Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9MGG2

Calculation Name: 2PET-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PET

Chain ID: A

ChEMBL ID:

UniProt ID: P50895

Base Structure: X-ray

Registration Date: 2023-09-26

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2464306.512078
FMO2-HF: Nuclear repulsion 2372951.336842
FMO2-HF: Total energy -91355.175236
FMO2-MP2: Total energy -91617.115978


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:1:GLU)


Summations of interaction energy for fragment #1(A:1: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.
-86.558-89.2331.338-15.965-12.6990.126
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.809 / q_NPA : -0.874
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].
3A3ARG10.8030.8621.746-129.748-134.90130.816-14.631-11.0320.137
4A4LEU00.0240.0064.968-4.384-4.347-0.001-0.007-0.0290.000
5A5SER0-0.025-0.0058.7241.3621.3620.0000.0000.0000.000
6A6VAL00.0140.01611.735-0.701-0.7010.0000.0000.0000.000
7A7PRO00.010-0.00615.4350.1910.1910.0000.0000.0000.000
8A8PRO00.0230.02117.628-0.317-0.3170.0000.0000.0000.000
9A9LEU0-0.040-0.01919.170-0.529-0.5290.0000.0000.0000.000
10A10VAL0-0.0040.01122.0300.1450.1450.0000.0000.0000.000
11A11GLU-1-0.804-0.91124.71710.30610.3060.0000.0000.0000.000
12A12VAL00.0030.00728.558-0.029-0.0290.0000.0000.0000.000
13A13MET0-0.0250.00031.170-0.151-0.1510.0000.0000.0000.000
14A14ARG10.9410.95134.528-7.736-7.7360.0000.0000.0000.000
15A15GLY0-0.0170.00036.109-0.188-0.1880.0000.0000.0000.000
16A16LYS10.8370.91833.662-8.509-8.5090.0000.0000.0000.000
17A17SER00.0290.01131.020-0.007-0.0070.0000.0000.0000.000
18A18VAL0-0.0060.00825.5850.0000.0000.0000.0000.0000.000
19A19ILE00.0100.00022.226-0.173-0.1730.0000.0000.0000.000
20A20LEU0-0.0240.00220.4740.2340.2340.0000.0000.0000.000
21A21ASP-1-0.797-0.88816.47017.58717.5870.0000.0000.0000.000
22A22CYS0-0.016-0.01714.032-0.101-0.1010.0000.0000.0000.000
23A23THR00.0170.00113.160-0.140-0.1400.0000.0000.0000.000
24A24PRO0-0.030-0.0058.7551.1931.1930.0000.0000.0000.000
25A25THR0-0.013-0.0126.465-1.168-1.1680.0000.0000.0000.000
26A26GLY00.0210.0053.7703.5303.6190.000-0.058-0.0300.000
27A27THR0-0.024-0.0074.5241.6131.707-0.001-0.019-0.0730.000
28A28HIS0-0.029-0.0125.497-1.856-1.8560.0000.0000.0000.000
29A29ASP-1-0.822-0.9278.65516.10716.1070.0000.0000.0000.000
30A30HIS0-0.080-0.02811.761-0.061-0.0610.0000.0000.0000.000
31A31TYR0-0.027-0.03010.1121.7851.7850.0000.0000.0000.000
32A32MET0-0.0250.00211.976-1.247-1.2470.0000.0000.0000.000
33A33LEU0-0.0010.00412.6951.6581.6580.0000.0000.0000.000
34A34GLU-1-0.772-0.84715.02014.18814.1880.0000.0000.0000.000
35A35TRP00.0120.00016.3750.7150.7150.0000.0000.0000.000
36A36PHE0-0.019-0.02016.395-0.827-0.8270.0000.0000.0000.000
37A37LEU0-0.0020.01020.8990.1100.1100.0000.0000.0000.000
38A38THR0-0.022-0.02920.3990.4180.4180.0000.0000.0000.000
39A39ASP-1-0.768-0.85723.10510.22010.2200.0000.0000.0000.000
40A40ARG10.8540.91624.625-9.925-9.9250.0000.0000.0000.000
41A41SER0-0.054-0.04726.4890.1370.1370.0000.0000.0000.000
42A42GLY00.0130.01322.4750.0670.0670.0000.0000.0000.000
43A43ALA0-0.021-0.00122.1130.4040.4040.0000.0000.0000.000
44A44ARG10.8310.86815.003-17.157-17.1570.0000.0000.0000.000
45A45PRO0-0.041-0.01522.438-0.036-0.0360.0000.0000.0000.000
46A46ARG10.8970.93418.811-13.822-13.8220.0000.0000.0000.000
47A47LEU0-0.053-0.01622.762-0.505-0.5050.0000.0000.0000.000
48A48ALA00.007-0.01922.332-0.511-0.5110.0000.0000.0000.000
49A49SER0-0.035-0.02919.5760.3990.3990.0000.0000.0000.000
50A50ALA00.0030.00018.729-0.742-0.7420.0000.0000.0000.000
51A51GLU-1-0.862-0.92015.99216.32316.3230.0000.0000.0000.000
52A52MET0-0.0280.00414.885-0.819-0.8190.0000.0000.0000.000
53A53GLN00.036-0.00415.2250.4410.4410.0000.0000.0000.000
54A54GLY00.0370.02516.513-0.834-0.8340.0000.0000.0000.000
55A55SER0-0.156-0.08318.318-0.246-0.2460.0000.0000.0000.000
56A56GLU-1-0.905-0.92520.40811.48811.4880.0000.0000.0000.000
57A57LEU0-0.015-0.01219.5540.6950.6950.0000.0000.0000.000
58A58GLN0-0.036-0.01320.816-0.736-0.7360.0000.0000.0000.000
59A59VAL00.016-0.01321.3850.5630.5630.0000.0000.0000.000
60A60THR0-0.049-0.02323.663-0.520-0.5200.0000.0000.0000.000
61A61MET0-0.0270.00024.3270.5570.5570.0000.0000.0000.000
62A62HIS00.006-0.01122.728-0.544-0.5440.0000.0000.0000.000
63A63ASP-1-0.859-0.93827.4319.7869.7860.0000.0000.0000.000
64A64THR0-0.050-0.03729.254-0.267-0.2670.0000.0000.0000.000
65A65ARG10.8520.94129.209-10.307-10.3070.0000.0000.0000.000
66A66GLY00.0460.03532.871-0.180-0.1800.0000.0000.0000.000
67A67ARG10.7270.83530.555-9.844-9.8440.0000.0000.0000.000
68A68SER0-0.0110.01233.774-0.090-0.0900.0000.0000.0000.000
69A69PRO0-0.005-0.00933.874-0.083-0.0830.0000.0000.0000.000
70A70PRO00.0310.00632.0110.1860.1860.0000.0000.0000.000
71A71TYR0-0.016-0.00426.6630.1080.1080.0000.0000.0000.000
72A72GLN0-0.019-0.01827.224-0.203-0.2030.0000.0000.0000.000
73A73LEU00.0000.01220.8860.3440.3440.0000.0000.0000.000
74A74ASP-1-0.755-0.86121.55913.37313.3730.0000.0000.0000.000
75A75SER0-0.020-0.01722.8060.3640.3640.0000.0000.0000.000
76A76GLN0-0.032-0.01718.1470.4990.4990.0000.0000.0000.000
77A77GLY00.0410.02717.8470.8210.8210.0000.0000.0000.000
78A78ARG10.7890.88517.844-14.416-14.4160.0000.0000.0000.000
79A79LEU00.0190.01319.943-0.766-0.7660.0000.0000.0000.000
80A80VAL0-0.009-0.00522.357-0.056-0.0560.0000.0000.0000.000
81A81LEU0-0.035-0.02024.881-0.232-0.2320.0000.0000.0000.000
82A82ALA00.0650.02628.463-0.120-0.1200.0000.0000.0000.000
83A83GLU-1-0.905-0.96131.8378.1928.1920.0000.0000.0000.000
84A84ALA00.0100.01931.023-0.136-0.1360.0000.0000.0000.000
85A85GLN00.0320.00232.758-0.532-0.5320.0000.0000.0000.000
86A86VAL00.0550.02533.1340.2710.2710.0000.0000.0000.000
87A87GLY0-0.0010.01033.4350.1410.1410.0000.0000.0000.000
88A88ASP-1-0.725-0.83729.12710.07910.0790.0000.0000.0000.000
89A89GLU-1-0.832-0.89328.47610.07010.0700.0000.0000.0000.000
90A90ARG10.7950.89126.073-10.592-10.5920.0000.0000.0000.000
91A91ASP-1-0.809-0.89722.21512.79512.7950.0000.0000.0000.000
92A92TYR0-0.039-0.03320.998-0.396-0.3960.0000.0000.0000.000
93A93VAL0-0.017-0.01215.3670.5170.5170.0000.0000.0000.000
94A95VAL00.003-0.00611.5691.2911.2910.0000.0000.0000.000
95A96VAL00.0310.0157.776-1.129-1.1290.0000.0000.0000.000
96A97ARG10.8760.9199.264-15.788-15.7880.0000.0000.0000.000
97A98ALA00.0570.0236.349-1.524-1.5240.0000.0000.0000.000
98A99GLY00.0700.0357.2971.0691.0690.0000.0000.0000.000
99A100ALA0-0.015-0.0137.3041.2651.2650.0000.0000.0000.000
100A101ALA0-0.0110.0103.1632.1702.6650.079-0.155-0.4190.000
101A102GLY00.0190.0182.8483.9095.6190.446-1.093-1.063-0.011
102A103THR0-0.041-0.0385.045-3.771-3.715-0.001-0.002-0.0530.000
103A104ALA0-0.0050.0115.1062.9562.9560.0000.0000.0000.000
104A105GLU-1-0.800-0.8677.14817.29017.2900.0000.0000.0000.000
105A106ALA0-0.0060.01110.2871.5961.5960.0000.0000.0000.000
106A107THR0-0.005-0.01412.875-1.382-1.3820.0000.0000.0000.000
107A108ALA00.0150.01216.6670.3320.3320.0000.0000.0000.000
108A109ARG10.8370.91719.586-11.932-11.9320.0000.0000.0000.000
109A110LEU0-0.026-0.01523.1490.0980.0980.0000.0000.0000.000
110A111ASN0-0.022-0.01325.916-0.221-0.2210.0000.0000.0000.000
111A112VAL0-0.021-0.02729.4170.0330.0330.0000.0000.0000.000
112A113PHE00.0090.01331.308-0.324-0.3240.0000.0000.0000.000
113A114ALA0-0.040-0.03735.433-0.064-0.0640.0000.0000.0000.000
114A115LYS10.9260.98039.006-7.055-7.0550.0000.0000.0000.000
115A116PRO00.0000.00542.065-0.027-0.0270.0000.0000.0000.000
116A117GLU-1-0.839-0.92744.7206.4236.4230.0000.0000.0000.000
117A118ALA0-0.041-0.02848.2440.0270.0270.0000.0000.0000.000
118A119THR0-0.038-0.04350.610-0.016-0.0160.0000.0000.0000.000
119A120GLU-1-0.808-0.87452.1645.6665.6660.0000.0000.0000.000
120A121VAL0-0.017-0.02955.0850.0630.0630.0000.0000.0000.000
121A122SER0-0.047-0.02757.859-0.072-0.0720.0000.0000.0000.000
122A123PRO0-0.004-0.00160.8700.0020.0020.0000.0000.0000.000
123A124ASN00.0300.01063.459-0.108-0.1080.0000.0000.0000.000
124A125LYS10.9440.95565.768-4.854-4.8540.0000.0000.0000.000
125A126GLY0-0.0140.01468.775-0.085-0.0850.0000.0000.0000.000
126A127THR00.006-0.01569.338-0.051-0.0510.0000.0000.0000.000
127A128LEU0-0.0160.03266.037-0.036-0.0360.0000.0000.0000.000
128A129SER00.026-0.02770.228-0.080-0.0800.0000.0000.0000.000
129A130VAL0-0.040-0.00871.6090.0470.0470.0000.0000.0000.000
130A131MET0-0.036-0.02173.313-0.022-0.0220.0000.0000.0000.000
131A132GLU-1-0.841-0.89170.7234.4784.4780.0000.0000.0000.000
132A133ASP-1-0.904-0.92871.6134.5524.5520.0000.0000.0000.000
133A134SER0-0.033-0.05067.6170.0500.0500.0000.0000.0000.000
134A135ALA00.0080.00362.6930.0020.0020.0000.0000.0000.000
135A136GLN00.0130.00664.1390.0440.0440.0000.0000.0000.000
136A137GLU-1-0.816-0.89561.2355.3285.3280.0000.0000.0000.000
137A138ILE0-0.030-0.01161.608-0.074-0.0740.0000.0000.0000.000
138A139ALA00.023-0.00360.107-0.064-0.0640.0000.0000.0000.000
139A140THR00.0040.02155.9930.0430.0430.0000.0000.0000.000
140A141CYS0-0.048-0.01253.5690.0070.0070.0000.0000.0000.000
141A142ASN0-0.021-0.01451.7320.0730.0730.0000.0000.0000.000
142A143SER00.0300.01847.6390.0290.0290.0000.0000.0000.000
143A144ARG10.8370.89446.727-6.010-6.0100.0000.0000.0000.000
144A145ASN00.020-0.00643.7460.1830.1830.0000.0000.0000.000
145A146GLY00.0540.03341.6200.0480.0480.0000.0000.0000.000
146A147ASN0-0.090-0.06534.355-0.139-0.1390.0000.0000.0000.000
147A148PRO00.0730.04435.3100.0400.0400.0000.0000.0000.000
148A149ALA00.006-0.01137.277-0.194-0.1940.0000.0000.0000.000
149A150PRO00.0030.01340.5770.0850.0850.0000.0000.0000.000
150A151LYS10.9240.94739.799-7.857-7.8570.0000.0000.0000.000
151A152ILE00.0000.00845.211-0.018-0.0180.0000.0000.0000.000
152A153THR00.0000.01848.5390.0660.0660.0000.0000.0000.000
153A154TRP00.021-0.00151.139-0.078-0.0780.0000.0000.0000.000
154A155TYR0-0.011-0.00851.0420.0910.0910.0000.0000.0000.000
155A156ARG10.8980.92757.330-5.138-5.1380.0000.0000.0000.000
156A157ASN00.0080.00460.7920.0190.0190.0000.0000.0000.000
157A158GLY00.0260.01558.6770.0000.0000.0000.0000.0000.000
158A159GLN0-0.062-0.02657.1140.1130.1130.0000.0000.0000.000
159A160ARG10.8260.88450.399-6.309-6.3090.0000.0000.0000.000
160A161LEU0-0.010-0.01154.919-0.050-0.0500.0000.0000.0000.000
161A162GLU-1-0.852-0.89952.5716.2596.2590.0000.0000.0000.000
162A163VAL0-0.036-0.01153.882-0.051-0.0510.0000.0000.0000.000
163A164PRO00.0210.02352.2400.1370.1370.0000.0000.0000.000
164A165VAL00.001-0.01649.369-0.045-0.0450.0000.0000.0000.000
165A166GLU-1-0.906-0.95350.6286.2336.2330.0000.0000.0000.000
166A167MET0-0.009-0.00154.487-0.107-0.1070.0000.0000.0000.000
167A168ASN0-0.051-0.03957.753-0.101-0.1010.0000.0000.0000.000
168A169PRO00.026-0.01160.692-0.001-0.0010.0000.0000.0000.000
169A170GLU-1-0.829-0.88562.4004.8174.8170.0000.0000.0000.000
170A171GLY00.010-0.01160.445-0.040-0.0400.0000.0000.0000.000
171A172TYR0-0.0340.01255.9320.0540.0540.0000.0000.0000.000
172A173MET0-0.013-0.00250.289-0.082-0.0820.0000.0000.0000.000
173A174THR00.0620.04153.1250.1280.1280.0000.0000.0000.000
174A175SER0-0.023-0.01948.9930.0700.0700.0000.0000.0000.000
175A176ARG10.9500.97348.501-6.354-6.3540.0000.0000.0000.000
176A177THR00.0250.01742.2540.0030.0030.0000.0000.0000.000
177A178VAL0-0.011-0.01145.299-0.045-0.0450.0000.0000.0000.000
178A179ARG10.8630.93636.078-8.255-8.2550.0000.0000.0000.000
179A180GLU-1-0.811-0.86642.5936.6016.6010.0000.0000.0000.000
180A181ALA00.0200.00542.5790.1720.1720.0000.0000.0000.000
181A182SER0-0.017-0.00442.2240.1310.1310.0000.0000.0000.000
182A183GLY00.0090.00838.5900.1940.1940.0000.0000.0000.000
183A184LEU0-0.073-0.01938.5600.2350.2350.0000.0000.0000.000
184A185LEU0-0.053-0.03137.986-0.061-0.0610.0000.0000.0000.000
185A186SER0-0.022-0.04641.958-0.008-0.0080.0000.0000.0000.000
186A187LEU0-0.067-0.02045.5810.0400.0400.0000.0000.0000.000
187A188THR00.0390.01947.422-0.131-0.1310.0000.0000.0000.000
188A189SER0-0.023-0.03450.7540.0790.0790.0000.0000.0000.000
189A190THR00.0470.02752.926-0.040-0.0400.0000.0000.0000.000
190A191LEU0-0.0040.02256.4060.0520.0520.0000.0000.0000.000
191A192TYR0-0.047-0.06057.564-0.048-0.0480.0000.0000.0000.000
192A193LEU0-0.032-0.02560.1890.0700.0700.0000.0000.0000.000
193A194ARG10.8200.90263.046-4.775-4.7750.0000.0000.0000.000
194A195LEU0-0.081-0.02966.1430.0330.0330.0000.0000.0000.000
195A196ARG10.8890.92067.755-4.737-4.7370.0000.0000.0000.000
196A197LYS10.9340.94170.775-4.288-4.2880.0000.0000.0000.000
197A198ASP-1-0.773-0.87570.3274.4574.4570.0000.0000.0000.000
198A199ASP-1-0.749-0.85766.8364.9034.9030.0000.0000.0000.000
199A200ARG10.8080.87469.174-4.261-4.2610.0000.0000.0000.000
200A201ASP-1-0.858-0.90271.2264.3734.3730.0000.0000.0000.000
201A202ALA0-0.051-0.01665.7290.0380.0380.0000.0000.0000.000
202A203SER0-0.0030.01463.8210.0000.0000.0000.0000.0000.000
203A204PHE0-0.003-0.01461.1940.0490.0490.0000.0000.0000.000
204A205HIS0-0.057-0.03854.502-0.128-0.1280.0000.0000.0000.000
205A207ALA00.0150.00250.847-0.015-0.0150.0000.0000.0000.000
206A208ALA00.0230.02547.1030.0520.0520.0000.0000.0000.000
207A209HIS0-0.005-0.02244.3100.1020.1020.0000.0000.0000.000
208A210TYR0-0.014-0.04041.3110.0530.0530.0000.0000.0000.000
209A211SER00.024-0.00336.405-0.013-0.0130.0000.0000.0000.000
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