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: 724MK

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2248071.090945
FMO2-HF: Nuclear repulsion 2166018.065587
FMO2-HF: Total energy -82053.025358
FMO2-MP2: Total energy -82293.963749


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.
-7.436-1.7259.34-4.246-10.801-0.024
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 : -0.011 / q_NPA : 0.004
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].
3H4LEU00.005-0.0052.625-1.1261.9930.456-1.508-2.0670.007
4H5GLN00.000-0.0145.286-0.110-0.103-0.001-0.001-0.0040.000
5H6GLU-1-0.767-0.8838.926-0.650-0.6500.0000.0000.0000.000
6H7SER0-0.039-0.01111.639-0.009-0.0090.0000.0000.0000.000
7H8GLY00.0490.00414.9490.0390.0390.0000.0000.0000.000
8H9PRO0-0.032-0.00118.395-0.020-0.0200.0000.0000.0000.000
9H10GLY00.0760.03721.159-0.011-0.0110.0000.0000.0000.000
10H11LEU0-0.081-0.03822.8010.0050.0050.0000.0000.0000.000
11H12VAL0-0.0030.00024.3590.0030.0030.0000.0000.0000.000
12H13LYS10.9360.99727.3820.0980.0980.0000.0000.0000.000
13H14PRO00.012-0.01430.3610.0010.0010.0000.0000.0000.000
14H15SER0-0.065-0.04031.5770.0070.0070.0000.0000.0000.000
15H16GLU-1-0.842-0.91629.117-0.084-0.0840.0000.0000.0000.000
16H17THR0-0.021-0.02624.4540.0010.0010.0000.0000.0000.000
17H18LEU00.0050.02620.120-0.003-0.0030.0000.0000.0000.000
18H19SER0-0.041-0.04520.0040.0210.0210.0000.0000.0000.000
19H20LEU0-0.0050.02015.512-0.016-0.0160.0000.0000.0000.000
20H21THR00.0240.00813.6510.0440.0440.0000.0000.0000.000
21H22CYS0-0.0600.0038.021-0.054-0.0540.0000.0000.0000.000
22H23THR00.0180.0148.4630.1890.1890.0000.0000.0000.000
23H24VAL00.0160.0122.633-0.648-0.5521.148-0.209-1.0340.000
24H25SER0-0.003-0.0033.7350.1330.4670.002-0.094-0.2410.000
25H26GLY00.0160.0052.367-4.272-2.6233.071-2.409-2.311-0.023
26H27GLY00.0470.0222.419-0.2391.1953.860-2.201-3.093-0.008
27H28SER0-0.0080.0062.9271.089-1.3140.1422.620-0.3590.001
28H29ILE00.0410.0245.4530.1700.1700.0000.0000.0000.000
29H30SER0-0.010-0.0177.271-0.092-0.0920.0000.0000.0000.000
30H31SER00.009-0.0068.5790.1390.1390.0000.0000.0000.000
31H32HIS0-0.012-0.0075.2280.0020.0020.0000.0000.0000.000
32H33TYR00.0120.0128.819-0.100-0.1000.0000.0000.0000.000
33H34TRP0-0.023-0.0113.034-0.3860.0060.044-0.081-0.3550.001
34H35SER00.052-0.0019.906-0.016-0.0160.0000.0000.0000.000
35H36TRP0-0.0170.00311.302-0.087-0.0870.0000.0000.0000.000
36H37ILE0-0.016-0.01513.0100.0440.0440.0000.0000.0000.000
37H38ARG10.8410.92415.7940.1030.1030.0000.0000.0000.000
38H39GLN00.0200.02418.478-0.016-0.0160.0000.0000.0000.000
39H40SER00.0000.00320.661-0.001-0.0010.0000.0000.0000.000
40H41PRO00.028-0.00224.193-0.008-0.0080.0000.0000.0000.000
41H42GLY00.0200.01525.2690.0150.0150.0000.0000.0000.000
42H43LYS10.9250.97125.1150.1500.1500.0000.0000.0000.000
43H44GLY00.0410.01523.295-0.020-0.0200.0000.0000.0000.000
44H45LEU0-0.0030.00516.7470.0010.0010.0000.0000.0000.000
45H46GLN00.0490.02820.0460.0160.0160.0000.0000.0000.000
46H47TRP0-0.0140.00015.274-0.018-0.0180.0000.0000.0000.000
47H48ILE0-0.015-0.00917.2770.0160.0160.0000.0000.0000.000
48H49GLY00.030-0.00416.8540.0200.0200.0000.0000.0000.000
49H50TYR0-0.0040.00013.348-0.025-0.0250.0000.0000.0000.000
50H51ILE0-0.022-0.02512.386-0.008-0.0080.0000.0000.0000.000
51H52TYR0-0.010-0.00712.3440.0280.0280.0000.0000.0000.000
52H53TYR00.0400.03510.817-0.021-0.0210.0000.0000.0000.000
53H54SER0-0.038-0.01712.643-0.032-0.0320.0000.0000.0000.000
54H55GLY00.0290.01315.800-0.026-0.0260.0000.0000.0000.000
55H56SER0-0.034-0.00317.717-0.034-0.0340.0000.0000.0000.000
56H57THR00.0060.00716.8760.0090.0090.0000.0000.0000.000
57H58ASN0-0.012-0.00518.340-0.012-0.0120.0000.0000.0000.000
58H59TYR00.0170.00718.689-0.016-0.0160.0000.0000.0000.000
59H60SER00.0190.02321.2490.0060.0060.0000.0000.0000.000
60H61PRO00.038-0.01122.998-0.001-0.0010.0000.0000.0000.000
61H62SER0-0.008-0.01025.5880.0000.0000.0000.0000.0000.000
62H63LEU0-0.038-0.00522.029-0.004-0.0040.0000.0000.0000.000
63H64LYS10.9930.99224.443-0.018-0.0180.0000.0000.0000.000
64H65SER0-0.0120.00225.4320.0030.0030.0000.0000.0000.000
65H66ARG10.8460.91026.2060.0780.0780.0000.0000.0000.000
66H67VAL0-0.0190.00720.189-0.009-0.0090.0000.0000.0000.000
67H68THR0-0.013-0.02021.0690.0140.0140.0000.0000.0000.000
68H69ILE0-0.044-0.01114.796-0.016-0.0160.0000.0000.0000.000
69H70SER0-0.019-0.00316.6530.0170.0170.0000.0000.0000.000
70H71VAL00.020-0.00311.622-0.016-0.0160.0000.0000.0000.000
71H72GLU-1-0.812-0.88812.9540.0900.0900.0000.0000.0000.000
72H73THR00.030-0.01511.2620.0060.0060.0000.0000.0000.000
73H74ALA00.0120.02411.9960.0530.0530.0000.0000.0000.000
74H75LYS10.8420.90612.524-0.048-0.0480.0000.0000.0000.000
75H76ASN0-0.041-0.0205.2240.0940.0940.0000.0000.0000.000
76H77GLN0-0.006-0.0208.005-0.038-0.0380.0000.0000.0000.000
77H78PHE00.0280.0157.2070.0780.0780.0000.0000.0000.000
78H79SER0-0.042-0.02812.062-0.064-0.0640.0000.0000.0000.000
79H80LEU0-0.0030.00914.8640.0290.0290.0000.0000.0000.000
80H81LYS10.9460.95817.2110.0440.0440.0000.0000.0000.000
81H82LEU0-0.0070.01020.9670.0100.0100.0000.0000.0000.000
82H82THR00.0420.00423.327-0.005-0.0050.0000.0000.0000.000
83H82SER0-0.019-0.01726.955-0.001-0.0010.0000.0000.0000.000
84H82MET0-0.0360.01023.6960.0010.0010.0000.0000.0000.000
85H83THR00.0420.01428.3600.0050.0050.0000.0000.0000.000
86H84ALA00.0720.02628.842-0.008-0.0080.0000.0000.0000.000
87H85ALA00.0000.00529.005-0.010-0.0100.0000.0000.0000.000
88H86ASP-1-0.800-0.86425.075-0.106-0.1060.0000.0000.0000.000
89H87THR00.0180.02124.298-0.014-0.0140.0000.0000.0000.000
90H88ALA0-0.038-0.03021.3610.0040.0040.0000.0000.0000.000
91H89VAL00.0120.02116.7600.0010.0010.0000.0000.0000.000
92H90TYR0-0.017-0.03816.2220.0200.0200.0000.0000.0000.000
93H91TYR00.0420.00112.074-0.042-0.0420.0000.0000.0000.000
94H93ALA00.0520.0077.520-0.203-0.2030.0000.0000.0000.000
95H94ARG10.8280.9263.690-1.275-0.9310.003-0.044-0.3020.000
96H95GLY0-0.0010.0377.166-0.082-0.0820.0000.0000.0000.000
97H96PRO0-0.043-0.03710.246-0.031-0.0310.0000.0000.0000.000
98H97VAL0-0.009-0.00812.8730.0030.0030.0000.0000.0000.000
99H98PRO00.0000.01411.3230.0670.0670.0000.0000.0000.000
100H99ALA0-0.008-0.0129.226-0.012-0.0120.0000.0000.0000.000
101H100VAL0-0.063-0.01911.289-0.033-0.0330.0000.0000.0000.000
102H100PHE00.0480.01413.870-0.032-0.0320.0000.0000.0000.000
103H100TYR0-0.0070.01517.129-0.022-0.0220.0000.0000.0000.000
104H100GLY00.0500.01115.1290.0410.0410.0000.0000.0000.000
105H100ASP-1-0.857-0.94015.3150.1530.1530.0000.0000.0000.000
106H100TYR00.001-0.00614.0960.0360.0360.0000.0000.0000.000
107H100ARG10.8770.9299.861-0.257-0.2570.0000.0000.0000.000
108H100LEU0-0.035-0.01210.8330.0620.0620.0000.0000.0000.000
109H101ASP-1-0.832-0.9116.978-0.731-0.7310.0000.0000.0000.000
110H102PRO00.0270.0292.369-0.2290.5100.615-0.319-1.035-0.002
111H103TRP0-0.033-0.0415.7010.5010.5010.0000.0000.0000.000
112H104GLY0-0.0080.0127.078-0.490-0.4900.0000.0000.0000.000
113H105GLN0-0.062-0.0358.6190.1240.1240.0000.0000.0000.000
114H106GLY0-0.030-0.01011.8380.1120.1120.0000.0000.0000.000
115H107THR0-0.048-0.02913.987-0.003-0.0030.0000.0000.0000.000
116H108LEU0-0.019-0.00716.7860.0310.0310.0000.0000.0000.000
117H109VAL0-0.017-0.00419.7900.0100.0100.0000.0000.0000.000
118H110THR00.006-0.01022.4520.0100.0100.0000.0000.0000.000
119H111VAL0-0.0110.00226.2190.0040.0040.0000.0000.0000.000
120H112SER00.000-0.00928.5880.0070.0070.0000.0000.0000.000
121H113SER00.0360.01031.880-0.002-0.0020.0000.0000.0000.000
122H114ALA0-0.0160.00134.0500.0040.0040.0000.0000.0000.000
123H115SER00.003-0.00933.157-0.004-0.0040.0000.0000.0000.000
124H116THR0-0.0080.00029.040-0.005-0.0050.0000.0000.0000.000
125H117LYS10.8540.91331.7990.1280.1280.0000.0000.0000.000
126H118GLY00.0610.03531.341-0.009-0.0090.0000.0000.0000.000
127H119PRO0-0.018-0.01630.2950.0090.0090.0000.0000.0000.000
128H120SER0-0.056-0.01433.3620.0060.0060.0000.0000.0000.000
129H121VAL00.004-0.00232.472-0.002-0.0020.0000.0000.0000.000
130H122PHE00.0190.01135.7350.0070.0070.0000.0000.0000.000
131H123PRO00.0420.02037.130-0.008-0.0080.0000.0000.0000.000
132H124LEU0-0.053-0.01336.2700.0060.0060.0000.0000.0000.000
133H125ALA00.030-0.00338.947-0.004-0.0040.0000.0000.0000.000
134H126PRO00.0200.02939.3920.0020.0020.0000.0000.0000.000
135H127SER00.0330.01641.6210.0060.0060.0000.0000.0000.000
136H128SER00.0120.00244.731-0.002-0.0020.0000.0000.0000.000
137H129LYS10.9390.95246.8410.0730.0730.0000.0000.0000.000
138H130SER0-0.0110.01541.1400.0010.0010.0000.0000.0000.000
139H131THR0-0.002-0.00541.659-0.006-0.0060.0000.0000.0000.000
140H132SER0-0.016-0.01642.4640.0040.0040.0000.0000.0000.000
141H133GLY00.0340.03242.534-0.003-0.0030.0000.0000.0000.000
142H134GLY0-0.004-0.01141.5010.0000.0000.0000.0000.0000.000
143H135THR0-0.052-0.00737.181-0.006-0.0060.0000.0000.0000.000
144H136ALA00.0680.03338.4800.0060.0060.0000.0000.0000.000
145H137ALA0-0.007-0.00337.012-0.008-0.0080.0000.0000.0000.000
146H138LEU00.0140.01734.2880.0080.0080.0000.0000.0000.000
147H139GLY00.049-0.00333.930-0.010-0.0100.0000.0000.0000.000
148H140CYS0-0.140-0.03829.505-0.003-0.0030.0000.0000.0000.000
149H141LEU00.0250.02734.095-0.006-0.0060.0000.0000.0000.000
150H142VAL0-0.018-0.01330.7090.0040.0040.0000.0000.0000.000
151H143LYS10.8690.90034.0620.1070.1070.0000.0000.0000.000
152H144ASP-1-0.779-0.87435.692-0.112-0.1120.0000.0000.0000.000
153H145TYR00.0180.01328.9660.0050.0050.0000.0000.0000.000
154H146PHE00.0430.03831.090-0.001-0.0010.0000.0000.0000.000
155H147PRO00.0020.00326.7760.0050.0050.0000.0000.0000.000
156H148GLU-1-0.787-0.88325.875-0.218-0.2180.0000.0000.0000.000
157H149PRO0-0.004-0.01621.7440.0020.0020.0000.0000.0000.000
158H150VAL0-0.004-0.02024.9950.0010.0010.0000.0000.0000.000
159H151THR0-0.026-0.00620.972-0.017-0.0170.0000.0000.0000.000
160H152VAL0-0.002-0.02124.2490.0190.0190.0000.0000.0000.000
161H153SER0-0.017-0.00122.766-0.024-0.0240.0000.0000.0000.000
162H154TRP00.0320.02524.8190.0270.0270.0000.0000.0000.000
163H155ASN00.010-0.00525.873-0.011-0.0110.0000.0000.0000.000
164H156SER00.006-0.00523.8610.0020.0020.0000.0000.0000.000
165H157GLY0-0.0160.00021.380-0.023-0.0230.0000.0000.0000.000
166H158ALA0-0.039-0.00922.169-0.011-0.0110.0000.0000.0000.000
167H159LEU0-0.045-0.01424.3660.0070.0070.0000.0000.0000.000
168H160THR00.004-0.00922.113-0.017-0.0170.0000.0000.0000.000
169H161SER00.0310.01424.584-0.002-0.0020.0000.0000.0000.000
170H162GLY00.0160.00326.8690.0110.0110.0000.0000.0000.000
171H163VAL0-0.0030.00826.4300.0120.0120.0000.0000.0000.000
172H164HIS0-0.004-0.00327.571-0.018-0.0180.0000.0000.0000.000
173H165THR00.0080.00326.5610.0200.0200.0000.0000.0000.000
174H166PHE0-0.0180.00228.283-0.009-0.0090.0000.0000.0000.000
175H167PRO00.0270.00528.983-0.008-0.0080.0000.0000.0000.000
176H168ALA00.0080.01229.4140.0130.0130.0000.0000.0000.000
177H169VAL0-0.023-0.01431.2600.0030.0030.0000.0000.0000.000
178H170LEU0-0.058-0.02434.1480.0000.0000.0000.0000.0000.000
179H171GLN0-0.023-0.02235.7990.0080.0080.0000.0000.0000.000
180H172SER00.0570.01739.158-0.001-0.0010.0000.0000.0000.000
181H173SER0-0.034-0.01640.2780.0010.0010.0000.0000.0000.000
182H174GLY00.0260.01738.0700.0010.0010.0000.0000.0000.000
183H175LEU0-0.066-0.02535.355-0.006-0.0060.0000.0000.0000.000
184H176TYR00.0150.01030.7130.0050.0050.0000.0000.0000.000
185H177SER0-0.020-0.01633.8710.0030.0030.0000.0000.0000.000
186H178LEU00.0320.03228.610-0.002-0.0020.0000.0000.0000.000
187H179SER00.0180.00433.1660.0090.0090.0000.0000.0000.000
188H180SER0-0.027-0.01228.705-0.008-0.0080.0000.0000.0000.000
189H181VAL00.017-0.00231.3550.0120.0120.0000.0000.0000.000
190H182VAL00.0450.01330.093-0.014-0.0140.0000.0000.0000.000
191H183THR0-0.057-0.01732.2200.0110.0110.0000.0000.0000.000
192H184VAL00.0060.00532.541-0.008-0.0080.0000.0000.0000.000
193H185PRO00.0500.01134.3920.0070.0070.0000.0000.0000.000
194H186SER00.0360.01337.632-0.001-0.0010.0000.0000.0000.000
195H187SER00.0080.00840.7930.0010.0010.0000.0000.0000.000
196H188SER0-0.060-0.03836.9080.0000.0000.0000.0000.0000.000
197H189LEU00.0190.00338.365-0.004-0.0040.0000.0000.0000.000
198H190GLY0-0.0130.00840.2780.0010.0010.0000.0000.0000.000
199H191THR0-0.026-0.01939.2670.0000.0000.0000.0000.0000.000
200H192GLN0-0.036-0.00332.4140.0020.0020.0000.0000.0000.000
201H193THR00.0070.01134.0770.0030.0030.0000.0000.0000.000
202H194TYR00.023-0.00132.152-0.014-0.0140.0000.0000.0000.000
203H195ILE00.0310.00730.6230.0090.0090.0000.0000.0000.000
204H197ASN00.0470.00125.525-0.004-0.0040.0000.0000.0000.000
205H198VAL0-0.0030.00226.416-0.018-0.0180.0000.0000.0000.000
206H199ASN0-0.003-0.02321.8580.0200.0200.0000.0000.0000.000
207H200HIS00.0660.06925.476-0.008-0.0080.0000.0000.0000.000
208H201LYS10.8870.93920.1170.2850.2850.0000.0000.0000.000
209H202PRO00.0310.03123.5120.0130.0130.0000.0000.0000.000
210H203SER0-0.032-0.03225.6160.0130.0130.0000.0000.0000.000
211H204ASN0-0.060-0.04724.673-0.012-0.0120.0000.0000.0000.000
212H205THR00.0230.02426.4580.0110.0110.0000.0000.0000.000
213H206LYS10.9270.94722.0890.2580.2580.0000.0000.0000.000
214H207VAL0-0.023-0.00128.5640.0150.0150.0000.0000.0000.000
215H208ASP-1-0.794-0.89428.453-0.218-0.2180.0000.0000.0000.000
216H209LYS10.8160.90231.3310.1440.1440.0000.0000.0000.000
217H210LYS10.8760.94733.8300.1000.1000.0000.0000.0000.000
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