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: 2JN7R

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1578285.290021
FMO2-HF: Nuclear repulsion 1496151.506526
FMO2-HF: Total energy -82133.783495
FMO2-MP2: Total energy -82371.318857


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.
-1.6240.474-0.002-1.121-0.9750.004
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 : 0.054 / q_NPA : 0.023
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].
3E12ALA0-0.027-0.0143.818-1.6600.438-0.002-1.121-0.9750.004
4E13PHE00.0190.0076.1140.0070.0070.0000.0000.0000.000
5E14PRO00.0100.0149.9290.0540.0540.0000.0000.0000.000
6E15PRO00.0070.00812.7750.0100.0100.0000.0000.0000.000
7E16PRO00.0190.00814.420-0.004-0.0040.0000.0000.0000.000
8E17PRO00.0310.01117.9800.0150.0150.0000.0000.0000.000
9E18PRO00.0400.00720.3510.0100.0100.0000.0000.0000.000
10E19TYR00.0450.01821.8900.0090.0090.0000.0000.0000.000
11E20TYR00.005-0.00918.7970.0060.0060.0000.0000.0000.000
12E21LYS10.9350.97319.426-0.020-0.0200.0000.0000.0000.000
13E22LEU0-0.0090.00423.6030.0090.0090.0000.0000.0000.000
14E23PHE00.0000.00426.8140.0020.0020.0000.0000.0000.000
15E24THR00.0100.00827.8330.0050.0050.0000.0000.0000.000
16E25ARG10.9900.97430.5380.0070.0070.0000.0000.0000.000
17E26GLU-1-0.876-0.91933.488-0.003-0.0030.0000.0000.0000.000
18E27ASN00.0320.00631.926-0.002-0.0020.0000.0000.0000.000
19E28ILE0-0.055-0.02231.983-0.003-0.0030.0000.0000.0000.000
20E29GLU-1-0.867-0.94435.988-0.016-0.0160.0000.0000.0000.000
21E30LYS10.8630.93338.3650.0080.0080.0000.0000.0000.000
22E31VAL0-0.014-0.00136.969-0.001-0.0010.0000.0000.0000.000
23E32ILE0-0.0060.00639.838-0.001-0.0010.0000.0000.0000.000
24E33SER0-0.026-0.02742.0270.0010.0010.0000.0000.0000.000
25E34ASN0-0.011-0.01542.588-0.001-0.0010.0000.0000.0000.000
26E35MET0-0.0020.00843.8670.0000.0000.0000.0000.0000.000
27E36GLU-1-0.844-0.92045.550-0.013-0.0130.0000.0000.0000.000
28E37LYS10.7360.86447.6440.0130.0130.0000.0000.0000.000
29E38GLU-1-0.838-0.88346.142-0.023-0.0230.0000.0000.0000.000
30E55GLU-1-0.877-0.92242.086-0.011-0.0110.0000.0000.0000.000
31E56ILE00.0180.01036.454-0.003-0.0030.0000.0000.0000.000
32E57GLU-1-0.772-0.88337.632-0.015-0.0150.0000.0000.0000.000
33E58SER0-0.002-0.03039.216-0.003-0.0030.0000.0000.0000.000
34E59LEU00.005-0.00435.710-0.004-0.0040.0000.0000.0000.000
35E60ALA0-0.031-0.00834.533-0.004-0.0040.0000.0000.0000.000
36E61LYS10.8040.86835.0090.0220.0220.0000.0000.0000.000
37E62LEU0-0.023-0.01636.537-0.003-0.0030.0000.0000.0000.000
38E63PHE0-0.032-0.01327.730-0.003-0.0030.0000.0000.0000.000
39E64LYS10.8100.91630.9060.0390.0390.0000.0000.0000.000
40E65LYS10.9670.99534.3280.0410.0410.0000.0000.0000.000
41E66PRO00.0060.01433.386-0.002-0.0020.0000.0000.0000.000
42E67SER0-0.035-0.03034.4170.0000.0000.0000.0000.0000.000
43E68CYS0-0.024-0.00834.548-0.002-0.0020.0000.0000.0000.000
44E69LEU00.0050.01234.4280.0050.0050.0000.0000.0000.000
45E70THR00.005-0.00736.546-0.004-0.0040.0000.0000.0000.000
46E71SER0-0.010-0.01037.747-0.001-0.0010.0000.0000.0000.000
47E72GLY00.0300.01837.7880.0010.0010.0000.0000.0000.000
48E73THR0-0.016-0.01732.3990.0010.0010.0000.0000.0000.000
49E74TYR00.0090.00326.746-0.005-0.0050.0000.0000.0000.000
50E75GLN00.0030.01425.784-0.013-0.0130.0000.0000.0000.000
51E76MET0-0.0110.00222.4190.0020.0020.0000.0000.0000.000
52E186PRO0-0.002-0.01732.015-0.002-0.0020.0000.0000.0000.000
53E187LEU0-0.066-0.02533.268-0.004-0.0040.0000.0000.0000.000
54E188ASP-1-0.919-0.95235.864-0.087-0.0870.0000.0000.0000.000
55E189SER0-0.021-0.01635.843-0.007-0.0070.0000.0000.0000.000
56E190GLN0-0.047-0.03034.8720.0000.0000.0000.0000.0000.000
57E191ASP-1-0.798-0.89436.916-0.074-0.0740.0000.0000.0000.000
58E192THR00.018-0.00839.544-0.005-0.0050.0000.0000.0000.000
59E193GLY00.0150.00841.1560.0000.0000.0000.0000.0000.000
60E194ALA0-0.063-0.03640.2750.0010.0010.0000.0000.0000.000
61E195VAL0-0.059-0.01237.066-0.003-0.0030.0000.0000.0000.000
62E196SER0-0.049-0.03739.742-0.001-0.0010.0000.0000.0000.000
63E197ALA00.0270.01542.7580.0000.0000.0000.0000.0000.000
64E198SER00.0130.01146.119-0.002-0.0020.0000.0000.0000.000
65E199SER0-0.092-0.06647.1810.0030.0030.0000.0000.0000.000
66E200VAL00.0050.00949.3800.0030.0030.0000.0000.0000.000
67E201ASN00.006-0.00749.688-0.004-0.0040.0000.0000.0000.000
68E202GLU-1-0.841-0.89150.561-0.056-0.0560.0000.0000.0000.000
69E203GLY00.0850.04352.339-0.002-0.0020.0000.0000.0000.000
70E204PHE0-0.031-0.01753.4820.0020.0020.0000.0000.0000.000
71E205ARG10.8700.91655.2570.0430.0430.0000.0000.0000.000
72E206ALA00.0400.01656.713-0.001-0.0010.0000.0000.0000.000
73E207ASP-1-0.814-0.89156.930-0.042-0.0420.0000.0000.0000.000
74E208GLN00.0290.03258.1910.0010.0010.0000.0000.0000.000
75E209LYS10.8180.89556.5330.0420.0420.0000.0000.0000.000
76E210SER00.0010.00256.8630.0020.0020.0000.0000.0000.000
77E211LYS10.8850.93857.3520.0390.0390.0000.0000.0000.000
78E212ASP-1-0.801-0.88159.722-0.040-0.0400.0000.0000.0000.000
79E213GLY0-0.114-0.07762.0030.0000.0000.0000.0000.0000.000
80E214GLU-1-0.837-0.88860.379-0.040-0.0400.0000.0000.0000.000
81E215THR0-0.012-0.02162.7270.0000.0000.0000.0000.0000.000
82E216SER00.0190.01958.9110.0000.0000.0000.0000.0000.000
83E217ASP-1-0.735-0.83657.982-0.044-0.0440.0000.0000.0000.000
84E218LEU0-0.028-0.00461.1330.0000.0000.0000.0000.0000.000
85E219ILE0-0.0120.03557.7980.0000.0000.0000.0000.0000.000
86E220LYS11.0070.97960.7260.0360.0360.0000.0000.0000.000
87E221ILE00.0090.01855.0780.0000.0000.0000.0000.0000.000
88E222PRO00.013-0.02254.2830.0010.0010.0000.0000.0000.000
89E223ARG10.9370.96054.9510.0420.0420.0000.0000.0000.000
90E224ARG10.7880.85348.1070.0620.0620.0000.0000.0000.000
91E225ALA00.0140.01450.517-0.002-0.0020.0000.0000.0000.000
92E226TYR0-0.078-0.05951.598-0.001-0.0010.0000.0000.0000.000
93E227GLU-1-0.842-0.92550.673-0.052-0.0520.0000.0000.0000.000
94E228LEU00.0180.00846.214-0.001-0.0010.0000.0000.0000.000
95E229ARG10.8280.90348.5690.0470.0470.0000.0000.0000.000
96E230PHE0-0.017-0.00350.9300.0000.0000.0000.0000.0000.000
97E231LEU00.0610.01846.4090.0000.0000.0000.0000.0000.000
98E232SER0-0.034-0.00345.980-0.001-0.0010.0000.0000.0000.000
99E233ARG10.8280.86947.3650.0470.0470.0000.0000.0000.000
100E234SER00.0300.01949.6920.0010.0010.0000.0000.0000.000
101E235LEU00.0160.02242.1800.0000.0000.0000.0000.0000.000
102E236MET0-0.004-0.00346.249-0.001-0.0010.0000.0000.0000.000
103E237LEU0-0.004-0.01047.4130.0010.0010.0000.0000.0000.000
104E238ASN00.0270.00746.9440.0010.0010.0000.0000.0000.000
105E239PHE00.0090.00940.693-0.001-0.0010.0000.0000.0000.000
106E240LEU0-0.0030.00045.7250.0000.0000.0000.0000.0000.000
107E241GLU-1-0.849-0.92948.794-0.049-0.0490.0000.0000.0000.000
108E242LEU0-0.0160.00141.4490.0010.0010.0000.0000.0000.000
109E243LEU00.011-0.00243.2710.0000.0000.0000.0000.0000.000
110E244GLY0-0.022-0.01146.4490.0020.0020.0000.0000.0000.000
111E245ILE0-0.040-0.02446.7870.0020.0020.0000.0000.0000.000
112E246MET00.0090.00442.2330.0010.0010.0000.0000.0000.000
113E247ALA0-0.046-0.01446.1050.0010.0010.0000.0000.0000.000
114E248LYS10.8520.93148.8610.0440.0440.0000.0000.0000.000
115E249ALA00.0100.01349.3630.0020.0020.0000.0000.0000.000
116E250PRO00.0510.02844.118-0.002-0.0020.0000.0000.0000.000
117E251GLU-1-0.871-0.94844.204-0.049-0.0490.0000.0000.0000.000
118E252GLN0-0.017-0.01745.234-0.002-0.0020.0000.0000.0000.000
119E253PHE0-0.034-0.01038.686-0.001-0.0010.0000.0000.0000.000
120E254PRO00.0130.00341.786-0.002-0.0020.0000.0000.0000.000
121E255SER00.0030.00943.033-0.001-0.0010.0000.0000.0000.000
122E256LYS10.8880.93045.7080.0510.0510.0000.0000.0000.000
123E257VAL00.0130.00739.759-0.002-0.0020.0000.0000.0000.000
124E258GLU-1-0.814-0.88740.393-0.082-0.0820.0000.0000.0000.000
125E259ASN0-0.041-0.02342.824-0.001-0.0010.0000.0000.0000.000
126E260ILE0-0.019-0.01340.142-0.001-0.0010.0000.0000.0000.000
127E261ARG10.8520.91837.8920.0840.0840.0000.0000.0000.000
128E262VAL00.0370.01240.367-0.002-0.0020.0000.0000.0000.000
129E263LEU0-0.0030.01143.0120.0000.0000.0000.0000.0000.000
130E264LEU0-0.010-0.00837.2290.0000.0000.0000.0000.0000.000
131E265LEU00.0070.00136.897-0.002-0.0020.0000.0000.0000.000
132E266ASN0-0.0040.01040.2650.0030.0030.0000.0000.0000.000
133E267LEU0-0.013-0.00342.0820.0010.0010.0000.0000.0000.000
134E268HIS0-0.011-0.01635.650-0.001-0.0010.0000.0000.0000.000
135E269HIS00.0260.04240.132-0.004-0.0040.0000.0000.0000.000
136E270LEU00.0310.01341.9560.0000.0000.0000.0000.0000.000
137E271ILE0-0.032-0.02739.6410.0020.0020.0000.0000.0000.000
138E272ASN0-0.011-0.02037.254-0.002-0.0020.0000.0000.0000.000
139E273ASP-1-0.803-0.87240.681-0.067-0.0670.0000.0000.0000.000
140E274TYR0-0.052-0.03044.0470.0040.0040.0000.0000.0000.000
141E275ARG10.9020.95336.3540.1000.1000.0000.0000.0000.000
142E276PRO00.0500.02841.6230.0000.0000.0000.0000.0000.000
143E277HIS0-0.0010.00442.8960.0020.0020.0000.0000.0000.000
144E278GLN00.0060.00339.175-0.002-0.0020.0000.0000.0000.000
145E279SER00.007-0.00439.1410.0000.0000.0000.0000.0000.000
146E280ARG10.9040.95841.3750.0640.0640.0000.0000.0000.000
147E281GLU-1-0.851-0.91043.956-0.070-0.0700.0000.0000.0000.000
148E282SER00.023-0.00440.6990.0000.0000.0000.0000.0000.000
149E283LEU0-0.0280.00041.189-0.001-0.0010.0000.0000.0000.000
150E284ILE0-0.005-0.01142.9660.0020.0020.0000.0000.0000.000
151E285MET00.0100.01144.0260.0010.0010.0000.0000.0000.000
152E286LEU0-0.023-0.01439.3120.0010.0010.0000.0000.0000.000
153E287LEU00.0110.00343.2440.0010.0010.0000.0000.0000.000
154E288GLU-1-0.877-0.92946.119-0.052-0.0520.0000.0000.0000.000
155E289LYS10.9400.97140.4560.0750.0750.0000.0000.0000.000
156E290GLN0-0.077-0.03644.679-0.002-0.0020.0000.0000.0000.000
157E291LEU00.0120.00746.2610.0020.0020.0000.0000.0000.000
158E292LYS10.9210.95448.6450.0540.0540.0000.0000.0000.000
159E293HIS0-0.058-0.01444.153-0.001-0.0010.0000.0000.0000.000
160E294GLU-1-0.824-0.91647.564-0.050-0.0500.0000.0000.0000.000
161E295GLU-1-0.933-0.96650.388-0.043-0.0430.0000.0000.0000.000
162E296SER0-0.045-0.04250.4130.0010.0010.0000.0000.0000.000
163E297GLN0-0.048-0.01948.6810.0030.0030.0000.0000.0000.000
164E298VAL00.0400.01851.1880.0020.0020.0000.0000.0000.000
165E299GLU-1-0.850-0.91054.511-0.032-0.0320.0000.0000.0000.000
166E300LEU00.0000.00850.6870.0010.0010.0000.0000.0000.000
167E301LEU00.0000.00952.7000.0010.0010.0000.0000.0000.000
168E302ARG10.8450.89855.1100.0350.0350.0000.0000.0000.000
169E303THR0-0.039-0.02957.4880.0010.0010.0000.0000.0000.000
170E304HIS00.0070.00554.9790.0010.0010.0000.0000.0000.000
171E305ASN00.0240.00857.1830.0010.0010.0000.0000.0000.000
172E306ARG10.8140.88259.5010.0280.0280.0000.0000.0000.000
173E307GLN00.0360.02259.1850.0000.0000.0000.0000.0000.000
174E308MET0-0.0080.01358.8580.0010.0010.0000.0000.0000.000
175E309THR0-0.047-0.03661.1160.0010.0010.0000.0000.0000.000
176E310GLU-1-0.786-0.85864.512-0.025-0.0250.0000.0000.0000.000
177E311THR0-0.045-0.03762.2190.0010.0010.0000.0000.0000.000
178E312LEU0-0.039-0.02263.8760.0010.0010.0000.0000.0000.000
179E313GLU-1-0.784-0.89765.556-0.019-0.0190.0000.0000.0000.000
180E314LYS10.8780.95066.9570.0210.0210.0000.0000.0000.000
181E315TYR0-0.032-0.01765.2610.0000.0000.0000.0000.0000.000
182E316LYS10.8010.90168.6500.0200.0200.0000.0000.0000.000
183E317SER0-0.031-0.02769.7010.0010.0010.0000.0000.0000.000
184E318LEU0-0.044-0.00767.2580.0000.0000.0000.0000.0000.000
185E319ASP-1-0.860-0.93369.858-0.014-0.0140.0000.0000.0000.000
186E320PHE0-0.037-0.03069.8170.0000.0000.0000.0000.0000.000
187E321ASN0-0.004-0.00770.6010.0000.0000.0000.0000.0000.000
188E322MET00.0770.05266.6340.0000.0000.0000.0000.0000.000
189E323GLU-1-0.894-0.94271.170-0.010-0.0100.0000.0000.0000.000
190E324LYS10.8120.89972.5620.0100.0100.0000.0000.0000.000
191E325GLU-1-0.854-0.92773.522-0.012-0.0120.0000.0000.0000.000
192E326GLY00.0020.00573.2490.0000.0000.0000.0000.0000.000
193E327ASP-1-0.871-0.94873.950-0.009-0.0090.0000.0000.0000.000
194E328VAL00.0250.02877.2940.0000.0000.0000.0000.0000.000
195E329ILE00.0210.00774.6500.0000.0000.0000.0000.0000.000
196E330GLN0-0.020-0.00774.5110.0000.0000.0000.0000.0000.000
197E331GLN0-0.077-0.05178.0360.0000.0000.0000.0000.0000.000
198E332LEU00.0060.01380.1210.0000.0000.0000.0000.0000.000
199E333LYS10.8830.93477.3270.0100.0100.0000.0000.0000.000
200E334SER0-0.108-0.04580.3890.0000.0000.0000.0000.0000.000
201E335SER0-0.043-0.01083.1340.0000.0000.0000.0000.0000.000