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: 4JLYN

Calculation Name: 2P2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q75TD0

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1933770.540439
FMO2-HF: Nuclear repulsion 1862440.596113
FMO2-HF: Total energy -71329.944326
FMO2-MP2: Total energy -71539.688113


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.
-137.352-125.69210.571-9.223-13.008-0.088
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 : 0.889 / q_NPA : 0.939
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].
3A4GLU-1-0.732-0.8732.887-46.416-43.9160.275-1.325-1.449-0.007
4A5LYS10.9190.9495.55524.43824.4380.0000.0000.0000.000
5A6GLU-1-0.863-0.9391.965-61.809-58.6635.778-3.933-4.991-0.042
6A7LYS10.7700.8762.30725.94429.4842.393-2.226-3.707-0.014
7A8MET0-0.0050.0193.1012.8372.4170.0490.611-0.240-0.001
8A9LEU0-0.020-0.0125.8862.2992.2990.0000.0000.0000.000
9A10ALA0-0.067-0.0272.132-2.351-1.7881.957-1.179-1.341-0.011
10A11GLY00.0150.0224.0073.2843.480-0.001-0.100-0.096-0.001
11A12HIS0-0.150-0.0703.234-10.144-8.0090.120-1.071-1.184-0.012
12A13LEU00.0250.0036.0562.3562.3560.0000.0000.0000.000
13A14TYR00.0020.0046.483-4.371-4.3710.0000.0000.0000.000
14A15ASN00.0660.0218.2213.9463.9460.0000.0000.0000.000
15A16PRO00.0500.03310.745-0.650-0.6500.0000.0000.0000.000
16A17ALA0-0.021-0.01312.9050.9900.9900.0000.0000.0000.000
17A18ASP-1-0.851-0.9359.372-25.742-25.7420.0000.0000.0000.000
18A19LEU00.032-0.00611.7750.6900.6900.0000.0000.0000.000
19A20GLU-1-0.986-0.9739.032-25.669-25.6690.0000.0000.0000.000
20A21LEU00.0080.0008.8220.9220.9220.0000.0000.0000.000
21A22VAL0-0.0140.00312.5921.2161.2160.0000.0000.0000.000
22A23LYS10.9820.99915.77316.33416.3340.0000.0000.0000.000
23A24GLU-1-0.862-0.90012.551-22.715-22.7150.0000.0000.0000.000
24A25ARG10.8910.94214.18419.90719.9070.0000.0000.0000.000
25A26GLU-1-0.943-0.96918.107-13.284-13.2840.0000.0000.0000.000
26A27ARG10.9090.95216.53817.34017.3400.0000.0000.0000.000
27A28ALA00.0540.03519.5190.6630.6630.0000.0000.0000.000
28A29ARG10.8130.88819.64915.85115.8510.0000.0000.0000.000
29A30ARG10.9060.96124.10612.00912.0090.0000.0000.0000.000
30A31LEU00.0310.01322.9540.5800.5800.0000.0000.0000.000
31A32VAL00.0120.01824.3850.4420.4420.0000.0000.0000.000
32A33ARG10.9200.96227.11810.87210.8720.0000.0000.0000.000
33A34LEU0-0.024-0.02129.1950.3830.3830.0000.0000.0000.000
34A35TYR0-0.039-0.03629.2650.3050.3050.0000.0000.0000.000
35A36ASN0-0.024-0.01729.6220.3450.3450.0000.0000.0000.000
36A37GLU-1-0.975-0.97632.871-8.992-8.9920.0000.0000.0000.000
37A38THR0-0.093-0.02534.0330.2820.2820.0000.0000.0000.000
38A39LEU00.0380.00736.6610.0420.0420.0000.0000.0000.000
39A40GLU-1-0.940-0.97439.074-7.761-7.7610.0000.0000.0000.000
40A41THR0-0.009-0.01040.657-0.064-0.0640.0000.0000.0000.000
41A42GLU-1-0.917-0.94538.132-8.269-8.2690.0000.0000.0000.000
42A43TYR00.022-0.00537.006-0.237-0.2370.0000.0000.0000.000
43A44ASP-1-0.868-0.93335.639-8.700-8.7000.0000.0000.0000.000
44A45LYS10.9170.96534.2738.6378.6370.0000.0000.0000.000
45A46ARG10.8920.93332.6298.6278.6270.0000.0000.0000.000
46A47THR00.0120.00330.990-0.425-0.4250.0000.0000.0000.000
47A48GLY0-0.016-0.00929.796-0.382-0.3820.0000.0000.0000.000
48A49LEU0-0.0010.00028.455-0.340-0.3400.0000.0000.0000.000
49A50LEU00.001-0.00126.360-0.533-0.5330.0000.0000.0000.000
50A51LYS10.8330.91825.02210.19310.1930.0000.0000.0000.000
51A52GLU-1-0.992-0.97323.889-12.616-12.6160.0000.0000.0000.000
52A53LEU0-0.067-0.03921.808-0.634-0.6340.0000.0000.0000.000
53A54PHE0-0.021-0.03220.630-0.669-0.6690.0000.0000.0000.000
54A55GLY00.0140.02117.874-0.024-0.0240.0000.0000.0000.000
55A56SER0-0.092-0.07118.7630.2930.2930.0000.0000.0000.000
56A57THR0-0.015-0.03221.490-0.028-0.0280.0000.0000.0000.000
57A58GLY00.0480.04924.902-0.040-0.0400.0000.0000.0000.000
58A59GLU-1-0.940-0.97028.009-10.060-10.0600.0000.0000.0000.000
59A60ARG10.8980.95131.3468.7438.7430.0000.0000.0000.000
60A61LEU00.0130.00826.881-0.223-0.2230.0000.0000.0000.000
61A62PHE0-0.039-0.01631.0010.1970.1970.0000.0000.0000.000
62A63ILE00.0140.01226.963-0.162-0.1620.0000.0000.0000.000
63A64GLU-1-0.874-0.92231.503-8.506-8.5060.0000.0000.0000.000
64A65PRO0-0.0530.00432.551-0.275-0.2750.0000.0000.0000.000
65A66ASN0-0.020-0.01931.4170.2550.2550.0000.0000.0000.000
66A67PHE00.0610.02423.475-0.055-0.0550.0000.0000.0000.000
67A68ARG10.9160.94425.25611.10911.1090.0000.0000.0000.000
68A69CYS0-0.0360.00620.525-0.133-0.1330.0000.0000.0000.000
69A70ASP-1-0.831-0.91716.884-16.754-16.7540.0000.0000.0000.000
70A71TYR0-0.006-0.02813.179-0.035-0.0350.0000.0000.0000.000
71A72GLY00.0030.00317.1470.4400.4400.0000.0000.0000.000
72A73TYR00.008-0.03612.040-0.274-0.2740.0000.0000.0000.000
73A74ASN0-0.074-0.03311.457-0.994-0.9940.0000.0000.0000.000
74A75ILE0-0.0260.00215.113-0.085-0.0850.0000.0000.0000.000
75A76HIS00.0010.02915.0051.1551.1550.0000.0000.0000.000
76A77VAL0-0.019-0.01119.9630.0900.0900.0000.0000.0000.000
77A78GLY00.0510.03423.5380.0380.0380.0000.0000.0000.000
78A79GLU-1-0.886-0.96326.080-10.501-10.5010.0000.0000.0000.000
79A80ASN0-0.097-0.05329.6970.1750.1750.0000.0000.0000.000
80A81PHE00.0500.03526.1420.1010.1010.0000.0000.0000.000
81A82PHE00.0270.01029.6510.2370.2370.0000.0000.0000.000
82A83MET0-0.031-0.00626.000-0.346-0.3460.0000.0000.0000.000
83A84ASN00.0310.01230.6600.2150.2150.0000.0000.0000.000
84A85PHE00.0160.00732.081-0.257-0.2570.0000.0000.0000.000
85A86ASP-1-0.891-0.93631.731-9.434-9.4340.0000.0000.0000.000
86A87GLY0-0.0160.00328.384-0.117-0.1170.0000.0000.0000.000
87A88VAL0-0.057-0.04923.406-0.049-0.0490.0000.0000.0000.000
88A89ILE00.0230.00819.561-0.023-0.0230.0000.0000.0000.000
89A90LEU00.0080.01718.390-0.114-0.1140.0000.0000.0000.000
90A91ASP-1-0.667-0.82816.002-18.636-18.6360.0000.0000.0000.000
91A92VAL00.0330.01611.324-0.786-0.7860.0000.0000.0000.000
92A93CYS0-0.039-0.0198.881-2.376-2.3760.0000.0000.0000.000
93A94GLU-1-0.844-0.91911.287-21.636-21.6360.0000.0000.0000.000
94A95VAL0-0.003-0.00413.5760.4010.4010.0000.0000.0000.000
95A96ARG10.8230.91514.51519.86819.8680.0000.0000.0000.000
96A97ILE0-0.003-0.01118.8350.2780.2780.0000.0000.0000.000
97A98GLY00.0020.00922.622-0.007-0.0070.0000.0000.0000.000
98A99ASP-1-0.833-0.93425.140-11.151-11.1510.0000.0000.0000.000
99A100HIS0-0.066-0.04728.5880.1730.1730.0000.0000.0000.000
100A101CYS0-0.0250.01526.6230.1800.1800.0000.0000.0000.000
101A102PHE00.0210.01729.8450.1910.1910.0000.0000.0000.000
102A103ILE00.004-0.01126.203-0.064-0.0640.0000.0000.0000.000
103A104GLY0-0.003-0.00630.7410.2310.2310.0000.0000.0000.000
104A105PRO00.0180.00631.858-0.249-0.2490.0000.0000.0000.000
105A106GLY00.029-0.00731.5790.0540.0540.0000.0000.0000.000
106A107VAL0-0.077-0.01826.728-0.085-0.0850.0000.0000.0000.000
107A108HIS00.0100.03724.916-0.498-0.4980.0000.0000.0000.000
108A109ILE00.0130.00020.0000.1280.1280.0000.0000.0000.000
109A110TYR0-0.039-0.05819.508-0.179-0.1790.0000.0000.0000.000
110A111THR0-0.005-0.01514.004-0.602-0.6020.0000.0000.0000.000
111A112ALA00.0130.01014.496-1.338-1.3380.0000.0000.0000.000
112A113THR0-0.051-0.03314.5121.6281.6280.0000.0000.0000.000
113A114HIS00.0680.03914.928-1.319-1.3190.0000.0000.0000.000
114A115PRO00.0220.01914.7740.3430.3430.0000.0000.0000.000
115A116LEU00.002-0.02117.1510.8660.8660.0000.0000.0000.000
116A117ASP-1-0.825-0.90820.125-13.257-13.2570.0000.0000.0000.000
117A118PRO0-0.021-0.01620.750-0.471-0.4710.0000.0000.0000.000
118A119HIS00.0050.01020.5380.1610.1610.0000.0000.0000.000
119A120GLU-1-0.910-0.96816.891-17.836-17.8360.0000.0000.0000.000
120A121ARG10.8520.94417.14013.31313.3130.0000.0000.0000.000
121A122ASN0-0.033-0.03018.599-0.396-0.3960.0000.0000.0000.000
122A123SER0-0.063-0.02215.721-0.213-0.2130.0000.0000.0000.000
123A124GLY0-0.0060.00216.363-0.231-0.2310.0000.0000.0000.000
124A125LEU0-0.075-0.03610.758-1.050-1.0500.0000.0000.0000.000
125A126GLU-1-0.905-0.94711.788-18.253-18.2530.0000.0000.0000.000
126A127TYR0-0.021-0.0419.863-2.623-2.6230.0000.0000.0000.000
127A128GLY00.0330.01410.1482.3692.3690.0000.0000.0000.000
128A129LYS10.9100.94910.53218.03718.0370.0000.0000.0000.000
129A130PRO00.0560.03110.9331.3851.3850.0000.0000.0000.000
130A131VAL0-0.0110.01113.6950.8450.8450.0000.0000.0000.000
131A132VAL0-0.020-0.00316.735-0.237-0.2370.0000.0000.0000.000
132A133ILE0-0.011-0.02019.2270.6080.6080.0000.0000.0000.000
133A134GLY00.0310.02222.955-0.156-0.1560.0000.0000.0000.000
134A135HIS00.0710.04225.2520.1660.1660.0000.0000.0000.000
135A136ASN0-0.061-0.04128.2610.2840.2840.0000.0000.0000.000
136A137VAL0-0.0140.01427.0740.2320.2320.0000.0000.0000.000
137A138TRP0-0.019-0.00630.2270.2290.2290.0000.0000.0000.000
138A139ILE00.0250.00226.184-0.007-0.0070.0000.0000.0000.000
139A140GLY00.0100.00130.5670.1600.1600.0000.0000.0000.000
140A141GLY00.035-0.00732.181-0.245-0.2450.0000.0000.0000.000
141A142ARG10.9310.95531.9769.4709.4700.0000.0000.0000.000
142A143ALA0-0.0330.01029.200-0.019-0.0190.0000.0000.0000.000
143A144VAL00.0160.00525.133-0.140-0.1400.0000.0000.0000.000
144A145ILE0-0.0090.00221.7790.2220.2220.0000.0000.0000.000
145A146ASN00.008-0.00621.152-0.520-0.5200.0000.0000.0000.000
146A147PRO00.0390.00915.770-0.069-0.0690.0000.0000.0000.000
147A148GLY0-0.066-0.03515.6780.3290.3290.0000.0000.0000.000
148A149VAL0-0.0540.01216.5620.4390.4390.0000.0000.0000.000
149A150THR00.0230.00518.985-0.547-0.5470.0000.0000.0000.000
150A151ILE0-0.047-0.02721.0490.6890.6890.0000.0000.0000.000
151A152GLY00.019-0.00224.567-0.174-0.1740.0000.0000.0000.000
152A153ASP-1-0.814-0.91526.491-11.377-11.3770.0000.0000.0000.000
153A154ASN0-0.078-0.05528.7620.3850.3850.0000.0000.0000.000
154A155ALA0-0.0260.01029.0650.3300.3300.0000.0000.0000.000
155A156VAL0-0.013-0.00731.1470.0560.0560.0000.0000.0000.000
156A157ILE0-0.036-0.00628.1640.0190.0190.0000.0000.0000.000
157A158ALA00.0410.01431.6470.1480.1480.0000.0000.0000.000
158A159SER00.0340.00033.433-0.241-0.2410.0000.0000.0000.000
159A160GLY0-0.058-0.02233.5100.1540.1540.0000.0000.0000.000
160A161ALA0-0.081-0.02430.900-0.053-0.0530.0000.0000.0000.000
161A162VAL00.0240.01627.387-0.262-0.2620.0000.0000.0000.000
162A163VAL00.007-0.01324.8290.1710.1710.0000.0000.0000.000
163A164THR0-0.023-0.01623.897-0.472-0.4720.0000.0000.0000.000
164A165LYS10.9600.98323.01310.63210.6320.0000.0000.0000.000
165A166ASP-1-0.805-0.89021.143-14.641-14.6410.0000.0000.0000.000
166A167VAL0-0.081-0.04023.9020.6550.6550.0000.0000.0000.000
167A168PRO0-0.010-0.00426.550-0.210-0.2100.0000.0000.0000.000
168A169ALA00.0930.04428.5780.1130.1130.0000.0000.0000.000
169A170ASN0-0.065-0.06629.7750.0210.0210.0000.0000.0000.000
170A171ALA00.0090.02531.3670.3770.3770.0000.0000.0000.000
171A172VAL00.0090.00732.695-0.104-0.1040.0000.0000.0000.000
172A173VAL00.0030.00229.5620.1180.1180.0000.0000.0000.000
173A174GLY00.0420.00733.0640.0430.0430.0000.0000.0000.000
174A175GLY0-0.0100.00134.4780.0460.0460.0000.0000.0000.000
175A176ASN00.0080.01131.176-0.508-0.5080.0000.0000.0000.000
176A177PRO00.0550.01928.9970.1790.1790.0000.0000.0000.000
177A178ALA0-0.053-0.00929.5750.3320.3320.0000.0000.0000.000
178A179LYS10.9170.94930.7428.3238.3230.0000.0000.0000.000
179A180VAL00.0640.02331.9880.0580.0580.0000.0000.0000.000
180A181ILE0-0.081-0.04434.2270.2320.2320.0000.0000.0000.000
181A182LYS10.9360.96636.8788.0518.0510.0000.0000.0000.000
182A183TRP00.0550.03132.453-0.284-0.2840.0000.0000.0000.000
183A184LEU0-0.0230.00035.2030.3220.3220.0000.0000.0000.000
184A185LYS10.9911.02635.7098.6068.6060.0000.0000.0000.000