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: MVZ9Z

Calculation Name: 1U6A-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1U6A

Chain ID: H

ChEMBL ID:

UniProt ID: Q6N089

Base Structure: X-ray

Registration Date: 2023-06-26

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2248185.494811
FMO2-HF: Nuclear repulsion 2166133.425684
FMO2-HF: Total energy -82052.069127
FMO2-MP2: Total energy -82293.119582


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:2:VAL)


Summations of interaction energy for fragment #1(H:2:VAL)
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.
-8.832-5.02912.214-3.957-12.061-0.026
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.003
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].
3H4LEU00.000-0.0142.223-0.9231.9371.333-1.737-2.4560.005
4H5GLN0-0.004-0.0225.236-0.147-0.141-0.001-0.002-0.0040.000
5H6GLU-1-0.751-0.8658.923-0.662-0.6620.0000.0000.0000.000
6H7SER0-0.051-0.00711.625-0.026-0.0260.0000.0000.0000.000
7H8GLY00.0620.00614.9820.0480.0480.0000.0000.0000.000
8H9PRO0-0.041-0.00318.423-0.024-0.0240.0000.0000.0000.000
9H10GLY00.0870.04021.123-0.010-0.0100.0000.0000.0000.000
10H11LEU0-0.076-0.03422.7410.0060.0060.0000.0000.0000.000
11H12VAL00.0030.00324.3540.0030.0030.0000.0000.0000.000
12H13LYS10.9651.00527.3430.1020.1020.0000.0000.0000.000
13H14PRO00.008-0.01530.3190.0020.0020.0000.0000.0000.000
14H15SER0-0.058-0.03331.5110.0070.0070.0000.0000.0000.000
15H16GLU-1-0.849-0.92828.919-0.084-0.0840.0000.0000.0000.000
16H17THR0-0.019-0.02024.4470.0040.0040.0000.0000.0000.000
17H18LEU0-0.0130.01820.072-0.005-0.0050.0000.0000.0000.000
18H19SER0-0.025-0.03620.0540.0250.0250.0000.0000.0000.000
19H20LEU0-0.0140.01215.523-0.021-0.0210.0000.0000.0000.000
20H21THR00.0120.01313.4700.0420.0420.0000.0000.0000.000
21H22CYS0-0.0380.0077.986-0.062-0.0620.0000.0000.0000.000
22H23THR00.0070.0048.1890.2160.2160.0000.0000.0000.000
23H24VAL00.0220.0132.252-0.554-0.6971.483-0.288-1.0520.000
24H25SER0-0.017-0.0093.5240.1940.5800.004-0.121-0.2700.000
25H26GLY00.0080.0022.352-4.993-3.2923.205-2.485-2.421-0.024
26H27GLY00.0420.0172.2831.0041.2985.173-2.270-3.197-0.007
27H28SER0-0.0070.0042.7651.760-1.6960.2473.591-0.3810.001
28H29ILE00.0350.0245.5630.3010.3010.0000.0000.0000.000
29H30SER0-0.015-0.0227.327-0.099-0.0990.0000.0000.0000.000
30H31SER00.0190.0008.6810.1760.1760.0000.0000.0000.000
31H32HIS0-0.033-0.0125.703-0.033-0.0330.0000.0000.0000.000
32H33TYR00.0130.0138.878-0.149-0.1490.0000.0000.0000.000
33H34TRP0-0.027-0.0123.059-0.2850.1010.044-0.080-0.3490.000
34H35SER00.038-0.0149.837-0.049-0.0490.0000.0000.0000.000
35H36TRP0-0.0140.01011.170-0.088-0.0880.0000.0000.0000.000
36H37ILE0-0.018-0.01813.0250.0460.0460.0000.0000.0000.000
37H38ARG10.8430.94015.5830.0830.0830.0000.0000.0000.000
38H39GLN00.0200.01818.261-0.012-0.0120.0000.0000.0000.000
39H40SER0-0.011-0.00820.404-0.002-0.0020.0000.0000.0000.000
40H41PRO00.0220.00323.948-0.010-0.0100.0000.0000.0000.000
41H42GLY00.0300.01724.9900.0170.0170.0000.0000.0000.000
42H43LYS10.9140.96924.8280.1490.1490.0000.0000.0000.000
43H44GLY00.0360.00822.979-0.020-0.0200.0000.0000.0000.000
44H45LEU0-0.0090.00116.6360.0000.0000.0000.0000.0000.000
45H46GLN00.0610.03819.7820.0150.0150.0000.0000.0000.000
46H47TRP0-0.0150.00215.010-0.025-0.0250.0000.0000.0000.000
47H48ILE0-0.012-0.01217.0890.0130.0130.0000.0000.0000.000
48H49GLY00.022-0.01616.7050.0160.0160.0000.0000.0000.000
49H50TYR0-0.0010.00513.256-0.023-0.0230.0000.0000.0000.000
50H51ILE0-0.038-0.03312.559-0.020-0.0200.0000.0000.0000.000
51H52TYR00.004-0.00112.3230.0470.0470.0000.0000.0000.000
52H53TYR00.0340.02910.939-0.035-0.0350.0000.0000.0000.000
53H54SER0-0.042-0.01812.684-0.046-0.0460.0000.0000.0000.000
54H55GLY00.0300.01315.823-0.037-0.0370.0000.0000.0000.000
55H56SER0-0.032-0.00217.735-0.042-0.0420.0000.0000.0000.000
56H57THR00.0140.01016.8680.0210.0210.0000.0000.0000.000
57H58ASN0-0.010-0.00418.290-0.021-0.0210.0000.0000.0000.000
58H59TYR00.0270.01318.697-0.006-0.0060.0000.0000.0000.000
59H60SER00.0330.02821.1660.0040.0040.0000.0000.0000.000
60H61PRO00.053-0.00422.846-0.003-0.0030.0000.0000.0000.000
61H62SER0-0.039-0.02125.415-0.005-0.0050.0000.0000.0000.000
62H63LEU0-0.0190.00721.702-0.005-0.0050.0000.0000.0000.000
63H64LYS10.9870.98724.366-0.052-0.0520.0000.0000.0000.000
64H65SER0-0.031-0.00625.3470.0040.0040.0000.0000.0000.000
65H66ARG10.8500.90825.9610.0660.0660.0000.0000.0000.000
66H67VAL0-0.0290.00320.243-0.011-0.0110.0000.0000.0000.000
67H68THR0-0.032-0.02821.0860.0140.0140.0000.0000.0000.000
68H69ILE0-0.030-0.00414.706-0.021-0.0210.0000.0000.0000.000
69H70SER0-0.0080.00316.6830.0160.0160.0000.0000.0000.000
70H71VAL00.006-0.00911.683-0.014-0.0140.0000.0000.0000.000
71H72GLU-1-0.877-0.93412.9390.1050.1050.0000.0000.0000.000
72H73THR00.015-0.02311.4130.0080.0080.0000.0000.0000.000
73H74ALA00.0100.01712.1580.0520.0520.0000.0000.0000.000
74H75LYS10.9280.96812.577-0.041-0.0410.0000.0000.0000.000
75H76ASN0-0.035-0.0195.4740.1500.1500.0000.0000.0000.000
76H77GLN00.012-0.0087.952-0.057-0.0570.0000.0000.0000.000
77H78PHE00.0290.0147.6130.0940.0940.0000.0000.0000.000
78H79SER0-0.030-0.02012.161-0.098-0.0980.0000.0000.0000.000
79H80LEU0-0.0080.00814.9490.0380.0380.0000.0000.0000.000
80H81LYS10.9380.95417.2250.0230.0230.0000.0000.0000.000
81H82LEU00.0080.01520.9800.0130.0130.0000.0000.0000.000
82H82THR00.0300.00223.289-0.010-0.0100.0000.0000.0000.000
83H82SER0-0.002-0.00926.9330.0000.0000.0000.0000.0000.000
84H82MET0-0.0190.01123.4610.0020.0020.0000.0000.0000.000
85H83THR00.0440.01728.2830.0030.0030.0000.0000.0000.000
86H84ALA00.0680.02428.713-0.008-0.0080.0000.0000.0000.000
87H85ALA0-0.0070.00028.838-0.011-0.0110.0000.0000.0000.000
88H86ASP-1-0.798-0.86624.929-0.097-0.0970.0000.0000.0000.000
89H87THR00.0370.04424.152-0.016-0.0160.0000.0000.0000.000
90H88ALA0-0.027-0.03121.1370.0060.0060.0000.0000.0000.000
91H89VAL00.0100.02716.5450.0000.0000.0000.0000.0000.000
92H90TYR0-0.042-0.06516.0910.0270.0270.0000.0000.0000.000
93H91TYR00.0520.01911.775-0.048-0.0480.0000.0000.0000.000
94H93ALA00.0380.0067.260-0.225-0.2250.0000.0000.0000.000
95H94ARG10.9280.9892.812-4.075-3.1210.181-0.271-0.8640.001
96H95GLY0-0.0100.0327.070-0.104-0.1040.0000.0000.0000.000
97H96PRO0-0.034-0.02810.193-0.049-0.0490.0000.0000.0000.000
98H97VAL00.0040.00312.820-0.002-0.0020.0000.0000.0000.000
99H98PRO0-0.0190.00011.4020.1110.1110.0000.0000.0000.000
100H99ALA00.006-0.0059.366-0.024-0.0240.0000.0000.0000.000
101H100VAL0-0.072-0.02111.386-0.056-0.0560.0000.0000.0000.000
102H100PHE00.0490.01314.014-0.035-0.0350.0000.0000.0000.000
103H100TYR0-0.0060.01817.262-0.024-0.0240.0000.0000.0000.000
104H100GLY00.0460.00615.3510.0560.0560.0000.0000.0000.000
105H100ASP-1-0.919-0.97415.2770.2150.2150.0000.0000.0000.000
106H100TYR00.001-0.01114.1480.0610.0610.0000.0000.0000.000
107H100ARG10.9430.97410.397-0.501-0.5010.0000.0000.0000.000
108H100LEU0-0.036-0.01610.6360.0920.0920.0000.0000.0000.000
109H101ASP-1-0.872-0.9247.386-0.812-0.8120.0000.0000.0000.000
110H102PRO00.0110.0042.447-0.2910.5240.545-0.294-1.067-0.002
111H103TRP0-0.039-0.0485.7650.5410.5410.0000.0000.0000.000
112H104GLY0-0.0160.0056.781-0.543-0.5430.0000.0000.0000.000
113H105GLN0-0.037-0.0268.4390.1700.1700.0000.0000.0000.000
114H106GLY0-0.044-0.02911.6370.1200.1200.0000.0000.0000.000
115H107THR0-0.074-0.03613.799-0.005-0.0050.0000.0000.0000.000
116H108LEU0-0.002-0.00416.6550.0360.0360.0000.0000.0000.000
117H109VAL0-0.0090.00019.7040.0090.0090.0000.0000.0000.000
118H110THR00.001-0.01122.3370.0110.0110.0000.0000.0000.000
119H111VAL0-0.015-0.00126.0970.0040.0040.0000.0000.0000.000
120H112SER0-0.011-0.01528.4870.0070.0070.0000.0000.0000.000
121H113SER00.0220.00431.790-0.002-0.0020.0000.0000.0000.000
122H114ALA0-0.0290.00233.9540.0040.0040.0000.0000.0000.000
123H115SER00.007-0.00433.105-0.003-0.0030.0000.0000.0000.000
124H116THR0-0.010-0.00529.149-0.005-0.0050.0000.0000.0000.000
125H117LYS10.8800.93431.7610.1410.1410.0000.0000.0000.000
126H118GLY00.0610.03131.298-0.010-0.0100.0000.0000.0000.000
127H119PRO0-0.041-0.02930.2980.0090.0090.0000.0000.0000.000
128H120SER0-0.0270.00233.2870.0050.0050.0000.0000.0000.000
129H121VAL0-0.003-0.00732.497-0.003-0.0030.0000.0000.0000.000
130H122PHE00.0060.00235.7640.0070.0070.0000.0000.0000.000
131H123PRO00.0490.01337.162-0.009-0.0090.0000.0000.0000.000
132H124LEU0-0.062-0.00536.2580.0070.0070.0000.0000.0000.000
133H125ALA00.027-0.00438.981-0.004-0.0040.0000.0000.0000.000
134H126PRO00.0370.02039.1090.0020.0020.0000.0000.0000.000
135H127SER00.0260.01941.6550.0070.0070.0000.0000.0000.000
136H128SER00.006-0.00744.767-0.003-0.0030.0000.0000.0000.000
137H129LYS10.9430.95346.7170.0850.0850.0000.0000.0000.000
138H130SER00.0030.03241.2720.0010.0010.0000.0000.0000.000
139H131THR00.0170.00941.698-0.007-0.0070.0000.0000.0000.000
140H132SER0-0.044-0.03042.4540.0050.0050.0000.0000.0000.000
141H133GLY00.0470.03642.573-0.004-0.0040.0000.0000.0000.000
142H134GLY0-0.003-0.01241.5370.0000.0000.0000.0000.0000.000
143H135THR0-0.058-0.00637.763-0.008-0.0080.0000.0000.0000.000
144H136ALA00.0810.03638.5160.0070.0070.0000.0000.0000.000
145H137ALA0-0.013-0.00637.050-0.010-0.0100.0000.0000.0000.000
146H138LEU00.0120.02134.2850.0100.0100.0000.0000.0000.000
147H139GLY00.044-0.01033.964-0.012-0.0120.0000.0000.0000.000
148H140CYS0-0.142-0.03629.529-0.005-0.0050.0000.0000.0000.000
149H141LEU00.0230.02834.132-0.006-0.0060.0000.0000.0000.000
150H142VAL0-0.018-0.00830.7550.0040.0040.0000.0000.0000.000
151H143LYS10.9510.95833.9400.1200.1200.0000.0000.0000.000
152H144ASP-1-0.853-0.92335.590-0.128-0.1280.0000.0000.0000.000
153H145TYR00.0670.04128.8590.0030.0030.0000.0000.0000.000
154H146PHE00.0390.03730.9720.0000.0000.0000.0000.0000.000
155H147PRO00.0130.00826.6500.0050.0050.0000.0000.0000.000
156H148GLU-1-0.888-0.93425.852-0.235-0.2350.0000.0000.0000.000
157H149PRO00.018-0.01321.5990.0030.0030.0000.0000.0000.000
158H150VAL0-0.018-0.02024.8550.0000.0000.0000.0000.0000.000
159H151THR0-0.023-0.01620.918-0.019-0.0190.0000.0000.0000.000
160H152VAL0-0.006-0.01824.2520.0200.0200.0000.0000.0000.000
161H153SER00.0080.01422.899-0.025-0.0250.0000.0000.0000.000
162H154TRP00.0230.02024.8500.0300.0300.0000.0000.0000.000
163H155ASN00.0160.00425.899-0.012-0.0120.0000.0000.0000.000
164H156SER00.013-0.00523.8530.0010.0010.0000.0000.0000.000
165H157GLY0-0.033-0.00821.404-0.029-0.0290.0000.0000.0000.000
166H158ALA0-0.040-0.01122.194-0.013-0.0130.0000.0000.0000.000
167H159LEU0-0.043-0.01524.3880.0090.0090.0000.0000.0000.000
168H160THR00.023-0.00622.124-0.018-0.0180.0000.0000.0000.000
169H161SER00.0030.00324.619-0.003-0.0030.0000.0000.0000.000
170H162GLY00.0210.01326.9080.0120.0120.0000.0000.0000.000
171H163VAL00.0100.01326.5130.0140.0140.0000.0000.0000.000
172H164HIS0-0.004-0.00327.615-0.022-0.0220.0000.0000.0000.000
173H165THR00.011-0.00226.3970.0220.0220.0000.0000.0000.000
174H166PHE0-0.028-0.00428.321-0.009-0.0090.0000.0000.0000.000
175H167PRO00.0130.00028.743-0.009-0.0090.0000.0000.0000.000
176H168ALA00.0140.01529.2060.0130.0130.0000.0000.0000.000
177H169VAL00.000-0.00231.0570.0040.0040.0000.0000.0000.000
178H170LEU0-0.057-0.02534.0810.0000.0000.0000.0000.0000.000
179H171GLN0-0.043-0.03435.6140.0090.0090.0000.0000.0000.000
180H172SER00.0570.01638.9840.0000.0000.0000.0000.0000.000
181H173SER0-0.035-0.01940.0580.0020.0020.0000.0000.0000.000
182H174GLY00.0320.02137.9230.0010.0010.0000.0000.0000.000
183H175LEU0-0.074-0.02335.239-0.006-0.0060.0000.0000.0000.000
184H176TYR00.0200.00431.1540.0050.0050.0000.0000.0000.000
185H177SER0-0.039-0.02633.7290.0020.0020.0000.0000.0000.000
186H178LEU00.0450.03628.488-0.001-0.0010.0000.0000.0000.000
187H179SER00.0320.00733.1740.0090.0090.0000.0000.0000.000
188H180SER0-0.032-0.01028.721-0.010-0.0100.0000.0000.0000.000
189H181VAL00.0200.00331.3950.0130.0130.0000.0000.0000.000
190H182VAL00.0480.01330.026-0.016-0.0160.0000.0000.0000.000
191H183THR0-0.068-0.02332.2590.0120.0120.0000.0000.0000.000
192H184VAL00.0140.00732.603-0.010-0.0100.0000.0000.0000.000
193H185PRO00.0340.00334.4250.0090.0090.0000.0000.0000.000
194H186SER00.0460.01937.664-0.002-0.0020.0000.0000.0000.000
195H187SER00.0100.01140.8620.0010.0010.0000.0000.0000.000
196H188SER0-0.063-0.04436.9300.0000.0000.0000.0000.0000.000
197H189LEU00.0170.00138.390-0.005-0.0050.0000.0000.0000.000
198H190GLY0-0.0150.00940.3050.0010.0010.0000.0000.0000.000
199H191THR0-0.026-0.01438.8840.0000.0000.0000.0000.0000.000
200H192GLN0-0.0140.00532.3040.0030.0030.0000.0000.0000.000
201H193THR0-0.0040.00534.1040.0050.0050.0000.0000.0000.000
202H194TYR00.015-0.00732.243-0.016-0.0160.0000.0000.0000.000
203H195ILE00.0450.01030.9760.0110.0110.0000.0000.0000.000
204H197ASN00.0310.01325.736-0.004-0.0040.0000.0000.0000.000
205H198VAL00.0210.00926.443-0.019-0.0190.0000.0000.0000.000
206H199ASN00.0380.00822.0430.0370.0370.0000.0000.0000.000
207H200HIS00.0570.05425.390-0.009-0.0090.0000.0000.0000.000
208H201LYS10.8780.92519.8530.3440.3440.0000.0000.0000.000
209H202PRO00.0300.03023.4830.0130.0130.0000.0000.0000.000
210H203SER0-0.025-0.02225.5850.0130.0130.0000.0000.0000.000
211H204ASN0-0.076-0.05025.183-0.015-0.0150.0000.0000.0000.000
212H205THR00.0210.02126.4810.0120.0120.0000.0000.0000.000
213H206LYS10.9140.94222.0650.3060.3060.0000.0000.0000.000
214H207VAL0-0.0100.00728.5500.0180.0180.0000.0000.0000.000
215H208ASP-1-0.835-0.92328.661-0.260-0.2600.0000.0000.0000.000
216H209LYS10.8280.91031.3500.1710.1710.0000.0000.0000.000
217H210LYS10.9410.99233.8540.1240.1240.0000.0000.0000.000
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219H212GLU-1-0.881-0.94937.402-0.125-0.1250.0000.0000.0000.000
220H213PRO00.0010.00440.5040.0020.0020.0000.0000.0000.000