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: 2JGLR

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2246675.155736
FMO2-HF: Nuclear repulsion 2164621.552048
FMO2-HF: Total energy -82053.603688
FMO2-MP2: Total energy -82294.502511


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.
-7.963-0.3876.374-4.379-9.567-0.023
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 : -0.001 / q_NPA : 0.008
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].
3H4LEU00.0090.0032.763-0.7882.0430.188-1.294-1.7250.006
4H5GLN00.000-0.0065.325-0.130-0.119-0.001-0.001-0.0080.000
5H6GLU-1-0.759-0.8789.096-0.613-0.6130.0000.0000.0000.000
6H7SER0-0.041-0.01911.775-0.018-0.0180.0000.0000.0000.000
7H8GLY00.0460.00515.1950.0390.0390.0000.0000.0000.000
8H9PRO0-0.0160.01218.774-0.017-0.0170.0000.0000.0000.000
9H10GLY00.0730.02521.932-0.006-0.0060.0000.0000.0000.000
10H11LEU0-0.085-0.04023.1660.0040.0040.0000.0000.0000.000
11H12VAL0-0.0060.00624.6950.0010.0010.0000.0000.0000.000
12H13LYS10.8700.95027.7230.0980.0980.0000.0000.0000.000
13H14PRO00.011-0.01230.7210.0010.0010.0000.0000.0000.000
14H15SER0-0.067-0.03032.0740.0060.0060.0000.0000.0000.000
15H16GLU-1-0.803-0.89129.181-0.088-0.0880.0000.0000.0000.000
16H17THR0-0.028-0.02325.0530.0030.0030.0000.0000.0000.000
17H18LEU00.0180.02520.345-0.002-0.0020.0000.0000.0000.000
18H19SER0-0.027-0.02920.5590.0230.0230.0000.0000.0000.000
19H20LEU0-0.0120.01515.854-0.016-0.0160.0000.0000.0000.000
20H21THR00.0230.00714.1330.0480.0480.0000.0000.0000.000
21H22CYS0-0.059-0.0038.381-0.043-0.0430.0000.0000.0000.000
22H23THR00.0100.0198.4740.1770.1770.0000.0000.0000.000
23H24VAL00.0370.0242.808-0.799-0.3940.422-0.134-0.6930.000
24H25SER0-0.020-0.0193.6600.1010.3820.001-0.068-0.2140.000
25H26GLY00.0230.0132.518-4.414-2.4312.067-1.987-2.063-0.020
26H27GLY00.0350.0212.3510.0491.7942.335-1.587-2.493-0.007
27H28SER0-0.0020.0173.043-0.027-1.1090.0641.283-0.2650.000
28H29ILE00.0460.0195.6690.2030.2030.0000.0000.0000.000
29H30SER00.003-0.0037.524-0.064-0.0640.0000.0000.0000.000
30H31SER00.009-0.0058.4420.1450.1450.0000.0000.0000.000
31H32HIS00.0010.0055.3500.1090.1090.0000.0000.0000.000
32H33TYR0-0.0030.0088.895-0.119-0.1190.0000.0000.0000.000
33H34TRP0-0.018-0.0083.082-0.3450.0360.036-0.080-0.3350.000
34H35SER00.035-0.0179.666-0.020-0.0200.0000.0000.0000.000
35H36TRP0-0.0190.00111.265-0.092-0.0920.0000.0000.0000.000
36H37ILE0-0.005-0.00112.5970.0450.0450.0000.0000.0000.000
37H38ARG10.8040.89415.8280.1040.1040.0000.0000.0000.000
38H39GLN00.0360.02418.470-0.017-0.0170.0000.0000.0000.000
39H40SER0-0.0030.00420.798-0.005-0.0050.0000.0000.0000.000
40H41PRO00.019-0.00624.302-0.008-0.0080.0000.0000.0000.000
41H42GLY00.0210.01825.6980.0140.0140.0000.0000.0000.000
42H43LYS10.9310.97925.3390.1420.1420.0000.0000.0000.000
43H44GLY00.0530.02722.970-0.019-0.0190.0000.0000.0000.000
44H45LEU0-0.010-0.00216.4910.0030.0030.0000.0000.0000.000
45H46GLN00.0460.02219.8210.0160.0160.0000.0000.0000.000
46H47TRP00.0060.00815.154-0.020-0.0200.0000.0000.0000.000
47H48ILE0-0.024-0.00517.3730.0160.0160.0000.0000.0000.000
48H49GLY00.0410.00217.0750.0180.0180.0000.0000.0000.000
49H50TYR0-0.0140.00113.561-0.025-0.0250.0000.0000.0000.000
50H51ILE0-0.023-0.01612.406-0.011-0.0110.0000.0000.0000.000
51H52TYR00.0060.00512.1810.0200.0200.0000.0000.0000.000
52H53TYR00.0040.00410.836-0.031-0.0310.0000.0000.0000.000
53H54SER0-0.0130.00012.667-0.021-0.0210.0000.0000.0000.000
54H55GLY00.0340.01615.895-0.026-0.0260.0000.0000.0000.000
55H56SER0-0.028-0.00617.669-0.034-0.0340.0000.0000.0000.000
56H57THR00.006-0.00616.9050.0080.0080.0000.0000.0000.000
57H58ASN0-0.033-0.00418.338-0.016-0.0160.0000.0000.0000.000
58H59TYR00.0380.01018.711-0.014-0.0140.0000.0000.0000.000
59H60SER00.0200.00521.2130.0040.0040.0000.0000.0000.000
60H61PRO00.038-0.00322.960-0.003-0.0030.0000.0000.0000.000
61H62SER0-0.009-0.00125.2260.0010.0010.0000.0000.0000.000
62H63LEU0-0.040-0.01822.312-0.006-0.0060.0000.0000.0000.000
63H64LYS10.9570.97924.671-0.025-0.0250.0000.0000.0000.000
64H65SER0-0.0050.00525.6290.0040.0040.0000.0000.0000.000
65H66ARG10.8410.90726.4520.0750.0750.0000.0000.0000.000
66H67VAL0-0.0140.00420.382-0.009-0.0090.0000.0000.0000.000
67H68THR0-0.029-0.01621.2640.0140.0140.0000.0000.0000.000
68H69ILE0-0.0070.00515.073-0.018-0.0180.0000.0000.0000.000
69H70SER0-0.039-0.02416.3880.0140.0140.0000.0000.0000.000
70H71VAL00.009-0.00411.643-0.017-0.0170.0000.0000.0000.000
71H72GLU-1-0.815-0.89413.0750.0880.0880.0000.0000.0000.000
72H73THR00.0530.00111.558-0.001-0.0010.0000.0000.0000.000
73H74ALA0-0.0050.01712.3650.0390.0390.0000.0000.0000.000
74H75LYS10.8500.91512.999-0.036-0.0360.0000.0000.0000.000
75H76ASN0-0.030-0.0135.5020.1020.1020.0000.0000.0000.000
76H77GLN0-0.002-0.0158.208-0.036-0.0360.0000.0000.0000.000
77H78PHE00.0090.0017.1390.0870.0870.0000.0000.0000.000
78H79SER0-0.031-0.02612.021-0.063-0.0630.0000.0000.0000.000
79H80LEU0-0.0170.00014.8670.0290.0290.0000.0000.0000.000
80H81LYS10.9090.94317.3840.0460.0460.0000.0000.0000.000
81H82LEU00.0080.00721.1600.0070.0070.0000.0000.0000.000
82H82THR00.0500.01623.645-0.006-0.0060.0000.0000.0000.000
83H82SER0-0.009-0.00827.360-0.002-0.0020.0000.0000.0000.000
84H82MET0-0.0410.00324.0320.0010.0010.0000.0000.0000.000
85H83THR00.023-0.00728.7000.0050.0050.0000.0000.0000.000
86H84ALA00.0690.02029.159-0.008-0.0080.0000.0000.0000.000
87H85ALA0-0.006-0.00529.402-0.010-0.0100.0000.0000.0000.000
88H86ASP-1-0.776-0.83825.292-0.100-0.1000.0000.0000.0000.000
89H87THR00.0040.01724.395-0.014-0.0140.0000.0000.0000.000
90H88ALA0-0.045-0.02821.4420.0040.0040.0000.0000.0000.000
91H89VAL00.0260.02516.849-0.001-0.0010.0000.0000.0000.000
92H90TYR0-0.004-0.02516.5120.0250.0250.0000.0000.0000.000
93H91TYR00.039-0.00612.133-0.044-0.0440.0000.0000.0000.000
94H93ALA00.0440.0117.473-0.184-0.1840.0000.0000.0000.000
95H94ARG10.8360.9103.372-1.439-1.0360.011-0.059-0.3550.000
96H95GLY00.0290.0446.955-0.092-0.0920.0000.0000.0000.000
97H96PRO0-0.056-0.04010.112-0.033-0.0330.0000.0000.0000.000
98H97VAL00.0020.00212.9120.0090.0090.0000.0000.0000.000
99H98PRO00.0160.01211.0320.0600.0600.0000.0000.0000.000
100H99ALA00.006-0.0098.959-0.023-0.0230.0000.0000.0000.000
101H100VAL0-0.0420.00111.012-0.029-0.0290.0000.0000.0000.000
102H100PHE00.017-0.00513.661-0.029-0.0290.0000.0000.0000.000
103H100TYR0-0.0180.00316.817-0.032-0.0320.0000.0000.0000.000
104H100GLY00.0560.01214.6960.0560.0560.0000.0000.0000.000
105H100ASP-1-0.856-0.92314.5700.1920.1920.0000.0000.0000.000
106H100TYR0-0.023-0.01313.8190.0340.0340.0000.0000.0000.000
107H100ARG10.8260.8959.283-0.312-0.3120.0000.0000.0000.000
108H100LEU0-0.026-0.01110.5340.0680.0680.0000.0000.0000.000
109H101ASP-1-0.817-0.8966.380-0.311-0.3110.0000.0000.0000.000
110H102PRO00.0400.0402.273-0.3100.3081.251-0.452-1.416-0.002
111H103TRP0-0.041-0.0445.5060.5310.5310.0000.0000.0000.000
112H104GLY0-0.0140.0046.760-0.520-0.5200.0000.0000.0000.000
113H105GLN0-0.050-0.0368.3600.1160.1160.0000.0000.0000.000
114H106GLY0-0.019-0.00111.7220.1050.1050.0000.0000.0000.000
115H107THR0-0.042-0.03214.122-0.005-0.0050.0000.0000.0000.000
116H108LEU0-0.036-0.01216.9340.0290.0290.0000.0000.0000.000
117H109VAL0-0.022-0.00220.0070.0060.0060.0000.0000.0000.000
118H110THR00.000-0.01322.6890.0090.0090.0000.0000.0000.000
119H111VAL0-0.007-0.00326.4920.0050.0050.0000.0000.0000.000
120H112SER0-0.015-0.01128.8840.0080.0080.0000.0000.0000.000
121H113SER00.0420.00532.137-0.003-0.0030.0000.0000.0000.000
122H114ALA00.0070.01834.2150.0030.0030.0000.0000.0000.000
123H115SER00.0250.00333.663-0.002-0.0020.0000.0000.0000.000
124H116THR0-0.019-0.03329.193-0.004-0.0040.0000.0000.0000.000
125H117LYS10.8220.89731.9860.1300.1300.0000.0000.0000.000
126H118GLY00.0590.03531.098-0.009-0.0090.0000.0000.0000.000
127H119PRO0-0.041-0.01430.2310.0100.0100.0000.0000.0000.000
128H120SER00.0030.00333.2620.0020.0020.0000.0000.0000.000
129H121VAL0-0.0050.00132.6540.0000.0000.0000.0000.0000.000
130H122PHE00.0100.00235.9320.0060.0060.0000.0000.0000.000
131H123PRO00.0390.02137.572-0.007-0.0070.0000.0000.0000.000
132H124LEU0-0.049-0.02236.8280.0060.0060.0000.0000.0000.000
133H125ALA00.0500.02039.144-0.005-0.0050.0000.0000.0000.000
134H126PRO00.0090.02739.6030.0010.0010.0000.0000.0000.000
135H127SER00.0550.01841.6960.0070.0070.0000.0000.0000.000
136H128SER00.002-0.00145.120-0.002-0.0020.0000.0000.0000.000
137H129LYS10.9210.95146.8270.0750.0750.0000.0000.0000.000
138H130SER0-0.0070.00541.2700.0010.0010.0000.0000.0000.000
139H131THR0-0.003-0.00641.700-0.006-0.0060.0000.0000.0000.000
140H132SER0-0.036-0.03342.4190.0040.0040.0000.0000.0000.000
141H133GLY00.0330.03042.926-0.003-0.0030.0000.0000.0000.000
142H134GLY00.0170.00941.8200.0000.0000.0000.0000.0000.000
143H135THR0-0.041-0.00437.157-0.006-0.0060.0000.0000.0000.000
144H136ALA00.0640.02638.6900.0070.0070.0000.0000.0000.000
145H137ALA0-0.0030.01337.111-0.008-0.0080.0000.0000.0000.000
146H138LEU00.0080.02234.5160.0090.0090.0000.0000.0000.000
147H139GLY00.034-0.00934.398-0.010-0.0100.0000.0000.0000.000
148H140CYS0-0.0710.00029.854-0.003-0.0030.0000.0000.0000.000
149H141LEU00.0290.04034.162-0.008-0.0080.0000.0000.0000.000
150H142VAL0-0.027-0.02730.5850.0010.0010.0000.0000.0000.000
151H143LYS10.8740.90933.9910.1040.1040.0000.0000.0000.000
152H144ASP-1-0.775-0.86635.627-0.111-0.1110.0000.0000.0000.000
153H145TYR0-0.021-0.02629.2000.0040.0040.0000.0000.0000.000
154H146PHE00.0510.02731.4440.0010.0010.0000.0000.0000.000
155H147PRO00.0120.01327.0530.0040.0040.0000.0000.0000.000
156H148GLU-1-0.778-0.88126.003-0.221-0.2210.0000.0000.0000.000
157H149PRO0-0.018-0.00421.6810.0030.0030.0000.0000.0000.000
158H150VAL0-0.023-0.02024.9510.0000.0000.0000.0000.0000.000
159H151THR0-0.044-0.02221.170-0.024-0.0240.0000.0000.0000.000
160H152VAL00.013-0.01424.5400.0200.0200.0000.0000.0000.000
161H153SER0-0.023-0.00223.125-0.026-0.0260.0000.0000.0000.000
162H154TRP00.0360.01525.1580.0280.0280.0000.0000.0000.000
163H155ASN00.000-0.01426.159-0.014-0.0140.0000.0000.0000.000
164H156SER0-0.016-0.01724.7310.0030.0030.0000.0000.0000.000
165H157GLY0-0.0030.00321.810-0.025-0.0250.0000.0000.0000.000
166H158ALA0-0.043-0.00922.585-0.012-0.0120.0000.0000.0000.000
167H159LEU0-0.027-0.00624.7650.0130.0130.0000.0000.0000.000
168H160THR00.005-0.00422.128-0.016-0.0160.0000.0000.0000.000
169H161SER00.0450.00924.9530.0020.0020.0000.0000.0000.000
170H162GLY00.0370.01227.1550.0110.0110.0000.0000.0000.000
171H163VAL0-0.041-0.00726.6490.0130.0130.0000.0000.0000.000
172H164HIS0-0.0070.00428.008-0.014-0.0140.0000.0000.0000.000
173H165THR00.004-0.00526.8610.0170.0170.0000.0000.0000.000
174H166PHE0-0.0090.01028.666-0.009-0.0090.0000.0000.0000.000
175H167PRO00.025-0.00329.069-0.007-0.0070.0000.0000.0000.000
176H168ALA0-0.0070.01829.5110.0110.0110.0000.0000.0000.000
177H169VAL0-0.014-0.01431.2830.0040.0040.0000.0000.0000.000
178H170LEU0-0.037-0.01334.2980.0000.0000.0000.0000.0000.000
179H171GLN0-0.030-0.02535.7280.0080.0080.0000.0000.0000.000
180H172SER00.0310.00439.230-0.001-0.0010.0000.0000.0000.000
181H173SER0-0.012-0.00340.3930.0020.0020.0000.0000.0000.000
182H174GLY00.0220.01638.3750.0010.0010.0000.0000.0000.000
183H175LEU0-0.052-0.01835.557-0.005-0.0050.0000.0000.0000.000
184H176TYR00.0070.00530.5750.0040.0040.0000.0000.0000.000
185H177SER0-0.026-0.00934.1290.0020.0020.0000.0000.0000.000
186H178LEU00.0750.04828.622-0.002-0.0020.0000.0000.0000.000
187H179SER0-0.020-0.02632.8120.0120.0120.0000.0000.0000.000
188H180SER0-0.0030.00328.982-0.009-0.0090.0000.0000.0000.000
189H181VAL00.017-0.00631.5680.0120.0120.0000.0000.0000.000
190H182VAL00.0260.01130.379-0.014-0.0140.0000.0000.0000.000
191H183THR0-0.038-0.00832.5690.0100.0100.0000.0000.0000.000
192H184VAL00.0070.00433.074-0.009-0.0090.0000.0000.0000.000
193H185PRO00.0570.02234.6640.0070.0070.0000.0000.0000.000
194H186SER00.0170.00237.911-0.001-0.0010.0000.0000.0000.000
195H187SER0-0.004-0.00440.9010.0010.0010.0000.0000.0000.000
196H188SER0-0.025-0.01537.169-0.001-0.0010.0000.0000.0000.000
197H189LEU00.0160.00439.017-0.002-0.0020.0000.0000.0000.000
198H190GLY0-0.0030.01040.7790.0010.0010.0000.0000.0000.000
199H191THR0-0.045-0.02539.8690.0020.0020.0000.0000.0000.000
200H192GLN0-0.052-0.02233.0600.0000.0000.0000.0000.0000.000
201H193THR00.0060.00834.3570.0010.0010.0000.0000.0000.000
202H194TYR00.0400.00532.420-0.013-0.0130.0000.0000.0000.000
203H195ILE00.015-0.00830.7570.0100.0100.0000.0000.0000.000
204H197ASN00.035-0.00326.048-0.002-0.0020.0000.0000.0000.000
205H198VAL0-0.0060.01026.786-0.019-0.0190.0000.0000.0000.000
206H199ASN00.002-0.01121.9020.0240.0240.0000.0000.0000.000
207H200HIS00.0560.04925.362-0.012-0.0120.0000.0000.0000.000
208H201LYS10.8520.92520.3440.2650.2650.0000.0000.0000.000
209H202PRO00.0280.02523.7140.0110.0110.0000.0000.0000.000
210H203SER0-0.0010.01225.9090.0170.0170.0000.0000.0000.000
211H204ASN0-0.033-0.02824.621-0.010-0.0100.0000.0000.0000.000
212H205THR00.0380.01226.464-0.005-0.0050.0000.0000.0000.000
213H206LYS10.9450.96522.5410.2580.2580.0000.0000.0000.000
214H207VAL0-0.024-0.01328.8550.0150.0150.0000.0000.0000.000
215H208ASP-1-0.791-0.87228.847-0.215-0.2150.0000.0000.0000.000
216H209LYS10.8120.88631.5660.1460.1460.0000.0000.0000.000
217H210LYS10.8610.93734.1220.1020.1020.0000.0000.0000.000
218H211VAL0-0.043-0.02435.3960.0050.0050.0000.0000.0000.000
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