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: ZVY9N

Calculation Name: 1NBQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NBQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y624

Base Structure: X-ray

Registration Date: 2023-09-21

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2013720.673431
FMO2-HF: Nuclear repulsion 1932527.733876
FMO2-HF: Total energy -81192.939554
FMO2-MP2: Total energy -81425.454059


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(A:25:ALA)


Summations of interaction energy for fragment #1(A:25:ALA)
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.
-4.24-0.6051.099-1.862-2.873-0.015
Interaction energy analysis for fragmet #1(A:25:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.015
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].
3A27GLY00.0070.0103.888-0.6090.452-0.005-0.454-0.6030.002
4A28SER0-0.037-0.0426.3140.3530.3530.0000.0000.0000.000
5A29VAL00.0020.0099.347-0.042-0.0420.0000.0000.0000.000
6A30THR0-0.068-0.02711.9480.1030.1030.0000.0000.0000.000
7A31VAL00.0620.03515.618-0.045-0.0450.0000.0000.0000.000
8A32HIS0-0.032-0.00918.1240.0440.0440.0000.0000.0000.000
9A33SER00.018-0.01321.850-0.011-0.0110.0000.0000.0000.000
10A34SER0-0.034-0.02425.1670.0080.0080.0000.0000.0000.000
11A35GLU-1-0.887-0.96127.895-0.062-0.0620.0000.0000.0000.000
12A36PRO0-0.0150.01628.748-0.002-0.0020.0000.0000.0000.000
13A37GLU-1-0.993-1.00829.713-0.041-0.0410.0000.0000.0000.000
14A38VAL00.0410.04931.9200.0020.0020.0000.0000.0000.000
15A39ARG10.9510.95334.6030.0450.0450.0000.0000.0000.000
16A40ILE0-0.040-0.00937.9190.0000.0000.0000.0000.0000.000
17A41PRO0-0.0120.01340.2800.0000.0000.0000.0000.0000.000
18A42GLU-1-0.817-0.88442.459-0.048-0.0480.0000.0000.0000.000
19A43ASN0-0.004-0.01742.7660.0030.0030.0000.0000.0000.000
20A44ASN0-0.057-0.00141.265-0.001-0.0010.0000.0000.0000.000
21A45PRO0-0.033-0.00637.549-0.002-0.0020.0000.0000.0000.000
22A46VAL00.0300.01134.1680.0020.0020.0000.0000.0000.000
23A47LYS10.8970.94326.7270.1380.1380.0000.0000.0000.000
24A48LEU00.0260.05128.4040.0040.0040.0000.0000.0000.000
25A49SER0-0.007-0.02226.185-0.010-0.0100.0000.0000.0000.000
26A50CYS0-0.061-0.01821.085-0.013-0.0130.0000.0000.0000.000
27A51ALA0-0.0090.01320.857-0.014-0.0140.0000.0000.0000.000
28A52TYR00.007-0.01014.8860.0030.0030.0000.0000.0000.000
29A53SER0-0.047-0.03514.550-0.017-0.0170.0000.0000.0000.000
30A54GLY00.0830.02810.8900.0400.0400.0000.0000.0000.000
31A55PHE0-0.046-0.0308.830-0.188-0.1880.0000.0000.0000.000
32A56SER0-0.071-0.0377.2370.0560.0560.0000.0000.0000.000
33A57SER0-0.048-0.0239.3100.1770.1770.0000.0000.0000.000
34A58PRO0-0.032-0.01210.741-0.063-0.0630.0000.0000.0000.000
35A59ARG10.9441.00112.5670.4300.4300.0000.0000.0000.000
36A60VAL0-0.015-0.02014.9290.0120.0120.0000.0000.0000.000
37A61GLU-1-0.879-0.93017.852-0.227-0.2270.0000.0000.0000.000
38A62TRP00.0320.00420.6280.0080.0080.0000.0000.0000.000
39A63LYS10.9560.98222.6930.1100.1100.0000.0000.0000.000
40A64PHE0-0.049-0.02225.7800.0010.0010.0000.0000.0000.000
41A65ASP-1-0.886-0.94628.543-0.063-0.0630.0000.0000.0000.000
42A66GLN0-0.019-0.02630.9460.0000.0000.0000.0000.0000.000
43A67GLY0-0.0330.00534.5270.0000.0000.0000.0000.0000.000
44A68ASP-1-0.845-0.91434.366-0.028-0.0280.0000.0000.0000.000
45A69THR0-0.101-0.04234.068-0.002-0.0020.0000.0000.0000.000
46A70THR00.0400.00827.8460.0000.0000.0000.0000.0000.000
47A71ARG10.8730.93629.5880.0710.0710.0000.0000.0000.000
48A72LEU00.0290.00323.662-0.002-0.0020.0000.0000.0000.000
49A73VAL00.0090.03126.8780.0040.0040.0000.0000.0000.000
50A74CYS0-0.118-0.05523.329-0.007-0.0070.0000.0000.0000.000
51A75TYR00.0450.00821.958-0.001-0.0010.0000.0000.0000.000
52A76ASN00.012-0.02018.820-0.007-0.0070.0000.0000.0000.000
53A77ASN0-0.0170.01216.6720.0010.0010.0000.0000.0000.000
54A78LYS10.9780.99220.7480.1630.1630.0000.0000.0000.000
55A79ILE0-0.0270.00224.340-0.002-0.0020.0000.0000.0000.000
56A80THR0-0.046-0.04526.6870.0040.0040.0000.0000.0000.000
57A81ALA00.0550.00928.7700.0040.0040.0000.0000.0000.000
58A82SER0-0.015-0.01132.3290.0010.0010.0000.0000.0000.000
59A83TYR00.0170.01931.1860.0050.0050.0000.0000.0000.000
60A84GLU-1-0.929-0.96230.863-0.111-0.1110.0000.0000.0000.000
61A85ASP-1-0.907-0.92032.919-0.080-0.0800.0000.0000.0000.000
62A86ARG10.7450.84235.3040.0750.0750.0000.0000.0000.000
63A87VAL0-0.086-0.03729.822-0.001-0.0010.0000.0000.0000.000
64A88THR00.0410.01030.501-0.005-0.0050.0000.0000.0000.000
65A89PHE00.039-0.01720.7080.0010.0010.0000.0000.0000.000
66A90LEU0-0.016-0.00124.8760.0000.0000.0000.0000.0000.000
67A91PRO00.0020.00320.268-0.004-0.0040.0000.0000.0000.000
68A92THR00.0330.03221.017-0.006-0.0060.0000.0000.0000.000
69A93GLY00.0500.00023.5610.0120.0120.0000.0000.0000.000
70A94ILE0-0.0050.01125.465-0.004-0.0040.0000.0000.0000.000
71A95THR0-0.008-0.00627.9630.0070.0070.0000.0000.0000.000
72A96PHE0-0.019-0.00330.920-0.001-0.0010.0000.0000.0000.000
73A97LYS10.9000.94934.4470.0880.0880.0000.0000.0000.000
74A98SER00.0470.01037.9050.0040.0040.0000.0000.0000.000
75A99VAL00.0420.02036.783-0.004-0.0040.0000.0000.0000.000
76A100THR00.0650.02839.4340.0020.0020.0000.0000.0000.000
77A101ARG10.8430.90440.3340.0370.0370.0000.0000.0000.000
78A102GLU-1-0.907-0.94039.533-0.046-0.0460.0000.0000.0000.000
79A103ASP-1-0.825-0.90035.832-0.071-0.0710.0000.0000.0000.000
80A104THR00.0020.00435.656-0.003-0.0030.0000.0000.0000.000
81A105GLY00.0700.02134.1750.0030.0030.0000.0000.0000.000
82A106THR0-0.050-0.03628.7730.0000.0000.0000.0000.0000.000
83A107TYR0-0.068-0.03228.008-0.006-0.0060.0000.0000.0000.000
84A108THR0-0.063-0.05022.3480.0050.0050.0000.0000.0000.000
85A110MET0-0.015-0.01518.0930.0190.0190.0000.0000.0000.000
86A111VAL0-0.0060.00913.516-0.007-0.0070.0000.0000.0000.000
87A112SER00.0130.02611.9120.0010.0010.0000.0000.0000.000
88A113GLU-1-0.730-0.8705.959-1.373-1.3730.0000.0000.0000.000
89A114GLU-1-0.842-0.9279.086-0.565-0.5650.0000.0000.0000.000
90A115GLY0-0.070-0.0277.392-0.306-0.3060.0000.0000.0000.000
91A116GLY0-0.035-0.0328.0410.1490.1490.0000.0000.0000.000
92A117ASN0-0.035-0.0152.757-2.884-0.3871.105-1.399-2.203-0.017
93A118SER00.042-0.0155.0250.5040.581-0.001-0.009-0.0670.000
94A119TYR0-0.090-0.1178.0850.0350.0350.0000.0000.0000.000
95A120GLY0-0.027-0.00411.8440.0750.0750.0000.0000.0000.000
96A121GLU-1-0.887-0.91915.273-0.142-0.1420.0000.0000.0000.000
97A122VAL00.0050.02418.9870.0220.0220.0000.0000.0000.000
98A123LYS10.9200.95722.3620.0660.0660.0000.0000.0000.000
99A124VAL00.0630.04325.5350.0070.0070.0000.0000.0000.000
100A125LYS10.9190.96628.5980.0470.0470.0000.0000.0000.000
101A126LEU00.0070.02232.149-0.001-0.0010.0000.0000.0000.000
102A127ILE0-0.003-0.00134.8350.0040.0040.0000.0000.0000.000
103A128VAL00.025-0.01038.468-0.002-0.0020.0000.0000.0000.000
104A129LEU0-0.033-0.03540.6610.0030.0030.0000.0000.0000.000
105A130VAL0-0.001-0.00644.097-0.002-0.0020.0000.0000.0000.000
106A131PRO0-0.0080.00247.3230.0010.0010.0000.0000.0000.000
107A132PRO00.0050.01350.6850.0000.0000.0000.0000.0000.000
108A133SER00.029-0.00152.7500.0000.0000.0000.0000.0000.000
109A134LYS10.8210.89655.3860.0190.0190.0000.0000.0000.000
110A135PRO00.0160.00457.7730.0000.0000.0000.0000.0000.000
111A136THR0-0.027-0.00858.7420.0010.0010.0000.0000.0000.000
112A137VAL0-0.019-0.02260.3450.0000.0000.0000.0000.0000.000
113A138ASN0-0.058-0.01963.0720.0000.0000.0000.0000.0000.000
114A139ILE00.0160.01965.1840.0000.0000.0000.0000.0000.000
115A140PRO00.0030.01667.7900.0000.0000.0000.0000.0000.000
116A141SER00.049-0.01270.6700.0000.0000.0000.0000.0000.000
117A142SER0-0.028-0.00574.2380.0000.0000.0000.0000.0000.000
118A143ALA00.0130.00772.5410.0000.0000.0000.0000.0000.000
119A144THR0-0.065-0.02474.6560.0000.0000.0000.0000.0000.000
120A145ILE0-0.003-0.00375.5770.0000.0000.0000.0000.0000.000
121A146GLY0-0.0040.00175.4850.0000.0000.0000.0000.0000.000
122A147ASN0-0.020-0.01872.5290.0010.0010.0000.0000.0000.000
123A148ARG10.9820.99761.8470.0060.0060.0000.0000.0000.000
124A149ALA0-0.017-0.01768.2940.0000.0000.0000.0000.0000.000
125A150VAL0-0.036-0.00962.5190.0000.0000.0000.0000.0000.000
126A151LEU00.0150.01364.2940.0000.0000.0000.0000.0000.000
127A152THR0-0.013-0.02359.9330.0000.0000.0000.0000.0000.000
128A153CYS00.0480.01158.3460.0000.0000.0000.0000.0000.000
129A154SER0-0.008-0.01655.0280.0000.0000.0000.0000.0000.000
130A155GLU-1-0.769-0.86151.978-0.026-0.0260.0000.0000.0000.000
131A156GLN0-0.060-0.02649.3090.0010.0010.0000.0000.0000.000
132A157ASP-1-0.891-0.92149.323-0.031-0.0310.0000.0000.0000.000
133A158GLY0-0.037-0.02848.465-0.002-0.0020.0000.0000.0000.000
134A159SER0-0.0470.00842.6770.0010.0010.0000.0000.0000.000
135A160PRO00.011-0.03243.551-0.002-0.0020.0000.0000.0000.000
136A161PRO00.0350.01344.5710.0010.0010.0000.0000.0000.000
137A162SER00.002-0.00347.6280.0000.0000.0000.0000.0000.000
138A163GLU-1-0.939-0.93949.787-0.017-0.0170.0000.0000.0000.000
139A164TYR0-0.043-0.03252.7470.0000.0000.0000.0000.0000.000
140A165THR0-0.038-0.02256.4300.0010.0010.0000.0000.0000.000
141A166TRP00.016-0.00859.5670.0000.0000.0000.0000.0000.000
142A167PHE0-0.054-0.02362.1610.0000.0000.0000.0000.0000.000
143A168LYS11.0100.98866.2060.0080.0080.0000.0000.0000.000
144A169ASP-1-0.912-0.94269.792-0.009-0.0090.0000.0000.0000.000
145A170GLY0-0.014-0.01468.7260.0000.0000.0000.0000.0000.000
146A171ILE0-0.060-0.02668.3490.0000.0000.0000.0000.0000.000
147A172VAL0-0.040-0.02262.1320.0000.0000.0000.0000.0000.000
148A173MET0-0.0030.01463.1880.0010.0010.0000.0000.0000.000
149A174PRO0-0.0340.01762.4390.0000.0000.0000.0000.0000.000
150A175THR00.0450.04757.4600.0000.0000.0000.0000.0000.000
151A176ASN0-0.056-0.02060.7610.0000.0000.0000.0000.0000.000
152A177PRO00.0700.06862.8840.0000.0000.0000.0000.0000.000
153A178LYS10.9810.98665.8580.0030.0030.0000.0000.0000.000
154A179SER0-0.054-0.03265.8150.0000.0000.0000.0000.0000.000
155A180THR00.0380.00267.8190.0000.0000.0000.0000.0000.000
156A181ARG10.9750.96663.3130.0070.0070.0000.0000.0000.000
157A182ALA00.0190.01969.6720.0000.0000.0000.0000.0000.000
158A183PHE00.040-0.01467.3720.0000.0000.0000.0000.0000.000
159A184SER00.0030.04270.3620.0000.0000.0000.0000.0000.000
160A185ASN0-0.086-0.06071.2890.0000.0000.0000.0000.0000.000
161A186SER0-0.0140.01969.8560.0000.0000.0000.0000.0000.000
162A187SER0-0.009-0.02169.0620.0000.0000.0000.0000.0000.000
163A188TYR0-0.085-0.10163.4100.0000.0000.0000.0000.0000.000
164A189VAL00.0260.01659.9860.0010.0010.0000.0000.0000.000
165A190LEU0-0.0080.01059.399-0.001-0.0010.0000.0000.0000.000
166A191ASN00.0840.00753.4460.0000.0000.0000.0000.0000.000
167A192PRO00.0250.00953.339-0.001-0.0010.0000.0000.0000.000
168A193THR00.0490.03548.814-0.001-0.0010.0000.0000.0000.000
169A194THR0-0.0350.00951.9120.0000.0000.0000.0000.0000.000
170A195GLY0-0.051-0.02354.4000.0000.0000.0000.0000.0000.000
171A196GLU-1-0.947-0.98757.336-0.009-0.0090.0000.0000.0000.000
172A197LEU0-0.0140.01659.3090.0000.0000.0000.0000.0000.000
173A198VAL0-0.063-0.04061.5890.0000.0000.0000.0000.0000.000
174A199PHE0-0.028-0.01464.4520.0010.0010.0000.0000.0000.000
175A200ASP-1-0.912-0.95167.079-0.004-0.0040.0000.0000.0000.000
176A201PRO00.0080.00969.3210.0000.0000.0000.0000.0000.000
177A202LEU0-0.0080.00671.3650.0000.0000.0000.0000.0000.000
178A203SER0-0.011-0.03173.1750.0010.0010.0000.0000.0000.000
179A204ALA00.0940.03375.9060.0000.0000.0000.0000.0000.000
180A205SER0-0.030-0.00775.7200.0000.0000.0000.0000.0000.000
181A206ASP-1-0.825-0.93871.842-0.006-0.0060.0000.0000.0000.000
182A207THR0-0.0030.04673.4470.0000.0000.0000.0000.0000.000
183A208GLY0-0.007-0.01073.6540.0000.0000.0000.0000.0000.000
184A209GLU-1-0.884-0.94471.714-0.012-0.0120.0000.0000.0000.000
185A210TYR0-0.101-0.09467.4230.0000.0000.0000.0000.0000.000
186A211SER00.0320.00865.5550.0000.0000.0000.0000.0000.000
187A213GLU-1-0.875-0.92858.371-0.019-0.0190.0000.0000.0000.000
188A214ALA00.0020.00254.8600.0010.0010.0000.0000.0000.000
189A215ARG10.9260.93953.6240.0170.0170.0000.0000.0000.000
190A216ASN00.1040.08448.1350.0020.0020.0000.0000.0000.000
191A217GLY0-0.067-0.04248.301-0.001-0.0010.0000.0000.0000.000
192A218TYR0-0.054-0.04747.413-0.001-0.0010.0000.0000.0000.000
193A219GLY00.0190.00749.5490.0010.0010.0000.0000.0000.000
194A220THR0-0.030-0.02452.0780.0010.0010.0000.0000.0000.000
195A221PRO0-0.0390.00155.664-0.001-0.0010.0000.0000.0000.000
196A222MET00.0440.03756.8600.0010.0010.0000.0000.0000.000
197A223THR0-0.010-0.00458.9560.0010.0010.0000.0000.0000.000
198A224SER0-0.006-0.00362.0800.0000.0000.0000.0000.0000.000
199A225ASN0-0.038-0.02063.3170.0000.0000.0000.0000.0000.000
200A226ALA00.0360.01366.9100.0000.0000.0000.0000.0000.000
201A227VAL0-0.046-0.02168.2520.0000.0000.0000.0000.0000.000
202A228ARG10.8760.93970.8000.0090.0090.0000.0000.0000.000
203A229MET0-0.0100.01269.5400.0000.0000.0000.0000.0000.000
204A230GLU-1-0.876-0.93874.137-0.007-0.0070.0000.0000.0000.000
205A231ALA0-0.0180.01576.4590.0000.0000.0000.0000.0000.000
206A232VAL0-0.002-0.00677.6670.0000.0000.0000.0000.0000.000
207A233GLU-1-0.939-0.97279.870-0.004-0.0040.0000.0000.0000.000