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: G56Y1

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 OptAll
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 -2905003.865403
FMO2-HF: Nuclear repulsion 2813744.33187
FMO2-HF: Total energy -91259.533533
FMO2-MP2: Total energy -91523.278453


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.
-11.7380.9547.131-7.308-12.516-0.031
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 : 0.076 / q_NPA : 0.047
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].
3A28SER0-0.0100.0022.449-4.201-0.5141.287-2.051-2.923-0.003
4A29ASN00.0430.0112.603-0.9650.9280.697-0.709-1.881-0.004
5A30GLY00.0140.0063.9610.4750.8860.000-0.157-0.2530.000
6A31LEU0-0.048-0.0495.4770.8430.8430.0000.0000.0000.000
7A32GLY00.0080.0187.3180.3230.3230.0000.0000.0000.000
8A33PHE00.0230.0187.2480.2080.2080.0000.0000.0000.000
9A34VAL0-0.055-0.02410.6360.1670.1670.0000.0000.0000.000
10A35ASP-1-0.855-0.92512.859-0.335-0.3350.0000.0000.0000.000
11A36THR0-0.014-0.00113.3330.0620.0620.0000.0000.0000.000
12A37PRO00.008-0.00215.5580.0070.0070.0000.0000.0000.000
13A38TYR0-0.015-0.01015.984-0.005-0.0050.0000.0000.0000.000
14A39LYS10.7790.86817.4160.2020.2020.0000.0000.0000.000
15A40ALA00.0080.00418.253-0.002-0.0020.0000.0000.0000.000
16A41GLY00.009-0.01319.9830.0000.0000.0000.0000.0000.000
17A42THR0-0.023-0.00716.5770.0260.0260.0000.0000.0000.000
18A43LEU00.0170.01715.864-0.002-0.0020.0000.0000.0000.000
19A44GLU-1-0.809-0.87020.195-0.007-0.0070.0000.0000.0000.000
20A45VAL0-0.037-0.02023.0310.0070.0070.0000.0000.0000.000
21A46ASP-1-0.827-0.91124.471-0.072-0.0720.0000.0000.0000.000
22A47ASP-1-0.910-0.94626.855-0.032-0.0320.0000.0000.0000.000
23A48THR0-0.073-0.04227.5750.0080.0080.0000.0000.0000.000
24A49GLU-1-0.875-0.90720.976-0.007-0.0070.0000.0000.0000.000
25A50ASP-1-0.809-0.90722.647-0.009-0.0090.0000.0000.0000.000
26A51LEU0-0.033-0.01315.517-0.004-0.0040.0000.0000.0000.000
27A52ILE0-0.025-0.00918.765-0.025-0.0250.0000.0000.0000.000
28A53ILE0-0.0110.00614.123-0.011-0.0110.0000.0000.0000.000
29A54ASN0-0.012-0.01315.813-0.029-0.0290.0000.0000.0000.000
30A55CYS0-0.017-0.01011.831-0.016-0.0160.0000.0000.0000.000
31A56ASP-1-0.856-0.92713.870-0.427-0.4270.0000.0000.0000.000
32A57GLU-1-0.813-0.89516.677-0.179-0.1790.0000.0000.0000.000
33A58VAL0-0.0100.00511.683-0.015-0.0150.0000.0000.0000.000
34A59ASP-1-0.771-0.84514.041-0.128-0.1280.0000.0000.0000.000
35A60CYS0-0.059-0.05112.141-0.063-0.0630.0000.0000.0000.000
36A61THR0-0.045-0.02110.702-0.001-0.0010.0000.0000.0000.000
37A62THR00.031-0.02510.017-0.044-0.0440.0000.0000.0000.000
38A63PHE0-0.0300.0016.602-0.105-0.1050.0000.0000.0000.000
39A64VAL00.001-0.0065.354-0.377-0.3770.0000.0000.0000.000
40A65GLU-1-0.801-0.8955.5730.2000.2000.0000.0000.0000.000
41A66TYR00.0410.0147.4710.1930.1930.0000.0000.0000.000
42A67ALA00.0250.0133.092-0.555-0.1480.057-0.167-0.2980.000
43A68LEU0-0.014-0.0162.763-3.875-1.4320.470-1.415-1.499-0.013
44A69ALA00.0110.0064.197-0.0360.0710.001-0.007-0.1000.000
45A70MET00.017-0.0015.013-0.110-0.1100.0000.0000.0000.000
46A71ALA0-0.040-0.0072.1940.061-0.3144.067-1.236-2.456-0.003
47A72LEU00.003-0.0123.796-0.332-0.1200.009-0.008-0.2120.000
48A73CYS0-0.093-0.0097.099-0.086-0.0860.0000.0000.0000.000
49A74PRO0-0.016-0.0027.949-0.078-0.0780.0000.0000.0000.000
50A75GLN00.0250.02710.4380.0020.0020.0000.0000.0000.000
51A76GLN0-0.036-0.0444.981-0.663-0.571-0.001-0.001-0.0900.000
52A77GLY00.0230.0108.0170.1030.1030.0000.0000.0000.000
53A78ASP-1-0.918-0.9679.989-0.412-0.4120.0000.0000.0000.000
54A79GLU-1-0.933-0.96512.346-0.221-0.2210.0000.0000.0000.000
55A80MET0-0.109-0.0368.864-0.005-0.0050.0000.0000.0000.000
56A81GLN00.007-0.00311.5990.0310.0310.0000.0000.0000.000
57A82GLU-1-0.869-0.94513.390-0.181-0.1810.0000.0000.0000.000
58A83GLY00.0510.01914.6770.0200.0200.0000.0000.0000.000
59A84ASP-1-0.859-0.92212.4370.0240.0240.0000.0000.0000.000
60A85PHE00.008-0.0018.7800.0690.0690.0000.0000.0000.000
61A86ALA00.0420.02911.4370.0690.0690.0000.0000.0000.000
62A87ARG10.8400.90714.313-0.018-0.0180.0000.0000.0000.000
63A88ASN0-0.019-0.0259.6640.1200.1200.0000.0000.0000.000
64A89LEU00.0200.00710.7710.1050.1050.0000.0000.0000.000
65A90GLN0-0.055-0.02611.8240.0210.0210.0000.0000.0000.000
66A91ARG10.8720.92413.319-0.438-0.4380.0000.0000.0000.000
67A92ILE0-0.0190.0068.1820.0690.0690.0000.0000.0000.000
68A93ARG10.8360.90612.3220.0720.0720.0000.0000.0000.000
69A94TYR0-0.046-0.05314.581-0.028-0.0280.0000.0000.0000.000
70A95ARG10.7820.87917.586-0.112-0.1120.0000.0000.0000.000
71A96ASP-1-0.926-0.96418.9770.2070.2070.0000.0000.0000.000
72A97GLY0-0.0180.00017.972-0.009-0.0090.0000.0000.0000.000
73A98LYS10.7700.88718.862-0.105-0.1050.0000.0000.0000.000
74A99ILE00.0320.02319.8390.0050.0050.0000.0000.0000.000
75A100ASP-1-0.858-0.94222.7030.0610.0610.0000.0000.0000.000
76A101GLY00.0600.03925.8730.0000.0000.0000.0000.0000.000
77A102TYR0-0.007-0.02223.8250.0170.0170.0000.0000.0000.000
78A103THR0-0.035-0.01623.3870.0090.0090.0000.0000.0000.000
79A104SER0-0.0170.00122.9490.0160.0160.0000.0000.0000.000
80A105ARG10.8390.90218.1910.0240.0240.0000.0000.0000.000
81A106LEU0-0.079-0.02415.8810.0010.0010.0000.0000.0000.000
82A107HIS0-0.020-0.02716.7650.0020.0020.0000.0000.0000.000
83A108TYR0-0.046-0.05018.565-0.009-0.0090.0000.0000.0000.000
84A109ILE00.0710.03113.7520.0300.0300.0000.0000.0000.000
85A110SER0-0.035-0.06715.4300.0670.0670.0000.0000.0000.000
86A111ASP-1-0.838-0.92017.7130.2410.2410.0000.0000.0000.000
87A112TRP00.0110.0117.7290.0960.0960.0000.0000.0000.000
88A113ILE0-0.006-0.00812.2740.0730.0730.0000.0000.0000.000
89A114ASN0-0.043-0.00813.9000.0620.0620.0000.0000.0000.000
90A115ASN00.0310.01614.6560.0040.0040.0000.0000.0000.000
91A116ALA00.0470.02510.9150.0160.0160.0000.0000.0000.000
92A117VAL0-0.049-0.02313.0200.0540.0540.0000.0000.0000.000
93A118ARG10.8400.91114.712-0.318-0.3180.0000.0000.0000.000
94A119GLN0-0.012-0.00514.812-0.028-0.0280.0000.0000.0000.000
95A120GLY0-0.019-0.00313.929-0.006-0.0060.0000.0000.0000.000
96A121LEU0-0.031-0.0129.7460.0590.0590.0000.0000.0000.000
97A122LEU0-0.022-0.0216.8290.5040.5040.0000.0000.0000.000
98A123GLU-1-0.821-0.89110.0440.6460.6460.0000.0000.0000.000
99A124ASP-1-0.789-0.88511.3810.6220.6220.0000.0000.0000.000
100A125VAL00.0080.00110.183-0.093-0.0930.0000.0000.0000.000
101A126THR0-0.024-0.04413.489-0.085-0.0850.0000.0000.0000.000
102A127ALA0-0.034-0.03416.308-0.059-0.0590.0000.0000.0000.000
103A128ALA0-0.0230.00915.803-0.037-0.0370.0000.0000.0000.000
104A129TYR0-0.022-0.01114.503-0.019-0.0190.0000.0000.0000.000
105A130SER0-0.048-0.03118.728-0.045-0.0450.0000.0000.0000.000
106A131PRO00.0000.00921.0500.0070.0070.0000.0000.0000.000
107A132PHE0-0.027-0.01023.180-0.017-0.0170.0000.0000.0000.000
108A133LYS10.8660.91422.827-0.183-0.1830.0000.0000.0000.000
109A134GLN0-0.033-0.00222.577-0.029-0.0290.0000.0000.0000.000
110A135LYS10.9060.94424.918-0.119-0.1190.0000.0000.0000.000
111A136LEU00.0040.01721.278-0.010-0.0100.0000.0000.0000.000
112A137SER00.008-0.01425.247-0.009-0.0090.0000.0000.0000.000
113A138LEU0-0.049-0.00222.312-0.007-0.0070.0000.0000.0000.000
114A139SER0-0.015-0.01426.062-0.001-0.0010.0000.0000.0000.000
115A140TYR0-0.0050.01525.651-0.008-0.0080.0000.0000.0000.000
116A141MET0-0.023-0.00523.343-0.003-0.0030.0000.0000.0000.000
117A142SER0-0.071-0.07027.316-0.008-0.0080.0000.0000.0000.000
118A143THR0-0.061-0.04830.416-0.004-0.0040.0000.0000.0000.000
119A144HIS10.8420.93029.607-0.023-0.0230.0000.0000.0000.000
120A145PRO00.1030.05729.967-0.003-0.0030.0000.0000.0000.000
121A146GLU-1-0.842-0.94431.1090.0050.0050.0000.0000.0000.000
122A147LEU0-0.056-0.01626.350-0.006-0.0060.0000.0000.0000.000
123A148TYR00.0400.01723.464-0.005-0.0050.0000.0000.0000.000
124A149LYS10.8400.91127.4700.0480.0480.0000.0000.0000.000
125A150SER00.0270.01026.383-0.001-0.0010.0000.0000.0000.000
126A151LEU0-0.067-0.02627.0520.0070.0070.0000.0000.0000.000
127A152LYS10.8580.93230.6450.0190.0190.0000.0000.0000.000
128A153ASN00.0180.01133.4020.0010.0010.0000.0000.0000.000
129A154SER0-0.015-0.01732.5690.0010.0010.0000.0000.0000.000
130A155PRO00.0420.01733.4330.0040.0040.0000.0000.0000.000
131A156GLU-1-0.820-0.89534.1920.0260.0260.0000.0000.0000.000
132A157ASN00.000-0.00629.2360.0120.0120.0000.0000.0000.000
133A158VAL00.0100.01329.8470.0080.0080.0000.0000.0000.000
134A159ALA00.0120.00231.3470.0070.0070.0000.0000.0000.000
135A160GLN0-0.035-0.00628.0860.0010.0010.0000.0000.0000.000
136A161MET00.0320.01023.3450.0120.0120.0000.0000.0000.000
137A162ALA00.0080.00727.9080.0090.0090.0000.0000.0000.000
138A163LYS10.8860.94430.472-0.061-0.0610.0000.0000.0000.000
139A164TYR00.0590.02024.7300.0110.0110.0000.0000.0000.000
140A165GLU-1-0.716-0.80426.1540.0790.0790.0000.0000.0000.000
141A166LYS10.8690.93527.132-0.064-0.0640.0000.0000.0000.000
142A167ALA0-0.035-0.00327.0770.0030.0030.0000.0000.0000.000
143A168LEU0-0.013-0.00721.9650.0120.0120.0000.0000.0000.000
144A169SER00.019-0.00125.4790.0080.0080.0000.0000.0000.000
145A170GLY0-0.033-0.01227.6850.0000.0000.0000.0000.0000.000
146A171LYS10.9120.95625.107-0.148-0.1480.0000.0000.0000.000
147A172GLU-1-0.863-0.91225.5510.1920.1920.0000.0000.0000.000
148A173VAL00.0140.00119.9460.0170.0170.0000.0000.0000.000
149A174HIS00.0330.01519.721-0.034-0.0340.0000.0000.0000.000
150A175TYR0-0.021-0.02218.3990.0250.0250.0000.0000.0000.000
151A176LEU00.0290.03517.223-0.009-0.0090.0000.0000.0000.000
152A177PRO0-0.0120.00319.660-0.009-0.0090.0000.0000.0000.000
153A178LYS10.8450.91221.146-0.057-0.0570.0000.0000.0000.000
154A179ASP-1-0.871-0.92022.1670.1000.1000.0000.0000.0000.000
155A180LYS10.7960.89122.001-0.122-0.1220.0000.0000.0000.000
156A181LEU00.0120.00916.3210.0190.0190.0000.0000.0000.000
157A182GLU-1-0.740-0.86820.3580.0610.0610.0000.0000.0000.000
158A183PRO0-0.083-0.04319.3150.0080.0080.0000.0000.0000.000
159A184ASP-1-0.876-0.93218.4500.0820.0820.0000.0000.0000.000
160A185GLY0-0.009-0.00215.9550.0200.0200.0000.0000.0000.000
161A186LEU00.020-0.00515.444-0.011-0.0110.0000.0000.0000.000
162A187PRO00.0210.00814.5800.0460.0460.0000.0000.0000.000
163A188TRP00.0080.01113.4970.0360.0360.0000.0000.0000.000
164A189ILE00.0020.00810.9570.1040.1040.0000.0000.0000.000
165A190LYS10.9240.9707.577-0.819-0.8190.0000.0000.0000.000
166A191ASN00.0410.0096.096-0.009-0.0090.0000.0000.0000.000
167A192GLY0-0.017-0.0052.948-0.2200.3210.181-0.289-0.4340.002
168A193ASP-1-0.751-0.8263.0170.6962.4750.184-0.872-1.091-0.009
169A194ILE00.0260.0174.499-0.717-0.630-0.001-0.008-0.0790.000
170A195ILE0-0.042-0.0246.902-0.038-0.0380.0000.0000.0000.000
171A196ALA00.0290.01510.411-0.113-0.1130.0000.0000.0000.000
172A197LEU0-0.005-0.00913.1320.0090.0090.0000.0000.0000.000
173A198THR00.0330.00616.437-0.012-0.0120.0000.0000.0000.000
174A199THR0-0.081-0.06219.388-0.025-0.0250.0000.0000.0000.000
175A200ASN00.0110.00222.6070.0050.0050.0000.0000.0000.000
176A201THR00.0080.01224.520-0.009-0.0090.0000.0000.0000.000
177A202PRO0-0.006-0.02026.6990.0070.0070.0000.0000.0000.000
178A203GLY00.0550.04627.740-0.006-0.0060.0000.0000.0000.000
179A204LEU00.0140.00222.1620.0020.0020.0000.0000.0000.000
180A205ASP-1-0.768-0.85319.3190.1750.1750.0000.0000.0000.000
181A206VAL0-0.027-0.02715.0740.0100.0100.0000.0000.0000.000
182A207SER0-0.034-0.01518.140-0.024-0.0240.0000.0000.0000.000
183A208HIS0-0.009-0.01013.8590.0050.0050.0000.0000.0000.000
184A209MET00.0020.0019.9690.1180.1180.0000.0000.0000.000
185A210GLY00.0230.0148.506-0.111-0.1110.0000.0000.0000.000
186A211ILE0-0.0110.0082.633-0.5050.2310.152-0.248-0.6400.000
187A212ALA0-0.0090.0016.659-0.140-0.1400.0000.0000.0000.000
188A213ILE00.0250.0057.0450.0430.0430.0000.0000.0000.000
189A214TYR0-0.041-0.0369.606-0.025-0.0250.0000.0000.0000.000
190A215ILE0-0.016-0.01312.340-0.045-0.0450.0000.0000.0000.000
191A216LYS10.9380.95215.0630.0950.0950.0000.0000.0000.000
192A217GLY00.0280.02216.7990.0070.0070.0000.0000.0000.000
193A218GLN00.0350.03017.4390.0100.0100.0000.0000.0000.000
194A219LEU00.0220.03011.490-0.020-0.0200.0000.0000.0000.000
195A220HIS10.7580.85713.1380.0680.0680.0000.0000.0000.000
196A221LEU00.0210.02210.1900.0520.0520.0000.0000.0000.000
197A222LEU0-0.0190.0006.9580.0380.0380.0000.0000.0000.000
198A223HIS00.0380.0038.846-0.031-0.0310.0000.0000.0000.000
199A224ALA00.1090.06810.911-0.008-0.0080.0000.0000.0000.000
200A225SER0-0.031-0.01813.1170.0890.0890.0000.0000.0000.000
201A226SER00.0550.01816.457-0.002-0.0020.0000.0000.0000.000
202A227LYS10.9150.95519.5160.0950.0950.0000.0000.0000.000
203A228GLU-1-0.861-0.91918.877-0.185-0.1850.0000.0000.0000.000
204A229GLY00.0310.02620.575-0.011-0.0110.0000.0000.0000.000
205A230LYS10.8610.93217.0330.2930.2930.0000.0000.0000.000
206A231VAL0-0.0160.00610.5260.0410.0410.0000.0000.0000.000
207A232VAL0-0.029-0.00713.3400.0150.0150.0000.0000.0000.000
208A233VAL00.0420.01911.808-0.033-0.0330.0000.0000.0000.000
209A234GLY0-0.022-0.00813.7420.0470.0470.0000.0000.0000.000
210A235LYS10.8480.90116.0920.2070.2070.0000.0000.0000.000
211A236THR00.0040.00419.0050.0100.0100.0000.0000.0000.000
212A237ALA00.0190.01117.624-0.014-0.0140.0000.0000.0000.000
213A238LEU00.0360.00313.018-0.004-0.0040.0000.0000.0000.000
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