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

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FMODB ID: 434ZN

Calculation Name: 5D0Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: A

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-20

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 766
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -16383323.001235
FMO2-HF: Nuclear repulsion 16084043.813952
FMO2-HF: Total energy -299279.187284
FMO2-MP2: Total energy -300158.406916


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:24:PHE)


Summations of interaction energy for fragment #1(A:24:PHE)
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.
-35.118-17.05616.522-10.012-24.571-0.033
Interaction energy analysis for fragmet #1(A:24:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / 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].
3A26VAL00.0020.0122.573-4.3800.0672.388-2.165-4.6710.008
4A27LYS10.8070.8973.2842.1872.5460.0380.385-0.7820.001
5A28ASP-1-0.829-0.9095.303-0.246-0.2460.0000.0000.0000.000
6A29ILE0-0.059-0.0315.411-0.347-0.3470.0000.0000.0000.000
7A30HIS0-0.032-0.0177.6440.1950.1950.0000.0000.0000.000
8A31PHE00.017-0.0179.911-0.013-0.0130.0000.0000.0000.000
9A32GLU-1-0.873-0.92912.7210.0510.0510.0000.0000.0000.000
10A33GLY00.0270.01115.530-0.005-0.0050.0000.0000.0000.000
11A34LEU00.0080.00415.725-0.002-0.0020.0000.0000.0000.000
12A35GLN0-0.142-0.08719.2930.0050.0050.0000.0000.0000.000
13A36ARG10.8940.95523.0190.1280.1280.0000.0000.0000.000
14A37VAL0-0.034-0.00519.296-0.006-0.0060.0000.0000.0000.000
15A38ALA00.0270.01020.261-0.006-0.0060.0000.0000.0000.000
16A39VAL00.0490.00915.037-0.014-0.0140.0000.0000.0000.000
17A40GLY00.0130.01216.226-0.035-0.0350.0000.0000.0000.000
18A41ALA00.0100.00417.874-0.021-0.0210.0000.0000.0000.000
19A42ALA00.0370.02315.321-0.013-0.0130.0000.0000.0000.000
20A43LEU00.0400.01811.073-0.031-0.0310.0000.0000.0000.000
21A44LEU0-0.072-0.03214.104-0.053-0.0530.0000.0000.0000.000
22A45SER0-0.052-0.02315.7890.0020.0020.0000.0000.0000.000
23A46MET0-0.0350.0018.6400.0340.0340.0000.0000.0000.000
24A47PRO0-0.028-0.01811.054-0.009-0.0090.0000.0000.0000.000
25A48VAL00.0110.0156.748-0.043-0.0430.0000.0000.0000.000
26A49ARG10.8540.9058.6510.7190.7190.0000.0000.0000.000
27A50THR00.023-0.0036.912-0.131-0.1310.0000.0000.0000.000
28A51GLY0-0.035-0.0057.0740.1130.1130.0000.0000.0000.000
29A52ASP-1-0.829-0.8987.080-1.430-1.4300.0000.0000.0000.000
30A53THR0-0.066-0.0493.596-0.2780.0770.005-0.129-0.2310.000
31A54VAL0-0.028-0.0032.372-1.3180.6991.849-0.979-2.8870.002
32A55ASN0-0.028-0.0432.523-7.139-4.3511.941-2.181-2.548-0.029
33A56ASP-1-0.856-0.9384.5490.7100.883-0.001-0.004-0.1680.000
34A57GLU-1-0.950-0.9696.631-0.337-0.3370.0000.0000.0000.000
35A58ASP-1-0.822-0.8995.855-1.986-1.9860.0000.0000.0000.000
36A59ILE0-0.010-0.0033.568-0.1610.1880.007-0.070-0.2860.000
37A60SER00.002-0.0126.8570.2280.2280.0000.0000.0000.000
38A61ASN0-0.020-0.00210.1520.2150.2150.0000.0000.0000.000
39A62THR00.0450.0127.4450.0890.0890.0000.0000.0000.000
40A63ILE0-0.0140.0029.7360.0770.0770.0000.0000.0000.000
41A64ARG10.8850.93011.9820.3800.3800.0000.0000.0000.000
42A65ALA00.0010.01213.4560.0360.0360.0000.0000.0000.000
43A66LEU00.0340.00811.7190.0410.0410.0000.0000.0000.000
44A67PHE0-0.019-0.00515.3970.0360.0360.0000.0000.0000.000
45A68ALA0-0.022-0.00317.9320.0240.0240.0000.0000.0000.000
46A69THR0-0.073-0.04217.9370.0190.0190.0000.0000.0000.000
47A70GLY00.0310.02320.7130.0120.0120.0000.0000.0000.000
48A71ASN00.0100.00920.5300.0320.0320.0000.0000.0000.000
49A72PHE00.011-0.01017.2370.0120.0120.0000.0000.0000.000
50A73GLU-1-0.838-0.89620.889-0.035-0.0350.0000.0000.0000.000
51A74ASP-1-0.821-0.88917.5470.0260.0260.0000.0000.0000.000
52A75VAL00.0080.00812.684-0.016-0.0160.0000.0000.0000.000
53A76ARG10.8090.89512.390-0.082-0.0820.0000.0000.0000.000
54A77VAL00.0200.0146.054-0.007-0.0070.0000.0000.0000.000
55A78LEU0-0.0030.0046.7870.1000.1000.0000.0000.0000.000
56A79ARG10.9060.9422.689-12.761-9.2814.940-1.995-6.4240.020
57A80ASP-1-0.883-0.9205.4690.6120.6120.0000.0000.0000.000
58A81GLY00.0340.0186.131-0.354-0.3540.0000.0000.0000.000
59A82ASP-1-0.889-0.9552.135-4.455-2.3083.362-2.297-3.211-0.015
60A83THR00.0070.0142.440-4.271-3.8641.576-0.163-1.820-0.020
61A84LEU0-0.024-0.0092.664-0.7480.6980.417-0.382-1.4810.000
62A85LEU00.0170.0084.219-0.0610.0330.000-0.032-0.0620.000
63A86VAL0-0.004-0.0127.9190.0650.0650.0000.0000.0000.000
64A87GLN0-0.039-0.02610.5350.0390.0390.0000.0000.0000.000
65A88VAL0-0.029-0.01013.704-0.014-0.0140.0000.0000.0000.000
66A89LYS10.8910.93316.4360.0020.0020.0000.0000.0000.000
67A90GLU-1-0.785-0.90720.154-0.121-0.1210.0000.0000.0000.000
68A91ARG10.8140.90122.5280.1130.1130.0000.0000.0000.000
69A92PRO0-0.0650.00524.8540.0070.0070.0000.0000.0000.000
70A93THR0-0.031-0.02628.0660.0030.0030.0000.0000.0000.000
71A94ILE00.0080.01230.7570.0070.0070.0000.0000.0000.000
72A95ALA0-0.053-0.02634.216-0.004-0.0040.0000.0000.0000.000
73A96SER0-0.052-0.05736.5590.0000.0000.0000.0000.0000.000
74A97ILE00.0310.02438.0570.0000.0000.0000.0000.0000.000
75A98THR0-0.033-0.00841.2300.0010.0010.0000.0000.0000.000
76A99PHE00.0290.02244.3030.0020.0020.0000.0000.0000.000
77A100SER00.000-0.00547.0920.0010.0010.0000.0000.0000.000
78A101GLY00.0200.01449.6230.0010.0010.0000.0000.0000.000
79A102ASN0-0.055-0.01250.4760.0020.0020.0000.0000.0000.000
80A103LYS10.8320.89152.4970.0230.0230.0000.0000.0000.000
81A104SER0-0.019-0.03855.6040.0000.0000.0000.0000.0000.000
82A105VAL00.0110.01550.840-0.001-0.0010.0000.0000.0000.000
83A106LYS10.9250.95352.5980.0350.0350.0000.0000.0000.000
84A107ASP-1-0.763-0.88249.006-0.032-0.0320.0000.0000.0000.000
85A108ASP-1-0.869-0.93847.856-0.041-0.0410.0000.0000.0000.000
86A109MET0-0.032-0.00448.337-0.002-0.0020.0000.0000.0000.000
87A110LEU00.0280.02046.276-0.002-0.0020.0000.0000.0000.000
88A111LYS10.8870.94243.7450.0440.0440.0000.0000.0000.000
89A112GLN0-0.005-0.01243.034-0.003-0.0030.0000.0000.0000.000
90A113ASN00.0110.01643.511-0.004-0.0040.0000.0000.0000.000
91A114LEU00.0100.01039.571-0.002-0.0020.0000.0000.0000.000
92A115GLU-1-0.923-0.95638.944-0.069-0.0690.0000.0000.0000.000
93A116ALA0-0.033-0.01138.679-0.005-0.0050.0000.0000.0000.000
94A117SER0-0.027-0.01038.287-0.001-0.0010.0000.0000.0000.000
95A118GLY0-0.0100.00934.575-0.002-0.0020.0000.0000.0000.000
96A119VAL0-0.025-0.01634.604-0.002-0.0020.0000.0000.0000.000
97A120ARG10.8600.90435.3490.0790.0790.0000.0000.0000.000
98A121VAL0-0.007-0.02135.603-0.001-0.0010.0000.0000.0000.000
99A122GLY0-0.027-0.01334.256-0.003-0.0030.0000.0000.0000.000
100A123GLU-1-0.787-0.86429.860-0.113-0.1130.0000.0000.0000.000
101A124SER0-0.104-0.09126.7220.0060.0060.0000.0000.0000.000
102A125LEU0-0.001-0.00428.516-0.001-0.0010.0000.0000.0000.000
103A126ASP-1-0.753-0.83826.539-0.079-0.0790.0000.0000.0000.000
104A127ARG10.8700.91427.5910.0330.0330.0000.0000.0000.000
105A128THR0-0.073-0.06226.6670.0060.0060.0000.0000.0000.000
106A129THR00.0030.00329.7290.0020.0020.0000.0000.0000.000
107A130ILE0-0.018-0.00932.4430.0010.0010.0000.0000.0000.000
108A131ALA00.0330.01234.9680.0010.0010.0000.0000.0000.000
109A132ASP-1-0.863-0.93734.535-0.044-0.0440.0000.0000.0000.000
110A133ILE0-0.020-0.00634.1050.0000.0000.0000.0000.0000.000
111A134GLU-1-0.823-0.89738.141-0.019-0.0190.0000.0000.0000.000
112A135LYS10.8770.91940.4450.0280.0280.0000.0000.0000.000
113A136GLY00.0390.01740.8330.0000.0000.0000.0000.0000.000
114A137LEU0-0.051-0.03042.0400.0000.0000.0000.0000.0000.000
115A138GLU-1-0.851-0.92044.481-0.020-0.0200.0000.0000.0000.000
116A139ASP-1-0.788-0.86544.762-0.030-0.0300.0000.0000.0000.000
117A140PHE0-0.0170.00346.0940.0000.0000.0000.0000.0000.000
118A141TYR0-0.037-0.05047.9450.0000.0000.0000.0000.0000.000
119A142TYR0-0.069-0.05148.1460.0020.0020.0000.0000.0000.000
120A143SER0-0.037-0.00751.5440.0010.0010.0000.0000.0000.000
121A144VAL00.0100.00153.7570.0010.0010.0000.0000.0000.000
122A145GLY00.0120.02855.8300.0010.0010.0000.0000.0000.000
123A146LYS10.8470.91454.1980.0210.0210.0000.0000.0000.000
124A147TYR00.0310.01453.9520.0000.0000.0000.0000.0000.000
125A148SER0-0.102-0.06053.5230.0020.0020.0000.0000.0000.000
126A149ALA0-0.0070.01451.4830.0010.0010.0000.0000.0000.000
127A150SER0-0.072-0.03447.5530.0010.0010.0000.0000.0000.000
128A151VAL0-0.026-0.00843.6370.0000.0000.0000.0000.0000.000
129A152LYS10.8010.87342.2030.0180.0180.0000.0000.0000.000
130A153ALA00.0220.02138.904-0.001-0.0010.0000.0000.0000.000
131A154VAL0-0.043-0.02639.6900.0030.0030.0000.0000.0000.000
132A155VAL00.0090.01333.079-0.003-0.0030.0000.0000.0000.000
133A156THR00.001-0.00436.1580.0050.0050.0000.0000.0000.000
134A157PRO00.0110.00932.920-0.004-0.0040.0000.0000.0000.000
135A158LEU00.0040.00634.0300.0020.0020.0000.0000.0000.000
136A159PRO0-0.0010.00033.6370.0000.0000.0000.0000.0000.000
137A160ARG10.8590.90229.3850.0490.0490.0000.0000.0000.000
138A161ASN00.0840.04726.372-0.001-0.0010.0000.0000.0000.000
139A162ARG10.9360.99028.9140.0490.0490.0000.0000.0000.000
140A163VAL00.0210.00432.1830.0060.0060.0000.0000.0000.000
141A164ASP-1-0.805-0.87734.478-0.036-0.0360.0000.0000.0000.000
142A165LEU00.0150.01137.0310.0020.0020.0000.0000.0000.000
143A166LYS10.8740.93239.0960.0250.0250.0000.0000.0000.000
144A167LEU0-0.009-0.01040.7880.0000.0000.0000.0000.0000.000
145A168VAL00.0080.00644.1820.0000.0000.0000.0000.0000.000
146A169PHE00.0330.00246.040-0.001-0.0010.0000.0000.0000.000
147A170GLN0-0.032-0.01649.4820.0010.0010.0000.0000.0000.000
148A171GLU-1-0.676-0.79852.301-0.023-0.0230.0000.0000.0000.000
149A172GLY00.0380.02954.3550.0010.0010.0000.0000.0000.000
150A173VAL00.000-0.01656.882-0.001-0.0010.0000.0000.0000.000
151A174SER0-0.003-0.00859.953-0.001-0.0010.0000.0000.0000.000
152A175ALA0-0.005-0.00761.3410.0010.0010.0000.0000.0000.000
153A176GLU-1-0.814-0.86861.589-0.020-0.0200.0000.0000.0000.000
154A177ILE0-0.097-0.05362.446-0.001-0.0010.0000.0000.0000.000
155A178GLN00.0430.01765.5560.0000.0000.0000.0000.0000.000
156A179GLN0-0.052-0.02967.5790.0010.0010.0000.0000.0000.000
157A180ILE00.0260.01266.8100.0000.0000.0000.0000.0000.000
158A181ASN0-0.042-0.02768.1610.0010.0010.0000.0000.0000.000
159A182ILE00.0290.01868.387-0.001-0.0010.0000.0000.0000.000
160A183VAL0-0.0090.00169.8850.0010.0010.0000.0000.0000.000
161A184GLY00.0640.02470.574-0.001-0.0010.0000.0000.0000.000
162A185ASN0-0.076-0.03273.0750.0000.0000.0000.0000.0000.000
163A186HIS0-0.109-0.07074.7650.0010.0010.0000.0000.0000.000
164A187ALA0-0.048-0.01876.8110.0000.0000.0000.0000.0000.000
165A188PHE00.0200.01975.0710.0000.0000.0000.0000.0000.000
166A189THR00.0010.00676.9420.0000.0000.0000.0000.0000.000
167A190THR00.032-0.01273.6140.0000.0000.0000.0000.0000.000
168A191ASP-1-0.953-0.96474.196-0.018-0.0180.0000.0000.0000.000
169A192GLU-1-0.796-0.87775.177-0.022-0.0220.0000.0000.0000.000
170A193LEU00.0150.01971.848-0.001-0.0010.0000.0000.0000.000
171A194ILE0-0.012-0.01170.311-0.001-0.0010.0000.0000.0000.000
172A195SER0-0.058-0.04070.832-0.001-0.0010.0000.0000.0000.000
173A196HIS00.003-0.00970.295-0.001-0.0010.0000.0000.0000.000
174A197PHE0-0.054-0.01366.400-0.001-0.0010.0000.0000.0000.000
175A198GLN0-0.108-0.05566.6970.0000.0000.0000.0000.0000.000
176A199LEU00.0040.01969.5620.0010.0010.0000.0000.0000.000
177A217GLN00.0640.04460.2100.0010.0010.0000.0000.0000.000
178A218LYS10.8100.87855.7980.0280.0280.0000.0000.0000.000
179A219LEU00.0560.02957.438-0.001-0.0010.0000.0000.0000.000
180A220ALA00.0270.01855.2640.0000.0000.0000.0000.0000.000
181A221GLY00.0520.02857.3710.0000.0000.0000.0000.0000.000
182A222ASP-1-0.826-0.92259.525-0.028-0.0280.0000.0000.0000.000
183A223LEU0-0.013-0.00859.2220.0010.0010.0000.0000.0000.000
184A224GLU-1-0.829-0.88958.289-0.037-0.0370.0000.0000.0000.000
185A225THR00.0060.00961.4340.0010.0010.0000.0000.0000.000
186A226LEU0-0.0120.01164.7910.0010.0010.0000.0000.0000.000
187A227ARG10.8310.88060.0320.0350.0350.0000.0000.0000.000
188A228SER0-0.038-0.03564.0180.0000.0000.0000.0000.0000.000
189A229TYR0-0.048-0.04166.4230.0000.0000.0000.0000.0000.000
190A230TYR0-0.003-0.03969.0980.0010.0010.0000.0000.0000.000
191A231LEU0-0.051-0.02564.8870.0000.0000.0000.0000.0000.000
192A232ASP-1-0.857-0.91269.209-0.029-0.0290.0000.0000.0000.000
193A233ARG10.7790.88171.2260.0250.0250.0000.0000.0000.000
194A234GLY00.0350.02373.2060.0010.0010.0000.0000.0000.000
195A235TYR0-0.029-0.00771.7850.0000.0000.0000.0000.0000.000
196A236ALA0-0.023-0.02269.2560.0000.0000.0000.0000.0000.000
197A237ARG10.8010.87567.9070.0230.0230.0000.0000.0000.000
198A238PHE00.0130.00865.5220.0010.0010.0000.0000.0000.000
199A239ASN0-0.059-0.04262.809-0.002-0.0020.0000.0000.0000.000
200A240ILE00.0080.00062.0100.0010.0010.0000.0000.0000.000
201A241ASP-1-0.823-0.87362.215-0.024-0.0240.0000.0000.0000.000
202A242SER0-0.029-0.01961.2600.0000.0000.0000.0000.0000.000
203A243THR00.0140.00959.0440.0000.0000.0000.0000.0000.000
204A244GLN0-0.0140.01460.1930.0000.0000.0000.0000.0000.000
205A245VAL00.0310.00959.1000.0000.0000.0000.0000.0000.000
206A246SER0-0.026-0.00760.4060.0010.0010.0000.0000.0000.000
207A247LEU0-0.008-0.00956.6400.0000.0000.0000.0000.0000.000
208A248THR0-0.0020.00461.2670.0010.0010.0000.0000.0000.000
209A249PRO00.013-0.00863.0580.0000.0000.0000.0000.0000.000
210A250ASP-1-0.799-0.88962.926-0.013-0.0130.0000.0000.0000.000
211A251LYS10.8470.91458.5800.0120.0120.0000.0000.0000.000
212A252LYS10.8460.91357.9350.0130.0130.0000.0000.0000.000
213A253GLY00.0610.05859.681-0.001-0.0010.0000.0000.0000.000
214A254ILE0-0.109-0.07859.1060.0010.0010.0000.0000.0000.000
215A255TYR00.0310.02862.3580.0000.0000.0000.0000.0000.000
216A256VAL0-0.014-0.01962.2120.0000.0000.0000.0000.0000.000
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