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: NN98Q

Calculation Name: 2PAQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PAQ

Chain ID: A

ChEMBL ID:

UniProt ID: P76491

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1879446.724605
FMO2-HF: Nuclear repulsion 1807935.777406
FMO2-HF: Total energy -71510.947199
FMO2-MP2: Total energy -71717.721551


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:2:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-56.885-55.302-0.005-0.731-0.8470.003
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.960 / q_NPA : 0.967
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].
3A4SER00.0240.0033.7193.2264.809-0.005-0.731-0.8470.003
4A5HIS00.013-0.0096.174-0.230-0.2300.0000.0000.0000.000
5A6PHE00.0520.0319.3681.9891.9890.0000.0000.0000.000
6A7PHE00.0890.03011.3971.3421.3420.0000.0000.0000.000
7A8ALA0-0.050-0.01612.2901.3631.3630.0000.0000.0000.000
8A9HIS0-0.009-0.03212.5282.0742.0740.0000.0000.0000.000
9A10LEU00.0880.05315.4181.0571.0570.0000.0000.0000.000
10A11SER0-0.051-0.01617.2291.4461.4460.0000.0000.0000.000
11A12ARG10.9170.93917.60916.53716.5370.0000.0000.0000.000
12A13LEU00.0960.03720.7860.5250.5250.0000.0000.0000.000
13A14LYS10.8820.95221.51814.67814.6780.0000.0000.0000.000
14A15LEU0-0.119-0.05722.4500.3160.3160.0000.0000.0000.000
15A16ILE00.0000.03922.9410.2410.2410.0000.0000.0000.000
16A17ASN0-0.025-0.01827.0310.0560.0560.0000.0000.0000.000
17A18ARG10.9540.97430.8079.3769.3760.0000.0000.0000.000
18A19TRP0-0.093-0.04432.9830.2760.2760.0000.0000.0000.000
19A20PRO00.0540.02433.9920.1820.1820.0000.0000.0000.000
20A21LEU0-0.067-0.04336.1400.0950.0950.0000.0000.0000.000
21A22MET00.0190.03139.4730.1270.1270.0000.0000.0000.000
22A23ARG10.9540.97740.4456.7276.7270.0000.0000.0000.000
23A24ASN0-0.053-0.01638.5230.0090.0090.0000.0000.0000.000
24A25VAL0-0.065-0.05541.3130.0190.0190.0000.0000.0000.000
25A26ARG10.8430.90133.8269.0349.0340.0000.0000.0000.000
26A27THR0-0.027-0.01534.8890.0700.0700.0000.0000.0000.000
27A28GLU-1-0.819-0.89633.074-9.019-9.0190.0000.0000.0000.000
28A29ASN00.0260.01328.537-0.245-0.2450.0000.0000.0000.000
29A30VAL00.1020.03025.7390.1690.1690.0000.0000.0000.000
30A31SER0-0.093-0.01525.234-0.074-0.0740.0000.0000.0000.000
31A32GLU-1-0.802-0.89926.807-9.730-9.7300.0000.0000.0000.000
32A33HIS00.0180.01330.1010.2430.2430.0000.0000.0000.000
33A34SER00.0170.00226.4430.1460.1460.0000.0000.0000.000
34A35LEU0-0.039-0.01127.9160.0360.0360.0000.0000.0000.000
35A36GLN00.0150.00929.3670.1670.1670.0000.0000.0000.000
36A37VAL00.0580.01030.4800.2530.2530.0000.0000.0000.000
37A38ALA00.003-0.00828.2430.1810.1810.0000.0000.0000.000
38A39MET0-0.059-0.02530.2670.2310.2310.0000.0000.0000.000
39A40VAL00.008-0.00333.2160.2430.2430.0000.0000.0000.000
40A41ALA00.0310.01131.7660.2250.2250.0000.0000.0000.000
41A42HIS00.0010.00031.9580.0460.0460.0000.0000.0000.000
42A43ALA00.0050.00433.6510.1890.1890.0000.0000.0000.000
43A44LEU0-0.024-0.01636.9960.2550.2550.0000.0000.0000.000
44A45ALA00.0300.02134.6970.1750.1750.0000.0000.0000.000
45A46ALA0-0.029-0.01836.7040.1730.1730.0000.0000.0000.000
46A47ILE00.0050.00238.3130.2190.2190.0000.0000.0000.000
47A48LYS10.9100.98738.9207.5577.5570.0000.0000.0000.000
48A49ASN0-0.023-0.02336.4480.2530.2530.0000.0000.0000.000
49A50ARG10.8740.95640.8767.3107.3100.0000.0000.0000.000
50A51LYS10.8590.91243.3856.5256.5250.0000.0000.0000.000
51A52PHE0-0.0120.00244.2890.1480.1480.0000.0000.0000.000
52A53GLY0-0.0010.01044.9500.0010.0010.0000.0000.0000.000
53A54GLY0-0.024-0.00340.612-0.031-0.0310.0000.0000.0000.000
54A55ASN0-0.017-0.02037.9040.0310.0310.0000.0000.0000.000
55A56VAL00.0180.01734.366-0.164-0.1640.0000.0000.0000.000
56A57ASN00.0650.04528.6220.0360.0360.0000.0000.0000.000
57A58ALA00.032-0.00331.028-0.205-0.2050.0000.0000.0000.000
58A59GLU-1-0.865-0.93428.087-9.578-9.5780.0000.0000.0000.000
59A60ARG10.9000.95121.63111.54611.5460.0000.0000.0000.000
60A61ILE00.0420.02326.813-0.325-0.3250.0000.0000.0000.000
61A62ALA00.0030.00628.195-0.094-0.0940.0000.0000.0000.000
62A63LEU00.003-0.00221.002-0.225-0.2250.0000.0000.0000.000
63A64LEU0-0.034-0.02123.882-0.408-0.4080.0000.0000.0000.000
64A65ALA00.0250.02425.383-0.128-0.1280.0000.0000.0000.000
65A66MET0-0.082-0.04723.190-0.030-0.0300.0000.0000.0000.000
66A67TYR0-0.069-0.04116.912-0.648-0.6480.0000.0000.0000.000
67A68HIS0-0.0450.00422.7080.0790.0790.0000.0000.0000.000
68A69ASP-1-0.757-0.87525.129-10.516-10.5160.0000.0000.0000.000
69A70ALA0-0.036-0.02319.481-0.283-0.2830.0000.0000.0000.000
70A71SER00.013-0.02219.738-0.483-0.4830.0000.0000.0000.000
71A72GLU-1-0.866-0.93520.792-10.977-10.9770.0000.0000.0000.000
72A73VAL0-0.110-0.04717.9110.0570.0570.0000.0000.0000.000
73A74LEU0-0.135-0.07216.174-0.460-0.4600.0000.0000.0000.000
74A75THR0-0.053-0.04420.1830.0240.0240.0000.0000.0000.000
75A76GLY0-0.046-0.00623.8200.3770.3770.0000.0000.0000.000
76A77ASP-1-0.825-0.89026.015-9.698-9.6980.0000.0000.0000.000
77A78LEU0-0.054-0.02429.0650.2220.2220.0000.0000.0000.000
78A79PRO00.0200.00431.4870.1220.1220.0000.0000.0000.000
79A80THR0-0.036-0.04634.8260.1200.1200.0000.0000.0000.000
80A81PRO00.0020.02935.4840.2750.2750.0000.0000.0000.000
81A91GLN00.032-0.00933.351-0.160-0.1600.0000.0000.0000.000
82A92GLU-1-0.902-0.95730.191-9.292-9.2920.0000.0000.0000.000
83A93TYR00.0310.00027.719-0.228-0.2280.0000.0000.0000.000
84A94LYS10.8590.93628.3449.5229.5220.0000.0000.0000.000
85A95ALA00.007-0.00227.138-0.330-0.3300.0000.0000.0000.000
86A96ILE00.0180.00124.915-0.403-0.4030.0000.0000.0000.000
87A97GLU-1-0.776-0.86223.660-10.819-10.8190.0000.0000.0000.000
88A98LYS10.9640.97922.65210.06210.0620.0000.0000.0000.000
89A99ILE0-0.050-0.02820.147-0.518-0.5180.0000.0000.0000.000
90A100ALA0-0.0090.00519.033-0.724-0.7240.0000.0000.0000.000
91A101GLN00.044-0.00317.878-0.959-0.9590.0000.0000.0000.000
92A102GLN0-0.027-0.00115.001-0.249-0.2490.0000.0000.0000.000
93A103LYS10.9280.96414.54914.96314.9630.0000.0000.0000.000
94A104LEU00.0060.00113.103-1.354-1.3540.0000.0000.0000.000
95A105VAL00.0140.00112.682-1.448-1.4480.0000.0000.0000.000
96A106ASP-1-0.889-0.94510.962-18.469-18.4690.0000.0000.0000.000
97A107MET0-0.095-0.0358.459-2.208-2.2080.0000.0000.0000.000
98A108VAL0-0.0220.0237.745-3.094-3.0940.0000.0000.0000.000
99A109PRO0-0.018-0.0024.881-0.583-0.5830.0000.0000.0000.000
100A110GLU-1-0.917-0.9766.335-21.709-21.7090.0000.0000.0000.000
101A111GLU-1-0.959-0.9777.477-22.476-22.4760.0000.0000.0000.000
102A112LEU00.0090.0049.1031.0751.0750.0000.0000.0000.000
103A113ARG10.9020.9518.05923.27123.2710.0000.0000.0000.000
104A114ASP-1-0.898-0.95312.239-15.322-15.3220.0000.0000.0000.000
105A115ILE0-0.0070.00514.3810.8690.8690.0000.0000.0000.000
106A116PHE0-0.032-0.03913.1110.5740.5740.0000.0000.0000.000
107A117ALA00.0070.00815.7450.5000.5000.0000.0000.0000.000
108A118PRO0-0.026-0.02617.0190.4840.4840.0000.0000.0000.000
109A119LEU0-0.057-0.02318.0770.5960.5960.0000.0000.0000.000
110A120ILE0-0.072-0.02716.7340.1230.1230.0000.0000.0000.000
111A121ASP-1-0.827-0.91620.158-11.397-11.3970.0000.0000.0000.000
112A122GLU-1-0.898-0.92822.246-10.855-10.8550.0000.0000.0000.000
113A123HIS0-0.114-0.06821.6330.6220.6220.0000.0000.0000.000
114A124ALA0-0.006-0.00823.6840.1960.1960.0000.0000.0000.000
115A125TYR0-0.030-0.00924.6570.5640.5640.0000.0000.0000.000
116A126SER00.0700.04428.2660.2640.2640.0000.0000.0000.000
117A127ASP-1-0.885-0.95831.488-8.348-8.3480.0000.0000.0000.000
118A128GLU-1-0.902-0.96634.424-7.586-7.5860.0000.0000.0000.000
119A129GLU-1-0.925-0.97329.405-9.689-9.6890.0000.0000.0000.000
120A130LYS10.9290.97029.1679.5249.5240.0000.0000.0000.000
121A131SER0-0.077-0.03932.0850.0290.0290.0000.0000.0000.000
122A132LEU00.0410.02034.1330.0750.0750.0000.0000.0000.000
123A133VAL00.0410.02629.4030.0610.0610.0000.0000.0000.000
124A134LYS10.9440.97532.5658.2838.2830.0000.0000.0000.000
125A135GLN00.0030.04334.7410.2650.2650.0000.0000.0000.000
126A136ALA00.0470.02733.8850.1300.1300.0000.0000.0000.000
127A137ASP-1-0.874-0.92932.225-9.065-9.0650.0000.0000.0000.000
128A138ALA0-0.037-0.02134.6830.1070.1070.0000.0000.0000.000
129A139LEU00.023-0.00138.2480.1550.1550.0000.0000.0000.000
130A140CYS0-0.0090.01235.4610.1170.1170.0000.0000.0000.000
131A141ALA0-0.0070.00736.9900.0380.0380.0000.0000.0000.000
132A142TYR0-0.022-0.02738.2810.1270.1270.0000.0000.0000.000
133A143LEU00.001-0.00339.1960.1510.1510.0000.0000.0000.000
134A144LYS10.8860.96737.9068.2988.2980.0000.0000.0000.000
135A145CYS0-0.079-0.03640.4840.1270.1270.0000.0000.0000.000
136A146LEU00.000-0.01043.3850.1670.1670.0000.0000.0000.000
137A147GLU-1-0.927-0.95440.543-7.727-7.7270.0000.0000.0000.000
138A148GLU-1-0.763-0.86441.343-7.496-7.4960.0000.0000.0000.000
139A149LEU0-0.034-0.02744.7850.1460.1460.0000.0000.0000.000
140A150ALA0-0.0190.00447.7640.1550.1550.0000.0000.0000.000
141A151ALA0-0.0190.00946.3450.0850.0850.0000.0000.0000.000
142A152GLY0-0.028-0.01448.3390.0330.0330.0000.0000.0000.000
143A153ASN0-0.134-0.08344.1740.2100.2100.0000.0000.0000.000
144A154ASN00.040-0.00747.839-0.039-0.0390.0000.0000.0000.000
145A155GLU-1-0.882-0.92444.845-6.927-6.9270.0000.0000.0000.000
146A156PHE00.018-0.00340.076-0.050-0.0500.0000.0000.0000.000
147A157LEU00.0060.00845.581-0.020-0.0200.0000.0000.0000.000
148A158LEU00.0300.01046.6880.0090.0090.0000.0000.0000.000
149A159ALA0-0.025-0.00242.288-0.017-0.0170.0000.0000.0000.000
150A160LYS11.0011.00244.1626.2506.2500.0000.0000.0000.000
151A161THR0-0.0020.00045.9570.0430.0430.0000.0000.0000.000
152A162ARG10.9410.97039.3247.4877.4870.0000.0000.0000.000
153A163LEU0-0.031-0.02339.258-0.076-0.0760.0000.0000.0000.000
154A164GLU-1-0.841-0.93143.449-6.337-6.3370.0000.0000.0000.000
155A165ALA0-0.0130.01146.2450.0510.0510.0000.0000.0000.000
156A166THR0-0.076-0.04439.718-0.066-0.0660.0000.0000.0000.000
157A167LEU0-0.010-0.02141.343-0.104-0.1040.0000.0000.0000.000
158A168GLU-1-0.871-0.94043.869-6.170-6.1700.0000.0000.0000.000
159A169ALA0-0.068-0.02643.5680.0160.0160.0000.0000.0000.000
160A170ARG10.7970.89336.3347.8777.8770.0000.0000.0000.000
161A171ARG10.9270.98442.3856.0506.0500.0000.0000.0000.000
162A172SER0-0.029-0.04841.7060.0190.0190.0000.0000.0000.000
163A173GLN00.0410.00644.6150.1730.1730.0000.0000.0000.000
164A174GLU-1-0.857-0.94640.142-7.232-7.2320.0000.0000.0000.000
165A175MET0-0.0150.00941.202-0.011-0.0110.0000.0000.0000.000
166A176ASP-1-0.829-0.90743.399-6.331-6.3310.0000.0000.0000.000
167A177TYR0-0.024-0.02644.8690.1230.1230.0000.0000.0000.000
168A178PHE00.003-0.00639.6680.0130.0130.0000.0000.0000.000
169A179MET0-0.002-0.01644.228-0.074-0.0740.0000.0000.0000.000
170A180GLU-1-0.906-0.95346.483-5.975-5.9750.0000.0000.0000.000
171A181ILE0-0.128-0.05746.6350.0780.0780.0000.0000.0000.000
172A182PHE0-0.039-0.03243.035-0.002-0.0020.0000.0000.0000.000
173A183VAL0-0.020-0.00643.772-0.102-0.1020.0000.0000.0000.000
174A184PRO00.0030.01046.063-0.003-0.0030.0000.0000.0000.000
175A185SER0-0.001-0.00646.9850.1100.1100.0000.0000.0000.000
176A186PHE0-0.0510.01840.866-0.063-0.0630.0000.0000.0000.000
177A187HIS0-0.039-0.03046.4520.1070.1070.0000.0000.0000.000