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: 2JMZR

Calculation Name: 1F58-H-Xray372

Preferred Name:

Target Type:

Ligand Name: alpha-aminoisobutyric acid

ligand 3-letter code: AIB

PDB ID: 1F58

Chain ID: H

ChEMBL ID:

UniProt ID: P05877

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2359847.381607
FMO2-HF: Nuclear repulsion 2271461.979914
FMO2-HF: Total energy -88385.401693
FMO2-MP2: Total energy -88639.508095


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:ASP)


Summations of interaction energy for fragment #1(H:1:ASP)
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.
-19.954-16.3210.019-1.899-1.7520.009
Interaction energy analysis for fragmet #1(H:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.850 / q_NPA : -0.916
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].
3H3GLN0-0.030-0.0193.576-3.385-0.4790.020-1.628-1.2980.008
4H4LEU00.0100.0076.107-3.234-3.2340.0000.0000.0000.000
5H5GLN0-0.004-0.0059.761-1.129-1.1290.0000.0000.0000.000
6H6GLN00.0130.01012.7360.0280.0280.0000.0000.0000.000
7H7SER0-0.019-0.00616.359-0.285-0.2850.0000.0000.0000.000
8H8GLY00.0230.00019.377-0.028-0.0280.0000.0000.0000.000
9H9PRO0-0.0320.00023.1770.0120.0120.0000.0000.0000.000
10H10ASP-1-0.821-0.91125.27711.58011.5800.0000.0000.0000.000
11H11LEU0-0.057-0.02226.358-0.259-0.2590.0000.0000.0000.000
12H12VAL0-0.0030.00229.053-0.054-0.0540.0000.0000.0000.000
13H13LYS10.8140.89031.860-8.965-8.9650.0000.0000.0000.000
14H14PRO00.0570.01135.3610.0970.0970.0000.0000.0000.000
15H15SER0-0.084-0.03836.883-0.255-0.2550.0000.0000.0000.000
16H16GLN00.0330.02134.3860.1770.1770.0000.0000.0000.000
17H17SER0-0.003-0.01831.377-0.062-0.0620.0000.0000.0000.000
18H18LEU0-0.0210.01325.165-0.029-0.0290.0000.0000.0000.000
19H19SER0-0.027-0.03926.1410.0350.0350.0000.0000.0000.000
20H20LEU0-0.026-0.00620.9320.0320.0320.0000.0000.0000.000
21H21THR0-0.003-0.00318.392-0.204-0.2040.0000.0000.0000.000
22H22CYS0-0.068-0.01313.9640.1080.1080.0000.0000.0000.000
23H23THR00.0190.01212.790-0.712-0.7120.0000.0000.0000.000
24H24VAL00.0140.0138.7411.3641.3640.0000.0000.0000.000
25H25THR0-0.018-0.0086.347-3.027-3.0270.0000.0000.0000.000
26H26GLY00.0300.0114.1473.8773.845-0.001-0.0340.0680.000
27H27TYR0-0.036-0.0485.0231.7661.950-0.001-0.012-0.1710.000
28H28SER00.0190.0177.143-1.868-1.8680.0000.0000.0000.000
29H29ILE00.032-0.00610.9750.7170.7170.0000.0000.0000.000
30H30THR0-0.066-0.03013.101-0.434-0.4340.0000.0000.0000.000
31H31SER0-0.038-0.01010.511-1.354-1.3540.0000.0000.0000.000
32H32GLY00.0260.02810.9830.3520.3520.0000.0000.0000.000
33H33TYR00.0130.00611.568-2.363-2.3630.0000.0000.0000.000
34H34SER0-0.033-0.03413.652-2.591-2.5910.0000.0000.0000.000
35H35TRP0-0.0200.0148.6492.7132.7130.0000.0000.0000.000
36H35HIS00.033-0.01514.546-2.355-2.3550.0000.0000.0000.000
37H36TRP00.0100.00415.9491.0681.0680.0000.0000.0000.000
38H37ILE0-0.045-0.01915.567-0.894-0.8940.0000.0000.0000.000
39H38ARG10.8050.88119.402-11.740-11.7400.0000.0000.0000.000
40H39GLN0-0.019-0.01120.1130.4730.4730.0000.0000.0000.000
41H40PHE0-0.0020.02022.812-0.005-0.0050.0000.0000.0000.000
42H41PRO00.0290.00125.9050.2710.2710.0000.0000.0000.000
43H42GLY00.0210.01527.875-0.279-0.2790.0000.0000.0000.000
44H43ASN0-0.043-0.02023.4960.0570.0570.0000.0000.0000.000
45H44LYS10.8860.94923.592-11.353-11.3530.0000.0000.0000.000
46H45LEU00.0660.02719.1300.0140.0140.0000.0000.0000.000
47H46GLU-1-0.811-0.91122.22711.07611.0760.0000.0000.0000.000
48H47TRP00.0160.04019.359-0.164-0.1640.0000.0000.0000.000
49H48MET0-0.019-0.00621.504-0.729-0.7290.0000.0000.0000.000
50H49GLY00.0380.00121.529-0.854-0.8540.0000.0000.0000.000
51H50TYR0-0.0220.00518.1230.6590.6590.0000.0000.0000.000
52H51ILE0-0.037-0.01217.695-0.991-0.9910.0000.0000.0000.000
53H52HIS00.0680.05717.5170.9400.9400.0000.0000.0000.000
54H53TYR00.0760.03216.317-0.394-0.3940.0000.0000.0000.000
55H54SER0-0.052-0.05117.832-0.482-0.4820.0000.0000.0000.000
56H55ALA0-0.052-0.02220.589-0.605-0.6050.0000.0000.0000.000
57H56GLY00.0210.02821.990-0.420-0.4200.0000.0000.0000.000
58H57THR0-0.033-0.02722.2510.6820.6820.0000.0000.0000.000
59H58ASN0-0.014-0.00723.331-0.970-0.9700.0000.0000.0000.000
60H59TYR00.0330.01023.6400.6270.6270.0000.0000.0000.000
61H60ASN00.0320.02425.744-0.830-0.8300.0000.0000.0000.000
62H61PRO00.022-0.00427.325-0.255-0.2550.0000.0000.0000.000
63H62SER0-0.027-0.01830.145-0.402-0.4020.0000.0000.0000.000
64H63LEU0-0.024-0.01426.549-0.146-0.1460.0000.0000.0000.000
65H64LYS10.9410.97430.094-10.139-10.1390.0000.0000.0000.000
66H65SER0-0.015-0.00131.0010.0150.0150.0000.0000.0000.000
67H66ARG10.8060.87531.603-10.255-10.2550.0000.0000.0000.000
68H67ILE0-0.0280.01124.6660.0800.0800.0000.0000.0000.000
69H68SER0-0.038-0.02526.938-0.159-0.1590.0000.0000.0000.000
70H69ILE00.0290.02420.3530.2960.2960.0000.0000.0000.000
71H70THR0-0.0110.00322.147-0.204-0.2040.0000.0000.0000.000
72H71ARG10.8990.93417.833-15.729-15.7290.0000.0000.0000.000
73H72ASP-1-0.806-0.87819.05613.55813.5580.0000.0000.0000.000
74H73THR00.018-0.01817.6510.9230.9230.0000.0000.0000.000
75H74SER0-0.038-0.00517.3370.2820.2820.0000.0000.0000.000
76H75LYS10.8490.91117.382-13.550-13.5500.0000.0000.0000.000
77H76ASN0-0.018-0.00610.627-0.045-0.0450.0000.0000.0000.000
78H77GLN00.0150.00013.8670.5290.5290.0000.0000.0000.000
79H78PHE0-0.003-0.00712.769-0.702-0.7020.0000.0000.0000.000
80H79PHE00.001-0.00717.7700.4090.4090.0000.0000.0000.000
81H80LEU0-0.0040.00520.704-0.017-0.0170.0000.0000.0000.000
82H81GLN00.0270.02422.875-0.231-0.2310.0000.0000.0000.000
83H82LEU00.0130.00326.6780.0410.0410.0000.0000.0000.000
84H82ASN00.0050.00228.887-0.228-0.2280.0000.0000.0000.000
85H82SER00.0050.00132.558-0.002-0.0020.0000.0000.0000.000
86H82VAL0-0.0300.00430.384-0.019-0.0190.0000.0000.0000.000
87H83THR0-0.020-0.02833.226-0.412-0.4120.0000.0000.0000.000
88H84THR00.040-0.01333.2290.2390.2390.0000.0000.0000.000
89H85GLU-1-0.861-0.90532.8619.2489.2480.0000.0000.0000.000
90H86ASP-1-0.763-0.82729.39910.67910.6790.0000.0000.0000.000
91H87THR0-0.0140.00728.2110.4810.4810.0000.0000.0000.000
92H88ALA0-0.027-0.01124.733-0.058-0.0580.0000.0000.0000.000
93H89THR00.0050.01119.480-0.213-0.2130.0000.0000.0000.000
94H90TYR0-0.008-0.03020.4110.1550.1550.0000.0000.0000.000
95H91TYR0-0.004-0.02114.8960.3620.3620.0000.0000.0000.000
96H93ALA00.0330.00911.3031.5811.5810.0000.0000.0000.000
97H94ARG10.8160.8843.751-59.081-58.6740.001-0.194-0.2130.001
98H95GLU-1-0.902-0.94310.31919.60219.6020.0000.0000.0000.000
99H96GLU-1-0.770-0.8647.35134.44034.4400.0000.0000.0000.000
100H97ALA0-0.019-0.01910.612-1.964-1.9640.0000.0000.0000.000
101H98MET00.0080.0118.3312.3342.3340.0000.0000.0000.000
102H99PRO00.007-0.00710.986-2.348-2.3480.0000.0000.0000.000
103H100TYR0-0.012-0.00414.168-0.307-0.3070.0000.0000.0000.000
104H100GLY00.0080.00517.653-0.682-0.6820.0000.0000.0000.000
105H100ASN0-0.008-0.00620.1920.6100.6100.0000.0000.0000.000
106H100GLN0-0.060-0.03919.324-0.406-0.4060.0000.0000.0000.000
107H100ALA00.0310.03519.585-0.364-0.3640.0000.0000.0000.000
108H100TYR0-0.006-0.01512.9620.4360.4360.0000.0000.0000.000
109H100TYR0-0.032-0.01215.482-1.742-1.7420.0000.0000.0000.000
110H100TYR0-0.0070.00413.9291.0241.0240.0000.0000.0000.000
111H100ALA00.0280.00812.986-1.326-1.3260.0000.0000.0000.000
112H100MET0-0.005-0.00912.0021.6031.6030.0000.0000.0000.000
113H101ASP-1-0.778-0.8476.24948.57448.5740.0000.0000.0000.000
114H102CYS0-0.0120.0114.168-1.527-1.3590.000-0.031-0.1380.000
115H103TRP0-0.003-0.0267.274-5.222-5.2220.0000.0000.0000.000
116H104GLY00.0280.0239.1872.0902.0900.0000.0000.0000.000
117H105GLN0-0.019-0.0419.913-2.152-2.1520.0000.0000.0000.000
118H106GLY00.0180.01913.457-1.184-1.1840.0000.0000.0000.000
119H107THR0-0.023-0.02216.6620.0380.0380.0000.0000.0000.000
120H108THR0-0.043-0.01619.852-0.173-0.1730.0000.0000.0000.000
121H109VAL0-0.028-0.00523.402-0.090-0.0900.0000.0000.0000.000
122H110THR0-0.018-0.01226.186-0.199-0.1990.0000.0000.0000.000
123H111VAL0-0.013-0.00829.847-0.072-0.0720.0000.0000.0000.000
124H112SER00.041-0.01232.624-0.223-0.2230.0000.0000.0000.000
125H113SER00.0120.00136.1390.1070.1070.0000.0000.0000.000
126H114ALA0-0.0060.01737.897-0.164-0.1640.0000.0000.0000.000
127H115LYS10.9650.97838.371-7.279-7.2790.0000.0000.0000.000
128H116THR00.0060.00836.3500.0410.0410.0000.0000.0000.000
129H117THR0-0.041-0.01738.377-0.296-0.2960.0000.0000.0000.000
130H118PRO00.0240.02239.2200.2140.2140.0000.0000.0000.000
131H119PRO0-0.017-0.00238.728-0.117-0.1170.0000.0000.0000.000
132H120SER00.0090.01041.219-0.204-0.2040.0000.0000.0000.000
133H121VAL0-0.022-0.01641.7130.0930.0930.0000.0000.0000.000
134H122TYR0-0.020-0.01744.392-0.165-0.1650.0000.0000.0000.000
135H123PRO00.0180.01445.7500.1510.1510.0000.0000.0000.000
136H124LEU0-0.030-0.01644.527-0.140-0.1400.0000.0000.0000.000
137H125ALA00.0150.00147.9700.0600.0600.0000.0000.0000.000
138H126PRO00.001-0.00549.928-0.043-0.0430.0000.0000.0000.000
139H127GLY00.0160.01252.261-0.085-0.0850.0000.0000.0000.000
140H128SER00.0200.01155.071-0.044-0.0440.0000.0000.0000.000
141H129ALA0-0.0040.01256.441-0.105-0.1050.0000.0000.0000.000
142H130ALA00.0250.02154.6720.1150.1150.0000.0000.0000.000
143H133GLN0-0.007-0.02452.5220.0530.0530.0000.0000.0000.000
144H134THR0-0.0050.00454.938-0.032-0.0320.0000.0000.0000.000
145H135ASN00.0530.02252.9750.1210.1210.0000.0000.0000.000
146H136SER00.0310.00050.327-0.002-0.0020.0000.0000.0000.000
147H137MET0-0.0550.01344.6990.0450.0450.0000.0000.0000.000
148H138VAL00.0150.01748.407-0.101-0.1010.0000.0000.0000.000
149H139THR00.0120.00844.1200.1570.1570.0000.0000.0000.000
150H140LEU0-0.030-0.00645.172-0.190-0.1900.0000.0000.0000.000
151H141GLY00.0600.01343.1720.2050.2050.0000.0000.0000.000
152H142CYS0-0.0690.00640.868-0.062-0.0620.0000.0000.0000.000
153H143LEU0-0.0050.01241.3690.1950.1950.0000.0000.0000.000
154H144VAL00.006-0.00237.835-0.147-0.1470.0000.0000.0000.000
155H145LYS10.9590.96339.917-6.864-6.8640.0000.0000.0000.000
156H146GLY00.0080.00941.573-0.106-0.1060.0000.0000.0000.000
157H147TYR0-0.019-0.03234.150-0.219-0.2190.0000.0000.0000.000
158H148PHE00.0410.01634.4820.1440.1440.0000.0000.0000.000
159H149PRO00.0200.01931.744-0.234-0.2340.0000.0000.0000.000
160H150GLU-1-0.771-0.87630.0469.7379.7370.0000.0000.0000.000
161H151PRO0-0.0100.00727.7480.1200.1200.0000.0000.0000.000
162H152VAL00.003-0.00830.593-0.245-0.2450.0000.0000.0000.000
163H153THR0-0.061-0.03731.0450.3970.3970.0000.0000.0000.000
164H154VAL0-0.005-0.00832.938-0.307-0.3070.0000.0000.0000.000
165H156THR0-0.022-0.01033.8800.2590.2590.0000.0000.0000.000
166H157TRP00.0170.00336.422-0.366-0.3660.0000.0000.0000.000
167H162ASN00.031-0.00139.0680.1130.1130.0000.0000.0000.000
168H163SER0-0.015-0.00938.152-0.059-0.0590.0000.0000.0000.000
169H164GLY00.0100.01235.4870.2000.2000.0000.0000.0000.000
170H165SER0-0.055-0.03436.1950.0980.0980.0000.0000.0000.000
171H166LEU0-0.058-0.01638.958-0.099-0.0990.0000.0000.0000.000
172H167SER00.0410.00834.0840.1300.1300.0000.0000.0000.000
173H168SER00.0340.00935.6520.1450.1450.0000.0000.0000.000
174H169GLY00.0190.00837.197-0.190-0.1900.0000.0000.0000.000
175H171VAL0-0.051-0.01435.697-0.185-0.1850.0000.0000.0000.000
176H172HIS00.0000.01435.4780.3740.3740.0000.0000.0000.000
177H173THR00.0150.00133.453-0.389-0.3890.0000.0000.0000.000
178H174PHE0-0.0210.00633.4150.2870.2870.0000.0000.0000.000
179H175PRO00.025-0.00330.741-0.007-0.0070.0000.0000.0000.000
180H176ALA00.0030.02132.580-0.307-0.3070.0000.0000.0000.000
181H177VAL0-0.027-0.01133.8110.1900.1900.0000.0000.0000.000
182H178LEU0-0.0070.00034.718-0.157-0.1570.0000.0000.0000.000
183H179GLN00.002-0.01137.859-0.225-0.2250.0000.0000.0000.000
184H180SER0-0.014-0.01441.689-0.169-0.1690.0000.0000.0000.000
185H183ASP-1-0.836-0.90739.0958.0888.0880.0000.0000.0000.000
186H184LEU0-0.0460.00338.6720.1860.1860.0000.0000.0000.000
187H185TYR00.0280.01031.791-0.055-0.0550.0000.0000.0000.000
188H186THR0-0.051-0.03437.751-0.344-0.3440.0000.0000.0000.000
189H187LEU00.0410.03833.6880.1250.1250.0000.0000.0000.000
190H188SER0-0.010-0.01737.604-0.285-0.2850.0000.0000.0000.000
191H189SER00.010-0.00136.9040.1910.1910.0000.0000.0000.000
192H190SER0-0.010-0.01838.794-0.291-0.2910.0000.0000.0000.000
193H191VAL00.0210.00839.4020.2150.2150.0000.0000.0000.000
194H192THR0-0.027-0.01441.539-0.158-0.1580.0000.0000.0000.000
195H193VAL00.0060.00643.0370.1320.1320.0000.0000.0000.000
196H194PRO00.0700.00245.306-0.100-0.1000.0000.0000.0000.000
197H195SER0-0.021-0.03348.3690.0230.0230.0000.0000.0000.000
198H196SER00.0100.01851.673-0.064-0.0640.0000.0000.0000.000
199H198PRO00.0380.03048.005-0.097-0.0970.0000.0000.0000.000
200H199ARG10.8510.95449.437-6.158-6.1580.0000.0000.0000.000
201H200PRO0-0.033-0.03751.619-0.013-0.0130.0000.0000.0000.000
202H202SER0-0.031-0.02653.639-0.056-0.0560.0000.0000.0000.000
203H203GLU-1-0.879-0.93149.2386.3336.3330.0000.0000.0000.000
204H204THR0-0.068-0.05147.992-0.022-0.0220.0000.0000.0000.000
205H205VAL00.0280.03744.4630.1440.1440.0000.0000.0000.000
206H206THR0-0.002-0.01843.681-0.202-0.2020.0000.0000.0000.000
207H209ASN00.0420.00938.425-0.051-0.0510.0000.0000.0000.000
208H210VAL00.001-0.00137.5990.2170.2170.0000.0000.0000.000
209H211ALA0-0.011-0.00834.710-0.177-0.1770.0000.0000.0000.000
210H212HIS00.0310.01834.531-0.032-0.0320.0000.0000.0000.000
211H213PRO00.0290.01030.574-0.188-0.1880.0000.0000.0000.000
212H214ALA00.0310.02732.591-0.098-0.0980.0000.0000.0000.000
213H215SER0-0.011-0.02733.861-0.207-0.2070.0000.0000.0000.000
214H216SER0-0.040-0.01936.010-0.182-0.1820.0000.0000.0000.000
215H217THR0-0.0180.00137.221-0.222-0.2220.0000.0000.0000.000
216H218LYS10.9480.96036.224-8.118-8.1180.0000.0000.0000.000
217H219VAL0-0.016-0.00840.089-0.234-0.2340.0000.0000.0000.000
218H220ASP-1-0.824-0.89341.7577.6117.6110.0000.0000.0000.000
219H221LYS10.8790.92944.030-6.869-6.8690.0000.0000.0000.000
220H222LYS11.0021.01345.950-5.940-5.9400.0000.0000.0000.000
221H223ILE0-0.011-0.00545.382-0.111-0.1110.0000.0000.0000.000
222H226VAL00.002-0.00549.224-0.057-0.0570.0000.0000.0000.000
223H227PRO0-0.025-0.01553.0090.0600.0600.0000.0000.0000.000
224H228ARG10.8690.91953.956-5.759-5.7590.0000.0000.0000.000
225H229ASP-1-0.844-0.90356.7705.0855.0850.0000.0000.0000.000
226H230CYS0-0.093-0.04259.9690.0560.0560.0000.0000.0000.000