Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: GYY71

Calculation Name: 5D19-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D19

Chain ID: A

ChEMBL ID:

UniProt ID: O07229

Base Structure: X-ray

Registration Date: 2023-09-27

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2147642.961952
FMO2-HF: Nuclear repulsion 2068516.727741
FMO2-HF: Total energy -79126.234212
FMO2-MP2: Total energy -79357.743939


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:12:GLY)


Summations of interaction energy for fragment #1(A:12: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.
-3.0350.390.102-1.429-2.0980.001
Interaction energy analysis for fragmet #1(A:12:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.003
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].
3A14ARG10.9460.9763.280-4.872-2.9510.054-0.871-1.1050.004
4A15SER00.0110.0123.054-1.373-0.3490.028-0.446-0.606-0.003
5A16ARG10.8200.8884.7492.4872.651-0.001-0.035-0.1270.000
6A17GLU-1-0.784-0.8856.7150.0940.0940.0000.0000.0000.000
7A18SER0-0.035-0.0227.7100.2020.2020.0000.0000.0000.000
8A19ILE00.0200.0058.2760.1440.1440.0000.0000.0000.000
9A20LEU0-0.0270.00710.7830.1350.1350.0000.0000.0000.000
10A21ASP-1-0.783-0.86612.546-0.126-0.1260.0000.0000.0000.000
11A22ALA0-0.054-0.01713.6640.0550.0550.0000.0000.0000.000
12A23THR0-0.013-0.03514.7420.0450.0450.0000.0000.0000.000
13A24GLU-1-0.814-0.89216.777-0.149-0.1490.0000.0000.0000.000
14A25ARG10.9500.96717.4140.1930.1930.0000.0000.0000.000
15A26LEU0-0.059-0.01418.2050.0230.0230.0000.0000.0000.000
16A27MET00.0110.00621.0920.0170.0170.0000.0000.0000.000
17A28ALA00.0230.03722.8990.0150.0150.0000.0000.0000.000
18A29THR0-0.066-0.03023.8850.0170.0170.0000.0000.0000.000
19A30LYS10.8650.92023.2050.1780.1780.0000.0000.0000.000
20A31GLY00.0330.02426.378-0.002-0.0020.0000.0000.0000.000
21A32TYR00.002-0.04123.476-0.013-0.0130.0000.0000.0000.000
22A33ALA0-0.007-0.00524.962-0.013-0.0130.0000.0000.0000.000
23A34ALA0-0.040-0.01127.381-0.001-0.0010.0000.0000.0000.000
24A35THR0-0.033-0.01021.187-0.004-0.0040.0000.0000.0000.000
25A36SER00.006-0.02722.710-0.013-0.0130.0000.0000.0000.000
26A37ILE00.034-0.01615.536-0.015-0.0150.0000.0000.0000.000
27A38SER0-0.044-0.01718.215-0.032-0.0320.0000.0000.0000.000
28A39ASP-1-0.791-0.85419.441-0.206-0.2060.0000.0000.0000.000
29A40ILE00.0420.01914.574-0.001-0.0010.0000.0000.0000.000
30A41ARG10.9670.99715.0270.2390.2390.0000.0000.0000.000
31A42ASP-1-0.902-0.95915.868-0.235-0.2350.0000.0000.0000.000
32A43ALA0-0.048-0.01117.1680.0230.0230.0000.0000.0000.000
33A44CYS0-0.085-0.04811.770-0.024-0.0240.0000.0000.0000.000
34A45GLY0-0.0010.01112.440-0.016-0.0160.0000.0000.0000.000
35A46LEU0-0.015-0.0157.115-0.022-0.0220.0000.0000.0000.000
36A47ALA00.0370.01411.6550.0510.0510.0000.0000.0000.000
37A48PRO00.0700.03312.544-0.096-0.0960.0000.0000.0000.000
38A49SER00.008-0.00713.464-0.035-0.0350.0000.0000.0000.000
39A50SER0-0.041-0.0248.288-0.056-0.0560.0000.0000.0000.000
40A51ILE00.0550.0268.782-0.198-0.1980.0000.0000.0000.000
41A52TYR0-0.005-0.00810.963-0.023-0.0230.0000.0000.0000.000
42A53TRP0-0.040-0.0268.3040.0100.0100.0000.0000.0000.000
43A54HIS0-0.046-0.0053.326-0.0240.2920.021-0.077-0.2600.000
44A55PHE00.0210.0018.202-0.030-0.0300.0000.0000.0000.000
45A56GLY00.0010.02011.8050.0870.0870.0000.0000.0000.000
46A57SER0-0.050-0.06214.5370.0530.0530.0000.0000.0000.000
47A58LYS10.8450.92815.9200.1860.1860.0000.0000.0000.000
48A59GLU-1-0.769-0.89817.591-0.262-0.2620.0000.0000.0000.000
49A60GLY00.0360.02715.8050.0130.0130.0000.0000.0000.000
50A61VAL0-0.036-0.01412.966-0.031-0.0310.0000.0000.0000.000
51A62LEU00.0020.00114.7880.0080.0080.0000.0000.0000.000
52A63ALA00.0220.01017.4900.0240.0240.0000.0000.0000.000
53A64ALA00.0010.00012.7870.0220.0220.0000.0000.0000.000
54A65MET0-0.038-0.00114.9300.0290.0290.0000.0000.0000.000
55A66MET00.0120.02616.2150.0480.0480.0000.0000.0000.000
56A67GLU-1-0.752-0.84916.670-0.204-0.2040.0000.0000.0000.000
57A68ARG10.6950.80112.1240.3330.3330.0000.0000.0000.000
58A69GLY00.0140.00016.1540.0410.0410.0000.0000.0000.000
59A70ALA00.0070.00019.6550.0270.0270.0000.0000.0000.000
60A71GLN0-0.064-0.04415.8640.0280.0280.0000.0000.0000.000
61A72ARG10.8570.92015.6520.1590.1590.0000.0000.0000.000
62A73PHE00.0150.01220.3030.0170.0170.0000.0000.0000.000
63A74PHE00.010-0.02423.2680.0100.0100.0000.0000.0000.000
64A75ALA0-0.0170.00521.0840.0090.0090.0000.0000.0000.000
65A76ALA0-0.033-0.00123.2030.0120.0120.0000.0000.0000.000
66A77ILE00.0030.01325.7560.0020.0020.0000.0000.0000.000
67A78PRO00.0340.05227.811-0.001-0.0010.0000.0000.0000.000
68A79THR0-0.031-0.06928.696-0.006-0.0060.0000.0000.0000.000
69A80TRP00.017-0.00831.2310.0050.0050.0000.0000.0000.000
70A81ASP-1-0.834-0.92933.8110.0060.0060.0000.0000.0000.000
71A82GLU-1-0.859-0.88327.8190.0200.0200.0000.0000.0000.000
72A83ALA0-0.051-0.00732.6090.0030.0030.0000.0000.0000.000
73A84HIS00.0230.00333.1640.0010.0010.0000.0000.0000.000
74A85GLY00.0150.00637.054-0.003-0.0030.0000.0000.0000.000
75A86PRO0-0.039-0.00640.7050.0010.0010.0000.0000.0000.000
76A87VAL00.0550.01342.026-0.001-0.0010.0000.0000.0000.000
77A88GLU-1-0.860-0.94843.0070.0050.0050.0000.0000.0000.000
78A89GLN00.0060.01342.712-0.001-0.0010.0000.0000.0000.000
79A90ARG10.8160.91736.447-0.014-0.0140.0000.0000.0000.000
80A91SER00.0630.02437.9480.0000.0000.0000.0000.0000.000
81A92GLU-1-0.832-0.87738.473-0.006-0.0060.0000.0000.0000.000
82A93ARG10.7950.87337.285-0.003-0.0030.0000.0000.0000.000
83A94GLN00.0010.02732.5720.0000.0000.0000.0000.0000.000
84A95LEU0-0.042-0.01534.284-0.003-0.0030.0000.0000.0000.000
85A96THR0-0.020-0.04536.209-0.003-0.0030.0000.0000.0000.000
86A97GLU-1-0.842-0.89431.258-0.002-0.0020.0000.0000.0000.000
87A98LEU0-0.0140.00131.325-0.004-0.0040.0000.0000.0000.000
88A99VAL00.0150.00232.649-0.005-0.0050.0000.0000.0000.000
89A100SER0-0.0130.01532.663-0.004-0.0040.0000.0000.0000.000
90A101LEU0-0.014-0.00126.884-0.003-0.0030.0000.0000.0000.000
91A102GLN00.005-0.02030.345-0.009-0.0090.0000.0000.0000.000
92A103SER0-0.066-0.04732.246-0.002-0.0020.0000.0000.0000.000
93A104GLN0-0.097-0.04728.6410.0000.0000.0000.0000.0000.000
94A105HIS0-0.046-0.01129.985-0.002-0.0020.0000.0000.0000.000
95A106PRO00.0210.02425.738-0.008-0.0080.0000.0000.0000.000
96A107ASP-1-0.771-0.86724.123-0.134-0.1340.0000.0000.0000.000
97A108PHE0-0.021-0.00921.702-0.011-0.0110.0000.0000.0000.000
98A109LEU00.0210.02523.427-0.010-0.0100.0000.0000.0000.000
99A110ARG10.8490.89026.0110.1210.1210.0000.0000.0000.000
100A111LEU0-0.027-0.01520.526-0.003-0.0030.0000.0000.0000.000
101A112PHE0-0.007-0.02224.324-0.007-0.0070.0000.0000.0000.000
102A113TYR0-0.012-0.03925.317-0.001-0.0010.0000.0000.0000.000
103A114LEU0-0.020-0.00126.7170.0020.0020.0000.0000.0000.000
104A115LEU0-0.004-0.01021.130-0.002-0.0020.0000.0000.0000.000
105A116SER0-0.109-0.05425.4180.0030.0030.0000.0000.0000.000
106A117MET0-0.018-0.00427.9690.0080.0080.0000.0000.0000.000
107A118GLU-1-0.846-0.88025.611-0.141-0.1410.0000.0000.0000.000
108A119ARG10.8520.91928.4330.1100.1100.0000.0000.0000.000
109A120SER0-0.037-0.02923.2920.0020.0020.0000.0000.0000.000
110A121GLN00.0120.00123.428-0.001-0.0010.0000.0000.0000.000
111A122ASP-1-0.808-0.87418.187-0.305-0.3050.0000.0000.0000.000
112A123PRO00.0340.00521.4590.0030.0030.0000.0000.0000.000
113A124ALA00.0110.01117.0500.0120.0120.0000.0000.0000.000
114A125VAL00.0220.01419.186-0.001-0.0010.0000.0000.0000.000
115A126ALA00.0420.02620.4440.0120.0120.0000.0000.0000.000
116A127ALA0-0.029-0.01620.2610.0150.0150.0000.0000.0000.000
117A128VAL0-0.019-0.00316.9790.0150.0150.0000.0000.0000.000
118A129VAL00.0320.02120.0140.0170.0170.0000.0000.0000.000
119A130ARG10.9080.96323.3510.1140.1140.0000.0000.0000.000
120A131ARG10.8150.87016.3980.2350.2350.0000.0000.0000.000
121A132VAL00.0420.03020.8860.0160.0160.0000.0000.0000.000
122A133ARG10.8300.88423.3810.0910.0910.0000.0000.0000.000
123A134ASN00.009-0.02226.1590.0090.0090.0000.0000.0000.000
124A135THR0-0.021-0.01023.4610.0110.0110.0000.0000.0000.000
125A136ALA00.0200.01326.0540.0090.0090.0000.0000.0000.000
126A137ILE0-0.006-0.00528.5540.0070.0070.0000.0000.0000.000
127A138ALA0-0.011-0.00728.4830.0060.0060.0000.0000.0000.000
128A139ARG10.8030.87826.1630.0290.0290.0000.0000.0000.000
129A140PHE00.0480.02230.4210.0050.0050.0000.0000.0000.000
130A141ARG10.8470.91433.5670.0320.0320.0000.0000.0000.000
131A142ASP-1-0.809-0.89632.719-0.006-0.0060.0000.0000.0000.000
132A143SER0-0.001-0.01734.7190.0020.0020.0000.0000.0000.000
133A144ILE0-0.034-0.01536.8490.0020.0020.0000.0000.0000.000
134A145THR0-0.029-0.03337.5910.0010.0010.0000.0000.0000.000
135A146HIS10.7230.85935.7720.0050.0050.0000.0000.0000.000
136A147LEU0-0.0180.00040.6160.0020.0020.0000.0000.0000.000
137A148LEU0-0.0130.00443.1710.0000.0000.0000.0000.0000.000
138A149PRO00.0070.00545.7850.0010.0010.0000.0000.0000.000
139A150SER0-0.007-0.01447.5920.0000.0000.0000.0000.0000.000
140A151ASP-1-0.930-0.95848.736-0.004-0.0040.0000.0000.0000.000
141A152ILE0-0.018-0.00147.5470.0000.0000.0000.0000.0000.000
142A153PRO0-0.0050.00647.3980.0000.0000.0000.0000.0000.000
143A154PRO00.043-0.01942.713-0.001-0.0010.0000.0000.0000.000
144A155GLY0-0.027-0.00344.626-0.002-0.0020.0000.0000.0000.000
145A156LYS10.8820.94046.8290.0100.0100.0000.0000.0000.000
146A157ALA00.0230.02543.697-0.001-0.0010.0000.0000.0000.000
147A158ASP-1-0.843-0.90939.585-0.022-0.0220.0000.0000.0000.000
148A159LEU0-0.007-0.00741.529-0.003-0.0030.0000.0000.0000.000
149A160VAL00.0780.04243.552-0.002-0.0020.0000.0000.0000.000
150A161VAL00.0200.00438.932-0.002-0.0020.0000.0000.0000.000
151A162ALA0-0.047-0.01838.853-0.003-0.0030.0000.0000.0000.000
152A163GLU-1-0.913-0.94239.510-0.031-0.0310.0000.0000.0000.000
153A164LEU00.0260.00441.582-0.002-0.0020.0000.0000.0000.000
154A165THR0-0.031-0.03435.178-0.001-0.0010.0000.0000.0000.000
155A166ALA0-0.040-0.02037.072-0.003-0.0030.0000.0000.0000.000
156A167PHE0-0.0010.00138.227-0.003-0.0030.0000.0000.0000.000
157A168ALA00.0110.00137.705-0.001-0.0010.0000.0000.0000.000
158A169VAL0-0.035-0.01432.855-0.002-0.0020.0000.0000.0000.000
159A170ALA00.0120.00935.292-0.003-0.0030.0000.0000.0000.000
160A171LEU00.007-0.00137.471-0.002-0.0020.0000.0000.0000.000
161A172SER00.0200.02333.2730.0010.0010.0000.0000.0000.000
162A173ASP-1-0.795-0.84232.355-0.073-0.0730.0000.0000.0000.000
163A174GLY00.0080.00634.520-0.002-0.0020.0000.0000.0000.000
164A175VAL0-0.035-0.02436.2100.0010.0010.0000.0000.0000.000
165A176TYR00.005-0.00228.536-0.002-0.0020.0000.0000.0000.000
166A177PHE0-0.031-0.02833.047-0.003-0.0030.0000.0000.0000.000
167A178ALA00.0320.02436.2590.0000.0000.0000.0000.0000.000
168A179GLY00.0090.00036.1860.0020.0020.0000.0000.0000.000
169A180HIS0-0.032-0.00831.809-0.002-0.0020.0000.0000.0000.000
170A181LEU0-0.081-0.03235.870-0.002-0.0020.0000.0000.0000.000
171A182GLU-1-0.907-0.95739.350-0.043-0.0430.0000.0000.0000.000
172A183PRO00.0180.02038.0150.0030.0030.0000.0000.0000.000
173A184ASP-1-0.937-0.96939.954-0.032-0.0320.0000.0000.0000.000
174A185THR0-0.068-0.03643.1740.0030.0030.0000.0000.0000.000
175A186THR0-0.050-0.03039.2680.0020.0020.0000.0000.0000.000
176A187ASP-1-0.846-0.90740.887-0.019-0.0190.0000.0000.0000.000
177A188VAL00.0750.02235.8910.0000.0000.0000.0000.0000.000
178A189GLU-1-0.776-0.85539.345-0.013-0.0130.0000.0000.0000.000
179A190ARG10.8590.90940.6230.0200.0200.0000.0000.0000.000
180A191MET0-0.0090.00940.5490.0000.0000.0000.0000.0000.000
181A192TYR00.0610.00934.4170.0000.0000.0000.0000.0000.000
182A193ARG10.7510.84140.4320.0150.0150.0000.0000.0000.000
183A194ARG10.8810.92443.6730.0180.0180.0000.0000.0000.000
184A195LEU00.0130.02338.7420.0000.0000.0000.0000.0000.000
185A196ARG10.8340.91842.7070.0110.0110.0000.0000.0000.000
186A197GLN00.0830.04443.682-0.001-0.0010.0000.0000.0000.000
187A198ALA0-0.022-0.00345.2470.0010.0010.0000.0000.0000.000
188A199LEU0-0.004-0.00340.5730.0000.0000.0000.0000.0000.000
189A200GLU-1-0.882-0.96045.210-0.011-0.0110.0000.0000.0000.000
190A201ALA0-0.039-0.01947.7450.0010.0010.0000.0000.0000.000
191A202LEU0-0.004-0.00846.2870.0000.0000.0000.0000.0000.000
192A203ILE00.0150.01244.4060.0000.0000.0000.0000.0000.000
193A204PRO0-0.004-0.00748.3880.0000.0000.0000.0000.0000.000
194A205VAL0-0.0120.00351.7650.0000.0000.0000.0000.0000.000
195A206LEU00.0690.02846.6550.0000.0000.0000.0000.0000.000
196A207LEU0-0.043-0.00548.2440.0000.0000.0000.0000.0000.000
197A208GLU-1-0.876-0.94651.503-0.010-0.0100.0000.0000.0000.000
198A209GLU-1-0.952-0.96652.742-0.020-0.0200.0000.0000.0000.000
199A210THR0-0.045-0.05149.3500.0000.0000.0000.0000.0000.000
200A211HIS0-0.062-0.02152.8250.0010.0010.0000.0000.0000.000
201A212HIS0-0.0130.00956.0790.0010.0010.0000.0000.0000.000
202A213HIS0-0.109-0.04052.8130.0000.0000.0000.0000.0000.000