FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: K2GZ3

Calculation Name: 2GP6-A-Xray372

Preferred Name: 3-oxoacyl-[acyl-carrier-protein] synthase 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GP6

Chain ID: A

ChEMBL ID: CHEMBL4543

UniProt ID: P9WQD7

Base Structure: X-ray

Registration Date: 2023-09-27

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 415
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6967343.680893
FMO2-HF: Nuclear repulsion 6811543.928083
FMO2-HF: Total energy -155799.75281
FMO2-MP2: Total energy -156251.437567


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:3:HIS)


Summations of interaction energy for fragment #1(A:3:HIS)
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.
-12.072-8.5818.627-4.897-7.2230
Interaction energy analysis for fragmet #1(A:3:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.037
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].
3A5VAL0-0.051-0.0032.840-4.0860.7980.652-2.091-3.4460.001
4A6THR00.034-0.0265.330-0.833-0.834-0.001-0.0100.0110.000
5A7GLY0-0.0030.0138.067-0.225-0.2250.0000.0000.0000.000
6A8LYS10.8700.9471.886-9.238-11.0507.973-2.663-3.497-0.001
7A9ALA0-0.039-0.0193.421-0.805-0.4310.004-0.132-0.2470.000
8A10PHE00.0030.0075.549-0.322-0.3220.0000.0000.0000.000
9A11PRO00.0420.0438.5880.1330.1330.0000.0000.0000.000
10A12TYR00.0230.00011.9020.0980.0980.0000.0000.0000.000
11A13VAL00.0040.00814.345-0.125-0.1250.0000.0000.0000.000
12A14VAL0-0.036-0.02717.0570.0180.0180.0000.0000.0000.000
13A15VAL00.0160.01720.453-0.026-0.0260.0000.0000.0000.000
14A16THR0-0.049-0.06823.723-0.006-0.0060.0000.0000.0000.000
15A17GLY00.0460.02826.763-0.021-0.0210.0000.0000.0000.000
16A18ILE0-0.022-0.02828.2260.0110.0110.0000.0000.0000.000
17A19ALA00.0370.02130.578-0.012-0.0120.0000.0000.0000.000
18A20MET0-0.016-0.00132.3620.0040.0040.0000.0000.0000.000
19A21THR0-0.045-0.01834.308-0.003-0.0030.0000.0000.0000.000
20A22THR00.010-0.01034.722-0.002-0.0020.0000.0000.0000.000
21A23ALA00.0750.03937.668-0.003-0.0030.0000.0000.0000.000
22A24LEU0-0.0150.00338.140-0.004-0.0040.0000.0000.0000.000
23A25ALA0-0.017-0.01239.822-0.002-0.0020.0000.0000.0000.000
24A26THR0-0.024-0.00639.9950.0010.0010.0000.0000.0000.000
25A27ASP-1-0.829-0.92538.3040.1310.1310.0000.0000.0000.000
26A28ALA00.0270.00533.580-0.002-0.0020.0000.0000.0000.000
27A29GLU-1-0.815-0.90935.6260.1790.1790.0000.0000.0000.000
28A30THR0-0.062-0.05137.362-0.003-0.0030.0000.0000.0000.000
29A31THR0-0.013-0.01235.732-0.007-0.0070.0000.0000.0000.000
30A32TRP0-0.009-0.01130.849-0.006-0.0060.0000.0000.0000.000
31A33LYS10.9320.96536.222-0.130-0.1300.0000.0000.0000.000
32A34LEU00.0010.00239.543-0.003-0.0030.0000.0000.0000.000
33A35LEU00.001-0.00333.857-0.004-0.0040.0000.0000.0000.000
34A36LEU0-0.030-0.01535.118-0.003-0.0030.0000.0000.0000.000
35A37ASP-1-1.003-0.98638.4560.0800.0800.0000.0000.0000.000
36A38ARG10.9490.94940.070-0.080-0.0800.0000.0000.0000.000
37A39GLN0-0.0180.01341.097-0.008-0.0080.0000.0000.0000.000
38A40SER00.0430.01340.7190.0050.0050.0000.0000.0000.000
39A41GLY0-0.012-0.01640.8850.0000.0000.0000.0000.0000.000
40A42ILE0-0.055-0.02639.442-0.001-0.0010.0000.0000.0000.000
41A43ARG10.8870.94743.410-0.062-0.0620.0000.0000.0000.000
42A44THR00.023-0.00846.8150.0000.0000.0000.0000.0000.000
43A45LEU0-0.051-0.01345.0790.0020.0020.0000.0000.0000.000
44A46ASP-1-0.918-0.95848.3230.0290.0290.0000.0000.0000.000
45A47ASP-1-0.845-0.95248.3660.0390.0390.0000.0000.0000.000
46A48PRO0-0.0170.02750.609-0.002-0.0020.0000.0000.0000.000
47A49PHE0-0.081-0.04646.723-0.003-0.0030.0000.0000.0000.000
48A50VAL0-0.057-0.05349.952-0.002-0.0020.0000.0000.0000.000
49A51GLU-1-1.028-1.00752.5710.0150.0150.0000.0000.0000.000
50A52GLU-1-0.888-0.93555.8500.0130.0130.0000.0000.0000.000
51A53PHE0-0.102-0.05653.561-0.002-0.0020.0000.0000.0000.000
52A54ASP-1-0.943-0.96253.6060.0020.0020.0000.0000.0000.000
53A55LEU00.025-0.01747.346-0.003-0.0030.0000.0000.0000.000
54A56PRO0-0.0390.02047.3040.0020.0020.0000.0000.0000.000
55A57VAL00.0120.03243.6300.0010.0010.0000.0000.0000.000
56A58ARG10.9280.94446.963-0.015-0.0150.0000.0000.0000.000
57A59ILE00.0200.00943.7420.0020.0020.0000.0000.0000.000
58A60GLY00.022-0.00642.134-0.002-0.0020.0000.0000.0000.000
59A61GLY0-0.0060.02640.6490.0010.0010.0000.0000.0000.000
60A62HIS00.0610.01641.0530.0020.0020.0000.0000.0000.000
61A63LEU0-0.023-0.01138.8440.0050.0050.0000.0000.0000.000
62A64LEU0-0.0200.00642.553-0.004-0.0040.0000.0000.0000.000
63A65GLU-1-0.802-0.89541.6180.0990.0990.0000.0000.0000.000
64A66GLU-1-0.849-0.89945.1850.0560.0560.0000.0000.0000.000
65A67PHE0-0.009-0.01240.1520.0030.0030.0000.0000.0000.000
66A68ASP-1-0.933-0.98045.4330.0560.0560.0000.0000.0000.000
67A69HIS0-0.046-0.02248.027-0.002-0.0020.0000.0000.0000.000
68A70GLN0-0.031-0.03743.9570.0070.0070.0000.0000.0000.000
69A71LEU0-0.0200.00843.8860.0040.0040.0000.0000.0000.000
70A72THR00.0120.01247.378-0.006-0.0060.0000.0000.0000.000
71A73ARG10.9710.97749.404-0.050-0.0500.0000.0000.0000.000
72A74ILE0-0.014-0.03247.680-0.003-0.0030.0000.0000.0000.000
73A75GLU-1-0.801-0.92444.5140.0790.0790.0000.0000.0000.000
74A76LEU00.0130.02845.511-0.001-0.0010.0000.0000.0000.000
75A77ARG10.8860.94147.342-0.045-0.0450.0000.0000.0000.000
76A78ARG10.9020.95543.499-0.058-0.0580.0000.0000.0000.000
77A79MET0-0.0150.00541.3870.0020.0020.0000.0000.0000.000
78A80GLY00.0590.02342.101-0.003-0.0030.0000.0000.0000.000
79A81TYR00.0510.02839.8190.0060.0060.0000.0000.0000.000
80A82LEU00.0950.04035.3540.0060.0060.0000.0000.0000.000
81A83GLN0-0.032-0.00937.5170.0030.0030.0000.0000.0000.000
82A84ARG10.8890.96238.806-0.052-0.0520.0000.0000.0000.000
83A85MET00.0480.05136.5550.0050.0050.0000.0000.0000.000
84A86SER0-0.007-0.01334.1240.0050.0050.0000.0000.0000.000
85A87THR0-0.006-0.00435.7300.0100.0100.0000.0000.0000.000
86A88VAL00.0040.00637.8020.0070.0070.0000.0000.0000.000
87A89LEU00.0110.00933.7870.0060.0060.0000.0000.0000.000
88A90SER0-0.042-0.02233.2590.0120.0120.0000.0000.0000.000
89A91ARG10.8410.92734.364-0.095-0.0950.0000.0000.0000.000
90A92ARG10.8910.96236.632-0.110-0.1100.0000.0000.0000.000
91A93LEU0-0.051-0.00829.1690.0070.0070.0000.0000.0000.000
92A94TRP0-0.065-0.03229.3590.0150.0150.0000.0000.0000.000
93A95GLU-1-0.917-0.95033.6480.1420.1420.0000.0000.0000.000
94A96ASN0-0.053-0.03233.5290.0000.0000.0000.0000.0000.000
95A97ALA0-0.048-0.01830.2580.0070.0070.0000.0000.0000.000
96A98GLY0-0.007-0.00431.9830.0100.0100.0000.0000.0000.000
97A99SER0-0.066-0.05534.642-0.005-0.0050.0000.0000.0000.000
98A100PRO0-0.049-0.00930.041-0.004-0.0040.0000.0000.0000.000
99A101GLU-1-0.937-0.98332.2650.1670.1670.0000.0000.0000.000
100A102VAL0-0.040-0.01725.8790.0110.0110.0000.0000.0000.000
101A103ASP-1-0.760-0.88125.7120.1970.1970.0000.0000.0000.000
102A104THR0-0.020-0.01726.2000.0090.0090.0000.0000.0000.000
103A105ASN0-0.053-0.02725.553-0.019-0.0190.0000.0000.0000.000
104A106ARG10.8150.90816.984-0.338-0.3380.0000.0000.0000.000
105A107LEU0-0.0070.02222.4810.0240.0240.0000.0000.0000.000
106A108MET0-0.010-0.00221.003-0.012-0.0120.0000.0000.0000.000
107A109VAL00.007-0.00424.5800.0090.0090.0000.0000.0000.000
108A110SER0-0.048-0.02323.202-0.023-0.0230.0000.0000.0000.000
109A111ILE00.0050.00125.7370.0120.0120.0000.0000.0000.000
110A112GLY00.0440.02227.315-0.014-0.0140.0000.0000.0000.000
111A113THR0-0.025-0.01528.2320.0060.0060.0000.0000.0000.000
112A114GLY0-0.073-0.02630.114-0.004-0.0040.0000.0000.0000.000
113A115LEU0-0.060-0.00731.213-0.011-0.0110.0000.0000.0000.000
114A116GLY00.0080.00634.821-0.004-0.0040.0000.0000.0000.000
115A117SER0-0.022-0.03336.084-0.002-0.0020.0000.0000.0000.000
116A118ALA00.0190.02339.543-0.004-0.0040.0000.0000.0000.000
117A119GLU-1-0.847-0.91241.5940.0370.0370.0000.0000.0000.000
118A120GLU-1-0.924-0.96843.3780.0430.0430.0000.0000.0000.000
119A121LEU0-0.028-0.03141.726-0.001-0.0010.0000.0000.0000.000
120A122VAL00.0270.02345.668-0.003-0.0030.0000.0000.0000.000
121A123PHE0-0.0290.00548.2670.0000.0000.0000.0000.0000.000
122A124SER0-0.041-0.03946.827-0.001-0.0010.0000.0000.0000.000
123A125TYR0-0.050-0.02748.387-0.002-0.0020.0000.0000.0000.000
124A126ASP-1-0.895-0.96750.1980.0060.0060.0000.0000.0000.000
125A127ASP-1-0.840-0.91752.5890.0210.0210.0000.0000.0000.000
126A128MET0-0.073-0.03850.412-0.001-0.0010.0000.0000.0000.000
127A129ARG10.8490.94253.873-0.003-0.0030.0000.0000.0000.000
128A130ALA00.0210.00857.311-0.001-0.0010.0000.0000.0000.000
129A131ARG10.9100.97754.206-0.025-0.0250.0000.0000.0000.000
130A132GLY00.018-0.00657.330-0.001-0.0010.0000.0000.0000.000
131A133MET0-0.022-0.01554.0660.0010.0010.0000.0000.0000.000
132A134LYS10.9360.96054.288-0.010-0.0100.0000.0000.0000.000
133A135ALA0-0.0060.01156.6950.0020.0020.0000.0000.0000.000
134A136VAL00.0510.02951.8060.0010.0010.0000.0000.0000.000
135A137SER0-0.041-0.01849.1110.0000.0000.0000.0000.0000.000
136A138PRO00.0390.02147.8820.0000.0000.0000.0000.0000.000
137A139LEU00.010-0.00443.308-0.001-0.0010.0000.0000.0000.000
138A140THR0-0.032-0.04743.7530.0030.0030.0000.0000.0000.000
139A141VAL00.0340.03641.4900.0000.0000.0000.0000.0000.000
140A142GLN00.008-0.01936.240-0.003-0.0030.0000.0000.0000.000
141A143LYS10.8750.96039.331-0.040-0.0400.0000.0000.0000.000
142A144TYR00.0540.02440.2980.0020.0020.0000.0000.0000.000
143A145MET0-0.065-0.00636.506-0.004-0.0040.0000.0000.0000.000
144A146PRO00.0420.02232.9420.0060.0060.0000.0000.0000.000
145A147ASN00.0490.02231.8850.0010.0010.0000.0000.0000.000
146A148GLY00.0420.02133.2920.0070.0070.0000.0000.0000.000
147A149ALA00.0240.00333.6440.0040.0040.0000.0000.0000.000
148A150ALA00.0580.02929.7460.0080.0080.0000.0000.0000.000
149A151ALA0-0.028-0.02331.7330.0070.0070.0000.0000.0000.000
150A152ALA0-0.055-0.02833.3450.0010.0010.0000.0000.0000.000
151A153VAL00.0340.01031.4320.0020.0020.0000.0000.0000.000
152A154GLY0-0.026-0.01230.7650.0080.0080.0000.0000.0000.000
153A155LEU0-0.048-0.01131.543-0.002-0.0020.0000.0000.0000.000
154A156GLU-1-0.912-0.95934.7540.1170.1170.0000.0000.0000.000
155A157ARG10.9831.01831.336-0.159-0.1590.0000.0000.0000.000
156A158HIS0-0.002-0.00232.362-0.003-0.0030.0000.0000.0000.000
157A159ALA0-0.025-0.03727.7650.0050.0050.0000.0000.0000.000
158A160LYS10.8630.93527.644-0.144-0.1440.0000.0000.0000.000
159A161ALA00.0330.02722.246-0.004-0.0040.0000.0000.0000.000
160A162GLY0-0.0080.00622.5730.0060.0060.0000.0000.0000.000
161A163VAL0-0.011-0.01724.7420.0130.0130.0000.0000.0000.000
162A164MET0-0.060-0.02321.203-0.015-0.0150.0000.0000.0000.000
163A165THR00.000-0.02326.0960.0110.0110.0000.0000.0000.000
164A166PRO0-0.0210.04122.712-0.014-0.0140.0000.0000.0000.000
165A167VAL0-0.015-0.02625.3150.0070.0070.0000.0000.0000.000
166A168SER00.0240.00423.337-0.019-0.0190.0000.0000.0000.000
167A169ALA00.0540.05026.4160.0020.0020.0000.0000.0000.000
168A170CYS0-0.076-0.01127.7210.0080.0080.0000.0000.0000.000
169A171ALA00.0600.03522.6900.0130.0130.0000.0000.0000.000
170A172SER0-0.009-0.01123.6750.0170.0170.0000.0000.0000.000
171A173GLY00.0600.03124.9970.0150.0150.0000.0000.0000.000
172A174ALA00.0000.00721.2440.0230.0230.0000.0000.0000.000
173A175GLU-1-0.873-0.96219.8030.1120.1120.0000.0000.0000.000
174A176ALA0-0.031-0.00320.6260.0230.0230.0000.0000.0000.000
175A177ILE00.029-0.00319.8830.0230.0230.0000.0000.0000.000
176A178ALA00.0050.00816.4700.0580.0580.0000.0000.0000.000
177A179ARG10.8770.93116.701-0.156-0.1560.0000.0000.0000.000
178A180ALA00.0110.01318.1560.0210.0210.0000.0000.0000.000
179A181TRP00.012-0.0079.832-0.017-0.0170.0000.0000.0000.000
180A182GLN00.005-0.00112.9410.0120.0120.0000.0000.0000.000
181A183GLN00.0300.00813.5810.0210.0210.0000.0000.0000.000
182A184ILE0-0.0020.00314.7380.0120.0120.0000.0000.0000.000
183A185VAL0-0.045-0.01010.0560.0340.0340.0000.0000.0000.000
184A186LEU0-0.063-0.02410.3130.0780.0780.0000.0000.0000.000
185A187GLY0-0.018-0.00511.466-0.081-0.0810.0000.0000.0000.000
186A188GLU-1-0.973-0.99213.6000.1390.1390.0000.0000.0000.000
187A189ALA0-0.088-0.05116.643-0.039-0.0390.0000.0000.0000.000
188A190ASP-1-0.787-0.88017.2170.4850.4850.0000.0000.0000.000
189A191ALA0-0.003-0.01419.4390.0210.0210.0000.0000.0000.000
190A192ALA0-0.014-0.01821.580-0.025-0.0250.0000.0000.0000.000
191A193ILE00.0060.02623.4640.0100.0100.0000.0000.0000.000
192A194CYS0-0.047-0.02623.3580.0000.0000.0000.0000.0000.000
193A195GLY00.0470.01025.6730.0060.0060.0000.0000.0000.000
194A196GLY00.013-0.01127.015-0.008-0.0080.0000.0000.0000.000
195A197VAL0-0.048-0.03129.3130.0030.0030.0000.0000.0000.000
196A198GLU-1-0.707-0.86832.9680.0510.0510.0000.0000.0000.000
197A199THR0-0.071-0.03735.0370.0010.0010.0000.0000.0000.000
198A200ARG10.9971.00538.677-0.047-0.0470.0000.0000.0000.000
199A201ILE00.0060.00541.083-0.003-0.0030.0000.0000.0000.000
200A202GLU-1-0.836-0.92742.3030.0230.0230.0000.0000.0000.000
201A203ALA00.0250.00443.837-0.001-0.0010.0000.0000.0000.000
202A204VAL00.004-0.01642.727-0.003-0.0030.0000.0000.0000.000
203A205PRO00.0000.02839.470-0.004-0.0040.0000.0000.0000.000
204A206ILE00.0630.01241.199-0.004-0.0040.0000.0000.0000.000
205A207ALA00.0420.01742.939-0.003-0.0030.0000.0000.0000.000
206A208GLY0-0.028-0.00142.117-0.003-0.0030.0000.0000.0000.000
207A209PHE0-0.089-0.05934.891-0.003-0.0030.0000.0000.0000.000
208A210ALA0-0.047-0.02540.842-0.001-0.0010.0000.0000.0000.000
209A211GLN0-0.018-0.00943.614-0.001-0.0010.0000.0000.0000.000
210A212MET0-0.0180.00837.714-0.003-0.0030.0000.0000.0000.000
211A213ARG10.9830.94738.8650.0360.0360.0000.0000.0000.000
212A214ILE0-0.0470.01334.6800.0010.0010.0000.0000.0000.000
213A215VAL00.0780.04937.8520.0030.0030.0000.0000.0000.000
214A216MET0-0.025-0.00740.1510.0010.0010.0000.0000.0000.000
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