780.0780.0000.0000.0000.000
112A106THR00.041-0.00217.668-0.012-0.0120.0000.0000.0000.000
113A107GLU-1-0.751-0.86520.3400.0720.0720.0000.0000.0000.000
114A108HIS0-0.064-0.03421.7000.0240.0240.0000.0000.0000.000
115A109MET0-0.055-0.01415.0800.0230.0230.0000.0000.0000.000
116A110PRO00.0350.02817.084-0.039-0.0390.0000.0000.0000.000
117A111SER0-0.050-0.04114.9020.0300.0300.0000.0000.0000.000
118A112MET0-0.0020.0329.3970.0770.0770.0000.0000.0000.000
119A113PHE0-0.006-0.0247.163-0.182-0.1820.0000.0000.0000.000
120A114VAL00.0170.0076.8880.3560.3560.0000.0000.0000.000
121A115PRO0-0.033-0.0122.433-1.099-0.8692.368-0.572-2.0260.000
122A116VAL0-0.020-0.0264.5590.3880.480-0.001-0.010-0.0810.000
123A117GLY00.0060.0245.3660.2100.2100.0000.0000.0000.000
124A118ASP-1-0.865-0.9276.132-1.177-1.1770.0000.0000.0000.000
125A119VAL0-0.055-0.0199.8440.1380.1380.0000.0000.0000.000
126A120VAL00.0210.00012.5010.0500.0500.0000.0000.0000.000
127A121GLN00.0550.02115.6310.0560.0560.0000.0000.0000.000
128A122TYR0-0.001-0.01019.2410.0100.0100.0000.0000.0000.000
129A123GLY00.0520.01221.5190.0070.0070.0000.0000.0000.000
130A124PHE0-0.0150.01325.2940.0020.0020.0000.0000.0000.000
131A125LEU0-0.007-0.01327.229-0.018-0.0180.0000.0000.0000.000
132A126ASN0-0.0030.01030.3940.0210.0210.0000.0000.0000.000
133A127LEU00.0430.02533.607-0.004-0.0040.0000.0000.0000.000
134A128SER0-0.065-0.03535.761-0.002-0.0020.0000.0000.0000.000
135A129GLY00.0470.02331.472-0.007-0.0070.0000.0000.0000.000
136A130LYS10.8670.93229.1030.2230.2230.0000.0000.0000.000
137A131PRO00.019-0.00325.0130.0110.0110.0000.0000.0000.000
138A132THR0-0.0020.00527.9200.0010.0010.0000.0000.0000.000
139A133HIS00.0210.00728.101-0.017-0.0170.0000.0000.0000.000
140A134ARG10.8480.91621.8760.3580.3580.0000.0000.0000.000
141A135THR00.0010.01820.9940.0020.0020.0000.0000.0000.000
142A136MET0-0.036-0.01116.4720.0060.0060.0000.0000.0000.000
143A137MET0-0.0120.00716.0110.0460.0460.0000.0000.0000.000
144A138TYR00.038-0.00710.738-0.108-0.1080.0000.0000.0000.000
145A139ASN00.000-0.0079.2480.2240.2240.0000.0000.0000.000
146A140PHE0-0.003-0.01410.583-0.069-0.0690.0000.0000.0000.000
147A141PRO0-0.026-0.00411.1380.0470.0470.0000.0000.0000.000
148A142THR00.0000.00313.9870.0860.0860.0000.0000.0000.000
149A143LYS10.9310.96115.827-0.075-0.0750.0000.0000.0000.000
150A144ALA00.0290.01918.087-0.019-0.0190.0000.0000.0000.000
151A145GLY00.0650.04219.3710.0310.0310.0000.0000.0000.000
152A146GLN0-0.020-0.01416.395-0.015-0.0150.0000.0000.0000.000
153A147CYM-1-0.831-0.88017.862-0.163-0.1630.0000.0000.0000.000
154A148GLY00.0610.00719.7530.0230.0230.0000.0000.0000.000
155A149GLY0-0.0230.00415.570-0.010-0.0100.0000.0000.0000.000
156A150VAL0-0.013-0.01514.800-0.027-0.0270.0000.0000.0000.000
157A151VAL00.0070.01111.196-0.083-0.0830.0000.0000.0000.000
158A152THR0-0.027-0.01810.3060.0430.0430.0000.0000.0000.000
159A153SER00.0320.0048.978-0.242-0.2420.0000.0000.0000.000
160A154VAL00.0290.0019.3050.1480.1480.0000.0000.0000.000
161A155GLY00.0080.02311.5220.1100.1100.0000.0000.0000.000
162A156LYS10.8870.94613.5440.7290.7290.0000.0000.0000.000
163A157ILE0-0.003-0.00713.584-0.103-0.1030.0000.0000.0000.000
164A158ILE0-0.029-0.02512.7920.0480.0480.0000.0000.0000.000
165A159GLY00.040-0.00115.7360.0460.0460.0000.0000.0000.000
166A160ILE0-0.0210.01716.340-0.035-0.0350.0000.0000.0000.000
167A161HIS0-0.0100.00615.470-0.049-0.0490.0000.0000.0000.000
168A162ILE0-0.004-0.01217.4650.0400.0400.0000.0000.0000.000
169A163GLY00.0790.04219.2680.0310.0310.0000.0000.0000.000
170A164GLY0-0.015-0.02018.299-0.048-0.0480.0000.0000.0000.000
171A165ASN0-0.0040.00418.9720.0250.0250.0000.0000.0000.000
172A166GLY00.0490.03618.5350.0190.0190.0000.0000.0000.000
173A167ARG10.8570.92516.1420.1410.1410.0000.0000.0000.000
174A168GLN00.0340.02514.881-0.017-0.0170.0000.0000.0000.000
175A169GLY00.0210.00615.0330.0690.0690.0000.0000.0000.000
176A170PHE0-0.009-0.00915.843-0.064-0.0640.0000.0000.0000.000
177A171CYS0-0.0170.00216.009-0.004-0.0040.0000.0000.0000.000
178A172ALA00.0690.05117.999-0.007-0.0070.0000.0000.0000.000
179A173GLY0-0.007-0.00819.028-0.027-0.0270.0000.0000.0000.000
180A174LEU0-0.016-0.01719.5560.0430.0430.0000.0000.0000.000
181A175LYS10.7660.86021.1050.2150.2150.0000.0000.0000.000
182A176ARG10.7800.84023.1470.3240.3240.0000.0000.0000.000
183A177SER0-0.011-0.02925.7510.0100.0100.0000.0000.0000.000
184A178TYR00.010-0.00224.4880.0150.0150.0000.0000.0000.000
185A179PHE00.0490.01823.5140.0060.0060.0000.0000.0000.000
186A180ALA0-0.0120.00928.7170.0070.0070.0000.0000.0000.000
187A181SER00.0070.01031.4120.0080.0080.0000.0000.0000.000