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: 392YL

Calculation Name: 1JN5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JN5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9UBU9

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1946222.756096
FMO2-HF: Nuclear repulsion 1873580.76133
FMO2-HF: Total energy -72641.994765
FMO2-MP2: Total energy -72854.260626


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(B:370:ALA)


Summations of interaction energy for fragment #1(B:370:ALA)
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.
0.0471.654-0.007-0.807-0.7940.005
Interaction energy analysis for fragmet #1(B:370:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.018
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].
3B372PRO00.0420.0203.837-1.1910.416-0.007-0.807-0.7940.005
4B373CYS0-0.015-0.0116.2640.5020.5020.0000.0000.0000.000
5B374LYS10.9610.9907.8001.0961.0960.0000.0000.0000.000
6B375GLY00.0150.00911.3260.0560.0560.0000.0000.0000.000
7B376SER00.0400.01314.548-0.015-0.0150.0000.0000.0000.000
8B377TYR0-0.0220.01315.160-0.037-0.0370.0000.0000.0000.000
9B378PHE00.049-0.01217.2810.0340.0340.0000.0000.0000.000
10B379GLY00.0120.02519.3860.0280.0280.0000.0000.0000.000
11B380THR00.0150.00720.4290.0040.0040.0000.0000.0000.000
12B381GLU-1-0.844-0.94524.023-0.224-0.2240.0000.0000.0000.000
13B382ASN0-0.046-0.01426.1120.0090.0090.0000.0000.0000.000
14B383LEU00.1010.02524.6290.0070.0070.0000.0000.0000.000
15B384LYS10.9370.98823.3130.2570.2570.0000.0000.0000.000
16B385SER0-0.056-0.02525.5860.0070.0070.0000.0000.0000.000
17B386LEU00.0350.03228.9400.0060.0060.0000.0000.0000.000
18B387VAL00.0290.00624.6630.0070.0070.0000.0000.0000.000
19B388LEU0-0.024-0.02724.5910.0030.0030.0000.0000.0000.000
20B389HIS00.0110.01927.9250.0010.0010.0000.0000.0000.000
21B390PHE0-0.001-0.01229.1050.0070.0070.0000.0000.0000.000
22B391LEU0-0.029-0.01625.2350.0070.0070.0000.0000.0000.000
23B392GLN00.0170.01929.8380.0120.0120.0000.0000.0000.000
24B393GLN0-0.002-0.00432.2900.0060.0060.0000.0000.0000.000
25B394TYR00.001-0.01731.4210.0040.0040.0000.0000.0000.000
26B395TYR0-0.031-0.04827.6250.0080.0080.0000.0000.0000.000
27B396ALA00.0010.03433.0680.0020.0020.0000.0000.0000.000
28B397ILE00.0060.01436.1940.0040.0040.0000.0000.0000.000
29B398TYR0-0.034-0.01132.1400.0040.0040.0000.0000.0000.000
30B399ASP-1-0.758-0.88233.486-0.086-0.0860.0000.0000.0000.000
31B400SER0-0.041-0.02136.4600.0020.0020.0000.0000.0000.000
32B401GLY0-0.024-0.00740.0820.0020.0020.0000.0000.0000.000
33B402ASP-1-0.882-0.94041.823-0.038-0.0380.0000.0000.0000.000
34B403ARG10.7530.87435.0700.0540.0540.0000.0000.0000.000
35B404GLN00.0520.02639.8580.0010.0010.0000.0000.0000.000
36B405GLY0-0.022-0.01241.7540.0010.0010.0000.0000.0000.000
37B406LEU00.010-0.00135.327-0.002-0.0020.0000.0000.0000.000
38B407LEU0-0.045-0.02138.6050.0000.0000.0000.0000.0000.000
39B408ASP-1-0.914-0.94240.895-0.043-0.0430.0000.0000.0000.000
40B409ALA0-0.054-0.01935.298-0.002-0.0020.0000.0000.0000.000
41B410TYR0-0.074-0.03432.360-0.003-0.0030.0000.0000.0000.000
42B411HIS00.0900.02936.7570.0030.0030.0000.0000.0000.000
43B412ASP-1-0.866-0.93838.601-0.026-0.0260.0000.0000.0000.000
44B413GLY0-0.047-0.02539.8820.0020.0020.0000.0000.0000.000
45B414ALA0-0.025-0.00735.1580.0020.0020.0000.0000.0000.000
46B415CYS0-0.052-0.02532.9250.0050.0050.0000.0000.0000.000
47B416CYS0-0.0050.00631.662-0.005-0.0050.0000.0000.0000.000
48B417SER0-0.031-0.01429.2270.0080.0080.0000.0000.0000.000
49B418LEU00.0650.04328.506-0.006-0.0060.0000.0000.0000.000
50B419SER0-0.0300.00625.5010.0090.0090.0000.0000.0000.000
51B420ILE00.0150.01626.159-0.008-0.0080.0000.0000.0000.000
52B421PRO0-0.034-0.02223.0980.0120.0120.0000.0000.0000.000
53B422PHE00.0670.00524.6810.0040.0040.0000.0000.0000.000
54B423ILE0-0.0110.01622.5090.0010.0010.0000.0000.0000.000
55B424PRO0-0.0260.00126.2540.0010.0010.0000.0000.0000.000
56B425GLN00.009-0.02427.761-0.013-0.0130.0000.0000.0000.000
57B426ASN00.0810.03127.384-0.005-0.0050.0000.0000.0000.000
58B427PRO00.0090.00425.0330.0000.0000.0000.0000.0000.000
59B428ALA00.0140.01328.066-0.006-0.0060.0000.0000.0000.000
60B429ARG10.8900.95327.2870.0290.0290.0000.0000.0000.000
61B430SER00.0540.03330.7600.0080.0080.0000.0000.0000.000
62B431SER00.0210.00731.4470.0010.0010.0000.0000.0000.000
63B432LEU00.0350.03027.646-0.003-0.0030.0000.0000.0000.000
64B433ALA0-0.038-0.02332.3250.0020.0020.0000.0000.0000.000
65B434GLU-1-0.927-0.96235.186-0.025-0.0250.0000.0000.0000.000
66B435TYR0-0.001-0.04331.372-0.001-0.0010.0000.0000.0000.000
67B436PHE0-0.079-0.03932.8180.0040.0040.0000.0000.0000.000
68B437LYS10.9370.96234.0730.0110.0110.0000.0000.0000.000
69B438ASP-1-0.849-0.91834.984-0.013-0.0130.0000.0000.0000.000
70B439SER0-0.0190.00330.179-0.002-0.0020.0000.0000.0000.000
71B440ARG10.8870.93130.410-0.001-0.0010.0000.0000.0000.000
72B441ASN00.0610.01725.8430.0070.0070.0000.0000.0000.000
73B442VAL00.0420.02127.2820.0040.0040.0000.0000.0000.000
74B443LYN00.0200.01124.0480.0020.0020.0000.0000.0000.000
75B444LYS10.8280.92826.839-0.060-0.0600.0000.0000.0000.000
76B445LEU00.0320.02830.3240.0010.0010.0000.0000.0000.000
77B446LYS10.9030.94129.796-0.065-0.0650.0000.0000.0000.000
78B447ASP-1-0.781-0.89734.8510.0260.0260.0000.0000.0000.000
79B448PRO00.0280.00637.147-0.003-0.0030.0000.0000.0000.000
80B449THR00.0650.03338.191-0.003-0.0030.0000.0000.0000.000
81B450LEU0-0.002-0.00237.967-0.003-0.0030.0000.0000.0000.000
82B451ARG10.8310.91031.950-0.046-0.0460.0000.0000.0000.000
83B452PHE0-0.026-0.00635.523-0.003-0.0030.0000.0000.0000.000
84B453ARG10.9860.99437.852-0.006-0.0060.0000.0000.0000.000
85B454LEU0-0.0040.00534.282-0.003-0.0030.0000.0000.0000.000
86B455LEU0-0.106-0.04032.599-0.003-0.0030.0000.0000.0000.000
87B456LYS10.8990.96935.2800.0160.0160.0000.0000.0000.000
88B457HIS00.014-0.00136.2700.0000.0000.0000.0000.0000.000
89B458THR00.005-0.01138.6750.0000.0000.0000.0000.0000.000
90B459ARG10.9630.96739.1370.0320.0320.0000.0000.0000.000
91B460LEU00.0320.03540.187-0.002-0.0020.0000.0000.0000.000
92B461ASN0-0.007-0.01440.804-0.002-0.0020.0000.0000.0000.000
93B462VAL0-0.064-0.01835.5960.0000.0000.0000.0000.0000.000
94B463VAL00.018-0.01637.597-0.002-0.0020.0000.0000.0000.000
95B464ALA0-0.031-0.00739.284-0.001-0.0010.0000.0000.0000.000
96B465PHE00.0120.00933.547-0.001-0.0010.0000.0000.0000.000
97B466LEU0-0.021-0.00933.302-0.002-0.0020.0000.0000.0000.000
98B467ASN0-0.007-0.01536.934-0.006-0.0060.0000.0000.0000.000
99B468GLU-1-0.953-0.97839.605-0.022-0.0220.0000.0000.0000.000
100B469LEU0-0.074-0.01833.2390.0000.0000.0000.0000.0000.000
101B470PRO00.0130.01134.951-0.001-0.0010.0000.0000.0000.000
102B471LYS11.0101.01035.9950.0360.0360.0000.0000.0000.000
103B472THR0-0.074-0.06432.5750.0000.0000.0000.0000.0000.000
104B473GLN00.0310.01232.8740.0040.0040.0000.0000.0000.000
105B474HIS10.7980.91227.7370.0960.0960.0000.0000.0000.000
106B475ASP-1-0.850-0.88826.338-0.164-0.1640.0000.0000.0000.000
107B476VAL00.0480.00126.235-0.015-0.0150.0000.0000.0000.000
108B477ASN0-0.006-0.00825.975-0.009-0.0090.0000.0000.0000.000
109B478SER0-0.059-0.03923.041-0.024-0.0240.0000.0000.0000.000
110B479PHE0-0.083-0.02921.744-0.010-0.0100.0000.0000.0000.000
111B480VAL0-0.030-0.01115.717-0.021-0.0210.0000.0000.0000.000
112B481VAL0-0.047-0.04219.1530.0250.0250.0000.0000.0000.000
113B482ASP-1-0.878-0.92215.547-0.396-0.3960.0000.0000.0000.000
114B483ILE0-0.038-0.01818.1550.0380.0380.0000.0000.0000.000
115B484SER0-0.017-0.01317.756-0.012-0.0120.0000.0000.0000.000
116B485ALA0-0.013-0.00418.8790.0140.0140.0000.0000.0000.000
117B486GLN0-0.015-0.02721.9070.0030.0030.0000.0000.0000.000
118B487THR00.0170.02324.9020.0030.0030.0000.0000.0000.000
119B488SER00.0280.01528.017-0.005-0.0050.0000.0000.0000.000
120B489THR0-0.016-0.02631.236-0.002-0.0020.0000.0000.0000.000
121B490LEU00.0270.02825.4280.0020.0020.0000.0000.0000.000
122B491LEU00.0250.01325.343-0.007-0.0070.0000.0000.0000.000
123B492CYS0-0.035-0.00822.4020.0040.0040.0000.0000.0000.000
124B493PHE00.009-0.00821.497-0.017-0.0170.0000.0000.0000.000
125B494SER00.0160.01418.8040.0200.0200.0000.0000.0000.000
126B495VAL0-0.028-0.01420.368-0.027-0.0270.0000.0000.0000.000
127B496ASN00.0040.00917.1570.0410.0410.0000.0000.0000.000
128B497GLY00.0290.01220.259-0.018-0.0180.0000.0000.0000.000
129B498VAL00.0090.00222.4550.0110.0110.0000.0000.0000.000
130B499PHE0-0.044-0.02725.096-0.001-0.0010.0000.0000.0000.000
131B500LYS10.9891.01728.8110.0840.0840.0000.0000.0000.000
132B501GLU-1-0.763-0.85831.816-0.050-0.0500.0000.0000.0000.000
133B502VAL0-0.020-0.03034.5230.0000.0000.0000.0000.0000.000
134B503ASP-1-0.875-0.95037.693-0.044-0.0440.0000.0000.0000.000
135B504GLY00.0690.04338.7990.0000.0000.0000.0000.0000.000
136B505LYS10.9120.93240.0250.0220.0220.0000.0000.0000.000
137B506SER0-0.0080.00134.7700.0020.0020.0000.0000.0000.000
138B507ARG10.9350.98435.4900.0490.0490.0000.0000.0000.000
139B508ASP-1-0.907-0.95235.282-0.062-0.0620.0000.0000.0000.000
140B509SER0-0.022-0.00630.965-0.003-0.0030.0000.0000.0000.000
141B510LEU0-0.034-0.01425.772-0.002-0.0020.0000.0000.0000.000
142B511ARG10.7460.85627.0350.0580.0580.0000.0000.0000.000
143B512ALA00.0260.00221.658-0.011-0.0110.0000.0000.0000.000
144B513PHE0-0.057-0.03022.8190.0170.0170.0000.0000.0000.000
145B514THR00.0190.00418.757-0.015-0.0150.0000.0000.0000.000
146B515ARG10.8170.89621.5430.0900.0900.0000.0000.0000.000
147B516THR00.0060.00722.104-0.020-0.0200.0000.0000.0000.000
148B517PHE00.0350.02023.9630.0120.0120.0000.0000.0000.000
149B518ILE00.0210.00125.553-0.007-0.0070.0000.0000.0000.000
150B519ALA0-0.054-0.03427.7410.0060.0060.0000.0000.0000.000
151B520VAL00.0140.01430.3420.0000.0000.0000.0000.0000.000
152B521PRO0-0.005-0.01132.997-0.003-0.0030.0000.0000.0000.000
153B522ALA0-0.0050.02834.8980.0050.0050.0000.0000.0000.000
154B523SER0-0.003-0.01537.684-0.003-0.0030.0000.0000.0000.000
155B524ASN00.0270.01439.2370.0030.0030.0000.0000.0000.000
156B525SER0-0.022-0.01636.101-0.004-0.0040.0000.0000.0000.000
157B526GLY00.0050.01835.481-0.007-0.0070.0000.0000.0000.000
158B527LEU0-0.046-0.04229.951-0.001-0.0010.0000.0000.0000.000
159B528CYS00.0100.02534.0920.0030.0030.0000.0000.0000.000
160B529ILE00.0020.00830.8070.0000.0000.0000.0000.0000.000
161B530VAL00.0240.00331.5590.0050.0050.0000.0000.0000.000
162B531ASN0-0.037-0.02629.1030.0060.0060.0000.0000.0000.000
163B532ASP-1-0.743-0.85628.553-0.069-0.0690.0000.0000.0000.000
164B533GLU-1-0.907-0.94924.980-0.022-0.0220.0000.0000.0000.000
165B534LEU00.0240.02225.480-0.012-0.0120.0000.0000.0000.000
166B535PHE00.0600.02520.7430.0100.0100.0000.0000.0000.000
167B536VAL00.0290.01224.329-0.015-0.0150.0000.0000.0000.000
168B537ARG10.7900.87118.4120.1430.1430.0000.0000.0000.000
169B538ASN00.0010.00824.906-0.009-0.0090.0000.0000.0000.000
170B539ALA00.0080.01122.831-0.001-0.0010.0000.0000.0000.000
171B540SER0-0.004-0.02319.0770.0090.0090.0000.0000.0000.000
172B541SER00.041-0.00122.130-0.009-0.0090.0000.0000.0000.000
173B542GLU-1-0.890-0.94117.977-0.126-0.1260.0000.0000.0000.000
174B543GLU-1-0.797-0.87319.007-0.179-0.1790.0000.0000.0000.000
175B544ILE0-0.020-0.01221.314-0.004-0.0040.0000.0000.0000.000
176B545GLN00.0030.01023.314-0.005-0.0050.0000.0000.0000.000
177B546ARG10.9320.95817.0330.3000.3000.0000.0000.0000.000
178B547ALA0-0.036-0.01923.3390.0000.0000.0000.0000.0000.000
179B548PHE0-0.019-0.01825.4070.0060.0060.0000.0000.0000.000
180B549ALA0-0.0130.02126.1170.0090.0090.0000.0000.0000.000
181B550MET0-0.019-0.01528.114-0.004-0.0040.0000.0000.0000.000
182B551PRO0-0.028-0.00927.9070.0090.0090.0000.0000.0000.000
183B552ALA00.0260.01631.187-0.003-0.0030.0000.0000.0000.000
184B553PRO00.0010.00131.063-0.006-0.0060.0000.0000.0000.000
185B554THR00.0160.00229.2640.0090.0090.0000.0000.0000.000
186B555PRO0-0.026-0.00528.623-0.015-0.0150.0000.0000.0000.000