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: ZV1RN

Calculation Name: 2V81-A-Xray372

Preferred Name: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2V81

Chain ID: A

ChEMBL ID: CHEMBL4296324

UniProt ID: Q6BF16

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2164784.931178
FMO2-HF: Nuclear repulsion 2089311.589677
FMO2-HF: Total energy -75473.341501
FMO2-MP2: Total energy -75693.207937


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-19.288-8.8844.355-6.556-8.199-0.031
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.017
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].
3A3TRP0-0.008-0.0212.947-2.9910.3530.232-1.865-1.7100.002
4A4GLN00.004-0.0043.049-0.8370.1110.105-0.282-0.770-0.001
5A5THR0-0.0240.0145.8590.3010.3010.0000.0000.0000.000
6A6LYS10.9290.9629.5740.2700.2700.0000.0000.0000.000
7A7LEU0-0.037-0.00812.704-0.069-0.0690.0000.0000.0000.000
8A8PRO00.0040.02910.3450.0570.0570.0000.0000.0000.000
9A9LEU0-0.017-0.02911.9950.0030.0030.0000.0000.0000.000
10A10ILE00.0060.01411.2200.0570.0570.0000.0000.0000.000
11A11ALA0-0.0060.00415.3720.0110.0110.0000.0000.0000.000
12A12ILE0-0.035-0.01017.6220.0380.0380.0000.0000.0000.000
13A13LEU00.0080.00320.361-0.008-0.0080.0000.0000.0000.000
14A14ARG10.9500.95923.4830.0440.0440.0000.0000.0000.000
15A15GLY0-0.064-0.04125.366-0.009-0.0090.0000.0000.0000.000
16A16ILE0-0.0170.02325.168-0.001-0.0010.0000.0000.0000.000
17A17THR00.001-0.03328.2970.0120.0120.0000.0000.0000.000
18A18PRO0-0.021-0.03629.076-0.005-0.0050.0000.0000.0000.000
19A19ASP-1-0.919-0.92030.1290.0010.0010.0000.0000.0000.000
20A20GLU-1-0.866-0.92730.135-0.034-0.0340.0000.0000.0000.000
21A21ALA00.005-0.01625.865-0.012-0.0120.0000.0000.0000.000
22A22LEU00.0330.00625.765-0.013-0.0130.0000.0000.0000.000
23A23ALA00.0300.02726.851-0.012-0.0120.0000.0000.0000.000
24A24HIS00.0190.02026.484-0.025-0.0250.0000.0000.0000.000
25A25VAL00.0050.00521.039-0.020-0.0200.0000.0000.0000.000
26A26GLY00.0440.02222.839-0.019-0.0190.0000.0000.0000.000
27A27ALA0-0.0010.00824.954-0.016-0.0160.0000.0000.0000.000
28A28VAL0-0.027-0.01720.665-0.019-0.0190.0000.0000.0000.000
29A29ILE0-0.004-0.00219.134-0.030-0.0300.0000.0000.0000.000
30A30ASP-1-0.954-0.96721.337-0.151-0.1510.0000.0000.0000.000
31A31ALA0-0.087-0.03723.291-0.009-0.0090.0000.0000.0000.000
32A32GLY0-0.034-0.02320.291-0.027-0.0270.0000.0000.0000.000
33A33PHE0-0.078-0.04117.332-0.059-0.0590.0000.0000.0000.000
34A34ASP-1-0.754-0.90413.628-0.513-0.5130.0000.0000.0000.000
35A35ALA00.0100.01312.0330.0070.0070.0000.0000.0000.000
36A36VAL0-0.019-0.00713.938-0.024-0.0240.0000.0000.0000.000
37A37GLU-1-0.892-0.95815.7650.0530.0530.0000.0000.0000.000
38A38ILE00.0630.02017.688-0.033-0.0330.0000.0000.0000.000
39A39PRO0-0.042-0.01920.9060.0380.0380.0000.0000.0000.000
40A40LEU00.0320.01520.985-0.007-0.0070.0000.0000.0000.000
41A41ASN0-0.086-0.04124.021-0.005-0.0050.0000.0000.0000.000
42A42SER0-0.010-0.00724.935-0.023-0.0230.0000.0000.0000.000
43A43PRO0-0.0200.00427.5720.0150.0150.0000.0000.0000.000
44A44GLN00.014-0.00429.666-0.006-0.0060.0000.0000.0000.000
45A45TRP00.1000.04723.0530.0070.0070.0000.0000.0000.000
46A46GLU-1-0.898-0.97024.7920.1330.1330.0000.0000.0000.000
47A47GLN0-0.058-0.02926.4220.0040.0040.0000.0000.0000.000
48A48SER00.037-0.00225.7790.0040.0040.0000.0000.0000.000
49A49ILE00.0110.01319.739-0.007-0.0070.0000.0000.0000.000
50A50PRO00.0230.00921.425-0.001-0.0010.0000.0000.0000.000
51A51ALA00.0010.01222.820-0.006-0.0060.0000.0000.0000.000
52A52ILE0-0.025-0.02020.120-0.014-0.0140.0000.0000.0000.000
53A53VAL0-0.033-0.00417.669-0.019-0.0190.0000.0000.0000.000
54A54ASP-1-0.907-0.94919.7950.1160.1160.0000.0000.0000.000
55A55ALA0-0.088-0.03022.450-0.012-0.0120.0000.0000.0000.000
56A56TYR0-0.057-0.06520.023-0.021-0.0210.0000.0000.0000.000
57A57GLY00.0350.02216.776-0.027-0.0270.0000.0000.0000.000
58A58ASP-1-0.904-0.94515.7190.0590.0590.0000.0000.0000.000
59A59LYS10.8120.91016.7320.1010.1010.0000.0000.0000.000
60A60ALA0-0.030-0.01914.746-0.058-0.0580.0000.0000.0000.000
61A61LEU00.0110.0228.9300.0470.0470.0000.0000.0000.000
62A62ILE00.0130.00712.712-0.035-0.0350.0000.0000.0000.000
63A63GLY00.032-0.01614.4650.0860.0860.0000.0000.0000.000
64A64ALA0-0.0010.01515.662-0.048-0.0480.0000.0000.0000.000
65A65GLY00.0890.05516.4590.0280.0280.0000.0000.0000.000
66A66THR0-0.134-0.08118.742-0.003-0.0030.0000.0000.0000.000
67A67VAL00.0400.03117.680-0.002-0.0020.0000.0000.0000.000
68A68LEU0-0.041-0.03119.1050.0180.0180.0000.0000.0000.000
69A69LYS10.9020.95721.713-0.197-0.1970.0000.0000.0000.000
70A70PRO00.0570.03019.7230.0130.0130.0000.0000.0000.000
71A71GLU-1-0.834-0.93120.4610.3440.3440.0000.0000.0000.000
72A72GLN0-0.021-0.02121.463-0.003-0.0030.0000.0000.0000.000
73A73VAL00.0120.01615.643-0.018-0.0180.0000.0000.0000.000
74A74ASP-1-0.786-0.88418.1730.4950.4950.0000.0000.0000.000
75A75ALA0-0.056-0.02420.298-0.011-0.0110.0000.0000.0000.000
76A76LEU00.016-0.01517.709-0.021-0.0210.0000.0000.0000.000
77A77ALA00.0340.02516.580-0.012-0.0120.0000.0000.0000.000
78A78ARG10.9060.96317.530-0.271-0.2710.0000.0000.0000.000
79A79MET0-0.087-0.03620.416-0.027-0.0270.0000.0000.0000.000
80A80GLY00.0600.04017.148-0.032-0.0320.0000.0000.0000.000
81A81CYS0-0.089-0.01515.659-0.014-0.0140.0000.0000.0000.000
82A82GLN00.0440.02310.9670.0310.0310.0000.0000.0000.000
83A83LEU0-0.011-0.0029.8920.1320.1320.0000.0000.0000.000
84A84ILE00.0180.00311.514-0.082-0.0820.0000.0000.0000.000
85A85VAL00.0290.02112.4170.0450.0450.0000.0000.0000.000
86A86THR0-0.005-0.02314.574-0.001-0.0010.0000.0000.0000.000
87A87PRO0-0.057-0.03116.497-0.063-0.0630.0000.0000.0000.000
88A88ASN00.0400.02018.459-0.025-0.0250.0000.0000.0000.000
89A89ILE00.0500.04013.9910.0650.0650.0000.0000.0000.000
90A90HIS00.0210.00816.8290.0140.0140.0000.0000.0000.000
91A91SER00.048-0.00516.0090.0830.0830.0000.0000.0000.000
92A92GLU-1-0.866-0.94215.6670.7830.7830.0000.0000.0000.000
93A93VAL0-0.0170.00615.8210.0490.0490.0000.0000.0000.000
94A94ILE00.000-0.00310.8730.0040.0040.0000.0000.0000.000
95A95ARG10.9670.98411.952-0.625-0.6250.0000.0000.0000.000
96A96ARG10.8400.93413.228-0.435-0.4350.0000.0000.0000.000
97A97ALA00.0190.00312.241-0.002-0.0020.0000.0000.0000.000
98A98VAL00.0210.0127.829-0.019-0.0190.0000.0000.0000.000
99A99GLY0-0.025-0.0089.7330.1100.1100.0000.0000.0000.000
100A100TYR0-0.101-0.07012.536-0.107-0.1070.0000.0000.0000.000
101A101GLY0-0.0180.0048.415-0.132-0.1320.0000.0000.0000.000
102A102MET0-0.064-0.0078.210-0.156-0.1560.0000.0000.0000.000
103A103THR0-0.0050.0095.7940.5150.5150.0000.0000.0000.000
104A104VAL0-0.004-0.0187.371-0.527-0.5270.0000.0000.0000.000
105A105CYS0-0.028-0.0127.8610.0750.0750.0000.0000.0000.000
106A106PRO00.0010.0079.757-0.146-0.1460.0000.0000.0000.000
107A107GLY0-0.030-0.01612.518-0.131-0.1310.0000.0000.0000.000
108A108CYS0-0.053-0.02013.2920.0470.0470.0000.0000.0000.000
109A109ALA00.0650.02716.008-0.074-0.0740.0000.0000.0000.000
110A110THR00.0010.03517.555-0.031-0.0310.0000.0000.0000.000
111A111ALA00.0910.03115.1710.0020.0020.0000.0000.0000.000
112A112THR00.0130.00615.1510.0140.0140.0000.0000.0000.000
113A113GLU-1-0.883-0.94916.2990.0750.0750.0000.0000.0000.000
114A114ALA00.0380.01711.4640.0900.0900.0000.0000.0000.000
115A115PHE00.006-0.01111.3670.0800.0800.0000.0000.0000.000
116A116THR0-0.042-0.02112.6340.1500.1500.0000.0000.0000.000
117A117ALA0-0.016-0.01111.3080.1330.1330.0000.0000.0000.000
118A118LEU00.000-0.0066.2920.2200.2200.0000.0000.0000.000
119A119GLU-1-0.923-0.9459.1681.3121.3120.0000.0000.0000.000
120A120ALA0-0.127-0.05211.8840.0830.0830.0000.0000.0000.000
121A121GLY00.0160.0067.9450.0230.0230.0000.0000.0000.000
122A122ALA0-0.058-0.0286.9360.9020.9020.0000.0000.0000.000
123A123GLN00.0540.0212.836-2.483-2.0562.561-0.857-2.1310.006
124A124ALA0-0.0160.0023.020-4.378-3.1610.150-0.740-0.627-0.007
125A125LEU00.000-0.0055.8010.5620.5620.0000.0000.0000.000
126A126LYS10.9120.9689.195-0.186-0.1860.0000.0000.0000.000
127A127ILE00.0170.01812.2720.0960.0960.0000.0000.0000.000
128A128PHE0-0.064-0.00515.029-0.008-0.0080.0000.0000.0000.000
129A129PRO0-0.018-0.01118.4760.0320.0320.0000.0000.0000.000
130A130SER00.022-0.04917.660-0.025-0.0250.0000.0000.0000.000
131A131SER0-0.028-0.03519.926-0.009-0.0090.0000.0000.0000.000
132A132ALA0-0.032-0.01523.4420.0010.0010.0000.0000.0000.000
133A133PHE0-0.0250.00020.1330.0100.0100.0000.0000.0000.000
134A134GLY00.0400.02922.2010.0010.0010.0000.0000.0000.000
135A135PRO00.028-0.00619.072-0.020-0.0200.0000.0000.0000.000
136A136GLN0-0.013-0.02218.607-0.036-0.0360.0000.0000.0000.000
137A137TYR0-0.033-0.03617.889-0.016-0.0160.0000.0000.0000.000
138A138ILE00.0310.00613.620-0.013-0.0130.0000.0000.0000.000
139A139LYS10.9850.99414.6010.4870.4870.0000.0000.0000.000
140A140ALA0-0.043-0.02015.957-0.034-0.0340.0000.0000.0000.000
141A141LEU0-0.0060.00413.4180.0110.0110.0000.0000.0000.000
142A142LYS10.9480.9717.9672.2852.2850.0000.0000.0000.000
143A143ALA0-0.062-0.01311.722-0.107-0.1070.0000.0000.0000.000
144A144VAL0-0.055-0.03013.5800.0630.0630.0000.0000.0000.000
145A145LEU0-0.036-0.0108.7110.0970.0970.0000.0000.0000.000
146A146PRO00.0290.0185.983-0.044-0.0440.0000.0000.0000.000
147A147SER0-0.001-0.0166.787-0.674-0.6740.0000.0000.0000.000
148A148ASP-1-0.930-0.9582.611-9.406-6.6800.580-1.732-1.574-0.023
149A149ILE00.0080.0112.750-6.064-4.5260.727-1.044-1.220-0.008
150A150ALA00.0120.0053.4841.6131.8170.000-0.036-0.1670.000
151A151VAL0-0.021-0.0115.4620.9540.9540.0000.0000.0000.000
152A152PHE0-0.009-0.0087.5830.0410.0410.0000.0000.0000.000
153A153ALA00.0530.02811.9640.1300.1300.0000.0000.0000.000
154A154VAL0-0.0010.00315.1680.0380.0380.0000.0000.0000.000
155A155GLY00.0380.00817.8950.0330.0330.0000.0000.0000.000
156A156GLY00.0150.03721.612-0.016-0.0160.0000.0000.0000.000
157A157VAL0-0.0240.00118.761-0.012-0.0120.0000.0000.0000.000
158A158THR00.0410.00322.1900.0090.0090.0000.0000.0000.000
159A159PRO00.0250.00123.603-0.036-0.0360.0000.0000.0000.000
160A160GLU-1-0.917-0.96425.175-0.265-0.2650.0000.0000.0000.000
161A161ASN0-0.0120.00823.188-0.029-0.0290.0000.0000.0000.000
162A162LEU00.0250.00918.031-0.036-0.0360.0000.0000.0000.000
163A163ALA00.0730.01819.566-0.061-0.0610.0000.0000.0000.000
164A164GLN00.0020.00720.307-0.024-0.0240.0000.0000.0000.000
165A165TRP0-0.025-0.01416.703-0.026-0.0260.0000.0000.0000.000
166A166ILE0-0.0080.00015.425-0.104-0.1040.0000.0000.0000.000
167A167ASP-1-0.888-0.94015.928-0.655-0.6550.0000.0000.0000.000
168A168ALA0-0.133-0.05816.806-0.004-0.0040.0000.0000.0000.000
169A169GLY0-0.018-0.01413.162-0.021-0.0210.0000.0000.0000.000
170A170CYS0-0.089-0.03311.152-0.240-0.2400.0000.0000.0000.000
171A171ALA0-0.0120.0008.071-0.050-0.0500.0000.0000.0000.000
172A172GLY00.0240.00510.2080.1300.1300.0000.0000.0000.000
173A173ALA0-0.008-0.00413.0730.0420.0420.0000.0000.0000.000
174A174GLY00.0070.01215.2430.0080.0080.0000.0000.0000.000
175A175LEU0-0.027-0.02716.3690.0180.0180.0000.0000.0000.000
176A176GLY00.0470.01920.0200.0310.0310.0000.0000.0000.000
177A177SER00.020-0.00322.704-0.001-0.0010.0000.0000.0000.000
178A178ASP-1-0.942-0.95525.037-0.189-0.1890.0000.0000.0000.000
179A179LEU0-0.060-0.00521.542-0.010-0.0100.0000.0000.0000.000
180A180TYR00.018-0.00325.2340.0130.0130.0000.0000.0000.000
181A181ARG10.8750.94326.9310.0720.0720.0000.0000.0000.000
182A182ALA00.0590.01429.7110.0010.0010.0000.0000.0000.000
183A183GLY00.0370.02531.3000.0000.0000.0000.0000.0000.000
184A184GLN0-0.124-0.05728.4470.0000.0000.0000.0000.0000.000
185A185SER00.0660.02232.8850.0030.0030.0000.0000.0000.000
186A186VAL00.0700.02029.923-0.008-0.0080.0000.0000.0000.000
187A187GLU-1-0.886-0.95030.599-0.093-0.0930.0000.0000.0000.000
188A188ARG10.8860.96430.8730.1280.1280.0000.0000.0000.000
189A189THR00.0360.00225.947-0.016-0.0160.0000.0000.0000.000
190A190ALA00.0340.02126.955-0.020-0.0200.0000.0000.0000.000
191A191GLN0-0.035-0.01428.094-0.009-0.0090.0000.0000.0000.000
192A192GLN0-0.064-0.05326.735-0.011-0.0110.0000.0000.0000.000
193A193ALA00.0360.02023.276-0.027-0.0270.0000.0000.0000.000
194A194ALA00.0300.01323.693-0.033-0.0330.0000.0000.0000.000
195A195ALA0-0.029-0.01125.571-0.022-0.0220.0000.0000.0000.000
196A196PHE00.0360.00421.356-0.019-0.0190.0000.0000.0000.000
197A197VAL00.0060.01620.202-0.053-0.0530.0000.0000.0000.000
198A198LYS10.8380.90821.7240.2430.2430.0000.0000.0000.000
199A199ALA00.0440.02623.449-0.014-0.0140.0000.0000.0000.000
200A200TYR00.0200.00313.704-0.004-0.0040.0000.0000.0000.000
201A201ARG10.9080.94416.9240.5230.5230.0000.0000.0000.000
202A202GLU-1-0.867-0.92721.214-0.334-0.3340.0000.0000.0000.000
203A203ALA00.001-0.00319.8850.0000.0000.0000.0000.0000.000
204A204VAL0-0.038-0.01416.155-0.031-0.0310.0000.0000.0000.000
205A205GLN0-0.074-0.02118.790-0.016-0.0160.0000.0000.0000.000
206A206LEU0-0.037-0.00320.5670.0220.0220.0000.0000.0000.000