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: MVLKZ

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357323.729988
FMO2-HF: Nuclear repulsion 2268939.48188
FMO2-HF: Total energy -88384.248108
FMO2-MP2: Total energy -88638.329044


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.
-6.487-3.3440.105-1.415-1.8340.006
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 : -0.921 / q_NPA : -0.971
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].
3H3GLN00.000-0.0043.4423.5256.3190.106-1.335-1.5660.006
4H4LEU00.001-0.0086.087-4.289-4.2890.0000.0000.0000.000
5H5GLN0-0.014-0.0099.300-0.271-0.2710.0000.0000.0000.000
6H6GLN00.0130.02412.491-0.287-0.2870.0000.0000.0000.000
7H7SER0-0.034-0.01015.863-0.366-0.3660.0000.0000.0000.000
8H8GLY00.0400.00219.069-0.057-0.0570.0000.0000.0000.000
9H9PRO0-0.039-0.00722.6910.0510.0510.0000.0000.0000.000
10H10ASP-1-0.841-0.91824.62011.91511.9150.0000.0000.0000.000
11H11LEU0-0.041-0.01725.911-0.293-0.2930.0000.0000.0000.000
12H12VAL00.0050.00828.508-0.053-0.0530.0000.0000.0000.000
13H13LYS10.8730.95031.267-8.998-8.9980.0000.0000.0000.000
14H14PRO00.0580.00734.4390.1330.1330.0000.0000.0000.000
15H15SER0-0.087-0.04635.776-0.272-0.2720.0000.0000.0000.000
16H16GLN00.0080.01633.7020.1680.1680.0000.0000.0000.000
17H17SER00.016-0.01630.574-0.060-0.0600.0000.0000.0000.000
18H18LEU0-0.0200.01624.115-0.013-0.0130.0000.0000.0000.000
19H19SER0-0.032-0.03425.280-0.033-0.0330.0000.0000.0000.000
20H20LEU0-0.0130.00620.1120.0420.0420.0000.0000.0000.000
21H21THR00.0130.00417.452-0.274-0.2740.0000.0000.0000.000
22H22CYS0-0.068-0.00513.2930.3010.3010.0000.0000.0000.000
23H23THR00.023-0.00111.942-0.766-0.7660.0000.0000.0000.000
24H24VAL00.0130.0168.6761.6091.6090.0000.0000.0000.000
25H25THR0-0.0030.0015.930-2.905-2.9050.0000.0000.0000.000
26H26GLY00.0330.0073.8533.6993.653-0.001-0.0280.0750.000
27H27TYR0-0.023-0.0484.8462.8813.017-0.001-0.011-0.1240.000
28H28SER00.0140.0187.359-1.385-1.3850.0000.0000.0000.000
29H29ILE00.038-0.00411.1400.5950.5950.0000.0000.0000.000
30H30THR0-0.094-0.05313.318-0.161-0.1610.0000.0000.0000.000
31H31SER0-0.0060.01011.083-1.297-1.2970.0000.0000.0000.000
32H32GLY00.0140.03711.9940.7580.7580.0000.0000.0000.000
33H33TYR00.0210.01012.691-2.253-2.2530.0000.0000.0000.000
34H34SER0-0.032-0.04014.457-2.333-2.3330.0000.0000.0000.000
35H35TRP0-0.043-0.0079.6222.4052.4050.0000.0000.0000.000
36H35HIS00.0550.00514.703-2.251-2.2510.0000.0000.0000.000
37H36TRP00.0130.02115.7831.1061.1060.0000.0000.0000.000
38H37ILE0-0.040-0.01915.384-0.876-0.8760.0000.0000.0000.000
39H38ARG10.8190.89218.800-11.671-11.6710.0000.0000.0000.000
40H39GLN0-0.038-0.02719.7220.2550.2550.0000.0000.0000.000
41H40PHE00.0160.01421.956-0.063-0.0630.0000.0000.0000.000
42H41PRO00.0280.01325.2390.2690.2690.0000.0000.0000.000
43H42GLY00.0170.00526.795-0.314-0.3140.0000.0000.0000.000
44H43ASN0-0.030-0.02523.2590.0970.0970.0000.0000.0000.000
45H44LYS10.9661.00423.274-11.392-11.3920.0000.0000.0000.000
46H45LEU00.0480.01818.6030.0600.0600.0000.0000.0000.000
47H46GLU-1-0.898-0.95322.31111.29511.2950.0000.0000.0000.000
48H47TRP0-0.035-0.00118.994-0.222-0.2220.0000.0000.0000.000
49H48MET00.001-0.01221.068-0.611-0.6110.0000.0000.0000.000
50H49GLY00.0340.00421.153-0.846-0.8460.0000.0000.0000.000
51H50TYR0-0.025-0.00918.5480.5570.5570.0000.0000.0000.000
52H51ILE0-0.029-0.00118.529-0.971-0.9710.0000.0000.0000.000
53H52HIS00.0910.07318.5670.8750.8750.0000.0000.0000.000
54H53TYR00.0380.02417.473-0.433-0.4330.0000.0000.0000.000
55H54SER0-0.098-0.09119.148-0.477-0.4770.0000.0000.0000.000
56H55ALA0-0.071-0.03821.755-0.576-0.5760.0000.0000.0000.000
57H56GLY00.0200.03423.028-0.476-0.4760.0000.0000.0000.000
58H57THR0-0.034-0.02323.2620.6190.6190.0000.0000.0000.000
59H58ASN00.0070.00723.864-0.956-0.9560.0000.0000.0000.000
60H59TYR00.0260.00024.0330.6040.6040.0000.0000.0000.000
61H60ASN00.0440.03125.479-0.753-0.7530.0000.0000.0000.000
62H61PRO00.003-0.01527.093-0.234-0.2340.0000.0000.0000.000
63H62SER0-0.0020.00229.664-0.413-0.4130.0000.0000.0000.000
64H63LEU0-0.029-0.02026.078-0.169-0.1690.0000.0000.0000.000
65H64LYS10.9440.98329.809-9.879-9.8790.0000.0000.0000.000
66H65SER0-0.033-0.01730.9120.0590.0590.0000.0000.0000.000
67H66ARG10.8090.89330.732-10.315-10.3150.0000.0000.0000.000
68H67ILE00.0120.02324.1310.1630.1630.0000.0000.0000.000
69H68SER0-0.050-0.02226.715-0.100-0.1000.0000.0000.0000.000
70H69ILE00.0330.02520.5520.3070.3070.0000.0000.0000.000
71H70THR0-0.0040.00722.586-0.163-0.1630.0000.0000.0000.000
72H71ARG11.0100.98918.583-15.008-15.0080.0000.0000.0000.000
73H72ASP-1-0.823-0.90418.83913.45613.4560.0000.0000.0000.000
74H73THR00.003-0.03017.4130.8720.8720.0000.0000.0000.000
75H74SER0-0.061-0.00316.6590.3980.3980.0000.0000.0000.000
76H75LYS10.9060.93816.555-13.196-13.1960.0000.0000.0000.000
77H76ASN0-0.0120.00110.431-0.130-0.1300.0000.0000.0000.000
78H77GLN0-0.006-0.01313.4770.6280.6280.0000.0000.0000.000
79H78PHE0-0.0090.00213.237-0.701-0.7010.0000.0000.0000.000
80H79PHE0-0.011-0.02018.1640.3620.3620.0000.0000.0000.000
81H80LEU00.0100.01520.746-0.154-0.1540.0000.0000.0000.000
82H81GLN00.0050.00422.551-0.361-0.3610.0000.0000.0000.000
83H82LEU0-0.0130.00026.280-0.045-0.0450.0000.0000.0000.000
84H82ASN00.0350.01228.186-0.055-0.0550.0000.0000.0000.000
85H82SER0-0.001-0.00731.9320.0290.0290.0000.0000.0000.000
86H82VAL0-0.0110.01429.577-0.031-0.0310.0000.0000.0000.000
87H83THR00.0220.00732.583-0.408-0.4080.0000.0000.0000.000
88H84THR00.0430.00032.4410.2130.2130.0000.0000.0000.000
89H85GLU-1-0.927-0.96032.0409.4529.4520.0000.0000.0000.000
90H86ASP-1-0.778-0.85928.51910.76910.7690.0000.0000.0000.000
91H87THR0-0.0120.01227.2910.4690.4690.0000.0000.0000.000
92H88ALA0-0.016-0.01723.852-0.075-0.0750.0000.0000.0000.000
93H89THR0-0.0190.00818.6190.0030.0030.0000.0000.0000.000
94H90TYR0-0.025-0.03719.4810.1400.1400.0000.0000.0000.000
95H91TYR00.0290.01113.9650.4730.4730.0000.0000.0000.000
96H93ALA00.020-0.00211.0381.5701.5700.0000.0000.0000.000
97H94ARG10.8580.9294.636-50.978-50.917-0.001-0.006-0.0540.000
98H95GLU-1-0.908-0.93810.90319.88719.8870.0000.0000.0000.000
99H96GLU-1-0.804-0.8918.12331.18731.1870.0000.0000.0000.000
100H97ALA0-0.044-0.02411.143-1.576-1.5760.0000.0000.0000.000
101H98MET0-0.006-0.0028.9032.3282.3280.0000.0000.0000.000
102H99PRO0-0.006-0.01211.163-2.195-2.1950.0000.0000.0000.000
103H100TYR00.0170.00114.407-0.239-0.2390.0000.0000.0000.000
104H100GLY0-0.009-0.00717.730-0.597-0.5970.0000.0000.0000.000
105H100ASN0-0.024-0.01420.5580.5900.5900.0000.0000.0000.000
106H100GLN0-0.015-0.01219.394-0.772-0.7720.0000.0000.0000.000
107H100ALA00.0140.02919.563-0.422-0.4220.0000.0000.0000.000
108H100TYR00.007-0.00813.5930.5380.5380.0000.0000.0000.000
109H100TYR0-0.038-0.01415.691-1.677-1.6770.0000.0000.0000.000
110H100TYR0-0.0080.00614.2941.6191.6190.0000.0000.0000.000
111H100ALA00.0340.01013.009-1.310-1.3100.0000.0000.0000.000
112H100MET0-0.023-0.01812.1921.3251.3250.0000.0000.0000.000
113H101ASP-1-0.798-0.8846.99842.62242.6220.0000.0000.0000.000
114H102CYS0-0.0130.0114.0591.8842.0820.002-0.035-0.1650.000
115H103TRP00.008-0.0027.160-5.414-5.4140.0000.0000.0000.000
116H104GLY00.0220.0098.6302.4462.4460.0000.0000.0000.000
117H105GLN00.014-0.0189.221-2.803-2.8030.0000.0000.0000.000
118H106GLY0-0.0090.00712.558-1.012-1.0120.0000.0000.0000.000
119H107THR0-0.022-0.01415.774-0.168-0.1680.0000.0000.0000.000
120H108THR0-0.013-0.00918.984-0.301-0.3010.0000.0000.0000.000
121H109VAL0-0.0040.01122.426-0.162-0.1620.0000.0000.0000.000
122H110THR0-0.005-0.00725.276-0.158-0.1580.0000.0000.0000.000
123H111VAL0-0.011-0.00128.860-0.096-0.0960.0000.0000.0000.000
124H112SER00.0620.00731.606-0.258-0.2580.0000.0000.0000.000
125H113SER0-0.011-0.02334.9510.1300.1300.0000.0000.0000.000
126H114ALA0-0.0060.02337.165-0.232-0.2320.0000.0000.0000.000
127H115LYS10.9430.96137.665-7.434-7.4340.0000.0000.0000.000
128H116THR00.0070.00436.2740.0580.0580.0000.0000.0000.000
129H117THR0-0.046-0.01838.055-0.300-0.3000.0000.0000.0000.000
130H118PRO00.0220.01238.9180.2170.2170.0000.0000.0000.000
131H119PRO00.0010.00638.438-0.118-0.1180.0000.0000.0000.000
132H120SER0-0.0150.00640.869-0.213-0.2130.0000.0000.0000.000
133H121VAL0-0.010-0.01641.2610.0820.0820.0000.0000.0000.000
134H122TYR0-0.022-0.02443.844-0.168-0.1680.0000.0000.0000.000
135H123PRO00.0180.00545.3310.1460.1460.0000.0000.0000.000
136H124LEU0-0.032-0.00144.113-0.116-0.1160.0000.0000.0000.000
137H125ALA00.0220.01147.4790.0680.0680.0000.0000.0000.000
138H126PRO0-0.001-0.00649.994-0.038-0.0380.0000.0000.0000.000
139H127GLY00.0270.01251.563-0.091-0.0910.0000.0000.0000.000
140H128SER0-0.008-0.02054.010-0.047-0.0470.0000.0000.0000.000
141H129ALA00.0080.00955.707-0.105-0.1050.0000.0000.0000.000
142H130ALA00.0180.02554.3190.0930.0930.0000.0000.0000.000
143H133GLN0-0.032-0.04252.6220.0760.0760.0000.0000.0000.000
144H134THR0-0.0240.00554.259-0.014-0.0140.0000.0000.0000.000
145H135ASN00.0810.03152.4240.0780.0780.0000.0000.0000.000
146H136SER00.034-0.00549.0100.0330.0330.0000.0000.0000.000
147H137MET0-0.0190.02643.994-0.029-0.0290.0000.0000.0000.000
148H138VAL00.0470.04347.705-0.097-0.0970.0000.0000.0000.000
149H139THR0-0.034-0.02543.4440.1110.1110.0000.0000.0000.000
150H140LEU0-0.056-0.02744.584-0.195-0.1950.0000.0000.0000.000
151H141GLY00.0660.00342.7370.1980.1980.0000.0000.0000.000
152H142CYS0-0.082-0.00540.452-0.037-0.0370.0000.0000.0000.000
153H143LEU0-0.0050.00341.0040.1810.1810.0000.0000.0000.000
154H144VAL00.0010.00637.622-0.164-0.1640.0000.0000.0000.000
155H145LYS10.9550.95739.544-6.914-6.9140.0000.0000.0000.000
156H146GLY00.0180.01240.884-0.105-0.1050.0000.0000.0000.000
157H147TYR00.0090.01533.142-0.194-0.1940.0000.0000.0000.000
158H148PHE00.0170.03233.6370.1500.1500.0000.0000.0000.000
159H149PRO00.017-0.00831.417-0.247-0.2470.0000.0000.0000.000
160H150GLU-1-0.810-0.90529.51410.11310.1130.0000.0000.0000.000
161H151PRO00.012-0.00127.4690.0740.0740.0000.0000.0000.000
162H152VAL0-0.007-0.02030.438-0.227-0.2270.0000.0000.0000.000
163H153THR0-0.030-0.00930.7110.3610.3610.0000.0000.0000.000
164H154VAL0-0.010-0.01632.536-0.311-0.3110.0000.0000.0000.000
165H156THR0-0.0040.00133.6480.2470.2470.0000.0000.0000.000
166H157TRP00.015-0.00236.082-0.379-0.3790.0000.0000.0000.000
167H162ASN00.0300.00638.8250.0550.0550.0000.0000.0000.000
168H163SER0-0.026-0.02637.9610.0190.0190.0000.0000.0000.000
169H164GLY0-0.0040.00535.2150.1700.1700.0000.0000.0000.000
170H165SER0-0.046-0.02135.8110.1060.1060.0000.0000.0000.000
171H166LEU0-0.040-0.00938.452-0.036-0.0360.0000.0000.0000.000
172H167SER00.0290.00833.6750.0730.0730.0000.0000.0000.000
173H168SER0-0.007-0.00534.9960.1880.1880.0000.0000.0000.000
174H169GLY00.0160.00136.824-0.189-0.1890.0000.0000.0000.000
175H171VAL0-0.021-0.00834.868-0.221-0.2210.0000.0000.0000.000
176H172HIS00.0050.01734.5530.4020.4020.0000.0000.0000.000
177H173THR00.006-0.00332.534-0.383-0.3830.0000.0000.0000.000
178H174PHE0-0.047-0.01932.6970.2580.2580.0000.0000.0000.000
179H175PRO00.019-0.00230.169-0.002-0.0020.0000.0000.0000.000
180H176ALA00.0050.02231.892-0.315-0.3150.0000.0000.0000.000
181H177VAL0-0.0090.00333.0950.1980.1980.0000.0000.0000.000
182H178LEU0-0.004-0.01034.219-0.133-0.1330.0000.0000.0000.000
183H179GLN00.0110.01037.093-0.122-0.1220.0000.0000.0000.000
184H180SER0-0.038-0.03440.841-0.132-0.1320.0000.0000.0000.000
185H183ASP-1-0.907-0.95738.4997.8967.8960.0000.0000.0000.000
186H184LEU0-0.0500.00338.2930.1340.1340.0000.0000.0000.000
187H185TYR00.0110.00531.413-0.009-0.0090.0000.0000.0000.000
188H186THR0-0.033-0.04036.983-0.214-0.2140.0000.0000.0000.000
189H187LEU00.0400.03933.1990.1240.1240.0000.0000.0000.000
190H188SER0-0.008-0.01537.093-0.283-0.2830.0000.0000.0000.000
191H189SER00.0160.01236.3430.1990.1990.0000.0000.0000.000
192H190SER00.019-0.00138.245-0.213-0.2130.0000.0000.0000.000
193H191VAL00.0400.02338.7720.2180.2180.0000.0000.0000.000
194H192THR00.0010.00540.980-0.266-0.2660.0000.0000.0000.000
195H193VAL0-0.0120.00242.5310.1390.1390.0000.0000.0000.000
196H194PRO00.0260.00045.155-0.102-0.1020.0000.0000.0000.000
197H195SER0-0.013-0.03048.177-0.048-0.0480.0000.0000.0000.000
198H196SER0-0.017-0.00851.334-0.057-0.0570.0000.0000.0000.000
199H198PRO00.0320.02647.669-0.056-0.0560.0000.0000.0000.000
200H199ARG10.9741.04348.984-6.245-6.2450.0000.0000.0000.000
201H200PRO0-0.090-0.07451.050-0.018-0.0180.0000.0000.0000.000
202H202SER00.0110.00353.423-0.056-0.0560.0000.0000.0000.000
203H203GLU-1-0.896-0.94249.1136.3126.3120.0000.0000.0000.000
204H204THR0-0.090-0.05248.7800.0340.0340.0000.0000.0000.000
205H205VAL00.0510.02743.9620.1130.1130.0000.0000.0000.000
206H206THR0-0.022-0.02543.209-0.181-0.1810.0000.0000.0000.000
207H209ASN00.009-0.01037.979-0.080-0.0800.0000.0000.0000.000
208H210VAL00.0170.00437.2240.2190.2190.0000.0000.0000.000
209H211ALA0-0.005-0.00234.097-0.190-0.1900.0000.0000.0000.000
210H212HIS00.0400.04334.2140.0230.0230.0000.0000.0000.000
211H213PRO00.009-0.01030.492-0.218-0.2180.0000.0000.0000.000
212H214ALA00.0170.02332.796-0.114-0.1140.0000.0000.0000.000
213H215SER0-0.020-0.04633.804-0.186-0.1860.0000.0000.0000.000
214H216SER0-0.034-0.00835.990-0.180-0.1800.0000.0000.0000.000
215H217THR0-0.027-0.00437.157-0.270-0.2700.0000.0000.0000.000
216H218LYS10.9780.97536.041-8.177-8.1770.0000.0000.0000.000
217H219VAL0-0.023-0.00439.636-0.234-0.2340.0000.0000.0000.000
218H220ASP-1-0.807-0.89341.3267.7357.7350.0000.0000.0000.000
219H221LYS10.8810.94943.561-6.859-6.8590.0000.0000.0000.000
220H222LYS10.9830.99745.543-5.994-5.9940.0000.0000.0000.000
221H223ILE0-0.007-0.00745.248-0.111-0.1110.0000.0000.0000.000
222H226VAL0-0.026-0.01748.851-0.038-0.0380.0000.0000.0000.000
223H227PRO0-0.045-0.04052.6200.0520.0520.0000.0000.0000.000
224H228ARG10.9190.95253.650-5.807-5.8070.0000.0000.0000.000
225H229ASP-1-0.916-0.93456.3985.1465.1460.0000.0000.0000.000
226H230CYS0-0.016-0.00459.9120.0190.0190.0000.0000.0000.000