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: 66QQZ

Calculation Name: 5J09-J-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J09

Chain ID: J

ChEMBL ID:

UniProt ID: A0A023

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 OptHSide
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1857768.809795
FMO2-HF: Nuclear repulsion 1788272.72134
FMO2-HF: Total energy -69496.088455
FMO2-MP2: Total energy -69703.66122


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(J:46:ARG)


Summations of interaction energy for fragment #1(J:46:ARG)
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.
122.353131.4936.589-4.859-10.872-0.035
Interaction energy analysis for fragmet #1(J:46:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.976 / q_NPA : 0.995
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].
3J48TYR0-0.027-0.0232.556-24.489-17.8216.294-4.076-8.887-0.030
4J49THR0-0.020-0.0294.5179.1069.231-0.001-0.013-0.1110.000
5J50LEU00.0430.0337.490-1.021-1.0210.0000.0000.0000.000
6J51ARG10.9230.96410.18920.31120.3110.0000.0000.0000.000
7J52LEU00.0360.02913.1640.3310.3310.0000.0000.0000.000
8J53THR0-0.085-0.07516.4500.3620.3620.0000.0000.0000.000
9J54ARG10.9581.00319.94112.33812.3380.0000.0000.0000.000
10J55GLN00.020-0.01323.551-0.445-0.4450.0000.0000.0000.000
11J56PHE00.0040.00526.9180.0250.0250.0000.0000.0000.000
12J57GLN00.0290.01930.4780.0030.0030.0000.0000.0000.000
13J58PHE0-0.011-0.00733.669-0.071-0.0710.0000.0000.0000.000
14J59LYS10.9670.97735.4867.5127.5120.0000.0000.0000.000
15J60ILE00.0010.02538.277-0.044-0.0440.0000.0000.0000.000
16J61ASN0-0.011-0.01541.3280.0680.0680.0000.0000.0000.000
17J62LYS10.9010.95044.8276.1746.1740.0000.0000.0000.000
18J63GLN0-0.005-0.01247.859-0.029-0.0290.0000.0000.0000.000
19J64THR0-0.042-0.02549.9770.0790.0790.0000.0000.0000.000
20J65THR00.0210.02251.7830.1210.1210.0000.0000.0000.000
21J66SER00.023-0.00353.357-0.039-0.0390.0000.0000.0000.000
22J67VAL00.0160.00954.034-0.058-0.0580.0000.0000.0000.000
23J68GLY00.0390.02854.4830.1150.1150.0000.0000.0000.000
24J69ASN0-0.075-0.03054.3500.0670.0670.0000.0000.0000.000
25J70LEU00.0060.01347.363-0.101-0.1010.0000.0000.0000.000
26J71ILE00.0040.00848.1710.0310.0310.0000.0000.0000.000
27J72PHE0-0.026-0.02742.909-0.146-0.1460.0000.0000.0000.000
28J73ASN00.0150.00642.3720.0330.0330.0000.0000.0000.000
29J74ALA0-0.028-0.02537.777-0.128-0.1280.0000.0000.0000.000
30J75ASP-1-0.758-0.86135.424-8.619-8.6190.0000.0000.0000.000
31J76TYR0-0.035-0.01931.258-0.286-0.2860.0000.0000.0000.000
32J77ILE0-0.0110.00126.688-0.036-0.0360.0000.0000.0000.000
33J78THR0-0.013-0.00426.726-0.245-0.2450.0000.0000.0000.000
34J79PHE0-0.032-0.03121.740-0.112-0.1120.0000.0000.0000.000
35J80ALA00.0550.03621.625-0.030-0.0300.0000.0000.0000.000
36J81LEU00.0100.01215.280-0.036-0.0360.0000.0000.0000.000
37J82ASP-1-0.741-0.88219.288-13.871-13.8710.0000.0000.0000.000
38J83ASP-1-0.808-0.87021.971-12.023-12.0230.0000.0000.0000.000
39J84PHE0-0.114-0.08319.1230.3740.3740.0000.0000.0000.000
40J85LEU00.0040.00416.269-0.688-0.6880.0000.0000.0000.000
41J86GLN00.0200.02720.028-0.041-0.0410.0000.0000.0000.000
42J87ALA0-0.013-0.00820.5470.2110.2110.0000.0000.0000.000
43J88VAL0-0.043-0.01914.974-0.628-0.6280.0000.0000.0000.000
44J89PRO00.0570.04115.9880.5630.5630.0000.0000.0000.000
45J90ASN00.0430.00916.701-1.577-1.5770.0000.0000.0000.000
46J91PRO00.025-0.00811.936-0.255-0.2550.0000.0000.0000.000
47J92HIS00.0380.01812.712-1.622-1.6220.0000.0000.0000.000
48J93THR0-0.041-0.01214.867-0.104-0.1040.0000.0000.0000.000
49J94LEU0-0.0110.0059.725-0.683-0.6830.0000.0000.0000.000
50J95ASN00.0240.02010.0251.7761.7760.0000.0000.0000.000
51J96PHE0-0.100-0.0615.223-2.278-2.2780.0000.0000.0000.000
52J97GLU-1-0.844-0.9049.491-17.863-17.8630.0000.0000.0000.000
53J98ASP-1-0.838-0.9069.845-19.066-19.0660.0000.0000.0000.000
54J99TYR0-0.055-0.06410.211-2.546-2.5460.0000.0000.0000.000
55J100ARG10.8920.9509.78823.23623.2360.0000.0000.0000.000
56J101ILE00.0170.02712.821-1.491-1.4910.0000.0000.0000.000
57J102LYS10.9010.97812.13820.88920.8890.0000.0000.0000.000
58J103LEU0-0.058-0.04914.3850.9880.9880.0000.0000.0000.000
59J104ALA00.0350.03116.852-0.564-0.5640.0000.0000.0000.000
60J105LYS10.8880.93818.88015.48815.4880.0000.0000.0000.000
61J106MET00.0240.03621.864-0.183-0.1830.0000.0000.0000.000
62J107GLU-1-0.818-0.89325.334-11.620-11.6200.0000.0000.0000.000
63J108MET0-0.0170.02527.171-0.100-0.1000.0000.0000.0000.000
64J109ARG10.8600.91828.79710.23410.2340.0000.0000.0000.000
65J110PRO00.0490.03432.815-0.079-0.0790.0000.0000.0000.000
66J111THR00.008-0.01335.481-0.076-0.0760.0000.0000.0000.000
67J112GLY0-0.011-0.00837.4750.1540.1540.0000.0000.0000.000
68J113GLY00.0050.00840.4140.1700.1700.0000.0000.0000.000
69J114HIS0-0.049-0.00840.7140.1230.1230.0000.0000.0000.000
70J115TYR00.0320.01841.258-0.170-0.1700.0000.0000.0000.000
71J116THR00.018-0.00637.8580.0630.0630.0000.0000.0000.000
72J117VAL0-0.040-0.02140.988-0.035-0.0350.0000.0000.0000.000
73J118GLN00.0000.01444.1250.1470.1470.0000.0000.0000.000
74J119SER0-0.035-0.02244.418-0.182-0.1820.0000.0000.0000.000
75J120ASP-1-0.768-0.89143.355-6.911-6.9110.0000.0000.0000.000
76J121GLY00.0170.01344.201-0.053-0.0530.0000.0000.0000.000
77J122PHE0-0.042-0.05040.095-0.201-0.2010.0000.0000.0000.000
78J123GLY00.0860.06339.2930.1750.1750.0000.0000.0000.000
79J124HIS0-0.066-0.06636.265-0.129-0.1290.0000.0000.0000.000
80J125THR00.0070.01831.017-0.199-0.1990.0000.0000.0000.000
81J126ALA00.0430.01031.6220.0290.0290.0000.0000.0000.000
82J127VAL0-0.041-0.02625.210-0.210-0.2100.0000.0000.0000.000
83J128ILE00.0260.02028.5580.1330.1330.0000.0000.0000.000
84J129GLN0-0.083-0.05122.9070.0630.0630.0000.0000.0000.000
85J130ASP-1-0.741-0.85026.536-9.669-9.6690.0000.0000.0000.000
86J131SER00.0530.01128.9350.0120.0120.0000.0000.0000.000
87J132ARG10.8910.93831.4969.2519.2510.0000.0000.0000.000
88J133ILE0-0.050-0.02029.9730.1990.1990.0000.0000.0000.000
89J134THR0-0.006-0.03232.7530.1860.1860.0000.0000.0000.000
90J135ARG10.9320.98434.9577.9347.9340.0000.0000.0000.000
91J136PHE0-0.055-0.03635.8210.1990.1990.0000.0000.0000.000
92J137LYS10.8180.90536.1548.5068.5060.0000.0000.0000.000
93J138THR0-0.039-0.01638.6350.0320.0320.0000.0000.0000.000
94J139THR00.0180.00442.1150.0310.0310.0000.0000.0000.000
95J140ALA0-0.030-0.00644.9710.1360.1360.0000.0000.0000.000
96J141ASP-1-0.815-0.89546.111-6.681-6.6810.0000.0000.0000.000
97J142GLN0-0.037-0.02743.677-0.064-0.0640.0000.0000.0000.000
98J143THR00.0750.03047.737-0.068-0.0680.0000.0000.0000.000
99J144GLN0-0.014-0.00146.3270.0980.0980.0000.0000.0000.000
100J145ASP-1-0.748-0.84040.432-7.928-7.9280.0000.0000.0000.000
101J146PRO0-0.012-0.00540.154-0.059-0.0590.0000.0000.0000.000
102J147LEU0-0.034-0.03134.839-0.153-0.1530.0000.0000.0000.000
103J148ALA0-0.042-0.00337.279-0.181-0.1810.0000.0000.0000.000
104J149PRO00.005-0.00538.775-0.078-0.0780.0000.0000.0000.000
105J150PHE0-0.050-0.02033.707-0.079-0.0790.0000.0000.0000.000
106J151ASP-1-0.855-0.93031.008-9.487-9.4870.0000.0000.0000.000
107J152GLY0-0.016-0.00230.769-0.276-0.2760.0000.0000.0000.000
108J153ALA0-0.0040.01631.689-0.312-0.3120.0000.0000.0000.000
109J154LYS10.8810.93428.66110.15310.1530.0000.0000.0000.000
110J155LYS10.9710.99833.9077.9037.9030.0000.0000.0000.000
111J156TRP0-0.091-0.02534.270-0.334-0.3340.0000.0000.0000.000
112J157PHE00.0400.00736.2300.1810.1810.0000.0000.0000.000
113J158VAL00.0860.05037.820-0.237-0.2370.0000.0000.0000.000
114J159SER00.0150.02638.851-0.222-0.2220.0000.0000.0000.000
115J160ARG10.9400.95936.2107.8087.8080.0000.0000.0000.000
116J161GLY00.0100.01033.879-0.280-0.2800.0000.0000.0000.000
117J162PHE0-0.035-0.02829.073-0.020-0.0200.0000.0000.0000.000
118J163LYS10.8380.90023.57711.95211.9520.0000.0000.0000.000
119J164ARG10.8210.91026.17610.59210.5920.0000.0000.0000.000
120J165LEU0-0.008-0.00519.839-0.360-0.3600.0000.0000.0000.000
121J166LEU0-0.0050.00021.5650.4980.4980.0000.0000.0000.000
122J167ARG10.9660.97718.21213.10013.1000.0000.0000.0000.000
123J168PRO0-0.0090.01119.4210.4860.4860.0000.0000.0000.000
124J169LYS10.9740.97517.99113.72813.7280.0000.0000.0000.000
125J170PRO00.0440.04418.7600.5240.5240.0000.0000.0000.000
126J189ASN00.1270.04713.1050.4200.4200.0000.0000.0000.000
127J190SER00.022-0.00316.141-0.137-0.1370.0000.0000.0000.000
128J191ALA00.0020.00717.161-0.226-0.2260.0000.0000.0000.000
129J192ARG10.9340.98116.01613.86013.8600.0000.0000.0000.000
130J193THR0-0.071-0.04812.874-0.570-0.5700.0000.0000.0000.000
131J194GLY00.010-0.01414.343-0.777-0.7770.0000.0000.0000.000
132J195TRP0-0.070-0.0327.541-0.668-0.6680.0000.0000.0000.000
133J196ILE0-0.0050.01413.0231.1881.1880.0000.0000.0000.000
134J197PRO00.0930.04514.230-1.067-1.0670.0000.0000.0000.000
135J198LEU0-0.004-0.01112.1110.7500.7500.0000.0000.0000.000
136J199GLN00.0270.01816.1771.1191.1190.0000.0000.0000.000
137J200GLY00.0050.00419.5640.5630.5630.0000.0000.0000.000
138J201GLY00.0670.03921.4170.6310.6310.0000.0000.0000.000
139J202PRO00.0010.00123.916-0.419-0.4190.0000.0000.0000.000
140J203ASN0-0.030-0.03525.3640.3910.3910.0000.0000.0000.000
141J204SER00.029-0.00222.2810.1260.1260.0000.0000.0000.000
142J205ALA00.0200.02922.828-0.116-0.1160.0000.0000.0000.000
143J206GLY00.0420.02519.2340.0850.0850.0000.0000.0000.000
144J207THR0-0.055-0.03417.298-0.365-0.3650.0000.0000.0000.000
145J208LYS10.8980.96319.65811.42411.4240.0000.0000.0000.000
146J209VAL0-0.0270.00820.5900.5830.5830.0000.0000.0000.000
147J210ARG10.7900.86522.21211.37211.3720.0000.0000.0000.000
148J211HIS0-0.038-0.03018.717-0.550-0.5500.0000.0000.0000.000
149J212TYR00.0290.01323.3020.1890.1890.0000.0000.0000.000
150J213GLY00.1070.02224.619-0.400-0.4000.0000.0000.0000.000
151J214ILE0-0.110-0.03626.851-0.060-0.0600.0000.0000.0000.000
152J215ALA00.0570.03228.6920.0400.0400.0000.0000.0000.000
153J216PHE0-0.021-0.03532.409-0.170-0.1700.0000.0000.0000.000
154J217SER00.0500.00034.5680.0240.0240.0000.0000.0000.000
155J218PHE0-0.015-0.02638.008-0.184-0.1840.0000.0000.0000.000
156J219PRO00.0160.02240.8230.0640.0640.0000.0000.0000.000
157J220GLN0-0.021-0.01944.076-0.156-0.1560.0000.0000.0000.000
158J221PRO00.0220.02443.9200.1140.1140.0000.0000.0000.000
159J222GLU-1-0.822-0.91446.764-5.962-5.9620.0000.0000.0000.000
160J223GLN0-0.002-0.00647.6880.0790.0790.0000.0000.0000.000
161J224THR0-0.012-0.01143.517-0.102-0.1020.0000.0000.0000.000
162J225ILE00.0220.03939.569-0.030-0.0300.0000.0000.0000.000
163J226THR0-0.014-0.01537.533-0.094-0.0940.0000.0000.0000.000
164J227TYR0-0.020-0.03434.052-0.056-0.0560.0000.0000.0000.000
165J228VAL00.0190.00629.673-0.032-0.0320.0000.0000.0000.000
166J229THR00.003-0.00427.939-0.042-0.0420.0000.0000.0000.000
167J230LYS10.9370.97422.40012.88712.8870.0000.0000.0000.000
168J231LEU00.0150.02223.213-0.053-0.0530.0000.0000.0000.000
169J232THR0-0.094-0.05217.078-0.310-0.3100.0000.0000.0000.000
170J233LEU00.0370.02916.7610.2510.2510.0000.0000.0000.000
171J234TYR0-0.002-0.01112.873-0.199-0.1990.0000.0000.0000.000
172J235VAL00.0190.00812.2180.5660.5660.0000.0000.0000.000
173J236GLN00.0080.0018.567-0.609-0.6090.0000.0000.0000.000
174J237PHE00.0780.0307.1093.4333.4330.0000.0000.0000.000
175J238ARG10.8180.9064.41516.96917.092-0.001-0.055-0.0670.000
176J239GLN00.0970.0642.580-8.551-6.3270.297-0.715-1.807-0.005