FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: VQ5K1

Calculation Name: 2P1G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P1G

Chain ID: A

ChEMBL ID:

UniProt ID: Q64UP6

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2897840.015503
FMO2-HF: Nuclear repulsion 2806581.750646
FMO2-HF: Total energy -91258.264857
FMO2-MP2: Total energy -91522.042847


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:26:VAL)


Summations of interaction energy for fragment #1(A:26:VAL)
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.
-10.112-5.17916.687-7.233-14.385-0.029
Interaction energy analysis for fragmet #1(A:26:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / 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].
3A28SER0-0.0040.0002.037-2.834-0.9293.523-1.857-3.572-0.010
4A29ASN00.0500.0101.9660.909-0.8137.258-1.746-3.789-0.006
5A30GLY00.0220.0083.5380.5271.0140.011-0.068-0.4300.001
6A31LEU0-0.039-0.0485.1870.2020.356-0.001-0.009-0.1440.000
7A32GLY00.0140.0256.9720.1460.1460.0000.0000.0000.000
8A33PHE00.0090.0056.9650.1210.1210.0000.0000.0000.000
9A34VAL0-0.074-0.03710.4460.1280.1280.0000.0000.0000.000
10A35ASP-1-0.918-0.97112.698-0.025-0.0250.0000.0000.0000.000
11A36THR0-0.035-0.00413.214-0.020-0.0200.0000.0000.0000.000
12A37PRO00.0130.00215.3420.0580.0580.0000.0000.0000.000
13A38TYR0-0.015-0.01216.3820.0150.0150.0000.0000.0000.000
14A39LYS10.9220.95317.905-0.050-0.0500.0000.0000.0000.000
15A40ALA0-0.022-0.00518.7570.0130.0130.0000.0000.0000.000
16A41GLY00.019-0.01220.543-0.019-0.0190.0000.0000.0000.000
17A42THR0-0.013-0.00117.017-0.009-0.0090.0000.0000.0000.000
18A43LEU00.0170.01215.953-0.016-0.0160.0000.0000.0000.000
19A44GLU-1-0.828-0.88120.2170.0890.0890.0000.0000.0000.000
20A45VAL0-0.054-0.03323.0240.0000.0000.0000.0000.0000.000
21A46ASP-1-0.874-0.92024.728-0.031-0.0310.0000.0000.0000.000
22A47ASP-1-0.982-0.99327.0040.0090.0090.0000.0000.0000.000
23A48THR0-0.071-0.03727.7640.0040.0040.0000.0000.0000.000
24A49GLU-1-0.870-0.92221.5440.0370.0370.0000.0000.0000.000
25A50ASP-1-0.840-0.92623.125-0.069-0.0690.0000.0000.0000.000
26A51LEU0-0.051-0.02715.6140.0140.0140.0000.0000.0000.000
27A52ILE00.0070.02118.148-0.013-0.0130.0000.0000.0000.000
28A53ILE0-0.011-0.00713.6700.0110.0110.0000.0000.0000.000
29A54ASN00.001-0.01715.234-0.022-0.0220.0000.0000.0000.000
30A55CYS0-0.045-0.03211.3530.0070.0070.0000.0000.0000.000
31A56ASP-1-0.850-0.91113.608-0.165-0.1650.0000.0000.0000.000
32A57GLU-1-0.947-0.97616.4080.0230.0230.0000.0000.0000.000
33A58VAL0-0.0040.00811.7460.0110.0110.0000.0000.0000.000
34A59ASP-1-0.853-0.92714.3320.2690.2690.0000.0000.0000.000
35A60CYS0-0.068-0.05613.0440.0490.0490.0000.0000.0000.000
36A61THR00.0190.01311.5370.1770.1770.0000.0000.0000.000
37A62THR00.0400.01910.8790.0760.0760.0000.0000.0000.000
38A63PHE0-0.0290.0047.2810.0830.0830.0000.0000.0000.000
39A64VAL0-0.001-0.0106.3960.0060.0060.0000.0000.0000.000
40A65GLU-1-0.790-0.8876.0920.4480.4480.0000.0000.0000.000
41A66TYR00.0550.0337.587-0.222-0.2220.0000.0000.0000.000
42A67ALA00.0380.0172.949-0.639-0.2920.052-0.127-0.2720.000
43A68LEU0-0.047-0.0263.193-3.613-2.1880.098-0.722-0.800-0.006
44A69ALA00.0140.0054.267-0.790-0.715-0.001-0.003-0.0710.000
45A70MET00.0200.0055.112-0.066-0.0660.0000.0000.0000.000
46A71ALA0-0.051-0.0262.126-0.441-1.2915.269-1.716-2.703-0.003
47A72LEU0-0.010-0.0093.9810.0330.2930.002-0.044-0.2190.000
48A73CYS0-0.104-0.0186.8040.4240.4240.0000.0000.0000.000
49A74PRO0-0.0080.0057.900-0.201-0.2010.0000.0000.0000.000
50A75GLN00.0270.01410.037-0.012-0.0120.0000.0000.0000.000
51A76GLN0-0.014-0.0174.387-0.873-0.739-0.001-0.015-0.1180.000
52A77GLY00.005-0.0037.7010.1890.1890.0000.0000.0000.000
53A78ASP-1-0.924-0.9699.665-0.556-0.5560.0000.0000.0000.000
54A79GLU-1-0.935-0.96812.259-0.470-0.4700.0000.0000.0000.000
55A80MET0-0.094-0.0248.882-0.077-0.0770.0000.0000.0000.000
56A81GLN00.0120.00811.4890.1420.1420.0000.0000.0000.000
57A82GLU-1-0.887-0.96613.567-0.368-0.3680.0000.0000.0000.000
58A83GLY00.0380.02015.1830.0200.0200.0000.0000.0000.000
59A84ASP-1-0.916-0.96712.711-0.497-0.4970.0000.0000.0000.000
60A85PHE0-0.001-0.0048.8000.0050.0050.0000.0000.0000.000
61A86ALA00.0470.02911.8480.0500.0500.0000.0000.0000.000
62A87ARG10.9310.97014.7270.3740.3740.0000.0000.0000.000
63A88ASN0-0.054-0.0419.2600.1910.1910.0000.0000.0000.000
64A89LEU00.0300.01010.6390.0970.0970.0000.0000.0000.000
65A90GLN0-0.033-0.01212.1070.0760.0760.0000.0000.0000.000
66A91ARG10.8780.91713.1390.2160.2160.0000.0000.0000.000
67A92ILE0-0.017-0.0078.2130.0590.0590.0000.0000.0000.000
68A93ARG10.8280.91812.3320.0230.0230.0000.0000.0000.000
69A94TYR0-0.038-0.04314.7360.0220.0220.0000.0000.0000.000
70A95ARG10.8250.90417.421-0.110-0.1100.0000.0000.0000.000
71A96ASP-1-0.936-0.97118.6580.0400.0400.0000.0000.0000.000
72A97GLY0-0.049-0.02117.633-0.024-0.0240.0000.0000.0000.000
73A98LYS10.9060.97018.417-0.023-0.0230.0000.0000.0000.000
74A99ILE00.0110.01019.9590.0170.0170.0000.0000.0000.000
75A100ASP-1-0.971-1.00422.8390.0070.0070.0000.0000.0000.000
76A101GLY00.0700.04326.0750.0090.0090.0000.0000.0000.000
77A102TYR00.0490.02023.9870.0070.0070.0000.0000.0000.000
78A103THR0-0.037-0.01623.8720.0120.0120.0000.0000.0000.000
79A104SER00.0010.01022.9610.0100.0100.0000.0000.0000.000
80A105ARG10.8290.89018.509-0.089-0.0890.0000.0000.0000.000
81A106LEU0-0.085-0.03115.9290.0130.0130.0000.0000.0000.000
82A107HIS0-0.034-0.02317.4830.0490.0490.0000.0000.0000.000
83A108TYR0-0.046-0.04319.3780.0220.0220.0000.0000.0000.000
84A109ILE00.0930.02914.3750.0020.0020.0000.0000.0000.000
85A110SER0-0.062-0.07416.0810.0370.0370.0000.0000.0000.000
86A111ASP-1-0.866-0.94118.0450.1760.1760.0000.0000.0000.000
87A112TRP00.0140.0038.4790.0670.0670.0000.0000.0000.000
88A113ILE0-0.016-0.01312.8170.0070.0070.0000.0000.0000.000
89A114ASN0-0.058-0.02814.238-0.020-0.0200.0000.0000.0000.000
90A115ASN00.0180.01214.452-0.052-0.0520.0000.0000.0000.000
91A116ALA00.0390.02010.675-0.047-0.0470.0000.0000.0000.000
92A117VAL0-0.029-0.02112.801-0.043-0.0430.0000.0000.0000.000
93A118ARG10.8840.94214.267-0.190-0.1900.0000.0000.0000.000
94A119GLN0-0.0070.01014.134-0.079-0.0790.0000.0000.0000.000
95A120GLY0-0.0210.00013.901-0.050-0.0500.0000.0000.0000.000
96A121LEU0-0.043-0.0159.171-0.042-0.0420.0000.0000.0000.000
97A122LEU0-0.031-0.0186.5370.0680.0680.0000.0000.0000.000
98A123GLU-1-0.884-0.9419.8770.3170.3170.0000.0000.0000.000
99A124ASP-1-0.835-0.94111.6880.6270.6270.0000.0000.0000.000
100A125VAL00.0260.01010.745-0.081-0.0810.0000.0000.0000.000
101A126THR0-0.012-0.01913.998-0.044-0.0440.0000.0000.0000.000
102A127ALA0-0.015-0.01616.631-0.051-0.0510.0000.0000.0000.000
103A128ALA0-0.0220.01016.670-0.040-0.0400.0000.0000.0000.000
104A129TYR0-0.043-0.02015.171-0.021-0.0210.0000.0000.0000.000
105A130SER0-0.041-0.03319.491-0.034-0.0340.0000.0000.0000.000
106A131PRO00.0100.01721.409-0.004-0.0040.0000.0000.0000.000
107A132PHE0-0.050-0.02023.574-0.019-0.0190.0000.0000.0000.000
108A133LYS10.9130.94923.323-0.168-0.1680.0000.0000.0000.000
109A134GLN0-0.069-0.03023.597-0.013-0.0130.0000.0000.0000.000
110A135LYS10.9190.97425.159-0.137-0.1370.0000.0000.0000.000
111A136LEU0-0.004-0.00121.8600.0040.0040.0000.0000.0000.000
112A137SER0-0.006-0.01725.925-0.022-0.0220.0000.0000.0000.000
113A138LEU0-0.0230.00023.2020.0080.0080.0000.0000.0000.000
114A139SER0-0.017-0.01227.098-0.009-0.0090.0000.0000.0000.000
115A140TYR0-0.0010.00926.668-0.011-0.0110.0000.0000.0000.000
116A141MET0-0.035-0.02024.474-0.006-0.0060.0000.0000.0000.000
117A142SER0-0.074-0.06328.290-0.012-0.0120.0000.0000.0000.000
118A143THR0-0.027-0.00631.416-0.010-0.0100.0000.0000.0000.000
119A144HIS10.8420.93530.618-0.116-0.1160.0000.0000.0000.000
120A145PRO00.0960.05731.1730.0040.0040.0000.0000.0000.000
121A146GLU-1-0.873-0.96931.9730.0740.0740.0000.0000.0000.000
122A147LEU0-0.073-0.03227.549-0.003-0.0030.0000.0000.0000.000
123A148TYR00.0210.01024.5330.0010.0010.0000.0000.0000.000
124A149LYS10.9580.97827.864-0.033-0.0330.0000.0000.0000.000
125A150SER00.0340.00927.004-0.008-0.0080.0000.0000.0000.000
126A151LEU0-0.052-0.02228.1830.0000.0000.0000.0000.0000.000
127A152LYS10.9290.98131.244-0.058-0.0580.0000.0000.0000.000
128A153ASN0-0.0030.00034.013-0.002-0.0020.0000.0000.0000.000
129A154SER0-0.0060.00732.856-0.003-0.0030.0000.0000.0000.000
130A155PRO00.0830.03334.1970.0060.0060.0000.0000.0000.000
131A156GLU-1-0.885-0.94634.8640.0400.0400.0000.0000.0000.000
132A157ASN00.008-0.00430.0590.0030.0030.0000.0000.0000.000
133A158VAL00.0120.00930.5610.0090.0090.0000.0000.0000.000
134A159ALA0-0.020-0.00232.1040.0070.0070.0000.0000.0000.000
135A160GLN0-0.047-0.02128.472-0.003-0.0030.0000.0000.0000.000
136A161MET00.0400.01224.1710.0040.0040.0000.0000.0000.000
137A162ALA00.0380.02028.5230.0100.0100.0000.0000.0000.000
138A163LYS10.8580.93130.760-0.052-0.0520.0000.0000.0000.000
139A164TYR00.0370.00925.2350.0020.0020.0000.0000.0000.000
140A165GLU-1-0.728-0.82126.6220.1360.1360.0000.0000.0000.000
141A166LYS10.8930.95827.771-0.077-0.0770.0000.0000.0000.000
142A167ALA0-0.0280.00227.5190.0000.0000.0000.0000.0000.000
143A168LEU00.000-0.00221.8510.0040.0040.0000.0000.0000.000
144A169SER0-0.011-0.01726.0030.0150.0150.0000.0000.0000.000
145A170GLY0-0.049-0.02728.395-0.011-0.0110.0000.0000.0000.000
146A171LYS10.9370.96925.301-0.134-0.1340.0000.0000.0000.000
147A172GLU-1-0.849-0.91925.1290.1910.1910.0000.0000.0000.000
148A173VAL0-0.007-0.00120.0500.0080.0080.0000.0000.0000.000
149A174HIS00.0240.00619.655-0.028-0.0280.0000.0000.0000.000
150A175TYR0-0.049-0.02418.8420.0360.0360.0000.0000.0000.000
151A176LEU00.0140.02217.941-0.035-0.0350.0000.0000.0000.000
152A177PRO00.0010.01020.1390.0220.0220.0000.0000.0000.000
153A178LYS10.8910.93221.347-0.243-0.2430.0000.0000.0000.000
154A179ASP-1-0.980-0.99322.3840.2200.2200.0000.0000.0000.000
155A180LYS10.9000.95222.365-0.222-0.2220.0000.0000.0000.000
156A181LEU0-0.0300.00016.5890.0150.0150.0000.0000.0000.000
157A182GLU-1-0.852-0.93320.3490.2130.2130.0000.0000.0000.000
158A183PRO0-0.088-0.05019.3400.0410.0410.0000.0000.0000.000
159A184ASP-1-0.888-0.94218.3670.2940.2940.0000.0000.0000.000
160A185GLY0-0.0190.00115.8620.0250.0250.0000.0000.0000.000
161A186LEU00.006-0.00815.685-0.051-0.0510.0000.0000.0000.000
162A187PRO00.0340.01715.1180.0530.0530.0000.0000.0000.000
163A188TRP0-0.004-0.00614.0390.0300.0300.0000.0000.0000.000
164A189ILE0-0.0090.01511.0590.0710.0710.0000.0000.0000.000
165A190LYS10.9680.9928.063-0.632-0.6320.0000.0000.0000.000
166A191ASN00.0620.0115.8500.2200.2200.0000.0000.0000.000
167A192GLY0-0.026-0.0123.316-0.389-0.0260.070-0.167-0.2650.001
168A193ASP-1-0.740-0.8183.4592.1963.1340.023-0.384-0.577-0.003
169A194ILE00.0270.0135.2450.1820.1820.0000.0000.0000.000
170A195ILE0-0.044-0.0247.545-0.523-0.5230.0000.0000.0000.000
171A196ALA00.0260.01010.967-0.021-0.0210.0000.0000.0000.000
172A197LEU0-0.018-0.01413.992-0.073-0.0730.0000.0000.0000.000
173A198THR00.0330.00217.086-0.023-0.0230.0000.0000.0000.000
174A199THR0-0.068-0.04220.111-0.019-0.0190.0000.0000.0000.000
175A200ASN00.0160.00923.472-0.002-0.0020.0000.0000.0000.000
176A201THR0-0.019-0.00925.458-0.024-0.0240.0000.0000.0000.000
177A202PRO00.027-0.00527.5970.0050.0050.0000.0000.0000.000
178A203GLY00.0240.02928.6390.0000.0000.0000.0000.0000.000
179A204LEU00.0390.00323.1740.0010.0010.0000.0000.0000.000
180A205ASP-1-0.746-0.82620.3600.3040.3040.0000.0000.0000.000
181A206VAL0-0.029-0.03415.9740.0190.0190.0000.0000.0000.000
182A207SER0-0.086-0.03719.292-0.024-0.0240.0000.0000.0000.000
183A208HIS0-0.035-0.02815.282-0.032-0.0320.0000.0000.0000.000
184A209MET00.0440.01810.7940.0470.0470.0000.0000.0000.000
185A210GLY00.0200.0119.830-0.163-0.1630.0000.0000.0000.000
186A211ILE0-0.0170.0074.122-0.1640.1620.002-0.080-0.2470.000
187A212ALA0-0.0140.0007.114-0.633-0.6330.0000.0000.0000.000
188A213ILE00.0410.0097.0320.2190.2190.0000.0000.0000.000
189A214TYR0-0.041-0.0319.481-0.119-0.1190.0000.0000.0000.000
190A215ILE0-0.011-0.00512.250-0.064-0.0640.0000.0000.0000.000
191A216LYS10.9440.95414.861-0.156-0.1560.0000.0000.0000.000
192A217GLY00.0320.02216.527-0.013-0.0130.0000.0000.0000.000
193A218GLN00.0220.01817.2820.0170.0170.0000.0000.0000.000
194A219LEU00.0410.03911.5090.0280.0280.0000.0000.0000.000
195A220HIS10.7360.84613.083-0.426-0.4260.0000.0000.0000.000
196A221LEU00.0270.01910.7260.0980.0980.0000.0000.0000.000
197A222LEU0-0.0140.0116.804-0.179-0.1790.0000.0000.0000.000
198A223HIS00.0260.0009.8140.2670.2670.0000.0000.0000.000
199A224ALA00.1150.07411.754-0.115-0.1150.0000.0000.0000.000
200A225SER0-0.038-0.00813.7140.0140.0140.0000.0000.0000.000
201A226SER00.0640.01917.232-0.031-0.0310.0000.0000.0000.000
202A227LYS10.9070.95420.369-0.212-0.2120.0000.0000.0000.000
203A228GLU-1-0.958-0.99119.0150.1600.1600.0000.0000.0000.000
204A229GLY00.0050.01120.498-0.021-0.0210.0000.0000.0000.000
205A230LYS10.9610.98617.098-0.097-0.0970.0000.0000.0000.000
206A231VAL0-0.0170.00510.4400.0710.0710.0000.0000.0000.000
207A232VAL0-0.0110.00913.707-0.062-0.0620.0000.0000.0000.000
208A233VAL00.0550.02311.5630.1110.1110.0000.0000.0000.000
209A234GLY0-0.020-0.00913.814-0.060-0.0600.0000.0000.0000.000
210A235LYS10.9950.98816.313-0.158-0.1580.0000.0000.0000.000
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212A237ALA00.0180.01917.5740.0360.0360.0000.0000.0000.000
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