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: MVN6Z

Calculation Name: 5N9J-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: E

ChEMBL ID:

UniProt ID: P87310

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1578591.591525
FMO2-HF: Nuclear repulsion 1496460.970238
FMO2-HF: Total energy -82130.621287
FMO2-MP2: Total energy -82368.653507


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(E:10:PHE)


Summations of interaction energy for fragment #1(E:10: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.
0.3472.347-0.008-0.94-1.0510.004
Interaction energy analysis for fragmet #1(E:10:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.000
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].
3E12ALA0-0.011-0.0033.8251.4003.400-0.008-0.940-1.0510.004
4E13PHE00.015-0.0016.560-0.656-0.6560.0000.0000.0000.000
5E14PRO0-0.0100.01110.3310.1300.1300.0000.0000.0000.000
6E15PRO00.0080.00112.805-0.011-0.0110.0000.0000.0000.000
7E16PRO00.0190.01414.965-0.073-0.0730.0000.0000.0000.000
8E17PRO00.0270.00718.4650.0030.0030.0000.0000.0000.000
9E18PRO00.0500.00621.4290.0030.0030.0000.0000.0000.000
10E19TYR00.0380.00922.829-0.001-0.0010.0000.0000.0000.000
11E20TYR00.0160.00619.632-0.004-0.0040.0000.0000.0000.000
12E21LYS10.9410.97519.805-0.381-0.3810.0000.0000.0000.000
13E22LEU0-0.044-0.00224.022-0.013-0.0130.0000.0000.0000.000
14E23PHE0-0.004-0.01227.213-0.021-0.0210.0000.0000.0000.000
15E24THR00.006-0.01928.4060.0030.0030.0000.0000.0000.000
16E25ARG11.0070.97631.038-0.130-0.1300.0000.0000.0000.000
17E26GLU-1-0.867-0.92933.8490.0980.0980.0000.0000.0000.000
18E27ASN00.0780.06432.4780.0030.0030.0000.0000.0000.000
19E28ILE0-0.081-0.04232.372-0.004-0.0040.0000.0000.0000.000
20E29GLU-1-0.842-0.94436.2610.0860.0860.0000.0000.0000.000
21E30LYS10.9631.00138.754-0.104-0.1040.0000.0000.0000.000
22E31VAL0-0.053-0.00737.288-0.004-0.0040.0000.0000.0000.000
23E32ILE0-0.0070.02439.991-0.004-0.0040.0000.0000.0000.000
24E33SER0-0.056-0.05042.348-0.004-0.0040.0000.0000.0000.000
25E34ASN0-0.105-0.08442.976-0.004-0.0040.0000.0000.0000.000
26E35MET0-0.001-0.00444.150-0.002-0.0020.0000.0000.0000.000
27E36GLU-1-0.937-0.97945.8210.0530.0530.0000.0000.0000.000
28E37LYS10.8650.94848.025-0.062-0.0620.0000.0000.0000.000
29E38GLU-1-1.015-0.98747.1090.0630.0630.0000.0000.0000.000
30E55GLU-1-0.855-0.94342.7360.0770.0770.0000.0000.0000.000
31E56ILE00.011-0.00437.6980.0040.0040.0000.0000.0000.000
32E57GLU-1-0.835-0.89838.5630.0840.0840.0000.0000.0000.000
33E58SER00.0080.00039.8170.0020.0020.0000.0000.0000.000
34E59LEU00.001-0.00636.4740.0020.0020.0000.0000.0000.000
35E60ALA0-0.0090.00635.3740.0080.0080.0000.0000.0000.000
36E61LYS10.9950.98535.743-0.072-0.0720.0000.0000.0000.000
37E62LEU0-0.053-0.03736.9050.0000.0000.0000.0000.0000.000
38E63PHE0-0.060-0.01728.4210.0040.0040.0000.0000.0000.000
39E64LYS10.8580.94932.068-0.134-0.1340.0000.0000.0000.000
40E65LYS10.9390.98234.712-0.081-0.0810.0000.0000.0000.000
41E66PRO00.0360.01333.8110.0050.0050.0000.0000.0000.000
42E67SER0-0.102-0.12034.733-0.001-0.0010.0000.0000.0000.000
43E68CYS00.0420.10435.0820.0020.0020.0000.0000.0000.000
44E69LEU00.0030.01334.405-0.003-0.0030.0000.0000.0000.000
45E70THR0-0.004-0.01636.769-0.001-0.0010.0000.0000.0000.000
46E71SER00.004-0.00737.939-0.003-0.0030.0000.0000.0000.000
47E72GLY00.0550.02737.2810.0030.0030.0000.0000.0000.000
48E73THR0-0.043-0.05332.1000.0020.0020.0000.0000.0000.000
49E74TYR00.0070.03727.1610.0060.0060.0000.0000.0000.000
50E75GLN0-0.009-0.00225.555-0.004-0.0040.0000.0000.0000.000
51E76MET00.0090.02022.2450.0130.0130.0000.0000.0000.000
52E186PRO0-0.009-0.03432.2520.0020.0020.0000.0000.0000.000
53E187LEU0-0.040-0.01133.3930.0030.0030.0000.0000.0000.000
54E188ASP-1-0.922-0.94035.8750.0310.0310.0000.0000.0000.000
55E189SER0-0.034-0.03035.8700.0000.0000.0000.0000.0000.000
56E190GLN0-0.043-0.01435.1130.0020.0020.0000.0000.0000.000
57E191ASP-1-0.814-0.91937.1560.0110.0110.0000.0000.0000.000
58E192THR00.026-0.02040.175-0.001-0.0010.0000.0000.0000.000
59E193GLY0-0.013-0.00741.831-0.001-0.0010.0000.0000.0000.000
60E194ALA0-0.041-0.01640.0100.0000.0000.0000.0000.0000.000
61E195VAL0-0.078-0.02137.2630.0000.0000.0000.0000.0000.000
62E196SER0-0.065-0.04439.814-0.003-0.0030.0000.0000.0000.000
63E197ALA00.0270.01942.8470.0010.0010.0000.0000.0000.000
64E198SER00.001-0.00446.104-0.002-0.0020.0000.0000.0000.000
65E199SER0-0.080-0.07247.4620.0000.0000.0000.0000.0000.000
66E200VAL00.0090.00949.8650.0000.0000.0000.0000.0000.000
67E201ASN0-0.033-0.00950.2810.0020.0020.0000.0000.0000.000
68E202GLU-1-0.871-0.93750.1610.0010.0010.0000.0000.0000.000
69E203GLY00.0600.02852.7010.0010.0010.0000.0000.0000.000
70E204PHE0-0.078-0.05354.215-0.001-0.0010.0000.0000.0000.000
71E205ARG10.8960.93855.707-0.004-0.0040.0000.0000.0000.000
72E206ALA00.0380.01656.8770.0000.0000.0000.0000.0000.000
73E207ASP-1-0.892-0.93657.2700.0050.0050.0000.0000.0000.000
74E208GLN00.0270.01858.3920.0000.0000.0000.0000.0000.000
75E209LYS10.9400.97256.729-0.002-0.0020.0000.0000.0000.000
76E210SER0-0.0240.00457.4780.0000.0000.0000.0000.0000.000
77E211LYS10.9080.94858.2360.0030.0030.0000.0000.0000.000
78E212ASP-1-0.814-0.91460.476-0.001-0.0010.0000.0000.0000.000
79E213GLY0-0.076-0.05762.020-0.001-0.0010.0000.0000.0000.000
80E214GLU-1-0.914-0.93361.180-0.002-0.0020.0000.0000.0000.000
81E215THR0-0.011-0.03063.299-0.001-0.0010.0000.0000.0000.000
82E216SER00.0110.01359.6730.0000.0000.0000.0000.0000.000
83E217ASP-1-0.787-0.85359.253-0.011-0.0110.0000.0000.0000.000
84E218LEU0-0.043-0.01662.3190.0000.0000.0000.0000.0000.000
85E219ILE0-0.0150.01958.8000.0000.0000.0000.0000.0000.000
86E220LYS11.0301.00761.9080.0040.0040.0000.0000.0000.000
87E221ILE0-0.062-0.03656.1300.0000.0000.0000.0000.0000.000
88E222PRO00.003-0.00954.9370.0010.0010.0000.0000.0000.000
89E223ARG10.9910.99356.080-0.001-0.0010.0000.0000.0000.000
90E224ARG10.9010.96948.842-0.003-0.0030.0000.0000.0000.000
91E225ALA00.0410.01251.092-0.001-0.0010.0000.0000.0000.000
92E226TYR0-0.011-0.00352.169-0.001-0.0010.0000.0000.0000.000
93E227GLU-1-0.827-0.92651.247-0.004-0.0040.0000.0000.0000.000
94E228LEU00.0250.01947.246-0.001-0.0010.0000.0000.0000.000
95E229ARG10.9230.95749.6800.0090.0090.0000.0000.0000.000
96E230PHE0-0.048-0.01151.327-0.001-0.0010.0000.0000.0000.000
97E231LEU00.0770.02747.177-0.001-0.0010.0000.0000.0000.000
98E232SER0-0.021-0.00247.027-0.002-0.0020.0000.0000.0000.000
99E233ARG10.8020.84548.2470.0100.0100.0000.0000.0000.000
100E234SER00.0200.02250.594-0.001-0.0010.0000.0000.0000.000
101E235LEU00.0390.01342.858-0.001-0.0010.0000.0000.0000.000
102E236MET0-0.027-0.01647.168-0.001-0.0010.0000.0000.0000.000
103E237LEU0-0.027-0.01948.345-0.001-0.0010.0000.0000.0000.000
104E238ASN00.0660.02547.304-0.001-0.0010.0000.0000.0000.000
105E239PHE00.0260.02041.695-0.001-0.0010.0000.0000.0000.000
106E240LEU0-0.011-0.00246.516-0.001-0.0010.0000.0000.0000.000
107E241GLU-1-0.919-0.97249.490-0.014-0.0140.0000.0000.0000.000
108E242LEU0-0.017-0.00842.3110.0000.0000.0000.0000.0000.000
109E243LEU00.0240.00044.662-0.001-0.0010.0000.0000.0000.000
110E244GLY0-0.022-0.01747.2580.0000.0000.0000.0000.0000.000
111E245ILE0-0.050-0.01647.4240.0000.0000.0000.0000.0000.000
112E246MET0-0.0330.00143.714-0.001-0.0010.0000.0000.0000.000
113E247ALA0-0.028-0.00746.8570.0000.0000.0000.0000.0000.000
114E248LYS10.8610.94049.4020.0180.0180.0000.0000.0000.000
115E249ALA00.000-0.00450.0160.0010.0010.0000.0000.0000.000
116E250PRO00.0890.04044.8680.0010.0010.0000.0000.0000.000
117E251GLU-1-0.869-0.94545.034-0.021-0.0210.0000.0000.0000.000
118E252GLN0-0.025-0.01646.1220.0020.0020.0000.0000.0000.000
119E253PHE0-0.041-0.01639.8290.0010.0010.0000.0000.0000.000
120E254PRO0-0.013-0.00442.5350.0010.0010.0000.0000.0000.000
121E255SER00.0270.00843.5610.0010.0010.0000.0000.0000.000
122E256LYS10.9660.98946.1190.0130.0130.0000.0000.0000.000
123E257VAL0-0.004-0.01540.5290.0000.0000.0000.0000.0000.000
124E258GLU-1-0.843-0.90941.291-0.008-0.0080.0000.0000.0000.000
125E259ASN0-0.020-0.00143.4850.0010.0010.0000.0000.0000.000
126E260ILE0-0.026-0.01841.6370.0000.0000.0000.0000.0000.000
127E261ARG10.9170.95237.6220.0070.0070.0000.0000.0000.000
128E262VAL00.0350.01641.0910.0010.0010.0000.0000.0000.000
129E263LEU0-0.0150.01843.6130.0010.0010.0000.0000.0000.000
130E264LEU0-0.027-0.01038.5550.0000.0000.0000.0000.0000.000
131E265LEU00.013-0.00337.4990.0010.0010.0000.0000.0000.000
132E266ASN00.0080.03340.8360.0030.0030.0000.0000.0000.000
133E267LEU0-0.010-0.01042.6160.0010.0010.0000.0000.0000.000
134E268HIS0-0.016-0.00636.2870.0020.0020.0000.0000.0000.000
135E269HIS00.0720.07540.9150.0010.0010.0000.0000.0000.000
136E270LEU00.0150.00942.3680.0010.0010.0000.0000.0000.000
137E271ILE0-0.027-0.02740.5940.0010.0010.0000.0000.0000.000
138E272ASN0-0.022-0.02538.421-0.001-0.0010.0000.0000.0000.000
139E273ASP-1-0.843-0.92541.5400.0080.0080.0000.0000.0000.000
140E274TYR0-0.105-0.05944.5480.0010.0010.0000.0000.0000.000
141E275ARG10.9420.98336.1480.0030.0030.0000.0000.0000.000
142E276PRO00.0180.03042.4500.0000.0000.0000.0000.0000.000
143E277HIS00.010-0.02643.4160.0020.0020.0000.0000.0000.000
144E278GLN00.0340.01540.0170.0010.0010.0000.0000.0000.000
145E279SER0-0.006-0.00839.8150.0000.0000.0000.0000.0000.000
146E280ARG10.9390.98141.593-0.010-0.0100.0000.0000.0000.000
147E281GLU-1-0.930-0.96844.7130.0010.0010.0000.0000.0000.000
148E282SER00.0390.02340.866-0.001-0.0010.0000.0000.0000.000
149E283LEU0-0.032-0.01341.7510.0000.0000.0000.0000.0000.000
150E284ILE0-0.019-0.00943.0970.0010.0010.0000.0000.0000.000
151E285MET00.0490.03543.9080.0000.0000.0000.0000.0000.000
152E286LEU0-0.049-0.02239.7400.0000.0000.0000.0000.0000.000
153E287LEU00.007-0.01143.4370.0000.0000.0000.0000.0000.000
154E288GLU-1-0.931-0.95946.0250.0030.0030.0000.0000.0000.000
155E289LYS10.9430.97640.892-0.007-0.0070.0000.0000.0000.000
156E290GLN0-0.080-0.03744.4550.0000.0000.0000.0000.0000.000
157E291LEU00.0590.02646.0440.0000.0000.0000.0000.0000.000
158E292LYS11.0041.00748.5570.0010.0010.0000.0000.0000.000
159E293HIS0-0.048-0.04045.6380.0010.0010.0000.0000.0000.000
160E294GLU-1-0.908-0.95448.1810.0130.0130.0000.0000.0000.000
161E295GLU-1-0.945-0.96850.2310.0040.0040.0000.0000.0000.000
162E296SER0-0.073-0.03550.346-0.001-0.0010.0000.0000.0000.000
163E297GLN0-0.028-0.00948.388-0.001-0.0010.0000.0000.0000.000
164E298VAL00.0550.02451.4420.0000.0000.0000.0000.0000.000
165E299GLU-1-0.900-0.95254.5950.0050.0050.0000.0000.0000.000
166E300LEU0-0.021-0.01051.1580.0000.0000.0000.0000.0000.000
167E301LEU00.0190.03452.8880.0000.0000.0000.0000.0000.000
168E302ARG10.9350.95955.450-0.006-0.0060.0000.0000.0000.000
169E303THR0-0.097-0.06457.2830.0000.0000.0000.0000.0000.000
170E304HIS00.0450.02855.292-0.001-0.0010.0000.0000.0000.000
171E305ASN00.0400.00758.0150.0000.0000.0000.0000.0000.000
172E306ARG10.8460.94560.149-0.002-0.0020.0000.0000.0000.000
173E307GLN00.0380.01559.4060.0000.0000.0000.0000.0000.000
174E308MET0-0.0010.00058.8850.0000.0000.0000.0000.0000.000
175E309THR0-0.029-0.03461.8840.0000.0000.0000.0000.0000.000
176E310GLU-1-0.869-0.92665.1460.0020.0020.0000.0000.0000.000
177E311THR0-0.050-0.03562.875-0.001-0.0010.0000.0000.0000.000
178E312LEU0-0.062-0.02764.2210.0000.0000.0000.0000.0000.000
179E313GLU-1-0.920-0.97665.9410.0060.0060.0000.0000.0000.000
180E314LYS10.8930.95867.544-0.001-0.0010.0000.0000.0000.000
181E315TYR0-0.031-0.03266.036-0.001-0.0010.0000.0000.0000.000
182E316LYS10.9130.97867.902-0.007-0.0070.0000.0000.0000.000
183E317SER0-0.005-0.00569.9520.0000.0000.0000.0000.0000.000
184E318LEU0-0.058-0.01267.9000.0000.0000.0000.0000.0000.000
185E319ASP-1-0.880-0.93770.0900.0060.0060.0000.0000.0000.000
186E320PHE0-0.029-0.02369.6540.0000.0000.0000.0000.0000.000
187E321ASN0-0.033-0.02470.5970.0000.0000.0000.0000.0000.000
188E322MET00.0890.03966.7520.0000.0000.0000.0000.0000.000
189E323GLU-1-0.968-0.97071.5010.0070.0070.0000.0000.0000.000
190E324LYS10.9850.99072.707-0.007-0.0070.0000.0000.0000.000
191E325GLU-1-0.854-0.93873.6770.0040.0040.0000.0000.0000.000
192E326GLY0-0.0090.00573.1760.0000.0000.0000.0000.0000.000
193E327ASP-1-0.887-0.96473.9850.0040.0040.0000.0000.0000.000
194E328VAL00.0150.01377.0850.0000.0000.0000.0000.0000.000
195E329ILE00.0210.01374.6850.0000.0000.0000.0000.0000.000
196E330GLN0-0.100-0.04974.4110.0000.0000.0000.0000.0000.000
197E331GLN0-0.036-0.02978.229-0.001-0.0010.0000.0000.0000.000
198E332LEU0-0.0100.00679.7520.0000.0000.0000.0000.0000.000
199E333LYS10.8890.94377.482-0.002-0.0020.0000.0000.0000.000
200E334SER0-0.089-0.03780.4720.0000.0000.0000.0000.0000.000
201E335SER0-0.0420.00083.0720.0000.0000.0000.0000.0000.000