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: 8NJ8Y

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2210686.310718
FMO2-HF: Nuclear repulsion 2126877.843929
FMO2-HF: Total energy -83808.466789
FMO2-MP2: Total energy -84053.157187


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.
33.98936.5880.015-1.233-1.3810.005
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 : -0.875 / q_NPA : -0.940
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].
3H3GLN0-0.032-0.0093.553-7.323-4.9310.016-1.172-1.2360.005
4H4LEU00.0190.0095.672-2.191-2.1910.0000.0000.0000.000
5H5GLN0-0.031-0.0239.016-1.201-1.2010.0000.0000.0000.000
6H6GLN00.003-0.02411.132-0.166-0.1660.0000.0000.0000.000
7H7SER00.0110.02114.946-0.132-0.1320.0000.0000.0000.000
8H8GLY00.0150.00817.9750.2170.2170.0000.0000.0000.000
9H9ALA0-0.037-0.02019.407-0.203-0.2030.0000.0000.0000.000
10H10GLU-1-0.898-0.94022.47010.96110.9610.0000.0000.0000.000
11H11VAL0-0.040-0.03125.728-0.134-0.1340.0000.0000.0000.000
12H12VAL0-0.0010.00529.094-0.242-0.2420.0000.0000.0000.000
13H13ARG10.9650.97331.836-8.117-8.1170.0000.0000.0000.000
14H14SER00.031-0.00334.9350.2230.2230.0000.0000.0000.000
15H15GLY0-0.051-0.02836.827-0.203-0.2030.0000.0000.0000.000
16H16ALA0-0.056-0.01333.829-0.076-0.0760.0000.0000.0000.000
17H17SER0-0.018-0.02831.707-0.027-0.0270.0000.0000.0000.000
18H18VAL00.0030.01425.876-0.125-0.1250.0000.0000.0000.000
19H19LYS10.8570.91723.628-11.906-11.9060.0000.0000.0000.000
20H20LEU00.0290.04020.6040.1350.1350.0000.0000.0000.000
21H21SER00.009-0.01217.994-0.015-0.0150.0000.0000.0000.000
22H22CYS0-0.0100.00414.1660.2570.2570.0000.0000.0000.000
23H23THR00.0170.01711.362-0.366-0.3660.0000.0000.0000.000
24H24ALA00.0120.0079.7831.1091.1090.0000.0000.0000.000
25H25SER0-0.019-0.0135.364-2.244-2.2440.0000.0000.0000.000
26H26GLY00.0120.0014.0643.0173.0430.000-0.0530.0270.000
27H27PHE0-0.031-0.0204.7752.8333.014-0.001-0.008-0.1720.000
28H28ASN00.0000.0088.202-2.881-2.8810.0000.0000.0000.000
29H29ILE0-0.004-0.01312.0180.3910.3910.0000.0000.0000.000
30H30LYS10.7780.88514.085-17.073-17.0730.0000.0000.0000.000
31H31ASP-1-0.849-0.91114.50518.14918.1490.0000.0000.0000.000
32H32TYR0-0.047-0.0559.8792.4352.4350.0000.0000.0000.000
33H33TYR0-0.021-0.00115.403-0.850-0.8500.0000.0000.0000.000
34H34ILE0-0.035-0.02314.3991.1281.1280.0000.0000.0000.000
35H35HIS00.0590.03417.171-1.816-1.8160.0000.0000.0000.000
36H36TRP00.001-0.00917.7380.8030.8030.0000.0000.0000.000
37H37VAL0-0.032-0.01418.778-0.674-0.6740.0000.0000.0000.000
38H38LYS10.8440.93520.993-10.351-10.3510.0000.0000.0000.000
39H39GLN00.0130.00921.3960.4760.4760.0000.0000.0000.000
40H40ARG10.8290.89024.243-9.655-9.6550.0000.0000.0000.000
41H41PRO00.0470.01026.9750.2120.2120.0000.0000.0000.000
42H42GLU-1-0.922-0.95628.29410.29210.2920.0000.0000.0000.000
43H43LYS10.8630.93627.608-9.996-9.9960.0000.0000.0000.000
44H44GLY00.0470.02625.0320.4040.4040.0000.0000.0000.000
45H45LEU0-0.0100.00019.235-0.281-0.2810.0000.0000.0000.000
46H46GLU-1-0.832-0.90423.39610.30910.3090.0000.0000.0000.000
47H47TRP0-0.033-0.02421.674-0.045-0.0450.0000.0000.0000.000
48H48ILE0-0.034-0.01823.111-0.561-0.5610.0000.0000.0000.000
49H49GLY00.0390.00723.711-0.653-0.6530.0000.0000.0000.000
50H50TRP0-0.076-0.04621.1830.9110.9110.0000.0000.0000.000
51H51ILE00.007-0.00820.247-0.721-0.7210.0000.0000.0000.000
52H52ASP-1-0.757-0.85920.42414.93114.9310.0000.0000.0000.000
53H52PRO0-0.064-0.05317.424-0.639-0.6390.0000.0000.0000.000
54H53GLU-1-0.859-0.91320.55614.90714.9070.0000.0000.0000.000
55H54ILE0-0.067-0.02722.141-0.536-0.5360.0000.0000.0000.000
56H55GLY0-0.027-0.00524.432-0.491-0.4910.0000.0000.0000.000
57H56ASP-1-0.913-0.95425.84010.93210.9320.0000.0000.0000.000
58H57THR0-0.040-0.03624.9280.4510.4510.0000.0000.0000.000
59H58GLU-1-0.888-0.92226.18411.05411.0540.0000.0000.0000.000
60H59TYR00.0280.01026.4980.4930.4930.0000.0000.0000.000
61H60VAL00.0230.02828.411-0.463-0.4630.0000.0000.0000.000
62H61PRO00.016-0.02030.277-0.066-0.0660.0000.0000.0000.000
63H62LYS10.7530.87630.696-10.290-10.2900.0000.0000.0000.000
64H63PHE00.025-0.00328.086-0.029-0.0290.0000.0000.0000.000
65H64GLN00.0580.02831.1080.1530.1530.0000.0000.0000.000
66H65GLY0-0.0150.00733.002-0.245-0.2450.0000.0000.0000.000
67H66LYS10.7310.87530.294-9.404-9.4040.0000.0000.0000.000
68H67ALA00.0400.00827.0310.1840.1840.0000.0000.0000.000
69H68THR0-0.049-0.02627.646-0.398-0.3980.0000.0000.0000.000
70H69MET0-0.0150.02122.9670.3220.3220.0000.0000.0000.000
71H70THR00.010-0.00423.275-0.422-0.4220.0000.0000.0000.000
72H71ALA00.007-0.00619.5320.5620.5620.0000.0000.0000.000
73H72ASP-1-0.754-0.82819.37013.63613.6360.0000.0000.0000.000
74H73THR00.0340.02316.9740.6540.6540.0000.0000.0000.000
75H74SER0-0.055-0.03716.2500.7530.7530.0000.0000.0000.000
76H75SER0-0.101-0.07916.1640.4890.4890.0000.0000.0000.000
77H76ASN00.0250.01512.2280.7360.7360.0000.0000.0000.000
78H77THR0-0.0120.00213.5641.3231.3230.0000.0000.0000.000
79H78ALA00.0280.02416.142-0.940-0.9400.0000.0000.0000.000
80H79TYR0-0.029-0.04518.2410.0340.0340.0000.0000.0000.000
81H80LEU00.0110.01520.965-0.220-0.2200.0000.0000.0000.000
82H81GLN0-0.0200.00123.2060.0330.0330.0000.0000.0000.000
83H82LEU00.0290.01725.076-0.035-0.0350.0000.0000.0000.000
84H82SER00.0370.00528.664-0.057-0.0570.0000.0000.0000.000
85H82SER0-0.001-0.00932.472-0.015-0.0150.0000.0000.0000.000
86H82LEU0-0.0360.00129.776-0.058-0.0580.0000.0000.0000.000
87H83THR00.001-0.01433.441-0.373-0.3730.0000.0000.0000.000
88H84SER00.0330.00133.2840.1540.1540.0000.0000.0000.000
89H85GLU-1-0.811-0.86832.9239.0619.0610.0000.0000.0000.000
90H86ASP-1-0.807-0.88929.6929.9089.9080.0000.0000.0000.000
91H87THR00.0130.01428.4250.3640.3640.0000.0000.0000.000
92H88ALA0-0.043-0.02625.424-0.150-0.1500.0000.0000.0000.000
93H89VAL00.0150.02319.483-0.029-0.0290.0000.0000.0000.000
94H90TYR0-0.028-0.03520.920-0.278-0.2780.0000.0000.0000.000
95H91TYR00.012-0.00815.6020.3760.3760.0000.0000.0000.000
96H93ASN0-0.027-0.02313.0611.1361.1360.0000.0000.0000.000
97H94ALA00.0520.02311.430-1.119-1.1190.0000.0000.0000.000
98H95GLY00.0220.00712.3051.9041.9040.0000.0000.0000.000
99H96HIS0-0.0200.00511.8490.8720.8720.0000.0000.0000.000
100H97ASP-1-0.807-0.90015.32816.03516.0350.0000.0000.0000.000
101H98TYR0-0.050-0.01314.730-0.578-0.5780.0000.0000.0000.000
102H99ASP-1-0.850-0.91416.25718.95418.9540.0000.0000.0000.000
103H100ARG10.9370.95018.690-13.346-13.3460.0000.0000.0000.000
104H100GLY0-0.0020.00419.274-0.784-0.7840.0000.0000.0000.000
105H100ARG10.7900.89213.627-21.269-21.2690.0000.0000.0000.000
106H100PHE00.0030.00014.1760.2340.2340.0000.0000.0000.000
107H101PRO0-0.019-0.0089.026-0.008-0.0080.0000.0000.0000.000
108H102TYR00.0300.0185.4000.8170.8170.0000.0000.0000.000
109H103TRP0-0.003-0.0188.993-4.249-4.2490.0000.0000.0000.000
110H104GLY00.0370.0279.4271.9421.9420.0000.0000.0000.000
111H105GLN0-0.031-0.01311.7610.6870.6870.0000.0000.0000.000
112H106GLY0-0.0090.00312.948-0.971-0.9710.0000.0000.0000.000
113H107THR0-0.037-0.03216.4520.1680.1680.0000.0000.0000.000
114H108LEU0-0.027-0.00719.514-0.304-0.3040.0000.0000.0000.000
115H109VAL00.0250.01922.686-0.098-0.0980.0000.0000.0000.000
116H110THR00.010-0.00425.873-0.023-0.0230.0000.0000.0000.000
117H111VAL00.0050.01329.363-0.110-0.1100.0000.0000.0000.000
118H112SER00.0350.02032.625-0.233-0.2330.0000.0000.0000.000
119H113ALA0-0.006-0.00536.2610.0390.0390.0000.0000.0000.000
120H114ALA00.0160.03038.424-0.191-0.1910.0000.0000.0000.000
121H115LYS10.9140.94839.342-6.979-6.9790.0000.0000.0000.000
122H116THR00.0070.00936.4770.0080.0080.0000.0000.0000.000
123H117THR0-0.028-0.00739.094-0.258-0.2580.0000.0000.0000.000
124H118PRO00.0220.01539.8670.1990.1990.0000.0000.0000.000
125H119PRO0-0.035-0.00939.244-0.081-0.0810.0000.0000.0000.000
126H120SER00.0180.01441.729-0.185-0.1850.0000.0000.0000.000
127H121VAL0-0.009-0.01342.2580.1230.1230.0000.0000.0000.000
128H122TYR0-0.020-0.00944.852-0.166-0.1660.0000.0000.0000.000
129H123PRO00.0070.00645.9690.1500.1500.0000.0000.0000.000
130H124LEU0-0.021-0.01944.542-0.102-0.1020.0000.0000.0000.000
131H125ALA00.0280.01347.7670.0970.0970.0000.0000.0000.000
132H126PRO0-0.0120.00549.650-0.023-0.0230.0000.0000.0000.000
133H127GLY00.0750.03951.896-0.094-0.0940.0000.0000.0000.000
134H128SER0-0.035-0.01155.4170.0180.0180.0000.0000.0000.000
135H129ALA00.000-0.00456.756-0.118-0.1180.0000.0000.0000.000
136H130ALA0-0.009-0.00658.1950.0620.0620.0000.0000.0000.000
137H131GLN0-0.016-0.02357.554-0.041-0.0410.0000.0000.0000.000
138H132THR0-0.049-0.01657.8560.0090.0090.0000.0000.0000.000
139H133ASN00.0450.02150.2210.0210.0210.0000.0000.0000.000
140H134SER00.0200.02050.193-0.012-0.0120.0000.0000.0000.000
141H135MET0-0.0260.00944.818-0.042-0.0420.0000.0000.0000.000
142H136VAL00.0210.02447.748-0.050-0.0500.0000.0000.0000.000
143H137THR00.0120.00543.2620.1510.1510.0000.0000.0000.000
144H138LEU00.0000.01644.639-0.161-0.1610.0000.0000.0000.000
145H139GLY00.0430.00042.8970.2120.2120.0000.0000.0000.000
146H140CYS0-0.0750.00940.845-0.080-0.0800.0000.0000.0000.000
147H141LEU00.0240.03941.3940.1920.1920.0000.0000.0000.000
148H142VAL0-0.006-0.00738.481-0.153-0.1530.0000.0000.0000.000
149H143LYS10.9360.94340.360-6.859-6.8590.0000.0000.0000.000
150H144GLY00.0090.01241.846-0.096-0.0960.0000.0000.0000.000
151H145TYR00.0450.02834.822-0.102-0.1020.0000.0000.0000.000
152H146PHE00.0720.03134.8480.1300.1300.0000.0000.0000.000
153H147PRO0-0.0010.01132.428-0.195-0.1950.0000.0000.0000.000
154H148GLU-1-0.830-0.89730.4179.6559.6550.0000.0000.0000.000
155H149PRO00.0050.00128.4030.0740.0740.0000.0000.0000.000
156H150VAL00.000-0.01331.217-0.217-0.2170.0000.0000.0000.000
157H151THR0-0.028-0.01230.5820.2680.2680.0000.0000.0000.000
158H152VAL0-0.029-0.02433.317-0.265-0.2650.0000.0000.0000.000
159H153THR0-0.015-0.00433.9030.2520.2520.0000.0000.0000.000
160H154TRP00.0280.00836.430-0.318-0.3180.0000.0000.0000.000
161H155ASN00.015-0.00638.9510.0910.0910.0000.0000.0000.000
162H156SER0-0.010-0.00538.360-0.035-0.0350.0000.0000.0000.000
163H157GLY00.0140.01435.3930.1680.1680.0000.0000.0000.000
164H158SER0-0.069-0.04835.8750.0870.0870.0000.0000.0000.000
165H159LEU0-0.028-0.00538.501-0.045-0.0450.0000.0000.0000.000
166H160SER00.0190.00133.2320.1050.1050.0000.0000.0000.000
167H161SER00.0040.00534.2700.1970.1970.0000.0000.0000.000
168H162GLY00.0260.00335.974-0.206-0.2060.0000.0000.0000.000
169H163VAL0-0.029-0.00634.659-0.208-0.2080.0000.0000.0000.000
170H164HIS0-0.0070.00934.6020.3990.3990.0000.0000.0000.000
171H165THR00.018-0.00733.041-0.372-0.3720.0000.0000.0000.000
172H166PHE0-0.0290.00532.8710.2850.2850.0000.0000.0000.000
173H167PRO00.0370.00430.338-0.026-0.0260.0000.0000.0000.000
174H168ALA0-0.0150.00832.278-0.303-0.3030.0000.0000.0000.000
175H169VAL0-0.010-0.00333.6750.1440.1440.0000.0000.0000.000
176H170LEU00.0050.00335.071-0.168-0.1680.0000.0000.0000.000
177H171GLN0-0.015-0.01137.998-0.155-0.1550.0000.0000.0000.000
178H172SER0-0.008-0.00641.835-0.085-0.0850.0000.0000.0000.000
179H173ASP-1-0.887-0.93039.3357.2297.2290.0000.0000.0000.000
180H174LEU0-0.0060.00438.7760.1940.1940.0000.0000.0000.000
181H175TYR0-0.063-0.05931.782-0.065-0.0650.0000.0000.0000.000
182H176THR0-0.065-0.05738.244-0.269-0.2690.0000.0000.0000.000
183H177LEU00.0440.04234.3050.1680.1680.0000.0000.0000.000
184H178SER0-0.021-0.03237.603-0.354-0.3540.0000.0000.0000.000
185H179SER00.0080.01336.6650.1960.1960.0000.0000.0000.000
186H180SER00.018-0.00738.555-0.246-0.2460.0000.0000.0000.000
187H181VAL00.0090.00739.0550.2250.2250.0000.0000.0000.000
188H182THR0-0.028-0.02240.890-0.146-0.1460.0000.0000.0000.000
189H183VAL00.0210.01442.1850.1400.1400.0000.0000.0000.000
190H184PRO00.0690.01344.893-0.104-0.1040.0000.0000.0000.000
191H185SER00.017-0.00847.946-0.033-0.0330.0000.0000.0000.000
192H186SER0-0.019-0.00450.823-0.071-0.0710.0000.0000.0000.000
193H187THR0-0.043-0.01647.503-0.019-0.0190.0000.0000.0000.000
194H188TRP0-0.0030.01248.9620.0260.0260.0000.0000.0000.000
195H189PRO0-0.043-0.02851.007-0.035-0.0350.0000.0000.0000.000
196H190SER0-0.057-0.04553.000-0.019-0.0190.0000.0000.0000.000
197H191GLU-1-0.873-0.93548.6526.3256.3250.0000.0000.0000.000
198H192THR0-0.045-0.02747.537-0.047-0.0470.0000.0000.0000.000
199H193VAL00.0560.04544.2330.1250.1250.0000.0000.0000.000
200H194THR00.003-0.01443.934-0.179-0.1790.0000.0000.0000.000
201H196ASN00.0420.00638.721-0.030-0.0300.0000.0000.0000.000
202H197VAL0-0.0060.00137.9760.2370.2370.0000.0000.0000.000
203H198ALA0-0.007-0.00935.281-0.177-0.1770.0000.0000.0000.000
204H199HIS00.0240.02235.058-0.004-0.0040.0000.0000.0000.000
205H200PRO00.0340.01331.185-0.171-0.1710.0000.0000.0000.000
206H201ALA00.0190.01833.260-0.107-0.1070.0000.0000.0000.000
207H202SER0-0.002-0.03234.726-0.187-0.1870.0000.0000.0000.000
208H203SER0-0.038-0.02136.879-0.178-0.1780.0000.0000.0000.000
209H204THR0-0.0270.00738.049-0.165-0.1650.0000.0000.0000.000
210H205LYS10.9320.94736.258-7.715-7.7150.0000.0000.0000.000
211H206VAL0-0.006-0.00540.712-0.198-0.1980.0000.0000.0000.000
212H207ASP-1-0.831-0.89442.3437.2847.2840.0000.0000.0000.000
213H208LYS10.8510.90344.332-6.608-6.6080.0000.0000.0000.000
214H209LYS10.9280.97146.026-5.893-5.8930.0000.0000.0000.000
215H210ILE0-0.020-0.00445.754-0.098-0.0980.0000.0000.0000.000
216H211VAL0-0.008-0.01249.376-0.037-0.0370.0000.0000.0000.000
217H212PRO00.0200.00053.1160.0230.0230.0000.0000.0000.000
218H213ARG10.7750.86555.445-5.433-5.4330.0000.0000.0000.000
219H214ASP-1-0.788-0.86254.3165.5975.5970.0000.0000.0000.000