FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: 7MJJK

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2312209.189251
FMO2-HF: Nuclear repulsion 2225340.24832
FMO2-HF: Total energy -86868.94093
FMO2-MP2: Total energy -87121.159772


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.
-78.242-76.2549.712-5.954-5.7430.064
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 : -0.900 / q_NPA : -0.939
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].
3H3GLN0-0.041-0.0231.810-31.319-29.7799.717-5.836-5.4210.064
4H4LEU0-0.040-0.0254.928-5.130-5.081-0.001-0.009-0.0400.000
5H5VAL00.0540.0337.448-0.300-0.3000.0000.0000.0000.000
6H6GLU-1-0.793-0.91110.03221.23021.2300.0000.0000.0000.000
7H7SER00.004-0.00713.8010.0260.0260.0000.0000.0000.000
8H8GLY0-0.041-0.01316.568-0.502-0.5020.0000.0000.0000.000
9H9GLY00.000-0.00120.178-0.167-0.1670.0000.0000.0000.000
10H10GLY00.0470.01721.9100.5010.5010.0000.0000.0000.000
11H11LEU0-0.036-0.00524.428-0.202-0.2020.0000.0000.0000.000
12H12VAL0-0.047-0.03228.095-0.085-0.0850.0000.0000.0000.000
13H13GLN00.0290.03330.542-0.203-0.2030.0000.0000.0000.000
14H14PRO00.002-0.02033.8020.1070.1070.0000.0000.0000.000
15H15GLY0-0.0230.00834.859-0.180-0.1800.0000.0000.0000.000
16H16ARG10.9130.96929.094-10.266-10.2660.0000.0000.0000.000
17H17SER00.029-0.00929.822-0.061-0.0610.0000.0000.0000.000
18H18LEU0-0.034-0.01724.7020.0760.0760.0000.0000.0000.000
19H19ARG10.9410.98820.403-14.259-14.2590.0000.0000.0000.000
20H20LEU00.0060.00519.2150.3750.3750.0000.0000.0000.000
21H21SER0-0.018-0.02516.920-0.789-0.7890.0000.0000.0000.000
22H22CYS0-0.0390.00612.831-0.051-0.0510.0000.0000.0000.000
23H23VAL00.0160.03710.837-1.089-1.0890.0000.0000.0000.000
24H24THR0-0.007-0.0099.0311.7011.7010.0000.0000.0000.000
25H25SER00.004-0.0095.1952.4972.623-0.001-0.005-0.1190.000
26H26GLY00.0810.0234.6442.5592.679-0.001-0.082-0.0360.000
27H27PHE0-0.043-0.0304.948-3.023-2.983-0.001-0.016-0.0220.000
28H28THR00.0350.0267.6850.6660.6660.0000.0000.0000.000
29H29PHE00.0380.01511.414-1.047-1.0470.0000.0000.0000.000
30H30ASP-1-0.858-0.94013.37315.61015.6100.0000.0000.0000.000
31H31ASP-1-0.877-0.93513.44816.07616.0760.0000.0000.0000.000
32H32TYR0-0.068-0.05310.4710.1120.1120.0000.0000.0000.000
33H33ALA00.0040.02514.9660.1410.1410.0000.0000.0000.000
34H34MET0-0.0120.01812.0460.7580.7580.0000.0000.0000.000
35H35HIS00.0040.00316.341-1.372-1.3720.0000.0000.0000.000
36H36TRP0-0.0100.00116.8451.2151.2150.0000.0000.0000.000
37H37VAL0-0.003-0.00418.250-0.918-0.9180.0000.0000.0000.000
38H38ARG10.8630.95119.094-10.866-10.8660.0000.0000.0000.000
39H39GLN00.011-0.00320.451-0.739-0.7390.0000.0000.0000.000
40H40SER00.0240.02222.5920.1730.1730.0000.0000.0000.000
41H41PRO00.000-0.00625.2360.0820.0820.0000.0000.0000.000
42H42GLY00.0260.02225.660-0.489-0.4890.0000.0000.0000.000
43H43LYS10.8560.91626.845-10.658-10.6580.0000.0000.0000.000
44H44GLY00.0350.02224.775-0.145-0.1450.0000.0000.0000.000
45H45LEU00.0160.00918.9980.0630.0630.0000.0000.0000.000
46H46GLU-1-0.891-0.95122.91410.69710.6970.0000.0000.0000.000
47H47TRP0-0.002-0.00521.2240.2820.2820.0000.0000.0000.000
48H48VAL0-0.029-0.01022.447-0.526-0.5260.0000.0000.0000.000
49H49SER0-0.043-0.04922.488-0.684-0.6840.0000.0000.0000.000
50H50GLY00.0400.02221.1170.6650.6650.0000.0000.0000.000
51H51ILE0-0.058-0.02020.504-0.663-0.6630.0000.0000.0000.000
52H52SER00.014-0.00120.3890.8190.8190.0000.0000.0000.000
53H52TRP00.0850.03518.7470.1940.1940.0000.0000.0000.000
54H53ASN00.0400.02319.8400.4460.4460.0000.0000.0000.000
55H54THR0-0.039-0.03322.636-0.223-0.2230.0000.0000.0000.000
56H55GLY0-0.0180.00024.449-0.298-0.2980.0000.0000.0000.000
57H56THR00.0030.00325.359-0.369-0.3690.0000.0000.0000.000
58H57ILE00.0120.01425.0310.5740.5740.0000.0000.0000.000
59H58ILE0-0.0130.00224.191-0.473-0.4730.0000.0000.0000.000
60H59TYR00.0040.00325.9260.5250.5250.0000.0000.0000.000
61H60ALA00.1000.05627.065-0.308-0.3080.0000.0000.0000.000
62H61ASP-1-0.759-0.89828.8359.1879.1870.0000.0000.0000.000
63H62SER0-0.062-0.01530.292-0.121-0.1210.0000.0000.0000.000
64H63VAL0-0.052-0.03827.2450.1540.1540.0000.0000.0000.000
65H64LYS10.8700.92730.528-9.559-9.5590.0000.0000.0000.000
66H65GLY0-0.0070.00932.385-0.255-0.2550.0000.0000.0000.000
67H66ARG10.7050.83031.065-10.010-10.0100.0000.0000.0000.000
68H67PHE0-0.006-0.02026.0350.1510.1510.0000.0000.0000.000
69H68ILE00.0260.01027.275-0.201-0.2010.0000.0000.0000.000
70H69ILE0-0.0170.01020.4640.4000.4000.0000.0000.0000.000
71H70SER0-0.056-0.03122.485-0.572-0.5720.0000.0000.0000.000
72H71ARG10.8610.93516.658-15.452-15.4520.0000.0000.0000.000
73H72ASP-1-0.822-0.90618.79613.99413.9940.0000.0000.0000.000
74H73ASN0-0.006-0.02017.8891.0161.0160.0000.0000.0000.000
75H74ALA00.0150.01817.3960.8220.8220.0000.0000.0000.000
76H75LYS10.8390.91017.002-14.078-14.0780.0000.0000.0000.000
77H76ASN0-0.0210.00712.4271.9591.9590.0000.0000.0000.000
78H77SER0-0.011-0.00813.3111.5011.5010.0000.0000.0000.000
79H78LEU0-0.0100.00215.632-1.136-1.1360.0000.0000.0000.000
80H79TYR0-0.030-0.04117.3180.1620.1620.0000.0000.0000.000
81H80LEU00.0370.01220.078-0.246-0.2460.0000.0000.0000.000
82H81GLN00.002-0.00522.5850.1390.1390.0000.0000.0000.000
83H82MET0-0.0120.00424.607-0.219-0.2190.0000.0000.0000.000
84H82ASN00.0570.02627.384-0.145-0.1450.0000.0000.0000.000
85H82SER0-0.0050.00331.101-0.123-0.1230.0000.0000.0000.000
86H82LEU0-0.0010.01127.808-0.014-0.0140.0000.0000.0000.000
87H83ARG10.9730.97831.650-9.399-9.3990.0000.0000.0000.000
88H84VAL00.0330.02431.7480.2790.2790.0000.0000.0000.000
89H85GLU-1-0.873-0.95331.7759.2139.2130.0000.0000.0000.000
90H86ASP-1-0.833-0.86428.19810.64210.6420.0000.0000.0000.000
91H87THR0-0.0060.00227.1040.5580.5580.0000.0000.0000.000
92H88ALA00.011-0.00124.139-0.169-0.1690.0000.0000.0000.000
93H89LEU0-0.0150.00417.859-0.018-0.0180.0000.0000.0000.000
94H90TYR0-0.039-0.04619.646-0.259-0.2590.0000.0000.0000.000
95H91TYR00.0090.01314.6650.1530.1530.0000.0000.0000.000
96H93ALA00.028-0.00112.8941.1051.1050.0000.0000.0000.000
97H94LYS10.8290.9398.429-23.744-23.7440.0000.0000.0000.000
98H95THR0-0.037-0.02212.724-0.032-0.0320.0000.0000.0000.000
99H96ARG10.9240.93410.507-17.582-17.5820.0000.0000.0000.000
100H97SER0-0.0070.00113.947-0.478-0.4780.0000.0000.0000.000
101H98TYR00.0640.03012.9340.4840.4840.0000.0000.0000.000
102H99VAL0-0.0010.00819.078-0.339-0.3390.0000.0000.0000.000
103H100VAL00.0120.00322.5680.2210.2210.0000.0000.0000.000
104H100ALA00.0020.00424.9310.1160.1160.0000.0000.0000.000
105H100ALA0-0.013-0.00320.873-0.127-0.1270.0000.0000.0000.000
106H100GLU-1-0.912-0.94922.75410.91110.9110.0000.0000.0000.000
107H100TYR0-0.052-0.04718.7680.3770.3770.0000.0000.0000.000
108H100TYR00.0650.04913.8420.1800.1800.0000.0000.0000.000
109H100PHE0-0.017-0.02314.9680.5330.5330.0000.0000.0000.000
110H101HIS00.0090.0118.237-0.326-0.3260.0000.0000.0000.000
111H102TYR00.0240.0064.414-0.218-0.105-0.001-0.006-0.1050.000
112H103TRP00.0250.0029.765-2.162-2.1620.0000.0000.0000.000
113H104GLY00.0390.0359.4192.7802.7800.0000.0000.0000.000
114H105GLN0-0.043-0.03210.8790.6390.6390.0000.0000.0000.000
115H106GLY00.0080.00012.346-1.657-1.6570.0000.0000.0000.000
116H107ILE0-0.047-0.00815.468-0.271-0.2710.0000.0000.0000.000
117H108LEU00.004-0.00117.680-0.579-0.5790.0000.0000.0000.000
118H109VAL0-0.0150.00521.349-0.145-0.1450.0000.0000.0000.000
119H110THR0-0.031-0.03224.447-0.190-0.1900.0000.0000.0000.000
120H111VAL00.0160.01127.750-0.139-0.1390.0000.0000.0000.000
121H112SER00.005-0.00530.894-0.088-0.0880.0000.0000.0000.000
122H113SER00.0290.00034.1250.0330.0330.0000.0000.0000.000
123H114GLY0-0.0020.01436.4330.0490.0490.0000.0000.0000.000
124H115SER00.018-0.00133.6720.1030.1030.0000.0000.0000.000
125H116ALA00.0210.01234.8230.1180.1180.0000.0000.0000.000
126H117SER0-0.051-0.02336.237-0.290-0.2900.0000.0000.0000.000
127H118ALA00.010-0.01139.1190.1000.1000.0000.0000.0000.000
128H119PRO00.0260.02539.895-0.112-0.1120.0000.0000.0000.000
129H120THR0-0.049-0.02241.999-0.236-0.2360.0000.0000.0000.000
130H121LEU0-0.057-0.02844.4080.0950.0950.0000.0000.0000.000
131H122PHE00.0350.01346.542-0.169-0.1690.0000.0000.0000.000
132H123PRO0-0.0030.00348.1830.1170.1170.0000.0000.0000.000
133H124LEU0-0.013-0.00646.591-0.033-0.0330.0000.0000.0000.000
134H125VAL00.020-0.00550.7790.0030.0030.0000.0000.0000.000
135H126SER0-0.0260.00152.7600.0050.0050.0000.0000.0000.000
136H127CYS00.0210.00954.618-0.109-0.1090.0000.0000.0000.000
137H128GLU-1-0.969-0.97657.5405.1785.1780.0000.0000.0000.000
138H129ASN00.000-0.03255.688-0.101-0.1010.0000.0000.0000.000
139H130SER00.0400.01759.0480.0260.0260.0000.0000.0000.000
140H133ASN0-0.0070.01459.7110.0640.0640.0000.0000.0000.000
141H134PRO00.0070.02159.5620.0100.0100.0000.0000.0000.000
142H135SER00.0120.01254.7470.1040.1040.0000.0000.0000.000
143H136SER00.0280.00852.339-0.084-0.0840.0000.0000.0000.000
144H137THR0-0.014-0.03254.4690.0350.0350.0000.0000.0000.000
145H138VAL0-0.014-0.00851.3850.1060.1060.0000.0000.0000.000
146H139ALA0-0.0140.00051.6640.1110.1110.0000.0000.0000.000
147H140VAL0-0.0020.00651.558-0.053-0.0530.0000.0000.0000.000
148H141GLY00.0160.00247.8870.1140.1140.0000.0000.0000.000
149H142CYS0-0.068-0.02145.7430.0700.0700.0000.0000.0000.000
150H143LEU00.0260.01642.6630.2030.2030.0000.0000.0000.000
151H144ALA00.0260.01241.011-0.134-0.1340.0000.0000.0000.000
152H145GLN00.0240.00140.6170.2450.2450.0000.0000.0000.000
153H146ASP-1-0.800-0.88640.4467.4587.4580.0000.0000.0000.000
154H147PHE0-0.0250.00734.670-0.070-0.0700.0000.0000.0000.000
155H148LEU0-0.0430.00932.3100.1680.1680.0000.0000.0000.000
156H149PRO00.0760.03230.319-0.211-0.2110.0000.0000.0000.000
157H150ASP-1-0.782-0.90929.40210.65110.6510.0000.0000.0000.000
158H151SER0-0.046-0.02430.360-0.198-0.1980.0000.0000.0000.000
159H152ILE0-0.012-0.00832.457-0.309-0.3090.0000.0000.0000.000
160H153THR0-0.019-0.01435.2130.2040.2040.0000.0000.0000.000
161H154PHE00.0070.01137.586-0.189-0.1890.0000.0000.0000.000
162H156SER0-0.025-0.02841.0630.1020.1020.0000.0000.0000.000
163H157TRP00.0150.01343.936-0.163-0.1630.0000.0000.0000.000
164H158LYS10.8110.89547.431-6.450-6.4500.0000.0000.0000.000
165H159TYR00.022-0.00650.231-0.055-0.0550.0000.0000.0000.000
166H160LYS10.8400.93253.746-5.291-5.2910.0000.0000.0000.000
167H161ASN00.0280.01656.296-0.092-0.0920.0000.0000.0000.000
168H162ASN00.000-0.01253.2990.0310.0310.0000.0000.0000.000
169H163SER00.0150.00948.954-0.057-0.0570.0000.0000.0000.000
170H164ASP-1-0.885-0.93450.0726.1486.1480.0000.0000.0000.000
171H165ILE00.0080.00048.1950.1510.1510.0000.0000.0000.000
172H168SER0-0.0060.00145.3270.0570.0570.0000.0000.0000.000
173H169SER0-0.012-0.01543.6230.2100.2100.0000.0000.0000.000
174H171THR0-0.072-0.04142.317-0.173-0.1730.0000.0000.0000.000
175H172ARG10.8880.97141.448-6.878-6.8780.0000.0000.0000.000
176H173GLY00.0380.01438.447-0.070-0.0700.0000.0000.0000.000
177H174PHE0-0.018-0.01337.031-0.009-0.0090.0000.0000.0000.000
178H175PRO00.0320.01032.3460.0800.0800.0000.0000.0000.000
179H176SER0-0.010-0.00232.814-0.294-0.2940.0000.0000.0000.000
180H177VAL0-0.026-0.01333.0660.2580.2580.0000.0000.0000.000
181H178LEU00.0150.01130.296-0.081-0.0810.0000.0000.0000.000
182H179ARG10.9060.94133.335-7.939-7.9390.0000.0000.0000.000
183H180GLY00.0510.00735.4280.1950.1950.0000.0000.0000.000
184H183GLY00.0040.00834.891-0.189-0.1890.0000.0000.0000.000
185H184LYS10.8180.88635.907-7.793-7.7930.0000.0000.0000.000
186H185TYR00.0230.02829.0460.1270.1270.0000.0000.0000.000
187H186ALA0-0.040-0.03435.972-0.299-0.2990.0000.0000.0000.000
188H187ALA00.0290.01536.8530.2410.2410.0000.0000.0000.000
189H188THR00.0120.00838.830-0.148-0.1480.0000.0000.0000.000
190H189SER0-0.0040.01940.6230.1380.1380.0000.0000.0000.000
191H190GLN00.0310.01842.938-0.061-0.0610.0000.0000.0000.000
192H191VAL0-0.024-0.01745.2600.1390.1390.0000.0000.0000.000
193H192LEU0-0.0120.00047.967-0.095-0.0950.0000.0000.0000.000
194H193LEU00.027-0.00250.0160.0630.0630.0000.0000.0000.000
195H194PRO0-0.021-0.00652.679-0.046-0.0460.0000.0000.0000.000
196H195SER00.023-0.00455.258-0.115-0.1150.0000.0000.0000.000
197H196LYS10.9300.96158.083-5.142-5.1420.0000.0000.0000.000
198H197ASP-1-0.812-0.89259.1115.3045.3040.0000.0000.0000.000
199H198VAL0-0.022-0.00260.4520.0690.0690.0000.0000.0000.000
200H199MET00.003-0.00160.341-0.122-0.1220.0000.0000.0000.000
201H200GLN0-0.0220.00461.8010.1240.1240.0000.0000.0000.000
202H201GLY0-0.018-0.02160.770-0.049-0.0490.0000.0000.0000.000
203H202THR0-0.026-0.04061.4480.0510.0510.0000.0000.0000.000
204H203ASN00.0000.00158.318-0.038-0.0380.0000.0000.0000.000
205H204GLU-1-0.801-0.88660.0545.1225.1220.0000.0000.0000.000
206H205HIS0-0.092-0.04955.843-0.077-0.0770.0000.0000.0000.000
207H206VAL0-0.0340.01151.8560.0370.0370.0000.0000.0000.000
208H207VAL00.0260.01250.5420.0030.0030.0000.0000.0000.000
209H209LYS10.9520.98344.117-7.346-7.3460.0000.0000.0000.000
210H211VAL0-0.002-0.00541.2890.1680.1680.0000.0000.0000.000
211H212GLN0-0.051-0.02139.236-0.155-0.1550.0000.0000.0000.000
212H213HIS10.8740.92835.098-8.653-8.6530.0000.0000.0000.000
213H214PRO00.0090.02133.654-0.241-0.2410.0000.0000.0000.000
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