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: R8VN8

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 OptHSide
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 -2166515.83789
FMO2-HF: Nuclear repulsion 2091041.893929
FMO2-HF: Total energy -75473.943961
FMO2-MP2: Total energy -75693.837015


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.
-22.498-13.4269.012-7.929-10.157-0.053
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 : 0.003 / q_NPA : 0.012
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].
3A3TRP0-0.005-0.0232.992-3.1810.2020.185-1.897-1.6720.003
4A4GLN0-0.002-0.0052.821-1.738-0.4390.670-0.611-1.358-0.006
5A5THR0-0.045-0.0235.9820.3040.3040.0000.0000.0000.000
6A6LYS10.9320.9619.6530.3160.3160.0000.0000.0000.000
7A7LEU0-0.031-0.01112.828-0.054-0.0540.0000.0000.0000.000
8A8PRO00.0010.02710.2130.0530.0530.0000.0000.0000.000
9A9LEU0-0.017-0.02511.9730.0090.0090.0000.0000.0000.000
10A10ILE00.0040.01011.2230.0540.0540.0000.0000.0000.000
11A11ALA0-0.0050.00415.2300.0190.0190.0000.0000.0000.000
12A12ILE0-0.037-0.01317.4830.0350.0350.0000.0000.0000.000
13A13LEU00.0090.00720.166-0.004-0.0040.0000.0000.0000.000
14A14ARG10.9170.94123.2900.0520.0520.0000.0000.0000.000
15A15GLY0-0.053-0.03225.137-0.007-0.0070.0000.0000.0000.000
16A16ILE0-0.0170.02124.9050.0010.0010.0000.0000.0000.000
17A17THR0-0.002-0.03128.0970.0110.0110.0000.0000.0000.000
18A18PRO0-0.007-0.02428.852-0.007-0.0070.0000.0000.0000.000
19A19ASP-1-0.914-0.92629.924-0.013-0.0130.0000.0000.0000.000
20A20GLU-1-0.786-0.86829.827-0.062-0.0620.0000.0000.0000.000
21A21ALA0-0.012-0.01325.751-0.013-0.0130.0000.0000.0000.000
22A22LEU00.0450.01025.523-0.014-0.0140.0000.0000.0000.000
23A23ALA00.0230.02626.772-0.013-0.0130.0000.0000.0000.000
24A24HIS00.0020.01026.285-0.028-0.0280.0000.0000.0000.000
25A25VAL00.0010.00020.888-0.021-0.0210.0000.0000.0000.000
26A26GLY00.0390.02222.776-0.021-0.0210.0000.0000.0000.000
27A27ALA0-0.0120.00124.927-0.016-0.0160.0000.0000.0000.000
28A28VAL0-0.023-0.01620.654-0.018-0.0180.0000.0000.0000.000
29A29ILE0-0.012-0.00719.146-0.031-0.0310.0000.0000.0000.000
30A30ASP-1-0.949-0.96721.323-0.172-0.1720.0000.0000.0000.000
31A31ALA0-0.080-0.03023.309-0.007-0.0070.0000.0000.0000.000
32A32GLY0-0.026-0.01920.343-0.025-0.0250.0000.0000.0000.000
33A33PHE0-0.080-0.04217.358-0.060-0.0600.0000.0000.0000.000
34A34ASP-1-0.737-0.86813.419-0.586-0.5860.0000.0000.0000.000
35A35ALA00.0190.02011.969-0.006-0.0060.0000.0000.0000.000
36A36VAL0-0.024-0.01013.849-0.013-0.0130.0000.0000.0000.000
37A37GLU-1-0.867-0.94815.5370.0180.0180.0000.0000.0000.000
38A38ILE00.0700.02417.485-0.026-0.0260.0000.0000.0000.000
39A39PRO0-0.049-0.02020.6590.0380.0380.0000.0000.0000.000
40A40LEU00.0390.02320.865-0.005-0.0050.0000.0000.0000.000
41A41ASN0-0.077-0.03323.743-0.011-0.0110.0000.0000.0000.000
42A42SER00.007-0.00424.660-0.020-0.0200.0000.0000.0000.000
43A43PRO0-0.026-0.00227.3200.0150.0150.0000.0000.0000.000
44A44GLN0-0.009-0.02229.438-0.010-0.0100.0000.0000.0000.000
45A45TRP00.0850.03922.7330.0040.0040.0000.0000.0000.000
46A46GLU-1-0.890-0.96124.5260.1070.1070.0000.0000.0000.000
47A47GLN0-0.039-0.01626.1480.0020.0020.0000.0000.0000.000
48A48SER00.035-0.00125.6030.0030.0030.0000.0000.0000.000
49A49ILE00.0150.01119.447-0.008-0.0080.0000.0000.0000.000
50A50PRO00.0280.00921.227-0.004-0.0040.0000.0000.0000.000
51A51ALA0-0.0030.01022.623-0.006-0.0060.0000.0000.0000.000
52A52ILE0-0.013-0.01519.909-0.013-0.0130.0000.0000.0000.000
53A53VAL0-0.032-0.00817.417-0.021-0.0210.0000.0000.0000.000
54A54ASP-1-0.914-0.94919.6570.0780.0780.0000.0000.0000.000
55A55ALA0-0.087-0.02922.354-0.011-0.0110.0000.0000.0000.000
56A56TYR0-0.060-0.07120.060-0.019-0.0190.0000.0000.0000.000
57A57GLY00.0390.02516.702-0.030-0.0300.0000.0000.0000.000
58A58ASP-1-0.906-0.94415.6940.0060.0060.0000.0000.0000.000
59A59LYS10.8070.90816.7960.1320.1320.0000.0000.0000.000
60A60ALA0-0.039-0.02214.768-0.055-0.0550.0000.0000.0000.000
61A61LEU00.0140.0208.7220.0460.0460.0000.0000.0000.000
62A62ILE0-0.0010.00012.633-0.024-0.0240.0000.0000.0000.000
63A63GLY00.043-0.01114.2540.0770.0770.0000.0000.0000.000
64A64ALA00.0030.01615.408-0.039-0.0390.0000.0000.0000.000
65A65GLY00.0850.05516.1850.0240.0240.0000.0000.0000.000
66A66THR0-0.146-0.09118.4620.0010.0010.0000.0000.0000.000
67A67VAL00.0450.03317.2430.0000.0000.0000.0000.0000.000
68A68LEU0-0.024-0.01819.0430.0210.0210.0000.0000.0000.000
69A69LYS10.8380.90621.647-0.201-0.2010.0000.0000.0000.000
70A70PRO00.0440.02019.4880.0070.0070.0000.0000.0000.000
71A71GLU-1-0.775-0.88520.1010.3020.3020.0000.0000.0000.000
72A72GLN0-0.011-0.01320.970-0.003-0.0030.0000.0000.0000.000
73A73VAL00.0240.01815.290-0.020-0.0200.0000.0000.0000.000
74A74ASP-1-0.773-0.86017.8520.4800.4800.0000.0000.0000.000
75A75ALA0-0.052-0.01919.979-0.013-0.0130.0000.0000.0000.000
76A76LEU00.024-0.01117.377-0.022-0.0220.0000.0000.0000.000
77A77ALA00.0230.01716.314-0.016-0.0160.0000.0000.0000.000
78A78ARG10.9100.96317.263-0.247-0.2470.0000.0000.0000.000
79A79MET0-0.084-0.03020.193-0.025-0.0250.0000.0000.0000.000
80A80GLY00.0590.03916.963-0.031-0.0310.0000.0000.0000.000
81A81CYS0-0.068-0.00514.324-0.041-0.0410.0000.0000.0000.000
82A82GLN00.0360.02410.9060.0260.0260.0000.0000.0000.000
83A83LEU0-0.020-0.0089.7000.1010.1010.0000.0000.0000.000
84A84ILE00.0050.00111.178-0.056-0.0560.0000.0000.0000.000
85A85VAL00.0320.02212.2320.0410.0410.0000.0000.0000.000
86A86THR00.004-0.02214.5400.0020.0020.0000.0000.0000.000
87A87PRO0-0.045-0.01616.432-0.063-0.0630.0000.0000.0000.000
88A88ASN00.0460.02418.391-0.035-0.0350.0000.0000.0000.000
89A89ILE00.0450.03513.8740.0620.0620.0000.0000.0000.000
90A90HIS00.0130.00616.7260.0100.0100.0000.0000.0000.000
91A91SER00.0660.00715.8310.0790.0790.0000.0000.0000.000
92A92GLU-1-0.804-0.88115.4890.7710.7710.0000.0000.0000.000
93A93VAL0-0.028-0.00415.8480.0450.0450.0000.0000.0000.000
94A94ILE00.0100.00310.733-0.004-0.0040.0000.0000.0000.000
95A95ARG10.9200.95111.794-0.605-0.6050.0000.0000.0000.000
96A96ARG10.7800.87513.087-0.430-0.4300.0000.0000.0000.000
97A97ALA00.0200.00711.903-0.009-0.0090.0000.0000.0000.000
98A98VAL00.0270.0117.628-0.048-0.0480.0000.0000.0000.000
99A99GLY0-0.025-0.0059.4450.0930.0930.0000.0000.0000.000
100A100TYR0-0.112-0.08512.251-0.104-0.1040.0000.0000.0000.000
101A101GLY0-0.0150.0068.189-0.133-0.1330.0000.0000.0000.000
102A102MET0-0.068-0.0087.995-0.191-0.1910.0000.0000.0000.000
103A103THR0-0.0010.0105.5640.4290.4290.0000.0000.0000.000
104A104VAL0-0.012-0.0217.042-0.463-0.4630.0000.0000.0000.000
105A105CYS0-0.013-0.0077.8060.0630.0630.0000.0000.0000.000
106A106PRO0-0.022-0.0019.712-0.140-0.1400.0000.0000.0000.000
107A107GLY0-0.020-0.01012.433-0.127-0.1270.0000.0000.0000.000
108A108CYS0-0.066-0.03013.3330.0510.0510.0000.0000.0000.000
109A109ALA00.0490.01616.005-0.074-0.0740.0000.0000.0000.000
110A110THR0-0.036-0.02017.674-0.026-0.0260.0000.0000.0000.000
111A111ALA00.0850.02515.1820.0030.0030.0000.0000.0000.000
112A112THR00.0140.00515.1460.0150.0150.0000.0000.0000.000
113A113GLU-1-0.806-0.88416.2750.0660.0660.0000.0000.0000.000
114A114ALA00.0260.01411.5320.0900.0900.0000.0000.0000.000
115A115PHE00.012-0.00911.3410.0800.0800.0000.0000.0000.000
116A116THR0-0.043-0.02812.5890.1530.1530.0000.0000.0000.000
117A117ALA0-0.014-0.00911.2530.1360.1360.0000.0000.0000.000
118A118LEU0-0.001-0.0076.1910.2170.2170.0000.0000.0000.000
119A119GLU-1-0.931-0.9479.1511.3371.3370.0000.0000.0000.000
120A120ALA0-0.119-0.05111.8640.0840.0840.0000.0000.0000.000
121A121GLY00.0120.0057.9380.0110.0110.0000.0000.0000.000
122A122ALA0-0.061-0.0296.7540.9470.9470.0000.0000.0000.000
123A123GLN00.0590.0222.834-2.257-2.1523.312-0.972-2.4440.006
124A124ALA0-0.022-0.0012.942-4.849-3.5520.209-0.766-0.740-0.009
125A125LEU00.0100.0025.7300.5850.5850.0000.0000.0000.000
126A126LYS10.8770.9399.200-0.168-0.1680.0000.0000.0000.000
127A127ILE00.0350.02512.4350.1010.1010.0000.0000.0000.000
128A128PHE0-0.068-0.01315.056-0.010-0.0100.0000.0000.0000.000
129A129PRO0-0.015-0.00918.4970.0320.0320.0000.0000.0000.000
130A130SER00.044-0.03617.634-0.024-0.0240.0000.0000.0000.000
131A131SER0-0.028-0.02519.970-0.007-0.0070.0000.0000.0000.000
132A132ALA0-0.042-0.02023.4910.0010.0010.0000.0000.0000.000
133A133PHE0-0.0250.00120.2000.0090.0090.0000.0000.0000.000
134A134GLY00.0390.02922.2650.0020.0020.0000.0000.0000.000
135A135PRO00.031-0.00719.143-0.018-0.0180.0000.0000.0000.000
136A136GLN0-0.020-0.02018.679-0.039-0.0390.0000.0000.0000.000
137A137TYR0-0.029-0.01518.352-0.018-0.0180.0000.0000.0000.000
138A138ILE00.0280.00413.798-0.013-0.0130.0000.0000.0000.000
139A139LYS10.9920.99714.6640.5020.5020.0000.0000.0000.000
140A140ALA0-0.041-0.01616.026-0.031-0.0310.0000.0000.0000.000
141A141LEU00.0010.00613.5050.0120.0120.0000.0000.0000.000
142A142LYS10.9270.9567.4322.4932.4930.0000.0000.0000.000
143A143ALA0-0.064-0.01211.784-0.103-0.1030.0000.0000.0000.000
144A144VAL0-0.058-0.03313.6070.0670.0670.0000.0000.0000.000
145A145LEU0-0.029-0.0048.6920.0950.0950.0000.0000.0000.000
146A146PRO00.0360.0185.993-0.052-0.0520.0000.0000.0000.000
147A147SER00.027-0.0016.838-0.401-0.4010.0000.0000.0000.000
148A148ASP-1-0.941-0.9702.075-12.068-10.6603.950-2.722-2.637-0.040
149A149ILE00.0120.0162.845-5.483-4.1020.686-0.923-1.145-0.007
150A150ALA00.0250.0173.5461.5631.7620.000-0.038-0.1610.000
151A151VAL0-0.013-0.0095.5290.8790.8790.0000.0000.0000.000
152A152PHE0-0.007-0.0067.4030.0360.0360.0000.0000.0000.000
153A153ALA00.0480.02812.0120.1300.1300.0000.0000.0000.000
154A154VAL00.0000.00215.1260.0330.0330.0000.0000.0000.000
155A155GLY00.0360.00917.8590.0350.0350.0000.0000.0000.000
156A156GLY00.0190.02921.605-0.015-0.0150.0000.0000.0000.000
157A157VAL0-0.0230.00318.811-0.011-0.0110.0000.0000.0000.000
158A158THR00.007-0.03022.2450.0110.0110.0000.0000.0000.000
159A159PRO00.004-0.00523.670-0.036-0.0360.0000.0000.0000.000
160A160GLU-1-0.868-0.92325.241-0.272-0.2720.0000.0000.0000.000
161A161ASN0-0.0110.00423.047-0.035-0.0350.0000.0000.0000.000
162A162LEU00.0310.01418.043-0.033-0.0330.0000.0000.0000.000
163A163ALA00.0590.01119.646-0.060-0.0600.0000.0000.0000.000
164A164GLN00.0270.02120.395-0.025-0.0250.0000.0000.0000.000
165A165TRP0-0.040-0.02916.773-0.022-0.0220.0000.0000.0000.000
166A166ILE00.0030.00415.374-0.099-0.0990.0000.0000.0000.000
167A167ASP-1-0.889-0.93616.021-0.629-0.6290.0000.0000.0000.000
168A168ALA0-0.138-0.06516.947-0.002-0.0020.0000.0000.0000.000
169A169GLY0-0.018-0.01113.249-0.015-0.0150.0000.0000.0000.000
170A170CYS0-0.114-0.04111.241-0.223-0.2230.0000.0000.0000.000
171A171ALA0-0.015-0.0028.140-0.045-0.0450.0000.0000.0000.000
172A172GLY00.0240.00210.2890.1240.1240.0000.0000.0000.000
173A173ALA0-0.011-0.00413.1400.0450.0450.0000.0000.0000.000
174A174GLY00.0060.01015.2440.0010.0010.0000.0000.0000.000
175A175LEU0-0.033-0.03016.3670.0220.0220.0000.0000.0000.000
176A176GLY00.0560.02120.0260.0290.0290.0000.0000.0000.000
177A177SER00.0190.00522.6990.0020.0020.0000.0000.0000.000
178A178ASP-1-0.940-0.96024.944-0.197-0.1970.0000.0000.0000.000
179A179LEU0-0.067-0.01021.435-0.010-0.0100.0000.0000.0000.000
180A180TYR0-0.011-0.04225.0380.0110.0110.0000.0000.0000.000
181A181ARG10.8660.94426.7720.0830.0830.0000.0000.0000.000
182A182ALA00.0630.01629.6110.0010.0010.0000.0000.0000.000
183A183GLY00.0300.02231.0990.0010.0010.0000.0000.0000.000
184A184GLN0-0.133-0.06128.3850.0020.0020.0000.0000.0000.000
185A185SER00.020-0.02232.7400.0010.0010.0000.0000.0000.000
186A186VAL00.0750.02429.872-0.009-0.0090.0000.0000.0000.000
187A187GLU-1-0.839-0.90330.516-0.104-0.1040.0000.0000.0000.000
188A188ARG10.8610.94130.9060.1410.1410.0000.0000.0000.000
189A189THR00.041-0.00125.926-0.016-0.0160.0000.0000.0000.000
190A190ALA00.0260.01726.876-0.021-0.0210.0000.0000.0000.000
191A191GLN0-0.033-0.00528.056-0.012-0.0120.0000.0000.0000.000
192A192GLN0-0.042-0.04126.670-0.009-0.0090.0000.0000.0000.000
193A193ALA00.0370.02223.310-0.027-0.0270.0000.0000.0000.000
194A194ALA00.0380.01323.662-0.033-0.0330.0000.0000.0000.000
195A195ALA0-0.030-0.00925.561-0.021-0.0210.0000.0000.0000.000
196A196PHE00.0360.00321.338-0.019-0.0190.0000.0000.0000.000
197A197VAL0-0.0010.01320.080-0.052-0.0520.0000.0000.0000.000
198A198LYS10.8000.88121.7180.2570.2570.0000.0000.0000.000
199A199ALA00.0250.01423.444-0.013-0.0130.0000.0000.0000.000
200A200TYR00.0220.00513.690-0.005-0.0050.0000.0000.0000.000
201A201ARG10.9100.94816.5350.5610.5610.0000.0000.0000.000
202A202GLU-1-0.826-0.89521.246-0.327-0.3270.0000.0000.0000.000
203A203ALA00.0190.00819.9990.0010.0010.0000.0000.0000.000
204A204VAL0-0.031-0.01516.277-0.027-0.0270.0000.0000.0000.000
205A205GLN0-0.108-0.03818.8040.0000.0000.0000.0000.0000.000
206A206LEU0-0.0290.00321.0780.0110.0110.0000.0000.0000.000