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: 16J2Z

Calculation Name: 12E8-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 12E8

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-26

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2212565.161628
FMO2-HF: Nuclear repulsion 2128758.239013
FMO2-HF: Total energy -83806.922615
FMO2-MP2: Total energy -84051.689484


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
40.6242.1610.044-0.657-0.9270
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.964 / q_NPA : -0.998
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].
3H3GLN0-0.044-0.0293.352-3.797-2.2120.045-0.622-1.0070.000
4H4LEU00.0180.0145.697-1.890-1.8900.0000.0000.0000.000
5H5GLN00.0020.0049.218-1.421-1.4210.0000.0000.0000.000
6H6GLN00.026-0.00110.798-0.254-0.2540.0000.0000.0000.000
7H7SER00.0240.02214.5850.0140.0140.0000.0000.0000.000
8H8GLY00.0120.00917.4110.0960.0960.0000.0000.0000.000
9H9ALA0-0.031-0.01819.455-0.212-0.2120.0000.0000.0000.000
10H10GLU-1-0.916-0.94422.51611.14311.1430.0000.0000.0000.000
11H11VAL0-0.022-0.00925.716-0.099-0.0990.0000.0000.0000.000
12H12VAL0-0.015-0.01128.732-0.168-0.1680.0000.0000.0000.000
13H13ARG10.9740.97431.443-8.081-8.0810.0000.0000.0000.000
14H14SER00.025-0.00934.8310.1780.1780.0000.0000.0000.000
15H15GLY0-0.044-0.01536.417-0.198-0.1980.0000.0000.0000.000
16H16ALA0-0.062-0.02433.569-0.053-0.0530.0000.0000.0000.000
17H17SER00.004-0.01831.0630.0190.0190.0000.0000.0000.000
18H18VAL0-0.0110.00825.599-0.098-0.0980.0000.0000.0000.000
19H19LYS10.9250.96423.491-11.530-11.5300.0000.0000.0000.000
20H20LEU00.0240.02620.3130.0790.0790.0000.0000.0000.000
21H21SER0-0.004-0.00617.6270.1380.1380.0000.0000.0000.000
22H22CYS0-0.0150.02014.1310.2570.2570.0000.0000.0000.000
23H23THR00.0140.00311.234-0.488-0.4880.0000.0000.0000.000
24H24ALA00.0210.0159.3571.1121.1120.0000.0000.0000.000
25H25SER0-0.044-0.0145.485-0.554-0.5540.0000.0000.0000.000
26H26GLY00.0430.0094.4632.3762.332-0.001-0.0350.0800.000
27H27PHE0-0.052-0.0305.4392.9462.9460.0000.0000.0000.000
28H28ASN0-0.0120.0008.070-1.972-1.9720.0000.0000.0000.000
29H29ILE00.008-0.01011.8640.2980.2980.0000.0000.0000.000
30H30LYS10.9050.95014.052-15.729-15.7290.0000.0000.0000.000
31H31ASP-1-0.825-0.88815.56017.33417.3340.0000.0000.0000.000
32H32TYR0-0.065-0.04010.8031.6341.6340.0000.0000.0000.000
33H33TYR00.0330.03216.070-0.974-0.9740.0000.0000.0000.000
34H34ILE0-0.037-0.03814.2591.1081.1080.0000.0000.0000.000
35H35HIS00.0350.03016.699-1.542-1.5420.0000.0000.0000.000
36H36TRP00.0290.01117.5040.7110.7110.0000.0000.0000.000
37H37VAL0-0.027-0.01618.437-0.572-0.5720.0000.0000.0000.000
38H38LYS10.8850.95120.645-10.178-10.1780.0000.0000.0000.000
39H39GLN00.0440.01421.0900.3750.3750.0000.0000.0000.000
40H40ARG10.8690.94523.853-9.825-9.8250.0000.0000.0000.000
41H41PRO00.0580.01826.9470.1790.1790.0000.0000.0000.000
42H42GLU-1-0.915-0.95128.0009.8279.8270.0000.0000.0000.000
43H43LYS10.8580.92927.658-9.662-9.6620.0000.0000.0000.000
44H44GLY00.0230.00925.3340.3920.3920.0000.0000.0000.000
45H45LEU0-0.030-0.00919.248-0.252-0.2520.0000.0000.0000.000
46H46GLU-1-0.848-0.92323.45710.10910.1090.0000.0000.0000.000
47H47TRP0-0.019-0.01921.226-0.078-0.0780.0000.0000.0000.000
48H48ILE0-0.043-0.02723.127-0.564-0.5640.0000.0000.0000.000
49H49GLY00.0460.00923.244-0.597-0.5970.0000.0000.0000.000
50H50TRP0-0.061-0.03720.9080.8720.8720.0000.0000.0000.000
51H51ILE00.009-0.00820.189-0.658-0.6580.0000.0000.0000.000
52H52ASP-1-0.782-0.89020.44914.89914.8990.0000.0000.0000.000
53H52PRO0-0.093-0.06617.530-0.572-0.5720.0000.0000.0000.000
54H53GLU-1-0.968-0.97620.63913.86113.8610.0000.0000.0000.000
55H54ILE0-0.037-0.01122.006-0.497-0.4970.0000.0000.0000.000
56H55GLY0-0.066-0.02824.227-0.475-0.4750.0000.0000.0000.000
57H56ASP-1-0.888-0.93525.62910.64510.6450.0000.0000.0000.000
58H57THR0-0.071-0.04324.9620.5020.5020.0000.0000.0000.000
59H58GLU-1-0.901-0.93925.78710.75710.7570.0000.0000.0000.000
60H59TYR00.0030.02126.2630.4900.4900.0000.0000.0000.000
61H60VAL00.0360.02628.169-0.373-0.3730.0000.0000.0000.000
62H61PRO00.033-0.01629.846-0.107-0.1070.0000.0000.0000.000
63H62LYS10.8080.90430.996-9.852-9.8520.0000.0000.0000.000
64H63PHE0-0.016-0.02227.969-0.078-0.0780.0000.0000.0000.000
65H64GLN00.1120.05830.9280.3300.3300.0000.0000.0000.000
66H65GLY0-0.033-0.00532.751-0.253-0.2530.0000.0000.0000.000
67H66LYS10.7750.92029.993-9.217-9.2170.0000.0000.0000.000
68H67ALA00.023-0.01926.5430.1010.1010.0000.0000.0000.000
69H68THR0-0.049-0.01427.504-0.304-0.3040.0000.0000.0000.000
70H69MET0-0.0180.00122.7770.2910.2910.0000.0000.0000.000
71H70THR0-0.005-0.00223.123-0.290-0.2900.0000.0000.0000.000
72H71ALA00.018-0.00219.4570.5610.5610.0000.0000.0000.000
73H72ASP-1-0.822-0.89419.10313.30113.3010.0000.0000.0000.000
74H73THR00.0200.00217.3760.6660.6660.0000.0000.0000.000
75H74SER0-0.021-0.00216.7700.6980.6980.0000.0000.0000.000
76H75SER0-0.087-0.04416.2640.6170.6170.0000.0000.0000.000
77H76ASN00.0410.02012.0530.4000.4000.0000.0000.0000.000
78H77THR0-0.009-0.00113.4501.0271.0270.0000.0000.0000.000
79H78ALA00.0070.01215.965-0.781-0.7810.0000.0000.0000.000
80H79TYR0-0.027-0.04618.0640.0670.0670.0000.0000.0000.000
81H80LEU00.0220.02520.895-0.247-0.2470.0000.0000.0000.000
82H81GLN0-0.067-0.03223.240-0.029-0.0290.0000.0000.0000.000
83H82LEU00.0320.01725.338-0.138-0.1380.0000.0000.0000.000
84H82SER00.0110.00228.880-0.236-0.2360.0000.0000.0000.000
85H82SER00.013-0.00432.541-0.097-0.0970.0000.0000.0000.000
86H82LEU0-0.042-0.00629.621-0.054-0.0540.0000.0000.0000.000
87H83THR0-0.001-0.00233.633-0.358-0.3580.0000.0000.0000.000
88H84SER00.0520.01233.4610.2390.2390.0000.0000.0000.000
89H85GLU-1-0.881-0.94332.9848.7568.7560.0000.0000.0000.000
90H86ASP-1-0.833-0.91429.6299.7039.7030.0000.0000.0000.000
91H87THR00.0280.02428.3940.3800.3800.0000.0000.0000.000
92H88ALA0-0.069-0.04225.199-0.133-0.1330.0000.0000.0000.000
93H89VAL00.0100.02719.588-0.054-0.0540.0000.0000.0000.000
94H90TYR0-0.051-0.05020.778-0.117-0.1170.0000.0000.0000.000
95H91TYR00.0170.02415.1220.3240.3240.0000.0000.0000.000
96H93ASN00.001-0.02012.7590.7730.7730.0000.0000.0000.000
97H94ALA00.0280.00711.383-0.969-0.9690.0000.0000.0000.000
98H95GLY00.0210.00312.5351.4601.4600.0000.0000.0000.000
99H96HIS0-0.043-0.01711.9680.6140.6140.0000.0000.0000.000
100H97ASP-1-0.762-0.88115.94915.90815.9080.0000.0000.0000.000
101H98TYR0-0.069-0.02015.477-0.609-0.6090.0000.0000.0000.000
102H99ASP-1-0.892-0.94717.07417.92517.9250.0000.0000.0000.000
103H100ARG10.9350.94219.278-13.068-13.0680.0000.0000.0000.000
104H100GLY00.0020.00419.318-0.692-0.6920.0000.0000.0000.000
105H100ARG10.8250.92813.024-21.197-21.1970.0000.0000.0000.000
106H100PHE00.0070.00614.0740.2920.2920.0000.0000.0000.000
107H101PRO0-0.053-0.0239.2110.1520.1520.0000.0000.0000.000
108H102TYR00.0260.0106.0414.3354.3350.0000.0000.0000.000
109H103TRP00.0060.0009.108-3.423-3.4230.0000.0000.0000.000
110H104GLY00.0500.0229.6451.6501.6500.0000.0000.0000.000
111H105GLN0-0.011-0.00911.7740.5570.5570.0000.0000.0000.000
112H106GLY0-0.020-0.00413.255-0.874-0.8740.0000.0000.0000.000
113H107THR0-0.017-0.02516.7180.1680.1680.0000.0000.0000.000
114H108LEU0-0.044-0.01419.636-0.303-0.3030.0000.0000.0000.000
115H109VAL00.0250.01922.875-0.144-0.1440.0000.0000.0000.000
116H110THR0-0.007-0.01625.971-0.172-0.1720.0000.0000.0000.000
117H111VAL0-0.0110.00029.302-0.128-0.1280.0000.0000.0000.000
118H112SER00.0100.00032.490-0.211-0.2110.0000.0000.0000.000
119H113ALA0-0.025-0.01735.9200.0280.0280.0000.0000.0000.000
120H114ALA00.0200.03438.291-0.199-0.1990.0000.0000.0000.000
121H115LYS10.9240.95838.679-6.835-6.8350.0000.0000.0000.000
122H116THR0-0.052-0.02636.853-0.029-0.0290.0000.0000.0000.000
123H117THR00.0070.00738.895-0.244-0.2440.0000.0000.0000.000
124H118PRO00.0260.01739.8930.1960.1960.0000.0000.0000.000
125H119PRO0-0.013-0.00339.352-0.090-0.0900.0000.0000.0000.000
126H120SER0-0.0090.00641.765-0.179-0.1790.0000.0000.0000.000
127H121VAL00.003-0.00941.9290.1060.1060.0000.0000.0000.000
128H122TYR0-0.025-0.02744.441-0.152-0.1520.0000.0000.0000.000
129H123PRO0-0.016-0.00645.7120.1440.1440.0000.0000.0000.000
130H124LEU0-0.0110.00044.011-0.088-0.0880.0000.0000.0000.000
131H125ALA00.0180.00847.5290.0950.0950.0000.0000.0000.000
132H126PRO00.0100.01749.851-0.037-0.0370.0000.0000.0000.000
133H127GLY00.0920.04451.978-0.089-0.0890.0000.0000.0000.000
134H128SER0-0.061-0.03555.5860.0090.0090.0000.0000.0000.000
135H129ALA00.0030.00756.739-0.117-0.1170.0000.0000.0000.000
136H130ALA0-0.002-0.00458.0160.0670.0670.0000.0000.0000.000
137H131GLN00.009-0.00957.353-0.012-0.0120.0000.0000.0000.000
138H132THR0-0.066-0.02457.7600.0030.0030.0000.0000.0000.000
139H133ASN00.0500.02350.243-0.005-0.0050.0000.0000.0000.000
140H134SER00.0110.01150.065-0.008-0.0080.0000.0000.0000.000
141H135MET0-0.040-0.03045.2900.0080.0080.0000.0000.0000.000
142H136VAL00.0380.03747.352-0.079-0.0790.0000.0000.0000.000
143H137THR0-0.027-0.03743.0830.1220.1220.0000.0000.0000.000
144H138LEU0-0.031-0.01044.383-0.148-0.1480.0000.0000.0000.000
145H139GLY00.0670.00842.5810.2040.2040.0000.0000.0000.000
146H140CYS0-0.109-0.01240.646-0.084-0.0840.0000.0000.0000.000
147H141LEU00.0110.02441.2960.1770.1770.0000.0000.0000.000
148H142VAL0-0.010-0.00238.470-0.146-0.1460.0000.0000.0000.000
149H143LYS10.9410.94440.209-6.591-6.5910.0000.0000.0000.000
150H144GLY00.0270.02041.505-0.106-0.1060.0000.0000.0000.000
151H145TYR00.0420.03434.482-0.011-0.0110.0000.0000.0000.000
152H146PHE00.0670.04834.4550.1630.1630.0000.0000.0000.000
153H147PRO0-0.027-0.01132.288-0.218-0.2180.0000.0000.0000.000
154H148GLU-1-0.884-0.93030.3439.4089.4080.0000.0000.0000.000
155H149PRO00.015-0.01228.5080.0750.0750.0000.0000.0000.000
156H150VAL00.006-0.01631.281-0.204-0.2040.0000.0000.0000.000
157H151THR0-0.070-0.02430.4070.2070.2070.0000.0000.0000.000
158H152VAL00.029-0.01333.036-0.249-0.2490.0000.0000.0000.000
159H153THR0-0.0080.00233.8340.2340.2340.0000.0000.0000.000
160H154TRP00.0210.00536.319-0.314-0.3140.0000.0000.0000.000
161H155ASN00.000-0.01539.0960.0510.0510.0000.0000.0000.000
162H156SER0-0.012-0.00838.4960.0150.0150.0000.0000.0000.000
163H157GLY0-0.0140.00035.4800.1430.1430.0000.0000.0000.000
164H158SER0-0.053-0.02135.8720.1470.1470.0000.0000.0000.000
165H159LEU0-0.0070.00638.4740.0040.0040.0000.0000.0000.000
166H160SER00.0390.01033.2150.0830.0830.0000.0000.0000.000
167H161SER0-0.007-0.00334.5230.1240.1240.0000.0000.0000.000
168H162GLY00.031-0.00135.778-0.199-0.1990.0000.0000.0000.000
169H163VAL0-0.042-0.01334.487-0.189-0.1890.0000.0000.0000.000
170H164HIS0-0.0250.00434.2880.3880.3880.0000.0000.0000.000
171H165THR00.0140.00232.705-0.365-0.3650.0000.0000.0000.000
172H166PHE0-0.029-0.00632.4620.2610.2610.0000.0000.0000.000
173H167PRO00.0380.01030.043-0.046-0.0460.0000.0000.0000.000
174H168ALA00.0150.02332.069-0.287-0.2870.0000.0000.0000.000
175H169VAL0-0.0030.00333.4900.1600.1600.0000.0000.0000.000
176H170LEU0-0.009-0.01235.456-0.146-0.1460.0000.0000.0000.000
177H171GLN0-0.021-0.01037.910-0.095-0.0950.0000.0000.0000.000
178H172SER0-0.022-0.03241.684-0.041-0.0410.0000.0000.0000.000
179H173ASP-1-0.885-0.94339.3867.1527.1520.0000.0000.0000.000
180H174LEU0-0.0330.02039.0340.1450.1450.0000.0000.0000.000
181H175TYR00.006-0.01032.325-0.022-0.0220.0000.0000.0000.000
182H176THR0-0.032-0.04137.821-0.204-0.2040.0000.0000.0000.000
183H177LEU0-0.0050.02233.9570.1370.1370.0000.0000.0000.000
184H178SER00.021-0.00437.611-0.286-0.2860.0000.0000.0000.000
185H179SER0-0.013-0.00836.3440.1780.1780.0000.0000.0000.000
186H180SER00.002-0.00138.261-0.196-0.1960.0000.0000.0000.000
187H181VAL00.0640.02938.7010.2100.2100.0000.0000.0000.000
188H182THR0-0.0020.01840.628-0.256-0.2560.0000.0000.0000.000
189H183VAL00.0260.02441.9280.1450.1450.0000.0000.0000.000
190H184PRO00.0320.00144.567-0.105-0.1050.0000.0000.0000.000
191H185SER00.0040.00447.494-0.065-0.0650.0000.0000.0000.000
192H186SER0-0.010-0.00650.785-0.034-0.0340.0000.0000.0000.000
193H187THR0-0.008-0.01247.563-0.033-0.0330.0000.0000.0000.000
194H188TRP00.0110.04248.6800.0050.0050.0000.0000.0000.000
195H189PRO0-0.029-0.03250.764-0.043-0.0430.0000.0000.0000.000
196H190SER0-0.049-0.03252.8310.0040.0040.0000.0000.0000.000
197H191GLU-1-0.899-0.94048.1616.3066.3060.0000.0000.0000.000
198H192THR0-0.057-0.04047.758-0.001-0.0010.0000.0000.0000.000
199H193VAL00.0540.03643.9030.1140.1140.0000.0000.0000.000
200H194THR0-0.023-0.02143.913-0.173-0.1730.0000.0000.0000.000
201H196ASN00.016-0.01938.466-0.037-0.0370.0000.0000.0000.000
202H197VAL00.0170.01237.6740.2330.2330.0000.0000.0000.000
203H198ALA0-0.033-0.01334.915-0.170-0.1700.0000.0000.0000.000
204H199HIS00.0500.04635.1510.0380.0380.0000.0000.0000.000
205H200PRO00.016-0.00431.407-0.173-0.1730.0000.0000.0000.000
206H201ALA00.0190.01733.399-0.096-0.0960.0000.0000.0000.000
207H202SER0-0.023-0.03434.650-0.162-0.1620.0000.0000.0000.000
208H203SER0-0.053-0.01836.968-0.156-0.1560.0000.0000.0000.000
209H204THR00.0170.01538.309-0.260-0.2600.0000.0000.0000.000
210H205LYS10.9280.94435.502-7.762-7.7620.0000.0000.0000.000
211H206VAL0-0.0020.00340.516-0.196-0.1960.0000.0000.0000.000
212H207ASP-1-0.818-0.88342.1227.2067.2060.0000.0000.0000.000
213H208LYS10.8900.93444.274-6.435-6.4350.0000.0000.0000.000
214H209LYS10.9680.98745.799-5.789-5.7890.0000.0000.0000.000
215H210ILE00.005-0.00545.567-0.104-0.1040.0000.0000.0000.000
216H211VAL0-0.043-0.02049.082-0.040-0.0400.0000.0000.0000.000
217H212PRO00.020-0.00752.8110.0210.0210.0000.0000.0000.000
218H213ARG10.8800.93955.008-5.322-5.3220.0000.0000.0000.000
219H214ASP-1-0.896-0.93354.0685.6785.6780.0000.0000.0000.000