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: JLQJ9

Calculation Name: 2P8T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P8T

Chain ID: A

ChEMBL ID:

UniProt ID: O58461

Base Structure: X-ray

Registration Date: 2023-06-22

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066305.250962
FMO2-HF: Nuclear repulsion 1993880.095565
FMO2-HF: Total energy -72425.155397
FMO2-MP2: Total energy -72640.812931


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:14:GLU)


Summations of interaction energy for fragment #1(A:14:GLU)
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.
-110.423-118.09729.299-12.079-9.5470.112
Interaction energy analysis for fragmet #1(A:14:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.883 / q_NPA : -0.931
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].
3A16THR0-0.014-0.0263.870-1.6230.273-0.021-1.023-0.8520.003
4A17VAL00.0560.0217.2450.0770.0770.0000.0000.0000.000
5A18GLU-1-0.752-0.87410.44020.35220.3520.0000.0000.0000.000
6A19ASP-1-0.752-0.8437.03129.77929.7790.0000.0000.0000.000
7A20VAL0-0.044-0.0188.829-0.256-0.2560.0000.0000.0000.000
8A21LEU00.0180.01311.072-1.054-1.0540.0000.0000.0000.000
9A22ALA00.0330.02212.258-0.871-0.8710.0000.0000.0000.000
10A23VAL0-0.034-0.02310.618-0.675-0.6750.0000.0000.0000.000
11A24ILE00.0000.00413.698-0.949-0.9490.0000.0000.0000.000
12A25PHE00.0290.01516.675-0.901-0.9010.0000.0000.0000.000
13A26LEU0-0.004-0.00114.027-0.835-0.8350.0000.0000.0000.000
14A27LEU0-0.060-0.02615.321-0.572-0.5720.0000.0000.0000.000
15A28LYS10.8350.91318.972-12.820-12.8200.0000.0000.0000.000
16A29GLU-1-0.856-0.91121.50013.06213.0620.0000.0000.0000.000
17A30PRO0-0.014-0.01020.9630.7260.7260.0000.0000.0000.000
18A31LEU0-0.0060.00717.486-0.001-0.0010.0000.0000.0000.000
19A32GLY00.0240.00717.7660.5730.5730.0000.0000.0000.000
20A33ARG10.8120.85511.169-25.820-25.8200.0000.0000.0000.000
21A34LYS10.8320.91412.278-16.145-16.1450.0000.0000.0000.000
22A35GLN00.0960.04314.0840.7780.7780.0000.0000.0000.000
23A36ILE00.0220.01810.6350.0110.0110.0000.0000.0000.000
24A37SER00.005-0.0048.7370.0780.0780.0000.0000.0000.000
25A38GLU-1-0.869-0.91711.02818.51818.5180.0000.0000.0000.000
26A39ARG10.8300.90814.119-16.675-16.6750.0000.0000.0000.000
27A40LEU0-0.0070.0018.891-0.575-0.5750.0000.0000.0000.000
28A41GLU-1-0.799-0.87610.63521.37221.3720.0000.0000.0000.000
29A42LEU00.0080.0244.9552.6132.6130.0000.0000.0000.000
30A43GLY00.0570.0195.138-2.871-2.836-0.001-0.002-0.0320.000
31A44GLU-1-0.740-0.8445.42233.32333.337-0.0010.000-0.0130.000
32A45GLY00.0000.0053.535-8.772-7.7670.041-0.529-0.5170.003
33A46SER00.049-0.0051.564-35.729-45.91828.998-11.662-7.1480.091
34A47VAL0-0.0030.0073.250-13.277-13.9800.2841.169-0.7500.015
35A48ARG10.7550.8536.564-41.138-41.1380.0000.0000.0000.000
36A49THR00.0260.0054.099-9.341-9.073-0.001-0.032-0.2350.000
37A50LEU00.0380.0385.553-5.008-5.0080.0000.0000.0000.000
38A51LEU0-0.007-0.0097.000-4.124-4.1240.0000.0000.0000.000
39A52ARG10.8220.9149.358-30.075-30.0750.0000.0000.0000.000
40A53LYS10.9471.0008.524-24.894-24.8940.0000.0000.0000.000
41A54LEU00.0590.01310.596-1.985-1.9850.0000.0000.0000.000
42A55SER0-0.035-0.00812.828-2.145-2.1450.0000.0000.0000.000
43A56HIS0-0.024-0.02811.721-0.878-0.8780.0000.0000.0000.000
44A57LEU0-0.0240.00812.632-0.877-0.8770.0000.0000.0000.000
45A58ASP-1-0.798-0.89716.28913.26213.2620.0000.0000.0000.000
46A59ILE00.0340.05814.492-0.522-0.5220.0000.0000.0000.000
47A60ILE00.000-0.00113.537-0.299-0.2990.0000.0000.0000.000
48A61ARG10.7780.87917.458-15.726-15.7260.0000.0000.0000.000
49A62SER00.012-0.02617.7870.5320.5320.0000.0000.0000.000
50A63LYN0-0.0170.04019.4220.1860.1860.0000.0000.0000.000
51A64GLN00.0260.00823.041-0.207-0.2070.0000.0000.0000.000
52A65ARG10.8910.94018.349-17.141-17.1410.0000.0000.0000.000
53A66GLY0-0.020-0.01219.9290.7850.7850.0000.0000.0000.000
54A67HIS00.001-0.00414.209-1.433-1.4330.0000.0000.0000.000
55A68PHE00.0390.01218.641-0.245-0.2450.0000.0000.0000.000
56A69LEU00.0300.02417.7600.5500.5500.0000.0000.0000.000
57A70THR0-0.061-0.04120.040-0.608-0.6080.0000.0000.0000.000
58A71LEU00.0370.01122.158-0.094-0.0940.0000.0000.0000.000
59A72LYS10.8920.96117.657-15.416-15.4160.0000.0000.0000.000
60A73GLY00.032-0.00119.5040.1350.1350.0000.0000.0000.000
61A74LYS10.7650.86220.339-11.075-11.0750.0000.0000.0000.000
62A75GLU-1-0.812-0.89923.55310.92510.9250.0000.0000.0000.000
63A76ILE0-0.035-0.01417.746-0.087-0.0870.0000.0000.0000.000
64A77ARG10.7460.83620.855-13.469-13.4690.0000.0000.0000.000
65A78ASP-1-0.797-0.87522.00610.97010.9700.0000.0000.0000.000
66A79LYS10.8540.91122.920-11.880-11.8800.0000.0000.0000.000
67A80LEU0-0.0100.01118.092-0.094-0.0940.0000.0000.0000.000
68A81LEU0-0.010-0.01122.659-0.180-0.1800.0000.0000.0000.000
69A82SER0-0.086-0.04425.807-0.457-0.4570.0000.0000.0000.000
70A83MET0-0.0030.00622.841-0.088-0.0880.0000.0000.0000.000
71A84PHE0-0.013-0.00620.2340.2170.2170.0000.0000.0000.000
72A85SER00.0520.02825.282-0.227-0.2270.0000.0000.0000.000
73A86GLU-1-0.745-0.85624.29312.94912.9490.0000.0000.0000.000
74A87PRO0-0.038-0.00220.441-0.264-0.2640.0000.0000.0000.000
75A88ILE0-0.0290.00123.405-0.006-0.0060.0000.0000.0000.000
76A89GLY00.0010.00924.2590.1670.1670.0000.0000.0000.000
77A90VAL0-0.034-0.02325.054-0.597-0.5970.0000.0000.0000.000
78A91SER0-0.049-0.03926.3400.2580.2580.0000.0000.0000.000
79A92VAL00.0400.01827.577-0.358-0.3580.0000.0000.0000.000
80A93ASP-1-0.827-0.89928.8099.7479.7470.0000.0000.0000.000
81A94GLY0-0.021-0.00230.406-0.004-0.0040.0000.0000.0000.000
82A95TYR0-0.0200.00324.7440.3380.3380.0000.0000.0000.000
83A96PRO0-0.0130.00522.159-0.336-0.3360.0000.0000.0000.000
84A97GLY00.0610.00123.0110.3030.3030.0000.0000.0000.000
85A98ILE0-0.075-0.02619.9240.0690.0690.0000.0000.0000.000
86A99ALA00.0120.01623.184-0.136-0.1360.0000.0000.0000.000
87A100ILE0-0.025-0.02320.1010.3260.3260.0000.0000.0000.000
88A101VAL00.0210.02524.634-0.071-0.0710.0000.0000.0000.000
89A102VAL0-0.052-0.04224.0850.4740.4740.0000.0000.0000.000
90A103LYS10.8250.91426.727-10.582-10.5820.0000.0000.0000.000
91A104ASN0-0.008-0.00728.889-0.041-0.0410.0000.0000.0000.000
92A105PRO0-0.0150.00928.3550.2610.2610.0000.0000.0000.000
93A106PRO00.0000.01026.508-0.328-0.3280.0000.0000.0000.000
94A107GLU-1-0.796-0.89429.7778.8238.8230.0000.0000.0000.000
95A108PHE0-0.054-0.02927.4580.4080.4080.0000.0000.0000.000
96A109LYS10.8820.92028.252-9.343-9.3430.0000.0000.0000.000
97A110SER00.018-0.01927.6490.2920.2920.0000.0000.0000.000
98A111ILE0-0.0020.00227.0600.3450.3450.0000.0000.0000.000
99A112GLU-1-0.865-0.93725.06810.49710.4970.0000.0000.0000.000
100A113LEU00.0100.00122.5560.5760.5760.0000.0000.0000.000
101A114ARG10.8190.89822.176-10.462-10.4620.0000.0000.0000.000
102A115ASP-1-0.817-0.89022.38311.78911.7890.0000.0000.0000.000
103A116GLU-1-0.854-0.90817.84815.37115.3710.0000.0000.0000.000
104A117ALA00.002-0.00217.6800.8840.8840.0000.0000.0000.000
105A118ILE0-0.015-0.00617.9470.6430.6430.0000.0000.0000.000
106A119LYS10.8010.89116.168-13.222-13.2220.0000.0000.0000.000
107A120PHE0-0.048-0.03510.6591.4351.4350.0000.0000.0000.000
108A121ASP-1-0.822-0.89313.86520.31420.3140.0000.0000.0000.000
109A122ALA0-0.053-0.01716.074-0.333-0.3330.0000.0000.0000.000
110A123LYS10.7800.87119.494-12.508-12.5080.0000.0000.0000.000
111A124GLY0-0.010-0.01022.506-0.509-0.5090.0000.0000.0000.000
112A125ALA00.004-0.01422.8140.4670.4670.0000.0000.0000.000
113A126MET0-0.051-0.00924.934-0.513-0.5130.0000.0000.0000.000
114A127ILE00.0000.00324.2800.3320.3320.0000.0000.0000.000
115A128LEU0-0.0100.00927.953-0.271-0.2710.0000.0000.0000.000
116A129THR00.000-0.00930.8010.1620.1620.0000.0000.0000.000
117A130VAL0-0.040-0.00533.460-0.020-0.0200.0000.0000.0000.000
118A131LYS10.8900.93236.292-7.025-7.0250.0000.0000.0000.000
119A132ASP-1-0.874-0.91440.0636.7666.7660.0000.0000.0000.000
120A133ASN0-0.074-0.04939.668-0.023-0.0230.0000.0000.0000.000
121A134GLU-1-0.834-0.90039.3777.5577.5570.0000.0000.0000.000
122A135ILE00.0160.00632.8130.1010.1010.0000.0000.0000.000
123A136VAL0-0.028-0.00835.751-0.105-0.1050.0000.0000.0000.000
124A137PHE00.028-0.00532.6830.3370.3370.0000.0000.0000.000
125A138PRO0-0.024-0.00532.352-0.231-0.2310.0000.0000.0000.000
126A139GLU-1-1.008-0.99735.6918.0218.0210.0000.0000.0000.000
127A140ASP-1-0.797-0.90038.1147.4917.4910.0000.0000.0000.000
128A141PHE0-0.049-0.02538.250-0.168-0.1680.0000.0000.0000.000
129A142ARG10.8810.92636.049-8.125-8.1250.0000.0000.0000.000
130A143PRO00.023-0.00438.6160.2590.2590.0000.0000.0000.000
131A144LEU00.0040.00232.4020.0030.0030.0000.0000.0000.000
132A145LYS10.7910.88336.337-7.240-7.2400.0000.0000.0000.000
133A146GLU-1-0.850-0.93338.5317.2027.2020.0000.0000.0000.000
134A147MET0-0.084-0.00734.994-0.088-0.0880.0000.0000.0000.000
135A148TYR0-0.042-0.05432.1240.0640.0640.0000.0000.0000.000
136A149PRO00.0380.02335.3010.1500.1500.0000.0000.0000.000
137A150GLU-1-0.861-0.93334.8308.2518.2510.0000.0000.0000.000
138A151VAL0-0.0190.00329.9110.2100.2100.0000.0000.0000.000
139A152ALA00.0280.01032.4450.1190.1190.0000.0000.0000.000
140A153LYS10.8250.89334.804-8.091-8.0910.0000.0000.0000.000
141A154LYS10.8310.91629.018-10.365-10.3650.0000.0000.0000.000
142A155ILE0-0.0210.00129.5410.3400.3400.0000.0000.0000.000
143A156VAL00.006-0.00331.347-0.322-0.3220.0000.0000.0000.000
144A157ASP-1-0.865-0.94029.61710.35110.3510.0000.0000.0000.000
145A158TYR0-0.043-0.02431.1960.3550.3550.0000.0000.0000.000
146A159GLU-1-0.933-0.95933.3877.9207.9200.0000.0000.0000.000
147A160ASP-1-0.781-0.91035.5907.6847.6840.0000.0000.0000.000
148A161GLY0-0.022-0.00636.093-0.024-0.0240.0000.0000.0000.000
149A162ASP-1-0.796-0.88731.3289.4869.4860.0000.0000.0000.000
150A163ALA0-0.0150.00228.245-0.143-0.1430.0000.0000.0000.000
151A164VAL0-0.013-0.01728.2490.2160.2160.0000.0000.0000.000
152A165ILE0-0.0180.01321.930-0.096-0.0960.0000.0000.0000.000
153A166ILE00.010-0.00525.3890.0100.0100.0000.0000.0000.000
154A167THR0-0.016-0.01120.272-0.219-0.2190.0000.0000.0000.000
155A168TRP00.0510.01923.050-0.024-0.0240.0000.0000.0000.000
156A169ALA0-0.0060.00819.0730.1600.1600.0000.0000.0000.000
157A170GLU-1-0.760-0.87119.38112.81912.8190.0000.0000.0000.000
158A171THR0-0.053-0.04815.921-0.287-0.2870.0000.0000.0000.000
159A172PRO00.042-0.00118.922-0.001-0.0010.0000.0000.0000.000
160A173ALA0-0.0010.02013.613-0.118-0.1180.0000.0000.0000.000
161A174LYS10.8310.90413.511-20.131-20.1310.0000.0000.0000.000
162A175ALA00.0210.04215.928-0.218-0.2180.0000.0000.0000.000
163A176LEU00.0000.00815.488-0.251-0.2510.0000.0000.0000.000
164A177LYS10.8520.9128.537-26.372-26.3720.0000.0000.0000.000
165A178SER00.002-0.00914.408-0.376-0.3760.0000.0000.0000.000
166A179ALA0-0.003-0.00516.652-0.467-0.4670.0000.0000.0000.000
167A180ILE00.013-0.00414.736-0.352-0.3520.0000.0000.0000.000
168A181HIS10.7750.86813.974-17.327-17.3270.0000.0000.0000.000
169A182VAL00.004-0.00416.094-0.331-0.3310.0000.0000.0000.000
170A183ALA00.0230.00919.190-0.483-0.4830.0000.0000.0000.000
171A184TYR0-0.019-0.01815.361-0.148-0.1480.0000.0000.0000.000
172A185ILE0-0.039-0.02818.150-0.377-0.3770.0000.0000.0000.000
173A186LEU0-0.018-0.01320.079-0.404-0.4040.0000.0000.0000.000
174A187LYS10.8310.91421.573-11.103-11.1030.0000.0000.0000.000
175A188LYS10.8070.90418.355-12.357-12.3570.0000.0000.0000.000
176A189GLU-1-0.848-0.91719.95412.20612.2060.0000.0000.0000.000
177A190GLU-1-0.851-0.91322.40310.44410.4440.0000.0000.0000.000
178A191ILE0-0.043-0.01416.5070.1730.1730.0000.0000.0000.000
179A192THR0-0.004-0.01618.7130.0360.0360.0000.0000.0000.000
180A193PRO00.0610.00517.6600.8270.8270.0000.0000.0000.000
181A194GLU-1-0.837-0.90816.31514.18314.1830.0000.0000.0000.000
182A195ILE00.000-0.00313.7210.9660.9660.0000.0000.0000.000
183A196LEU0-0.002-0.00512.4491.5341.5340.0000.0000.0000.000
184A197GLU-1-0.856-0.92011.85817.32417.3240.0000.0000.0000.000
185A198VAL0-0.028-0.0259.0930.9720.9720.0000.0000.0000.000
186A199VAL0-0.0160.0096.0962.4162.4160.0000.0000.0000.000