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: 94NM2

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 OptHSide
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 -2002578.668891
FMO2-HF: Nuclear repulsion 1929976.865957
FMO2-HF: Total energy -72601.802934
FMO2-MP2: Total energy -72811.866205


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.
-8.684-3.0211.656-2.226-5.093-0.002
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 : 0.018 / q_NPA : 0.017
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-3GLY00.0230.0222.920-2.541-0.0330.048-1.141-1.4150.005
4A-2SER00.0620.0154.923-0.796-0.749-0.001-0.007-0.0390.000
5A-1HIS0-0.0030.0032.9570.2870.7010.093-0.167-0.3390.000
6A0MET0-0.034-0.0042.418-0.8170.4230.970-0.555-1.655-0.007
7A1GLY0-0.0120.0055.4140.3040.3040.0000.0000.0000.000
8A2PRO00.0360.0018.8220.0700.0700.0000.0000.0000.000
9A3SER00.0330.0087.0310.2850.2850.0000.0000.0000.000
10A4LEU00.0270.0104.7600.0810.171-0.001-0.010-0.0780.000
11A5ASP-1-0.954-0.9538.710-0.113-0.1130.0000.0000.0000.000
12A6PHE00.008-0.00412.2940.1270.1270.0000.0000.0000.000
13A7ALA00.0390.03010.1030.1070.1070.0000.0000.0000.000
14A8LEU00.0360.00511.1160.1330.1330.0000.0000.0000.000
15A9SER0-0.084-0.03213.5530.1000.1000.0000.0000.0000.000
16A10LEU0-0.043-0.03415.1240.0580.0580.0000.0000.0000.000
17A11LEU00.0310.01613.7980.0300.0300.0000.0000.0000.000
18A12ARG10.9700.99016.7440.1390.1390.0000.0000.0000.000
19A13ARG10.8480.91319.4240.1970.1970.0000.0000.0000.000
20A14ASN0-0.005-0.02319.9930.0000.0000.0000.0000.0000.000
21A15VAL0-0.0200.02216.5250.0000.0000.0000.0000.0000.000
22A16ARG10.9010.95019.8530.1040.1040.0000.0000.0000.000
23A17GLN0-0.032-0.01319.969-0.006-0.0060.0000.0000.0000.000
24A18VAL0-0.021-0.03323.093-0.001-0.0010.0000.0000.0000.000
25A19GLN0-0.0080.00725.7200.0110.0110.0000.0000.0000.000
26A20THR0-0.025-0.03128.421-0.001-0.0010.0000.0000.0000.000
27A21ASP-1-0.905-0.95331.144-0.021-0.0210.0000.0000.0000.000
28A22GLN0-0.042-0.01029.6750.0010.0010.0000.0000.0000.000
29A23GLY0-0.0020.00427.7730.0030.0030.0000.0000.0000.000
30A24HIS0-0.024-0.01523.680-0.016-0.0160.0000.0000.0000.000
31A25PHE00.0080.00622.677-0.010-0.0100.0000.0000.0000.000
32A26THR0-0.029-0.01017.5310.0140.0140.0000.0000.0000.000
33A27MET00.0040.02720.826-0.020-0.0200.0000.0000.0000.000
34A28LEU00.0050.00618.732-0.008-0.0080.0000.0000.0000.000
35A29GLY00.0320.02721.8000.0080.0080.0000.0000.0000.000
36A30VAL0-0.043-0.05323.259-0.023-0.0230.0000.0000.0000.000
37A31ARG10.9690.96025.1790.1440.1440.0000.0000.0000.000
38A32ASP-1-0.889-0.91528.162-0.107-0.1070.0000.0000.0000.000
39A33ARG10.8660.93530.5130.0670.0670.0000.0000.0000.000
40A34LEU00.0180.02529.1370.0030.0030.0000.0000.0000.000
41A35ALA00.0090.00725.985-0.010-0.0100.0000.0000.0000.000
42A36VAL0-0.0080.00122.6320.0030.0030.0000.0000.0000.000
43A37LEU00.0170.00524.059-0.001-0.0010.0000.0000.0000.000
44A38PRO00.0370.02522.231-0.011-0.0110.0000.0000.0000.000
45A39ARG00.0660.06624.8210.0150.0150.0000.0000.0000.000
46A40HIS0-0.062-0.05623.5150.0080.0080.0000.0000.0000.000
47A41SER0-0.039-0.04126.7670.0130.0130.0000.0000.0000.000
48A42GLN0-0.076-0.03928.7760.0070.0070.0000.0000.0000.000
49A43PRO00.0090.01630.3500.0080.0080.0000.0000.0000.000
50A44GLY00.0790.04432.646-0.001-0.0010.0000.0000.0000.000
51A45LYS10.9560.96836.0650.0250.0250.0000.0000.0000.000
52A46THR0-0.039-0.01836.1440.0000.0000.0000.0000.0000.000
53A47ILE00.0050.02130.0130.0010.0010.0000.0000.0000.000
54A48TRP00.0020.00130.1630.0030.0030.0000.0000.0000.000
55A49ILE00.017-0.00827.049-0.007-0.0070.0000.0000.0000.000
56A50GLU-1-0.823-0.90523.449-0.016-0.0160.0000.0000.0000.000
57A51HIS0-0.035-0.02826.5180.0020.0020.0000.0000.0000.000
58A52LYS10.9320.98330.5420.0090.0090.0000.0000.0000.000
59A53LEU0-0.018-0.00632.171-0.006-0.0060.0000.0000.0000.000
60A54VAL0-0.018-0.01032.4570.0000.0000.0000.0000.0000.000
61A55ASN0-0.037-0.02434.9840.0020.0020.0000.0000.0000.000
62A56VAL0-0.038-0.03233.373-0.005-0.0050.0000.0000.0000.000
63A57LEU0-0.066-0.03836.0320.0030.0030.0000.0000.0000.000
64A58ASP-1-0.906-0.95936.295-0.087-0.0870.0000.0000.0000.000
65A59ALA0-0.013-0.00334.002-0.005-0.0050.0000.0000.0000.000
66A60VAL00.0220.01633.2640.0030.0030.0000.0000.0000.000
67A61GLU-1-0.872-0.93331.405-0.116-0.1160.0000.0000.0000.000
68A62LEU0-0.018-0.00627.522-0.001-0.0010.0000.0000.0000.000
69A63VAL00.022-0.00830.588-0.002-0.0020.0000.0000.0000.000
70A64ASP-1-0.823-0.90428.815-0.191-0.1910.0000.0000.0000.000
71A65GLU-1-0.812-0.89730.612-0.199-0.1990.0000.0000.0000.000
72A66GLN0-0.094-0.05630.1800.0040.0040.0000.0000.0000.000
73A67GLY00.0040.01234.0070.0080.0080.0000.0000.0000.000
74A68VAL0-0.050-0.01830.2090.0070.0070.0000.0000.0000.000
75A69ASN00.0220.00630.508-0.011-0.0110.0000.0000.0000.000
76A70LEU0-0.036-0.02125.583-0.009-0.0090.0000.0000.0000.000
77A71GLH0-0.058-0.03325.679-0.011-0.0110.0000.0000.0000.000
78A72LEU0-0.024-0.01122.655-0.005-0.0050.0000.0000.0000.000
79A73THR00.0490.01826.6640.0050.0050.0000.0000.0000.000
80A74LEU0-0.048-0.02427.962-0.010-0.0100.0000.0000.0000.000
81A75ILE0-0.015-0.00129.4370.0090.0090.0000.0000.0000.000
82A76THR00.0440.00931.125-0.009-0.0090.0000.0000.0000.000
83A77LEU0-0.030-0.02229.1570.0080.0080.0000.0000.0000.000
84A78ASP-1-0.807-0.92233.680-0.050-0.0500.0000.0000.0000.000
85A79THR0-0.005-0.01132.7280.0040.0040.0000.0000.0000.000
86A80ASN0-0.037-0.02235.597-0.004-0.0040.0000.0000.0000.000
87A81GLU-1-0.907-0.94230.873-0.053-0.0530.0000.0000.0000.000
88A82LYS10.8730.94531.1970.0860.0860.0000.0000.0000.000
89A83PHE00.0120.01824.589-0.002-0.0020.0000.0000.0000.000
90A84ARG10.8600.92118.7960.2560.2560.0000.0000.0000.000
91A85ASP-1-0.716-0.85524.937-0.218-0.2180.0000.0000.0000.000
92A86ILE0-0.094-0.02720.396-0.012-0.0120.0000.0000.0000.000
93A87THR00.034-0.01221.907-0.035-0.0350.0000.0000.0000.000
94A88LYS10.8640.93722.9080.2070.2070.0000.0000.0000.000
95A89PHE0-0.034-0.02118.079-0.003-0.0030.0000.0000.0000.000
96A90ILE0-0.0290.01518.678-0.059-0.0590.0000.0000.0000.000
97A91PRO00.0110.00718.4370.0210.0210.0000.0000.0000.000
98A92GLU-1-0.796-0.86821.268-0.268-0.2680.0000.0000.0000.000
99A93ASN0-0.031-0.03723.6100.0050.0050.0000.0000.0000.000
100A94ILE00.0230.01820.539-0.031-0.0310.0000.0000.0000.000
101A95SER0-0.0120.00117.317-0.003-0.0030.0000.0000.0000.000
102A96THR00.0170.01915.6000.0170.0170.0000.0000.0000.000
103A97ALA0-0.064-0.04111.0470.0000.0000.0000.0000.0000.000
104A98SER00.0440.01610.0980.0950.0950.0000.0000.0000.000
105A99ASP-1-0.846-0.9204.148-6.357-5.8940.002-0.101-0.3650.000
106A100ALA0-0.046-0.0096.376-0.059-0.0590.0000.0000.0000.000
107A101THR0-0.049-0.0304.554-0.435-0.344-0.001-0.008-0.0820.000
108A102LEU0-0.002-0.0067.2280.1960.1960.0000.0000.0000.000
109A103VAL0-0.027-0.02110.4510.1000.1000.0000.0000.0000.000
110A104ILE00.012-0.00512.6080.0060.0060.0000.0000.0000.000
111A105ASN0-0.024-0.02515.0200.0770.0770.0000.0000.0000.000
112A106THR00.0700.02217.776-0.006-0.0060.0000.0000.0000.000
113A107GLU-1-0.789-0.89020.3610.0790.0790.0000.0000.0000.000
114A108HIS0-0.069-0.04221.8930.0260.0260.0000.0000.0000.000
115A109MET0-0.067-0.01715.3510.0250.0250.0000.0000.0000.000
116A110PRO00.0420.02317.375-0.040-0.0400.0000.0000.0000.000
117A111SER0-0.042-0.03014.5630.0270.0270.0000.0000.0000.000
118A112MET00.0050.0239.3800.1050.1050.0000.0000.0000.000
119A113PHE0-0.019-0.0157.412-0.163-0.1630.0000.0000.0000.000
120A114VAL00.0230.0087.1020.3250.3250.0000.0000.0000.000
121A115PRO0-0.030-0.0022.571-1.186-0.4220.547-0.236-1.0760.000
122A116VAL0-0.013-0.0255.1370.2830.329-0.001-0.001-0.0440.000
123A117GLY0-0.0030.0185.7660.2050.2050.0000.0000.0000.000
124A118ASP-1-0.890-0.9496.532-1.194-1.1940.0000.0000.0000.000
125A119VAL0-0.064-0.02310.0640.1670.1670.0000.0000.0000.000
126A120VAL00.014-0.00612.7790.0270.0270.0000.0000.0000.000
127A121GLN00.0310.02416.1270.0500.0500.0000.0000.0000.000
128A122TYR0-0.005-0.00419.8350.0070.0070.0000.0000.0000.000
129A123GLY00.0470.00922.0350.0090.0090.0000.0000.0000.000
130A124PHE0-0.0120.01125.6790.0020.0020.0000.0000.0000.000
131A125LEU0-0.014-0.01927.577-0.015-0.0150.0000.0000.0000.000
132A126ASN0-0.0250.00730.8830.0200.0200.0000.0000.0000.000
133A127LEU00.1200.03733.929-0.004-0.0040.0000.0000.0000.000
134A128SER0-0.068-0.02735.873-0.004-0.0040.0000.0000.0000.000
135A129GLY0-0.002-0.00131.794-0.007-0.0070.0000.0000.0000.000
136A130LYS10.8640.93929.1310.2180.2180.0000.0000.0000.000
137A131PRO00.0350.00125.2360.0110.0110.0000.0000.0000.000
138A132THR0-0.0120.02128.193-0.002-0.0020.0000.0000.0000.000
139A133HIS00.0210.00028.901-0.011-0.0110.0000.0000.0000.000
140A134ARG10.9010.92922.9750.3140.3140.0000.0000.0000.000
141A135THR00.0400.04721.4400.0110.0110.0000.0000.0000.000
142A136MET0-0.059-0.04316.9900.0100.0100.0000.0000.0000.000
143A137MET0-0.015-0.00516.4190.0520.0520.0000.0000.0000.000
144A138TYR00.0430.00411.117-0.083-0.0830.0000.0000.0000.000
145A139ASN00.002-0.0059.8210.2020.2020.0000.0000.0000.000
146A140PHE00.004-0.01510.887-0.078-0.0780.0000.0000.0000.000
147A141PRO0-0.030-0.00511.4370.0460.0460.0000.0000.0000.000
148A142THR0-0.0090.00414.0540.0850.0850.0000.0000.0000.000
149A143LYS10.9970.96715.970-0.046-0.0460.0000.0000.0000.000
150A144ALA0-0.060-0.00718.766-0.001-0.0010.0000.0000.0000.000
151A145GLY00.0500.05619.4730.0240.0240.0000.0000.0000.000
152A146GLN0-0.011-0.01516.571-0.001-0.0010.0000.0000.0000.000
153A147CYM-1-0.820-0.87518.102-0.149-0.1490.0000.0000.0000.000
154A148GLY00.048-0.01219.8920.0230.0230.0000.0000.0000.000
155A149GLY0-0.042-0.01315.681-0.019-0.0190.0000.0000.0000.000
156A150VAL00.0210.01414.803-0.012-0.0120.0000.0000.0000.000
157A151VAL00.0150.02611.465-0.074-0.0740.0000.0000.0000.000
158A152THR0-0.026-0.01510.5560.0380.0380.0000.0000.0000.000
159A153SER00.0380.0089.295-0.219-0.2190.0000.0000.0000.000
160A154VAL00.0200.0039.5330.0500.0500.0000.0000.0000.000
161A155GLY00.0010.01111.6540.1150.1150.0000.0000.0000.000
162A156LYS10.8910.95013.7820.7120.7120.0000.0000.0000.000
163A157ILE00.001-0.01314.033-0.086-0.0860.0000.0000.0000.000
164A158ILE0-0.028-0.02813.1510.0350.0350.0000.0000.0000.000
165A159GLY00.0330.00315.9760.0380.0380.0000.0000.0000.000
166A160ILE0-0.0010.01916.615-0.033-0.0330.0000.0000.0000.000
167A161HIS0-0.0050.01515.748-0.041-0.0410.0000.0000.0000.000
168A162ILE0-0.014-0.01617.7680.0350.0350.0000.0000.0000.000
169A163GLY00.0840.04419.7020.0300.0300.0000.0000.0000.000
170A164GLY0-0.013-0.01018.764-0.044-0.0440.0000.0000.0000.000
171A165ASN00.0140.01619.3310.0200.0200.0000.0000.0000.000
172A166GLY00.0350.02518.7030.0200.0200.0000.0000.0000.000
173A167ARG10.8710.93216.7090.1330.1330.0000.0000.0000.000
174A168GLN00.0240.01715.520-0.017-0.0170.0000.0000.0000.000
175A169GLY00.0200.01015.3910.0610.0610.0000.0000.0000.000
176A170PHE0-0.002-0.01816.288-0.057-0.0570.0000.0000.0000.000
177A171CYS0-0.0120.00516.574-0.005-0.0050.0000.0000.0000.000
178A172ALA00.0540.04318.653-0.011-0.0110.0000.0000.0000.000
179A173GLY0-0.011-0.01119.459-0.023-0.0230.0000.0000.0000.000
180A174LEU00.0010.00019.7290.0380.0380.0000.0000.0000.000
181A175LYS10.7660.85721.3460.2060.2060.0000.0000.0000.000
182A176ARG10.8090.88123.1630.3160.3160.0000.0000.0000.000
183A177SER00.003-0.01025.6690.0110.0110.0000.0000.0000.000
184A178TYR00.007-0.00324.8340.0150.0150.0000.0000.0000.000
185A179PHE00.0370.02123.8460.0070.0070.0000.0000.0000.000
186A180ALA00.0010.01529.1400.0040.0040.0000.0000.0000.000
187A181SER0-0.0070.00631.9430.0060.0060.0000.0000.0000.000