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: 72K8K

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2358762.882953
FMO2-HF: Nuclear repulsion 2270377.936326
FMO2-HF: Total energy -88384.946627
FMO2-MP2: Total energy -88638.985584


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.
-10.808-7.442-0.012-1.678-1.6750.009
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 : -0.869 / q_NPA : -0.927
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].
3H3GLN0-0.017-0.0143.817-1.0632.013-0.008-1.627-1.4410.009
4H4LEU00.010-0.0016.209-3.968-3.9680.0000.0000.0000.000
5H5GLN0-0.012-0.0089.880-0.918-0.9180.0000.0000.0000.000
6H6GLN00.0200.03712.764-0.158-0.1580.0000.0000.0000.000
7H7SER0-0.021-0.00816.395-0.307-0.3070.0000.0000.0000.000
8H8GLY00.0260.00019.285-0.053-0.0530.0000.0000.0000.000
9H9PRO0-0.035-0.00622.9990.0510.0510.0000.0000.0000.000
10H10ASP-1-0.844-0.91925.06411.81411.8140.0000.0000.0000.000
11H11LEU0-0.047-0.02026.395-0.298-0.2980.0000.0000.0000.000
12H12VAL0-0.0070.00129.072-0.049-0.0490.0000.0000.0000.000
13H13LYS10.8260.90731.896-8.982-8.9820.0000.0000.0000.000
14H14PRO00.0600.00835.0750.1240.1240.0000.0000.0000.000
15H15SER0-0.088-0.04736.409-0.271-0.2710.0000.0000.0000.000
16H16GLN00.0050.02134.2840.1410.1410.0000.0000.0000.000
17H17SER0-0.005-0.03031.237-0.060-0.0600.0000.0000.0000.000
18H18LEU0-0.0240.01024.830-0.009-0.0090.0000.0000.0000.000
19H19SER0-0.009-0.02225.8920.0350.0350.0000.0000.0000.000
20H20LEU0-0.032-0.00220.8070.0680.0680.0000.0000.0000.000
21H21THR00.0060.00217.908-0.246-0.2460.0000.0000.0000.000
22H22CYS0-0.066-0.00713.7990.3620.3620.0000.0000.0000.000
23H23THR00.0180.00512.416-0.769-0.7690.0000.0000.0000.000
24H24VAL00.0090.0108.7651.5501.5500.0000.0000.0000.000
25H25THR0-0.0060.0016.313-2.872-2.8720.0000.0000.0000.000
26H26GLY00.0360.0093.9963.8903.843-0.001-0.0260.0750.000
27H27TYR0-0.033-0.0544.7172.7932.935-0.001-0.014-0.1280.000
28H28SER00.0090.0257.338-1.409-1.4090.0000.0000.0000.000
29H29ILE00.041-0.01111.0670.6520.6520.0000.0000.0000.000
30H30THR0-0.071-0.03913.312-0.118-0.1180.0000.0000.0000.000
31H31SER0-0.024-0.00411.020-1.412-1.4120.0000.0000.0000.000
32H32GLY00.0220.03911.5190.7480.7480.0000.0000.0000.000
33H33TYR00.0110.00312.182-2.238-2.2380.0000.0000.0000.000
34H34SER0-0.038-0.03814.014-2.381-2.3810.0000.0000.0000.000
35H35TRP0-0.039-0.0098.9902.3792.3790.0000.0000.0000.000
36H35HIS00.032-0.01914.748-2.218-2.2180.0000.0000.0000.000
37H36TRP00.0310.02416.1911.0451.0450.0000.0000.0000.000
38H37ILE0-0.049-0.02315.819-0.886-0.8860.0000.0000.0000.000
39H38ARG10.8330.89619.349-11.618-11.6180.0000.0000.0000.000
40H39GLN0-0.022-0.01219.8260.3140.3140.0000.0000.0000.000
41H40PHE00.0050.01322.409-0.057-0.0570.0000.0000.0000.000
42H41PRO00.0320.01225.6350.2630.2630.0000.0000.0000.000
43H42GLY00.0110.00327.142-0.312-0.3120.0000.0000.0000.000
44H43ASN0-0.060-0.03723.2860.0740.0740.0000.0000.0000.000
45H44LYS10.9370.99023.592-11.310-11.3100.0000.0000.0000.000
46H45LEU00.0480.01718.9860.0590.0590.0000.0000.0000.000
47H46GLU-1-0.862-0.93922.70311.14711.1470.0000.0000.0000.000
48H47TRP0-0.0020.02019.567-0.182-0.1820.0000.0000.0000.000
49H48MET0-0.010-0.00621.597-0.636-0.6360.0000.0000.0000.000
50H49GLY00.0390.00821.495-0.840-0.8400.0000.0000.0000.000
51H50TYR0-0.024-0.00618.3370.5950.5950.0000.0000.0000.000
52H51ILE0-0.029-0.00618.082-0.933-0.9330.0000.0000.0000.000
53H52HIS00.0750.05118.0210.8100.8100.0000.0000.0000.000
54H53TYR00.0630.03217.005-0.421-0.4210.0000.0000.0000.000
55H54SER0-0.059-0.04818.618-0.448-0.4480.0000.0000.0000.000
56H55ALA0-0.066-0.03621.232-0.558-0.5580.0000.0000.0000.000
57H56GLY00.0200.03622.562-0.475-0.4750.0000.0000.0000.000
58H57THR0-0.037-0.03022.7210.6400.6400.0000.0000.0000.000
59H58ASN0-0.011-0.00123.575-0.961-0.9610.0000.0000.0000.000
60H59TYR00.0220.00323.9360.6070.6070.0000.0000.0000.000
61H60ASN00.0300.02025.789-0.751-0.7510.0000.0000.0000.000
62H61PRO00.012-0.01427.365-0.234-0.2340.0000.0000.0000.000
63H62SER0-0.013-0.00430.198-0.383-0.3830.0000.0000.0000.000
64H63LEU0-0.016-0.01326.430-0.161-0.1610.0000.0000.0000.000
65H64LYS10.9420.98030.188-9.963-9.9630.0000.0000.0000.000
66H65SER0-0.025-0.01131.1220.0670.0670.0000.0000.0000.000
67H66ARG10.7970.87931.457-10.270-10.2700.0000.0000.0000.000
68H67ILE00.0080.02424.6300.1720.1720.0000.0000.0000.000
69H68SER0-0.037-0.01826.980-0.119-0.1190.0000.0000.0000.000
70H69ILE00.0300.02120.4640.3220.3220.0000.0000.0000.000
71H70THR0-0.0080.00722.530-0.168-0.1680.0000.0000.0000.000
72H71ARG10.9380.95218.358-15.065-15.0650.0000.0000.0000.000
73H72ASP-1-0.814-0.87818.99613.50313.5030.0000.0000.0000.000
74H73THR00.003-0.03117.4700.8560.8560.0000.0000.0000.000
75H74SER0-0.058-0.00216.6900.4060.4060.0000.0000.0000.000
76H75LYS10.8910.92016.661-13.255-13.2550.0000.0000.0000.000
77H76ASN0-0.019-0.00210.4780.0150.0150.0000.0000.0000.000
78H77GLN00.012-0.00513.7100.5810.5810.0000.0000.0000.000
79H78PHE0-0.011-0.00212.991-0.792-0.7920.0000.0000.0000.000
80H79PHE0-0.020-0.02618.0790.3660.3660.0000.0000.0000.000
81H80LEU00.0020.01420.946-0.158-0.1580.0000.0000.0000.000
82H81GLN00.0280.01522.957-0.243-0.2430.0000.0000.0000.000
83H82LEU0-0.002-0.00126.713-0.035-0.0350.0000.0000.0000.000
84H82ASN00.0190.00928.787-0.059-0.0590.0000.0000.0000.000
85H82SER00.016-0.00232.5300.0330.0330.0000.0000.0000.000
86H82VAL0-0.0230.00730.116-0.023-0.0230.0000.0000.0000.000
87H83THR00.004-0.00233.185-0.403-0.4030.0000.0000.0000.000
88H84THR00.024-0.00933.0240.2290.2290.0000.0000.0000.000
89H85GLU-1-0.871-0.93032.5829.3399.3390.0000.0000.0000.000
90H86ASP-1-0.770-0.83829.12310.72710.7270.0000.0000.0000.000
91H87THR00.0010.02227.8620.4820.4820.0000.0000.0000.000
92H88ALA0-0.027-0.01524.375-0.074-0.0740.0000.0000.0000.000
93H89THR0-0.0050.00619.085-0.216-0.2160.0000.0000.0000.000
94H90TYR0-0.028-0.04320.0580.1560.1560.0000.0000.0000.000
95H91TYR00.015-0.00414.5530.3720.3720.0000.0000.0000.000
96H93ALA00.0310.00311.6111.4901.4900.0000.0000.0000.000
97H94ARG10.8410.9064.601-51.045-50.971-0.001-0.005-0.0670.000
98H95GLU-1-0.885-0.92510.75219.73519.7350.0000.0000.0000.000
99H96GLU-1-0.798-0.8817.77831.31431.3140.0000.0000.0000.000
100H97ALA0-0.046-0.02710.903-1.631-1.6310.0000.0000.0000.000
101H98MET00.000-0.0028.5072.2052.2050.0000.0000.0000.000
102H99PRO00.006-0.00611.405-2.093-2.0930.0000.0000.0000.000
103H100TYR00.008-0.00314.656-0.259-0.2590.0000.0000.0000.000
104H100GLY0-0.005-0.00417.983-0.605-0.6050.0000.0000.0000.000
105H100ASN0-0.022-0.01620.9020.5150.5150.0000.0000.0000.000
106H100GLN0-0.031-0.01819.638-0.545-0.5450.0000.0000.0000.000
107H100ALA00.0230.03119.786-0.414-0.4140.0000.0000.0000.000
108H100TYR00.009-0.00513.3580.4520.4520.0000.0000.0000.000
109H100TYR0-0.036-0.01315.762-1.634-1.6340.0000.0000.0000.000
110H100TYR00.0070.01014.1331.0171.0170.0000.0000.0000.000
111H100ALA00.0240.00813.003-1.339-1.3390.0000.0000.0000.000
112H100MET0-0.017-0.01512.0371.3951.3950.0000.0000.0000.000
113H101ASP-1-0.796-0.8686.58944.79244.7920.0000.0000.0000.000
114H102CYS0-0.0060.0124.5920.6440.765-0.001-0.006-0.1140.000
115H103TRP00.006-0.0107.602-5.262-5.2620.0000.0000.0000.000
116H104GLY00.0320.0159.1662.2872.2870.0000.0000.0000.000
117H105GLN00.002-0.0279.639-2.175-2.1750.0000.0000.0000.000
118H106GLY0-0.017-0.00113.062-0.989-0.9890.0000.0000.0000.000
119H107THR0-0.012-0.01216.316-0.161-0.1610.0000.0000.0000.000
120H108THR0-0.029-0.01319.554-0.116-0.1160.0000.0000.0000.000
121H109VAL0-0.0160.00322.967-0.171-0.1710.0000.0000.0000.000
122H110THR0-0.003-0.00525.856-0.161-0.1610.0000.0000.0000.000
123H111VAL0-0.012-0.00329.424-0.091-0.0910.0000.0000.0000.000
124H112SER00.0730.01632.194-0.245-0.2450.0000.0000.0000.000
125H113SER00.0040.00135.5310.1110.1110.0000.0000.0000.000
126H114ALA00.0070.02637.674-0.230-0.2300.0000.0000.0000.000
127H115LYS10.9690.97838.205-7.358-7.3580.0000.0000.0000.000
128H116THR00.0060.00136.3610.0450.0450.0000.0000.0000.000
129H117THR0-0.046-0.01538.323-0.305-0.3050.0000.0000.0000.000
130H118PRO00.0230.01639.2160.2250.2250.0000.0000.0000.000
131H119PRO00.0050.01138.608-0.114-0.1140.0000.0000.0000.000
132H120SER0-0.029-0.00441.175-0.210-0.2100.0000.0000.0000.000
133H121VAL0-0.012-0.01741.4610.0810.0810.0000.0000.0000.000
134H122TYR0-0.008-0.02044.129-0.163-0.1630.0000.0000.0000.000
135H123PRO00.0070.00945.6270.1440.1440.0000.0000.0000.000
136H124LEU0-0.025-0.00644.318-0.113-0.1130.0000.0000.0000.000
137H125ALA00.0150.00847.6920.0700.0700.0000.0000.0000.000
138H126PRO00.016-0.00149.808-0.044-0.0440.0000.0000.0000.000
139H127GLY00.0300.01651.740-0.092-0.0920.0000.0000.0000.000
140H128SER0-0.007-0.00754.206-0.049-0.0490.0000.0000.0000.000
141H129ALA00.0100.00755.869-0.106-0.1060.0000.0000.0000.000
142H130ALA00.0180.02354.4210.0910.0910.0000.0000.0000.000
143H133GLN0-0.028-0.03552.4850.0700.0700.0000.0000.0000.000
144H134THR0-0.0030.00854.370-0.040-0.0400.0000.0000.0000.000
145H135ASN00.0120.00752.2520.0850.0850.0000.0000.0000.000
146H136SER00.0480.00549.1530.0140.0140.0000.0000.0000.000
147H137MET0-0.0050.02344.068-0.022-0.0220.0000.0000.0000.000
148H138VAL00.0430.03747.767-0.094-0.0940.0000.0000.0000.000
149H139THR0-0.033-0.02443.4280.0990.0990.0000.0000.0000.000
150H140LEU0-0.048-0.02244.727-0.195-0.1950.0000.0000.0000.000
151H141GLY00.0630.00542.9440.1990.1990.0000.0000.0000.000
152H142CYS0-0.0600.00840.688-0.045-0.0450.0000.0000.0000.000
153H143LEU0-0.0030.00441.2820.1840.1840.0000.0000.0000.000
154H144VAL0-0.0040.00437.964-0.167-0.1670.0000.0000.0000.000
155H145LYS10.9470.94839.918-6.949-6.9490.0000.0000.0000.000
156H146GLY00.0280.01541.323-0.102-0.1020.0000.0000.0000.000
157H147TYR0-0.016-0.01633.773-0.222-0.2220.0000.0000.0000.000
158H148PHE00.0320.03734.2640.1510.1510.0000.0000.0000.000
159H149PRO00.011-0.00731.823-0.250-0.2500.0000.0000.0000.000
160H150GLU-1-0.769-0.87029.8679.9269.9260.0000.0000.0000.000
161H151PRO00.001-0.00527.6920.0970.0970.0000.0000.0000.000
162H152VAL0-0.002-0.02130.789-0.221-0.2210.0000.0000.0000.000
163H153THR0-0.042-0.01330.9370.3590.3590.0000.0000.0000.000
164H154VAL0-0.009-0.01832.620-0.310-0.3100.0000.0000.0000.000
165H156THR0-0.017-0.01133.6060.2560.2560.0000.0000.0000.000
166H157TRP00.0180.00436.150-0.374-0.3740.0000.0000.0000.000
167H162ASN00.018-0.00438.8830.0590.0590.0000.0000.0000.000
168H163SER0-0.020-0.02138.015-0.041-0.0410.0000.0000.0000.000
169H164GLY00.0060.01035.2720.1750.1750.0000.0000.0000.000
170H165SER0-0.048-0.02435.8590.1060.1060.0000.0000.0000.000
171H166LEU0-0.051-0.01438.500-0.035-0.0350.0000.0000.0000.000
172H167SER00.0320.01133.7300.0660.0660.0000.0000.0000.000
173H168SER0-0.004-0.00435.0530.1850.1850.0000.0000.0000.000
174H169GLY00.015-0.00136.843-0.188-0.1880.0000.0000.0000.000
175H171VAL0-0.024-0.00835.190-0.218-0.2180.0000.0000.0000.000
176H172HIS00.0020.01434.6870.3820.3820.0000.0000.0000.000
177H173THR00.0180.01132.817-0.386-0.3860.0000.0000.0000.000
178H174PHE0-0.038-0.01132.9110.2590.2590.0000.0000.0000.000
179H175PRO00.0340.00230.5310.0160.0160.0000.0000.0000.000
180H176ALA0-0.0050.01632.250-0.311-0.3110.0000.0000.0000.000
181H177VAL0-0.018-0.00433.4670.1930.1930.0000.0000.0000.000
182H178LEU0-0.001-0.00334.344-0.138-0.1380.0000.0000.0000.000
183H179GLN00.006-0.00737.533-0.184-0.1840.0000.0000.0000.000
184H180SER0-0.031-0.03041.281-0.126-0.1260.0000.0000.0000.000
185H183ASP-1-0.894-0.95238.9877.9867.9860.0000.0000.0000.000
186H184LEU0-0.0510.00538.7880.1330.1330.0000.0000.0000.000
187H185TYR00.0090.00331.503-0.032-0.0320.0000.0000.0000.000
188H186THR0-0.033-0.02337.421-0.232-0.2320.0000.0000.0000.000
189H187LEU00.0400.04133.5180.1270.1270.0000.0000.0000.000
190H188SER00.000-0.01137.401-0.272-0.2720.0000.0000.0000.000
191H189SER00.0110.00036.4820.1880.1880.0000.0000.0000.000
192H190SER0-0.004-0.01238.419-0.285-0.2850.0000.0000.0000.000
193H191VAL00.0320.01738.9240.2210.2210.0000.0000.0000.000
194H192THR0-0.0010.00541.109-0.241-0.2410.0000.0000.0000.000
195H193VAL00.0080.01142.5840.1350.1350.0000.0000.0000.000
196H194PRO00.0310.00445.213-0.098-0.0980.0000.0000.0000.000
197H195SER0-0.007-0.02148.196-0.048-0.0480.0000.0000.0000.000
198H196SER0-0.008-0.00851.383-0.061-0.0610.0000.0000.0000.000
199H198PRO00.0330.03047.733-0.058-0.0580.0000.0000.0000.000
200H199ARG10.9431.03249.074-6.266-6.2660.0000.0000.0000.000
201H200PRO0-0.061-0.05751.149-0.013-0.0130.0000.0000.0000.000
202H202SER0-0.005-0.01353.517-0.062-0.0620.0000.0000.0000.000
203H203GLU-1-0.906-0.95049.1886.3836.3830.0000.0000.0000.000
204H204THR0-0.072-0.04147.984-0.025-0.0250.0000.0000.0000.000
205H205VAL00.0320.01744.0090.1180.1180.0000.0000.0000.000
206H206THR0-0.002-0.01743.235-0.181-0.1810.0000.0000.0000.000
207H209ASN00.019-0.00138.009-0.051-0.0510.0000.0000.0000.000
208H210VAL00.008-0.00437.3000.2180.2180.0000.0000.0000.000
209H211ALA0-0.006-0.00134.233-0.188-0.1880.0000.0000.0000.000
210H212HIS00.0380.03134.4270.0110.0110.0000.0000.0000.000
211H213PRO00.013-0.00830.536-0.215-0.2150.0000.0000.0000.000
212H214ALA00.0140.02232.818-0.119-0.1190.0000.0000.0000.000
213H215SER0-0.019-0.03333.914-0.184-0.1840.0000.0000.0000.000
214H216SER0-0.031-0.00936.101-0.177-0.1770.0000.0000.0000.000
215H217THR0-0.019-0.00137.262-0.270-0.2700.0000.0000.0000.000
216H218LYS10.9690.97335.891-8.232-8.2320.0000.0000.0000.000
217H219VAL0-0.023-0.00839.729-0.237-0.2370.0000.0000.0000.000
218H220ASP-1-0.810-0.89241.4107.7627.7620.0000.0000.0000.000
219H221LYS10.8740.94543.642-6.907-6.9070.0000.0000.0000.000
220H222LYS10.9941.00545.617-6.023-6.0230.0000.0000.0000.000
221H223ILE0-0.023-0.01545.276-0.118-0.1180.0000.0000.0000.000
222H226VAL0-0.025-0.01649.001-0.037-0.0370.0000.0000.0000.000
223H227PRO0-0.045-0.03452.7570.0560.0560.0000.0000.0000.000
224H228ARG10.9140.93953.674-5.816-5.8160.0000.0000.0000.000
225H229ASP-1-0.916-0.93756.6255.1555.1550.0000.0000.0000.000
226H230CYS0-0.025-0.00660.1490.0120.0120.0000.0000.0000.000