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: M9MMZ

Calculation Name: 1ADQ-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ADQ

Chain ID: H

ChEMBL ID:

UniProt ID: P01861

Base Structure: X-ray

Registration Date: 2023-09-26

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2312290.348625
FMO2-HF: Nuclear repulsion 2225422.676741
FMO2-HF: Total energy -86867.671884
FMO2-MP2: Total energy -87119.96084


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:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-50.324-48.1110.001-0.747-1.4650.003
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.976 / q_NPA : -0.995
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].
3H3GLN0-0.015-0.0013.386-5.655-3.6430.004-0.647-1.3690.003
4H4LEU0-0.026-0.0244.812-2.824-2.778-0.001-0.004-0.0400.000
5H5VAL00.0470.0338.312-0.185-0.1850.0000.0000.0000.000
6H6GLU-1-0.820-0.92810.70220.38220.3820.0000.0000.0000.000
7H7SER00.009-0.00514.4250.0780.0780.0000.0000.0000.000
8H8GLY0-0.037-0.03317.444-0.489-0.4890.0000.0000.0000.000
9H9GLY0-0.005-0.00320.934-0.151-0.1510.0000.0000.0000.000
10H10GLY00.0470.01822.8330.4560.4560.0000.0000.0000.000
11H11LEU0-0.028-0.00525.351-0.186-0.1860.0000.0000.0000.000
12H12VAL0-0.050-0.03028.769-0.099-0.0990.0000.0000.0000.000
13H13GLN00.0360.03231.355-0.223-0.2230.0000.0000.0000.000
14H14PRO00.000-0.02534.4640.1230.1230.0000.0000.0000.000
15H15GLY0-0.0150.01035.318-0.171-0.1710.0000.0000.0000.000
16H16ARG10.8930.96330.633-9.982-9.9820.0000.0000.0000.000
17H17SER00.0350.00130.341-0.071-0.0710.0000.0000.0000.000
18H18LEU0-0.026-0.01125.3220.0830.0830.0000.0000.0000.000
19H19ARG10.9661.00222.110-13.700-13.7000.0000.0000.0000.000
20H20LEU00.0140.02719.5860.3180.3180.0000.0000.0000.000
21H21SER0-0.051-0.04417.618-0.537-0.5370.0000.0000.0000.000
22H22CYS0-0.0350.01412.884-0.093-0.0930.0000.0000.0000.000
23H23VAL00.0230.03711.445-0.846-0.8460.0000.0000.0000.000
24H24THR0-0.026-0.0228.8971.6681.6680.0000.0000.0000.000
25H25SER00.012-0.0045.4522.5242.5240.0000.0000.0000.000
26H26GLY00.0830.0254.3651.8121.923-0.001-0.079-0.0310.000
27H27PHE0-0.051-0.0294.675-1.929-1.885-0.001-0.017-0.0250.000
28H28THR00.0460.0287.4360.4030.4030.0000.0000.0000.000
29H29PHE00.0350.01311.140-1.021-1.0210.0000.0000.0000.000
30H30ASP-1-0.900-0.96913.18816.04516.0450.0000.0000.0000.000
31H31ASP-1-0.872-0.93913.59316.08316.0830.0000.0000.0000.000
32H32TYR0-0.064-0.03211.053-0.364-0.3640.0000.0000.0000.000
33H33ALA0-0.0020.02115.2700.0340.0340.0000.0000.0000.000
34H34MET0-0.0050.02911.7990.7010.7010.0000.0000.0000.000
35H35HIS00.0000.00116.371-1.305-1.3050.0000.0000.0000.000
36H36TRP0-0.0120.00016.9371.0821.0820.0000.0000.0000.000
37H37VAL0-0.001-0.00118.660-0.842-0.8420.0000.0000.0000.000
38H38ARG10.9160.98419.440-10.695-10.6950.0000.0000.0000.000
39H39GLN00.023-0.00520.489-0.683-0.6830.0000.0000.0000.000
40H40SER00.0080.01323.0920.1640.1640.0000.0000.0000.000
41H41PRO00.004-0.00325.5720.0640.0640.0000.0000.0000.000
42H42GLY00.0380.02925.971-0.456-0.4560.0000.0000.0000.000
43H43LYS10.8610.91727.210-10.555-10.5550.0000.0000.0000.000
44H44GLY00.0320.02725.164-0.147-0.1470.0000.0000.0000.000
45H45LEU00.0190.00719.4620.0600.0600.0000.0000.0000.000
46H46GLU-1-0.923-0.95923.41810.52310.5230.0000.0000.0000.000
47H47TRP0-0.003-0.01121.3130.2400.2400.0000.0000.0000.000
48H48VAL0-0.0080.00222.701-0.506-0.5060.0000.0000.0000.000
49H49SER0-0.044-0.05222.630-0.670-0.6700.0000.0000.0000.000
50H50GLY00.0440.02521.0920.6320.6320.0000.0000.0000.000
51H51ILE0-0.054-0.00920.317-0.647-0.6470.0000.0000.0000.000
52H52SER00.0220.00020.4810.8750.8750.0000.0000.0000.000
53H52TRP00.0960.04118.7530.1300.1300.0000.0000.0000.000
54H53ASN00.0410.03019.9490.3790.3790.0000.0000.0000.000
55H54THR0-0.036-0.04322.688-0.204-0.2040.0000.0000.0000.000
56H55GLY0-0.0130.00424.367-0.313-0.3130.0000.0000.0000.000
57H56THR0-0.013-0.00225.705-0.334-0.3340.0000.0000.0000.000
58H57ILE00.0170.01425.1930.5550.5550.0000.0000.0000.000
59H58ILE0-0.021-0.00424.261-0.469-0.4690.0000.0000.0000.000
60H59TYR0-0.010-0.01325.9130.4560.4560.0000.0000.0000.000
61H60ALA00.1010.06127.350-0.278-0.2780.0000.0000.0000.000
62H61ASP-1-0.818-0.92829.0188.9958.9950.0000.0000.0000.000
63H62SER0-0.052-0.02030.830-0.093-0.0930.0000.0000.0000.000
64H63VAL0-0.034-0.02827.3880.1280.1280.0000.0000.0000.000
65H64LYS10.9180.96530.633-9.505-9.5050.0000.0000.0000.000
66H65GLY0-0.0030.01332.409-0.247-0.2470.0000.0000.0000.000
67H66ARG10.7030.84631.432-9.866-9.8660.0000.0000.0000.000
68H67PHE0-0.003-0.01725.8350.1530.1530.0000.0000.0000.000
69H68ILE00.0160.00627.284-0.196-0.1960.0000.0000.0000.000
70H69ILE0-0.0170.00820.3850.3510.3510.0000.0000.0000.000
71H70SER0-0.061-0.03122.307-0.528-0.5280.0000.0000.0000.000
72H71ARG10.8680.94416.893-15.193-15.1930.0000.0000.0000.000
73H72ASP-1-0.879-0.94718.52413.78013.7800.0000.0000.0000.000
74H73ASN00.021-0.00617.3630.9850.9850.0000.0000.0000.000
75H74ALA00.0150.02116.9850.8060.8060.0000.0000.0000.000
76H75LYS10.9050.95716.924-13.769-13.7690.0000.0000.0000.000
77H76ASN0-0.0050.01712.1471.5911.5910.0000.0000.0000.000
78H77SER0-0.008-0.00713.2591.4171.4170.0000.0000.0000.000
79H78LEU0-0.0110.00515.581-1.026-1.0260.0000.0000.0000.000
80H79TYR0-0.034-0.04417.1730.4130.4130.0000.0000.0000.000
81H80LEU00.0340.00820.144-0.224-0.2240.0000.0000.0000.000
82H81GLN0-0.005-0.00822.6550.0160.0160.0000.0000.0000.000
83H82MET0-0.0330.00024.849-0.171-0.1710.0000.0000.0000.000
84H82ASN00.0790.02927.635-0.067-0.0670.0000.0000.0000.000
85H82SER0-0.023-0.01031.361-0.124-0.1240.0000.0000.0000.000
86H82LEU00.0150.01528.339-0.015-0.0150.0000.0000.0000.000
87H83ARG10.9880.98331.971-9.213-9.2130.0000.0000.0000.000
88H84VAL00.0380.01532.1060.2620.2620.0000.0000.0000.000
89H85GLU-1-0.925-0.97432.1558.9648.9640.0000.0000.0000.000
90H86ASP-1-0.834-0.88428.50810.43010.4300.0000.0000.0000.000
91H87THR0-0.032-0.01427.4090.4920.4920.0000.0000.0000.000
92H88ALA00.005-0.01024.495-0.165-0.1650.0000.0000.0000.000
93H89LEU0-0.0120.00718.278-0.050-0.0500.0000.0000.0000.000
94H90TYR0-0.051-0.05419.884-0.228-0.2280.0000.0000.0000.000
95H91TYR00.0180.01914.9790.0760.0760.0000.0000.0000.000
96H93ALA00.034-0.00213.1500.9720.9720.0000.0000.0000.000
97H94LYS10.8290.9348.833-24.359-24.3590.0000.0000.0000.000
98H95THR0-0.042-0.03312.7430.0920.0920.0000.0000.0000.000
99H96ARG10.9350.94111.022-18.364-18.3640.0000.0000.0000.000
100H97SER0-0.0020.00414.745-0.468-0.4680.0000.0000.0000.000
101H98TYR00.0300.00613.2220.1900.1900.0000.0000.0000.000
102H99VAL0-0.0060.00619.666-0.362-0.3620.0000.0000.0000.000
103H100VAL00.0150.00323.2040.2180.2180.0000.0000.0000.000
104H100ALA00.0040.00325.5180.1000.1000.0000.0000.0000.000
105H100ALA0-0.012-0.00621.717-0.120-0.1200.0000.0000.0000.000
106H100GLU-1-0.920-0.95023.47210.92910.9290.0000.0000.0000.000
107H100TYR0-0.055-0.04519.2130.3210.3210.0000.0000.0000.000
108H100TYR00.0710.04414.5060.2430.2430.0000.0000.0000.000
109H100PHE0-0.024-0.02814.9930.6290.6290.0000.0000.0000.000
110H101HIS00.0240.0239.001-0.267-0.2670.0000.0000.0000.000
111H102TYR00.0280.0084.8440.7650.7650.0000.0000.0000.000
112H103TRP00.0290.0039.778-2.035-2.0350.0000.0000.0000.000
113H104GLY00.0250.0289.9392.3272.3270.0000.0000.0000.000
114H105GLN00.002-0.00611.2070.4590.4590.0000.0000.0000.000
115H106GLY0-0.001-0.00312.781-1.422-1.4220.0000.0000.0000.000
116H107ILE0-0.036-0.00315.942-0.267-0.2670.0000.0000.0000.000
117H108LEU00.000-0.00418.375-0.528-0.5280.0000.0000.0000.000
118H109VAL0-0.0220.00822.051-0.137-0.1370.0000.0000.0000.000
119H110THR0-0.016-0.02725.102-0.184-0.1840.0000.0000.0000.000
120H111VAL00.0150.01828.460-0.138-0.1380.0000.0000.0000.000
121H112SER0-0.019-0.02131.525-0.162-0.1620.0000.0000.0000.000
122H113SER00.0270.00334.8400.0200.0200.0000.0000.0000.000
123H114GLY00.0060.01637.3330.0470.0470.0000.0000.0000.000
124H115SER00.0140.00434.8360.0980.0980.0000.0000.0000.000
125H116ALA00.0080.00135.8740.1220.1220.0000.0000.0000.000
126H117SER0-0.046-0.02137.385-0.267-0.2670.0000.0000.0000.000
127H118ALA00.000-0.01340.0880.1020.1020.0000.0000.0000.000
128H119PRO00.0040.01540.867-0.085-0.0850.0000.0000.0000.000
129H120THR0-0.028-0.01642.770-0.222-0.2220.0000.0000.0000.000
130H121LEU0-0.062-0.03545.3420.0780.0780.0000.0000.0000.000
131H122PHE00.0140.00347.128-0.185-0.1850.0000.0000.0000.000
132H123PRO0-0.017-0.00848.4930.1130.1130.0000.0000.0000.000
133H124LEU0-0.001-0.00146.566-0.032-0.0320.0000.0000.0000.000
134H125VAL00.031-0.00150.8830.0050.0050.0000.0000.0000.000
135H126SER0-0.0230.00752.925-0.009-0.0090.0000.0000.0000.000
136H127CYS00.005-0.00154.685-0.111-0.1110.0000.0000.0000.000
137H128GLU-1-0.956-0.97157.5435.1225.1220.0000.0000.0000.000
138H129ASN00.019-0.02355.675-0.100-0.1000.0000.0000.0000.000
139H130SER00.014-0.00759.0950.0250.0250.0000.0000.0000.000
140H133ASN0-0.0010.01859.7760.0660.0660.0000.0000.0000.000
141H134PRO0-0.0120.01759.4260.0110.0110.0000.0000.0000.000
142H135SER00.0230.01254.8020.0990.0990.0000.0000.0000.000
143H136SER00.0230.00652.501-0.081-0.0810.0000.0000.0000.000
144H137THR0-0.008-0.01554.4910.0320.0320.0000.0000.0000.000
145H138VAL0-0.028-0.01451.5670.1050.1050.0000.0000.0000.000
146H139ALA0-0.0090.00651.6290.1050.1050.0000.0000.0000.000
147H140VAL0-0.0030.00151.518-0.053-0.0530.0000.0000.0000.000
148H141GLY00.0180.00147.9140.1120.1120.0000.0000.0000.000
149H142CYS0-0.085-0.02845.7690.0620.0620.0000.0000.0000.000
150H143LEU00.0270.01442.9680.2050.2050.0000.0000.0000.000
151H144ALA00.0200.00941.429-0.130-0.1300.0000.0000.0000.000
152H145GLN0-0.012-0.01941.1160.1200.1200.0000.0000.0000.000
153H146ASP-1-0.909-0.96040.9887.3507.3500.0000.0000.0000.000
154H147PHE00.0260.02835.069-0.054-0.0540.0000.0000.0000.000
155H148LEU0-0.0440.01433.2570.1710.1710.0000.0000.0000.000
156H149PRO00.0730.02731.237-0.205-0.2050.0000.0000.0000.000
157H150ASP-1-0.813-0.94129.74610.40710.4070.0000.0000.0000.000
158H151SER0-0.039-0.00231.379-0.171-0.1710.0000.0000.0000.000
159H152ILE00.000-0.00533.153-0.299-0.2990.0000.0000.0000.000
160H153THR0-0.012-0.01235.6360.2030.2030.0000.0000.0000.000
161H154PHE00.0050.01438.016-0.190-0.1900.0000.0000.0000.000
162H156SER0-0.030-0.03541.4270.1000.1000.0000.0000.0000.000
163H157TRP00.0130.02044.240-0.153-0.1530.0000.0000.0000.000
164H158LYS10.9180.97147.660-6.386-6.3860.0000.0000.0000.000
165H159TYR00.0310.00150.512-0.081-0.0810.0000.0000.0000.000
166H160LYS10.9010.96953.962-5.271-5.2710.0000.0000.0000.000
167H161ASN00.0370.01756.496-0.040-0.0400.0000.0000.0000.000
168H162ASN00.003-0.01153.4140.0310.0310.0000.0000.0000.000
169H163SER00.0050.00749.158-0.048-0.0480.0000.0000.0000.000
170H164ASP-1-0.886-0.93550.1866.0766.0760.0000.0000.0000.000
171H165ILE00.0080.00148.3020.1490.1490.0000.0000.0000.000
172H168SER0-0.016-0.00145.5250.0500.0500.0000.0000.0000.000
173H169SER0-0.023-0.01943.7200.1810.1810.0000.0000.0000.000
174H171THR0-0.064-0.03942.317-0.141-0.1410.0000.0000.0000.000
175H172ARG10.9270.98541.500-6.833-6.8330.0000.0000.0000.000
176H173GLY00.0380.00738.433-0.073-0.0730.0000.0000.0000.000
177H174PHE0-0.024-0.01536.993-0.002-0.0020.0000.0000.0000.000
178H175PRO00.0280.01032.4900.0750.0750.0000.0000.0000.000
179H176SER0-0.010-0.00133.106-0.273-0.2730.0000.0000.0000.000
180H177VAL0-0.016-0.00433.2280.2520.2520.0000.0000.0000.000
181H178LEU00.0260.00830.527-0.070-0.0700.0000.0000.0000.000
182H179ARG10.9640.98533.655-7.793-7.7930.0000.0000.0000.000
183H180GLY00.0500.00335.9650.1810.1810.0000.0000.0000.000
184H183GLY0-0.013-0.00435.533-0.185-0.1850.0000.0000.0000.000
185H184LYS10.8650.93436.551-7.701-7.7010.0000.0000.0000.000
186H185TYR00.0270.03029.9190.1690.1690.0000.0000.0000.000
187H186ALA0-0.042-0.03636.502-0.287-0.2870.0000.0000.0000.000
188H187ALA00.0340.01437.1030.2320.2320.0000.0000.0000.000
189H188THR00.0120.01139.043-0.136-0.1360.0000.0000.0000.000
190H189SER0-0.0160.01340.6780.1290.1290.0000.0000.0000.000
191H190GLN00.0510.02342.947-0.019-0.0190.0000.0000.0000.000
192H191VAL0-0.034-0.02145.2430.1440.1440.0000.0000.0000.000
193H192LEU0-0.0130.00047.957-0.094-0.0940.0000.0000.0000.000
194H193LEU00.005-0.00550.0400.0600.0600.0000.0000.0000.000
195H194PRO00.0000.00152.701-0.046-0.0460.0000.0000.0000.000
196H195SER00.0380.02355.343-0.130-0.1300.0000.0000.0000.000
197H196LYS10.9390.95958.135-5.112-5.1120.0000.0000.0000.000
198H197ASP-1-0.840-0.91659.2245.2995.2990.0000.0000.0000.000
199H198VAL0-0.018-0.00260.5250.0640.0640.0000.0000.0000.000
200H199MET0-0.009-0.01060.229-0.111-0.1110.0000.0000.0000.000
201H200GLN0-0.0150.00861.8900.1220.1220.0000.0000.0000.000
202H201GLY0-0.032-0.03260.865-0.047-0.0470.0000.0000.0000.000
203H202THR00.0140.00861.4920.0620.0620.0000.0000.0000.000
204H203ASN00.002-0.00258.536-0.010-0.0100.0000.0000.0000.000
205H204GLU-1-0.922-0.98060.1585.0365.0360.0000.0000.0000.000
206H205HIS0-0.080-0.04056.198-0.075-0.0750.0000.0000.0000.000
207H206VAL0-0.0400.00751.8280.0350.0350.0000.0000.0000.000
208H207VAL00.0300.01751.0130.0040.0040.0000.0000.0000.000
209H209LYS10.9370.97145.039-7.226-7.2260.0000.0000.0000.000
210H211VAL0-0.006-0.00441.8700.1590.1590.0000.0000.0000.000
211H212GLN0-0.053-0.01539.773-0.056-0.0560.0000.0000.0000.000
212H213HIS10.8990.94236.012-8.486-8.4860.0000.0000.0000.000
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