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: 1N76Z

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 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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2901247.522518
FMO2-HF: Nuclear repulsion 2809988.325381
FMO2-HF: Total energy -91259.197136
FMO2-MP2: Total energy -91523.019948


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.
-9.5740.9029.788-7.006-13.256-0.02
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 : 0.073 / q_NPA : 0.040
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].
3A28SER00.0020.0022.435-4.983-0.8291.644-2.301-3.497-0.003
4A29ASN00.0390.0092.189-1.1590.3142.402-1.099-2.776-0.004
5A30GLY00.0080.0023.7790.3770.9410.004-0.216-0.3520.001
6A31LEU0-0.032-0.0425.3880.6770.825-0.001-0.009-0.1380.000
7A32GLY00.0120.0237.2660.3150.3150.0000.0000.0000.000
8A33PHE00.0080.0076.9860.1870.1870.0000.0000.0000.000
9A34VAL0-0.072-0.02610.6200.1570.1570.0000.0000.0000.000
10A35ASP-1-0.846-0.92212.873-0.324-0.3240.0000.0000.0000.000
11A36THR0-0.015-0.00613.2150.0540.0540.0000.0000.0000.000
12A37PRO00.0090.00015.5310.0040.0040.0000.0000.0000.000
13A38TYR0-0.021-0.01515.905-0.007-0.0070.0000.0000.0000.000
14A39LYS10.7850.87617.7370.1980.1980.0000.0000.0000.000
15A40ALA0-0.001-0.00318.577-0.006-0.0060.0000.0000.0000.000
16A41GLY00.012-0.01520.2490.0030.0030.0000.0000.0000.000
17A42THR0-0.0090.00117.1230.0220.0220.0000.0000.0000.000
18A43LEU00.0160.01516.0340.0020.0020.0000.0000.0000.000
19A44GLU-1-0.830-0.89520.237-0.017-0.0170.0000.0000.0000.000
20A45VAL0-0.044-0.02923.0250.0080.0080.0000.0000.0000.000
21A46ASP-1-0.860-0.91224.673-0.078-0.0780.0000.0000.0000.000
22A47ASP-1-0.954-0.98927.076-0.035-0.0350.0000.0000.0000.000
23A48THR0-0.069-0.03127.9960.0080.0080.0000.0000.0000.000
24A49GLU-1-0.869-0.91321.438-0.017-0.0170.0000.0000.0000.000
25A50ASP-1-0.843-0.92623.047-0.014-0.0140.0000.0000.0000.000
26A51LEU0-0.040-0.02115.614-0.004-0.0040.0000.0000.0000.000
27A52ILE0-0.0080.01118.333-0.017-0.0170.0000.0000.0000.000
28A53ILE0-0.0010.00113.872-0.009-0.0090.0000.0000.0000.000
29A54ASN00.022-0.00615.313-0.023-0.0230.0000.0000.0000.000
30A55CYS0-0.035-0.02511.530-0.021-0.0210.0000.0000.0000.000
31A56ASP-1-0.866-0.92513.708-0.412-0.4120.0000.0000.0000.000
32A57GLU-1-0.841-0.91116.539-0.177-0.1770.0000.0000.0000.000
33A58VAL0-0.0080.00911.972-0.004-0.0040.0000.0000.0000.000
34A59ASP-1-0.806-0.87814.257-0.149-0.1490.0000.0000.0000.000
35A60CYS0-0.080-0.06012.414-0.050-0.0500.0000.0000.0000.000
36A61THR00.0060.00210.794-0.027-0.0270.0000.0000.0000.000
37A62THR00.034-0.00510.401-0.038-0.0380.0000.0000.0000.000
38A63PHE0-0.0300.0026.694-0.107-0.1070.0000.0000.0000.000
39A64VAL0-0.005-0.0115.546-0.306-0.3060.0000.0000.0000.000
40A65GLU-1-0.780-0.8765.7670.0960.0960.0000.0000.0000.000
41A66TYR00.0410.0277.6090.1790.1790.0000.0000.0000.000
42A67ALA00.0390.0153.199-0.487-0.1370.041-0.136-0.2550.000
43A68LEU0-0.034-0.0223.141-2.112-0.4880.102-0.860-0.866-0.007
44A69ALA00.0180.0074.4640.1990.297-0.001-0.005-0.0920.000
45A70MET00.0230.0025.066-0.078-0.0780.0000.0000.0000.000
46A71ALA0-0.068-0.0232.1710.369-0.7015.326-1.467-2.789-0.004
47A72LEU00.017-0.0043.667-0.399-0.1920.0120.054-0.2730.000
48A73CYS0-0.109-0.0176.839-0.092-0.0920.0000.0000.0000.000
49A74PRO00.0010.0057.592-0.103-0.1030.0000.0000.0000.000
50A75GLN00.0270.0249.782-0.032-0.0320.0000.0000.0000.000
51A76GLN0-0.018-0.0294.796-0.653-0.547-0.001-0.003-0.1020.000
52A77GLY00.0130.0027.8230.1120.1120.0000.0000.0000.000
53A78ASP-1-0.922-0.9709.873-0.392-0.3920.0000.0000.0000.000
54A79GLU-1-0.936-0.96512.238-0.204-0.2040.0000.0000.0000.000
55A80MET0-0.104-0.0318.7330.0090.0090.0000.0000.0000.000
56A81GLN00.005-0.00211.4660.0380.0380.0000.0000.0000.000
57A82GLU-1-0.880-0.96413.254-0.182-0.1820.0000.0000.0000.000
58A83GLY00.0470.02414.9340.0200.0200.0000.0000.0000.000
59A84ASP-1-0.843-0.91512.4590.0130.0130.0000.0000.0000.000
60A85PHE0-0.008-0.0028.7670.0620.0620.0000.0000.0000.000
61A86ALA00.0460.02811.7250.0630.0630.0000.0000.0000.000
62A87ARG10.8340.90314.636-0.020-0.0200.0000.0000.0000.000
63A88ASN0-0.036-0.0299.6770.1020.1020.0000.0000.0000.000
64A89LEU00.0240.00910.6500.0860.0860.0000.0000.0000.000
65A90GLN0-0.037-0.01612.1060.0110.0110.0000.0000.0000.000
66A91ARG10.8880.92213.664-0.399-0.3990.0000.0000.0000.000
67A92ILE0-0.020-0.0028.5630.0660.0660.0000.0000.0000.000
68A93ARG10.8230.90812.7450.0830.0830.0000.0000.0000.000
69A94TYR0-0.048-0.05214.801-0.024-0.0240.0000.0000.0000.000
70A95ARG10.7940.88217.816-0.091-0.0910.0000.0000.0000.000
71A96ASP-1-0.919-0.96019.1580.1820.1820.0000.0000.0000.000
72A97GLY0-0.040-0.01418.108-0.010-0.0100.0000.0000.0000.000
73A98LYS10.8100.90718.943-0.095-0.0950.0000.0000.0000.000
74A99ILE00.0200.01520.0570.0050.0050.0000.0000.0000.000
75A100ASP-1-0.887-0.94423.0300.0460.0460.0000.0000.0000.000
76A101GLY00.0650.03726.2690.0020.0020.0000.0000.0000.000
77A102TYR00.0280.01423.7110.0130.0130.0000.0000.0000.000
78A103THR0-0.040-0.01723.6250.0070.0070.0000.0000.0000.000
79A104SER0-0.0140.00823.1500.0140.0140.0000.0000.0000.000
80A105ARG10.8520.90318.2760.0360.0360.0000.0000.0000.000
81A106LEU0-0.076-0.02716.0590.0030.0030.0000.0000.0000.000
82A107HIS0-0.041-0.02917.070-0.005-0.0050.0000.0000.0000.000
83A108TYR0-0.056-0.05918.692-0.010-0.0100.0000.0000.0000.000
84A109ILE00.0850.02513.7760.0280.0280.0000.0000.0000.000
85A110SER0-0.043-0.06315.6600.0590.0590.0000.0000.0000.000
86A111ASP-1-0.869-0.93617.8690.2070.2070.0000.0000.0000.000
87A112TRP00.0130.0048.0690.0940.0940.0000.0000.0000.000
88A113ILE0-0.015-0.01412.4900.0670.0670.0000.0000.0000.000
89A114ASN0-0.033-0.01214.1680.0620.0620.0000.0000.0000.000
90A115ASN00.0250.01414.734-0.001-0.0010.0000.0000.0000.000
91A116ALA00.0380.02211.2030.0120.0120.0000.0000.0000.000
92A117VAL0-0.037-0.02713.3500.0480.0480.0000.0000.0000.000
93A118ARG10.8560.92714.873-0.278-0.2780.0000.0000.0000.000
94A119GLN0-0.0100.00314.994-0.021-0.0210.0000.0000.0000.000
95A120GLY0-0.0220.00014.331-0.011-0.0110.0000.0000.0000.000
96A121LEU0-0.048-0.01810.0870.0530.0530.0000.0000.0000.000
97A122LEU0-0.025-0.0146.9860.4080.4080.0000.0000.0000.000
98A123GLU-1-0.837-0.90910.2810.6470.6470.0000.0000.0000.000
99A124ASP-1-0.788-0.89911.6900.5620.5620.0000.0000.0000.000
100A125VAL00.0020.00110.728-0.085-0.0850.0000.0000.0000.000
101A126THR0-0.026-0.03214.030-0.080-0.0800.0000.0000.0000.000
102A127ALA0-0.036-0.02916.615-0.055-0.0550.0000.0000.0000.000
103A128ALA0-0.0160.01216.682-0.036-0.0360.0000.0000.0000.000
104A129TYR0-0.034-0.01715.041-0.018-0.0180.0000.0000.0000.000
105A130SER0-0.048-0.03819.481-0.042-0.0420.0000.0000.0000.000
106A131PRO00.0030.00721.3970.0060.0060.0000.0000.0000.000
107A132PHE0-0.047-0.01723.579-0.017-0.0170.0000.0000.0000.000
108A133LYS10.8920.92723.300-0.167-0.1670.0000.0000.0000.000
109A134GLN0-0.065-0.02322.902-0.028-0.0280.0000.0000.0000.000
110A135LYS10.8930.94724.722-0.102-0.1020.0000.0000.0000.000
111A136LEU00.0030.00621.416-0.009-0.0090.0000.0000.0000.000
112A137SER00.017-0.01025.419-0.008-0.0080.0000.0000.0000.000
113A138LEU0-0.050-0.00622.756-0.004-0.0040.0000.0000.0000.000
114A139SER0-0.026-0.01626.469-0.001-0.0010.0000.0000.0000.000
115A140TYR00.0080.02525.807-0.007-0.0070.0000.0000.0000.000
116A141MET0-0.021-0.00923.680-0.003-0.0030.0000.0000.0000.000
117A142SER0-0.078-0.06927.525-0.007-0.0070.0000.0000.0000.000
118A143THR0-0.043-0.03130.641-0.003-0.0030.0000.0000.0000.000
119A144HIS10.8320.92729.832-0.016-0.0160.0000.0000.0000.000
120A145PRO00.1060.06230.452-0.004-0.0040.0000.0000.0000.000
121A146GLU-1-0.839-0.94631.3980.0000.0000.0000.0000.0000.000
122A147LEU0-0.066-0.02526.897-0.006-0.0060.0000.0000.0000.000
123A148TYR00.0320.01423.837-0.005-0.0050.0000.0000.0000.000
124A149LYS10.9200.97427.6590.0500.0500.0000.0000.0000.000
125A150SER00.0210.00126.4470.0000.0000.0000.0000.0000.000
126A151LEU0-0.048-0.02227.5060.0080.0080.0000.0000.0000.000
127A152LYS10.8690.94330.7840.0230.0230.0000.0000.0000.000
128A153ASN00.0040.00333.5490.0010.0010.0000.0000.0000.000
129A154SER0-0.0120.00532.5250.0020.0020.0000.0000.0000.000
130A155PRO00.0570.02733.7540.0030.0030.0000.0000.0000.000
131A156GLU-1-0.846-0.93334.6190.0200.0200.0000.0000.0000.000
132A157ASN0-0.002-0.01129.6540.0110.0110.0000.0000.0000.000
133A158VAL00.0120.01030.2170.0070.0070.0000.0000.0000.000
134A159ALA0-0.0140.00031.6980.0060.0060.0000.0000.0000.000
135A160GLN00.0040.00428.5090.0020.0020.0000.0000.0000.000
136A161MET00.0380.01323.6740.0100.0100.0000.0000.0000.000
137A162ALA00.0240.01028.1760.0080.0080.0000.0000.0000.000
138A163LYS10.8300.91530.540-0.050-0.0500.0000.0000.0000.000
139A164TYR00.0470.01325.0650.0100.0100.0000.0000.0000.000
140A165GLU-1-0.722-0.80726.4250.0670.0670.0000.0000.0000.000
141A166LYS10.9000.96227.411-0.053-0.0530.0000.0000.0000.000
142A167ALA0-0.0310.00227.4990.0030.0030.0000.0000.0000.000
143A168LEU00.005-0.00322.0440.0110.0110.0000.0000.0000.000
144A169SER0-0.002-0.01125.8260.0070.0070.0000.0000.0000.000
145A170GLY0-0.032-0.02028.050-0.003-0.0030.0000.0000.0000.000
146A171LYS10.9220.97425.130-0.137-0.1370.0000.0000.0000.000
147A172GLU-1-0.854-0.90925.4030.1730.1730.0000.0000.0000.000
148A173VAL00.0040.00219.8050.0170.0170.0000.0000.0000.000
149A174HIS00.0380.01419.753-0.031-0.0310.0000.0000.0000.000
150A175TYR0-0.022-0.02018.8150.0220.0220.0000.0000.0000.000
151A176LEU00.0160.02917.831-0.009-0.0090.0000.0000.0000.000
152A177PRO00.0070.01220.115-0.009-0.0090.0000.0000.0000.000
153A178LYS10.8760.92221.326-0.049-0.0490.0000.0000.0000.000
154A179ASP-1-0.892-0.93622.3550.0970.0970.0000.0000.0000.000
155A180LYS10.8170.89622.304-0.113-0.1130.0000.0000.0000.000
156A181LEU0-0.0270.00216.5320.0140.0140.0000.0000.0000.000
157A182GLU-1-0.805-0.91820.3260.0570.0570.0000.0000.0000.000
158A183PRO0-0.078-0.04019.3270.0080.0080.0000.0000.0000.000
159A184ASP-1-0.888-0.94318.3890.0870.0870.0000.0000.0000.000
160A185GLY0-0.0160.00015.8560.0230.0230.0000.0000.0000.000
161A186LEU00.002-0.00715.678-0.015-0.0150.0000.0000.0000.000
162A187PRO00.0320.01014.9500.0400.0400.0000.0000.0000.000
163A188TRP0-0.012-0.00813.9290.0410.0410.0000.0000.0000.000
164A189ILE0-0.0160.00811.0270.0850.0850.0000.0000.0000.000
165A190LYS10.9640.9867.904-0.804-0.8040.0000.0000.0000.000
166A191ASN00.0550.0076.062-0.044-0.0440.0000.0000.0000.000
167A192GLY0-0.017-0.0073.3290.0260.4030.073-0.172-0.2770.001
168A193ASP-1-0.746-0.8203.4371.3352.2930.026-0.412-0.571-0.003
169A194ILE00.0290.0145.047-0.565-0.5650.0000.0000.0000.000
170A195ILE0-0.046-0.0277.1320.0090.0090.0000.0000.0000.000
171A196ALA00.0290.01710.588-0.113-0.1130.0000.0000.0000.000
172A197LEU0-0.009-0.01113.1650.0130.0130.0000.0000.0000.000
173A198THR00.029-0.00416.325-0.009-0.0090.0000.0000.0000.000
174A199THR0-0.076-0.06319.345-0.024-0.0240.0000.0000.0000.000
175A200ASN00.0250.01522.5460.0040.0040.0000.0000.0000.000
176A201THR00.0010.00224.473-0.008-0.0080.0000.0000.0000.000
177A202PRO00.012-0.01126.6750.0060.0060.0000.0000.0000.000
178A203GLY00.0250.02827.767-0.006-0.0060.0000.0000.0000.000
179A204LEU00.0310.00122.3660.0010.0010.0000.0000.0000.000
180A205ASP-1-0.751-0.83319.7120.1380.1380.0000.0000.0000.000
181A206VAL0-0.022-0.03115.0860.0110.0110.0000.0000.0000.000
182A207SER0-0.070-0.03118.373-0.022-0.0220.0000.0000.0000.000
183A208HIS0-0.016-0.02013.9210.0030.0030.0000.0000.0000.000
184A209MET00.0330.02210.0700.1080.1080.0000.0000.0000.000
185A210GLY00.0100.0068.819-0.095-0.0950.0000.0000.0000.000
186A211ILE0-0.0080.0052.835-0.3350.2480.059-0.183-0.4590.000
187A212ALA0-0.0120.0046.700-0.098-0.0980.0000.0000.0000.000
188A213ILE00.0250.0057.0180.0430.0430.0000.0000.0000.000
189A214TYR0-0.031-0.0289.472-0.044-0.0440.0000.0000.0000.000
190A215ILE0-0.002-0.00412.321-0.039-0.0390.0000.0000.0000.000
191A216LYS10.9450.95914.9320.0820.0820.0000.0000.0000.000
192A217GLY00.0270.02016.6070.0050.0050.0000.0000.0000.000
193A218GLN00.0320.03117.3840.0060.0060.0000.0000.0000.000
194A219LEU00.0190.03311.569-0.018-0.0180.0000.0000.0000.000
195A220HIS10.7570.83913.0760.0670.0670.0000.0000.0000.000
196A221LEU00.0250.02110.3770.0470.0470.0000.0000.0000.000
197A222LEU0-0.0080.0116.5060.0330.0330.0000.0000.0000.000
198A223HIS00.0230.0068.879-0.026-0.0260.0000.0000.0000.000
199A224ALA00.1070.06710.963-0.006-0.0060.0000.0000.0000.000
200A225SER0-0.033-0.01113.1720.0820.0820.0000.0000.0000.000
201A226SER00.0710.02516.583-0.006-0.0060.0000.0000.0000.000
202A227LYS10.9060.95419.7740.1020.1020.0000.0000.0000.000
203A228GLU-1-0.867-0.93518.591-0.181-0.1810.0000.0000.0000.000
204A229GLY00.0330.02820.026-0.002-0.0020.0000.0000.0000.000
205A230LYS10.8640.92416.9650.2870.2870.0000.0000.0000.000
206A231VAL0-0.0180.00110.3690.0410.0410.0000.0000.0000.000
207A232VAL0-0.0120.00713.2450.0170.0170.0000.0000.0000.000
208A233VAL00.0520.02511.466-0.039-0.0390.0000.0000.0000.000
209A234GLY0-0.024-0.00813.4880.0500.0500.0000.0000.0000.000
210A235LYS10.8660.91015.9550.1850.1850.0000.0000.0000.000
211A236THR0-0.0130.00319.1610.0120.0120.0000.0000.0000.000
212A237ALA00.0150.00917.550-0.010-0.0100.0000.0000.0000.000
213A238LEU00.0580.01013.451-0.004-0.0040.0000.0000.0000.000
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