Manual

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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: PJ4M9

Calculation Name: 3GPK-A-Xray42

Preferred Name:

Target Type:

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 3GPK

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G9Z0

Base Structure: X-ray

Registration Date: 2019-02-15

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -988202.833369
FMO2-HF: Nuclear repulsion 939579.537016
FMO2-HF: Total energy -48623.296352
FMO2-MP2: Total energy -48762.991221


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:206:ACE)


Summations of interaction energy for fragment #1(A:206:ACE)
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.
7.621-3.67213.8210.481-3.01-0.02
Interaction energy analysis for fragmet #1(A:206:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.050
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].
3A208GLU-1-0.772-0.8743.652-1.233-0.389-0.019-0.024-0.801-0.003
4A209GLU-1-0.864-0.9166.460-0.955-0.9550.0000.0000.0000.000
5A210TYR00.011-0.0028.3170.2060.2060.0000.0000.0000.000
6A211ARG10.8770.96712.9840.2610.2610.0000.0000.0000.000
7A212ILE0-0.003-0.01914.8660.0270.0270.0000.0000.0000.000
8A213GLY00.0140.02618.5530.0090.0090.0000.0000.0000.000
9A214GLU-1-0.824-0.93522.110-0.191-0.1910.0000.0000.0000.000
10A215ILE0-0.0230.00223.8530.0090.0090.0000.0000.0000.000
11A216PHE0-0.008-0.00426.4700.0000.0000.0000.0000.0000.000
12A217LEU0-0.030-0.00128.1350.0060.0060.0000.0000.0000.000
13A218ALA00.0190.02130.953-0.001-0.0010.0000.0000.0000.000
14A219ALA0-0.021-0.02832.3230.0060.0060.0000.0000.0000.000
15A220THR00.0290.02933.316-0.003-0.0030.0000.0000.0000.000
16A221GLU-1-0.776-0.87332.293-0.067-0.0670.0000.0000.0000.000
17A222GLU-1-0.871-0.93035.539-0.047-0.0470.0000.0000.0000.000
18A223ASN0-0.034-0.01937.7290.0050.0050.0000.0000.0000.000
19A224LYS10.7500.87929.3270.0790.0790.0000.0000.0000.000
20A225PRO00.0390.01534.874-0.002-0.0020.0000.0000.0000.000
21A226GLN00.0070.02336.6600.0030.0030.0000.0000.0000.000
22A227VAL00.008-0.00433.0670.0000.0000.0000.0000.0000.000
23A228PHE0-0.0020.01029.703-0.003-0.0030.0000.0000.0000.000
24A229ALA0-0.0010.00633.573-0.001-0.0010.0000.0000.0000.000
25A230ASN00.021-0.00335.8550.0030.0030.0000.0000.0000.000
26A231ALA00.0650.02530.642-0.001-0.0010.0000.0000.0000.000
27A232GLU-1-0.770-0.85931.641-0.070-0.0700.0000.0000.0000.000
28A233LYS10.9210.97333.1090.0480.0480.0000.0000.0000.000
29A234ILE00.0190.01631.1750.0010.0010.0000.0000.0000.000
30A235VAL00.0080.00528.589-0.003-0.0030.0000.0000.0000.000
31A236GLU-1-0.938-0.94430.795-0.050-0.0500.0000.0000.0000.000
32A237GLN0-0.025-0.02133.6160.0010.0010.0000.0000.0000.000
33A238LEU00.0070.01928.2000.0000.0000.0000.0000.0000.000
34A239LYS10.8870.95326.1960.0840.0840.0000.0000.0000.000
35A240GLN0-0.0380.02130.6330.0030.0030.0000.0000.0000.000
36A241GLY00.0170.01632.3990.0040.0040.0000.0000.0000.000
37A242GLY0-0.0230.00533.258-0.001-0.0010.0000.0000.0000.000
38A243SER0-0.056-0.04031.324-0.008-0.0080.0000.0000.0000.000
39A244PHE00.0930.03025.0390.0030.0030.0000.0000.0000.000
40A245VAL00.0240.01528.3680.0000.0000.0000.0000.0000.000
41A246ALA0-0.025-0.01530.1130.0020.0020.0000.0000.0000.000
42A247TYR0-0.002-0.02731.6040.0040.0040.0000.0000.0000.000
43A248ALA00.0060.01828.6560.0020.0020.0000.0000.0000.000
44A249ARG10.8710.92730.6310.0990.0990.0000.0000.0000.000
45A250GLN0-0.0340.00133.2890.0030.0030.0000.0000.0000.000
46A251TYR0-0.002-0.02533.1680.0050.0050.0000.0000.0000.000
47A252SER0-0.016-0.00928.2340.0010.0010.0000.0000.0000.000
48A253GLU-1-0.737-0.82830.994-0.080-0.0800.0000.0000.0000.000
49A254ALA00.0300.03526.9050.0010.0010.0000.0000.0000.000
50A255SER0-0.002-0.01927.4010.0040.0040.0000.0000.0000.000
51A256THR00.0260.01224.0050.0100.0100.0000.0000.0000.000
52A257ALA00.0310.02727.414-0.001-0.0010.0000.0000.0000.000
53A258ALA00.0110.00530.2040.0030.0030.0000.0000.0000.000
54A259VAL0-0.021-0.01226.4330.0080.0080.0000.0000.0000.000
55A260GLY0-0.039-0.02127.509-0.007-0.0070.0000.0000.0000.000
56A261GLY00.0200.00526.119-0.002-0.0020.0000.0000.0000.000
57A262ASP-1-0.838-0.89021.628-0.238-0.2380.0000.0000.0000.000
58A263LEU0-0.035-0.00318.9700.0070.0070.0000.0000.0000.000
59A264GLY00.0280.01019.308-0.019-0.0190.0000.0000.0000.000
60A265TRP0-0.064-0.06213.136-0.054-0.0540.0000.0000.0000.000
61A266ILE0-0.039-0.00813.8340.0090.0090.0000.0000.0000.000
62A267ARG10.9610.9758.3240.9700.9700.0000.0000.0000.000
63A268LEU00.0480.0139.0860.1620.1620.0000.0000.0000.000
64A269ALA0-0.016-0.00110.4490.1170.1170.0000.0000.0000.000
65A270GLN00.0060.00612.061-0.005-0.0050.0000.0000.0000.000
66A271LEU0-0.0220.00114.5830.0540.0540.0000.0000.0000.000
67A272PRO00.0080.01616.107-0.005-0.0050.0000.0000.0000.000
68A273THR00.067-0.01316.318-0.030-0.0300.0000.0000.0000.000
69A274GLU-1-0.863-0.91017.011-0.151-0.1510.0000.0000.0000.000
70A275LEU00.0310.01618.4750.0040.0040.0000.0000.0000.000
71A276ALA00.0050.01713.068-0.020-0.0200.0000.0000.0000.000
72A277THR0-0.027-0.02813.658-0.020-0.0200.0000.0000.0000.000
73A278THR00.0160.03615.1260.0270.0270.0000.0000.0000.000
74A279ALA00.0360.00814.3390.0160.0160.0000.0000.0000.000
75A280ALA0-0.0180.00411.048-0.021-0.0210.0000.0000.0000.000
76A281SER00.0190.00912.1980.0220.0220.0000.0000.0000.000
77A282MET0-0.0780.00214.9330.0250.0250.0000.0000.0000.000
78A283GLY00.0430.04915.098-0.023-0.0230.0000.0000.0000.000
79A284PRO00.020-0.01115.619-0.010-0.0100.0000.0000.0000.000
80A285GLY00.0750.03817.7150.0270.0270.0000.0000.0000.000
81A286GLN0-0.0300.00620.2060.0250.0250.0000.0000.0000.000
82A287LEU00.007-0.00621.441-0.016-0.0160.0000.0000.0000.000
83A288ALA0-0.011-0.00721.0420.0080.0080.0000.0000.0000.000
84A289GLY00.0440.04623.056-0.007-0.0070.0000.0000.0000.000
85A290PRO0-0.025-0.02025.4180.0070.0070.0000.0000.0000.000
86A291VAL00.0180.00721.5890.0070.0070.0000.0000.0000.000
87A292GLU-1-0.848-0.89824.904-0.079-0.0790.0000.0000.0000.000
88A293ILE00.0030.00722.722-0.008-0.0080.0000.0000.0000.000
89A294ARG10.8990.91322.3560.1270.1270.0000.0000.0000.000
90A295GLY00.0330.02227.3410.0080.0080.0000.0000.0000.000
91A296GLY00.0480.02328.6690.0040.0040.0000.0000.0000.000
92A297PHE00.0060.01127.419-0.001-0.0010.0000.0000.0000.000
93A298SER00.006-0.01123.7830.0050.0050.0000.0000.0000.000
94A299ILE0-0.043-0.00525.2790.0040.0040.0000.0000.0000.000
95A300LEU00.013-0.00318.648-0.009-0.0090.0000.0000.0000.000
96A301TYR0-0.019-0.01121.5470.0180.0180.0000.0000.0000.000
97A302LEU0-0.0210.00114.602-0.020-0.0200.0000.0000.0000.000
98A303ILE0-0.024-0.00918.5710.0220.0220.0000.0000.0000.000
99A304ASP-1-0.798-0.90016.709-0.240-0.2400.0000.0000.0000.000
100A305LYS10.8030.8899.6620.3960.3960.0000.0000.0000.000
101A306ARG10.8840.96110.7590.5820.5820.0000.0000.0000.000
102A307GLU-1-0.893-0.9605.819-0.583-0.5830.0000.0000.0000.000
103A308GLY00.0510.0235.8330.3000.3000.0000.0000.0000.000
104A309HIS0-0.068-0.0342.826-1.133-0.9150.271-0.333-0.156-0.001
105A310HIS0-0.550-0.5446.499-0.037-0.0370.0000.0000.0000.000
106A311HIS0-1.132-1.13210.254-0.021-0.0210.0000.0000.0000.000
107A312HIS0-1.210-1.24012.704-0.017-0.0170.0000.0000.0000.000
108A313HIS0-0.409-0.58911.6610.0370.0370.0000.0000.0000.000
109A314HIS-12.9853.22510.717-0.090-0.0900.0000.0000.0000.000
110A600SO4-2-1.748-1.83019.563-0.262-0.2620.0000.0000.0000.000
111A601SO4-2-1.886-1.93419.566-0.463-0.4630.0000.0000.0000.000
112A3HOH0-0.044-0.03624.2360.0030.0030.0000.0000.0000.000
113A4HOH0-0.0080.00026.5550.0060.0060.0000.0000.0000.000
114A5HOH00.0430.03338.439-0.001-0.0010.0000.0000.0000.000
115A7HOH00.0110.02236.806-0.001-0.0010.0000.0000.0000.000
116A8HOH0-0.023-0.01735.4190.0000.0000.0000.0000.0000.000
117A15HOH0-0.037-0.02635.9470.0000.0000.0000.0000.0000.000
118A16HOH0-0.047-0.04934.7680.0020.0020.0000.0000.0000.000
119A18HOH0-0.059-0.03936.8990.0010.0010.0000.0000.0000.000
120A21HOH0-0.022-0.01836.5500.0020.0020.0000.0000.0000.000
121A24HOH0-0.039-0.02836.6020.0020.0020.0000.0000.0000.000
122A30HOH0-0.604-0.6069.9020.0230.0230.0000.0000.0000.000
123A32HOH0-0.027-0.01924.1170.0000.0000.0000.0000.0000.000
124A35HOH0-0.005-0.02913.998-0.007-0.0070.0000.0000.0000.000
125A36HOH0-0.042-0.02629.407-0.002-0.0020.0000.0000.0000.000
126A40HOH0-0.062-0.05434.7150.0020.0020.0000.0000.0000.000
127A43HOH0-0.044-0.03119.9570.0020.0020.0000.0000.0000.000
128A44HOH00.0030.00623.7580.0040.0040.0000.0000.0000.000
129A46HOH0-0.008-0.01218.689-0.004-0.0040.0000.0000.0000.000
130A49HOH0-0.051-0.03233.9200.0020.0020.0000.0000.0000.000
131A51HOH00.0050.00122.8180.0060.0060.0000.0000.0000.000
132A52HOH0-0.065-0.04618.0130.0090.0090.0000.0000.0000.000
133A53HOH00.0160.01136.0650.0010.0010.0000.0000.0000.000
134A54HOH0-0.015-0.02812.826-0.022-0.0220.0000.0000.0000.000
135A55HOH0-0.021-0.02437.9550.0000.0000.0000.0000.0000.000
136A66HOH00.005-0.01229.1370.0010.0010.0000.0000.0000.000
137A68HOH0-0.003-0.0047.1010.2450.2450.0000.0000.0000.000
138A70HOH0-0.013-0.01440.1020.0000.0000.0000.0000.0000.000
139A80HOH0-0.030-0.01918.9220.0040.0040.0000.0000.0000.000
140A82HOH0-0.016-0.00911.3660.0290.0290.0000.0000.0000.000
141A83HOH00.0070.00531.5680.0010.0010.0000.0000.0000.000
142A87HOH0-0.044-0.02334.8740.0010.0010.0000.0000.0000.000
143A93HOH0-0.053-0.03517.0560.0140.0140.0000.0000.0000.000
144A95HOH0-0.028-0.01732.0200.0000.0000.0000.0000.0000.000
145A102HOH0-0.012-0.02915.4470.0070.0070.0000.0000.0000.000
146A103HOH0-0.004-0.00231.841-0.001-0.0010.0000.0000.0000.000
147A111HOH0-0.040-0.03022.6010.0070.0070.0000.0000.0000.000
148A113HOH00.009-0.00737.4820.0010.0010.0000.0000.0000.000
149A116HOH0-0.0090.0007.8050.0990.0990.0000.0000.0000.000
150A118HOH0-0.041-0.02419.6860.0050.0050.0000.0000.0000.000
151A120HOH00.0170.01334.199-0.001-0.0010.0000.0000.0000.000
152A124HOH0-0.037-0.03528.8230.0010.0010.0000.0000.0000.000
153A125HOH0-0.012-0.00638.0310.0010.0010.0000.0000.0000.000
154A127HOH0-0.019-0.02314.137-0.008-0.0080.0000.0000.0000.000
155A131HOH00.0380.02128.502-0.001-0.0010.0000.0000.0000.000
156A137HOH0-0.026-0.02420.9250.0040.0040.0000.0000.0000.000
157A138HOH0-0.0470.0082.3878.873-3.10411.3741.925-1.322-0.013
158A139HOH0-0.055-0.0274.3880.0810.097-0.001-0.003-0.0120.000
159A140HOH0-0.031-0.00512.432-0.009-0.0090.0000.0000.0000.000
160A141HOH00.0150.0242.102-0.037-0.4522.197-1.079-0.704-0.003
161A142HOH00.0110.01121.0990.0030.0030.0000.0000.0000.000
162A146HOH0-0.045-0.04013.4030.0030.0030.0000.0000.0000.000
163A152HOH00.0220.01818.640-0.009-0.0090.0000.0000.0000.000
164A154HOH0-0.055-0.06718.2280.0040.0040.0000.0000.0000.000
165A155HOH0-0.063-0.05231.4470.0010.0010.0000.0000.0000.000
166A157HOH00.0130.0219.9960.0330.0330.0000.0000.0000.000
167A158HOH0-0.019-0.01439.5140.0010.0010.0000.0000.0000.000
168A162HOH0-0.041-0.02413.2170.0160.0160.0000.0000.0000.000
169A165HOH00.0220.01340.2130.0000.0000.0000.0000.0000.000
170A169HOH00.0440.02111.236-0.042-0.0420.0000.0000.0000.000
171A170HOH00.0260.01926.1280.0030.0030.0000.0000.0000.000
172A171HOH00.0330.02110.0670.0280.0280.0000.0000.0000.000
173A172HOH0-0.054-0.0386.4100.0930.0930.0000.0000.0000.000
174A177HOH0-0.042-0.02626.644-0.002-0.0020.0000.0000.0000.000
175A179HOH0-0.047-0.0488.0070.1020.1020.0000.0000.0000.000
176A183HOH0-0.028-0.0225.1450.4420.463-0.001-0.005-0.0150.000
177A184HOH00.0010.01436.2360.0020.0020.0000.0000.0000.000
178A187HOH00.0610.03632.9530.0000.0000.0000.0000.0000.000
179A191HOH0-0.046-0.02833.5700.0020.0020.0000.0000.0000.000
180A199HOH0-0.045-0.03934.3960.0010.0010.0000.0000.0000.000
181A316HOH0-0.028-0.02642.619-0.001-0.0010.0000.0000.0000.000
182A318HOH0-0.030-0.01637.0170.0010.0010.0000.0000.0000.000
183A319HOH0-0.027-0.02817.8650.0070.0070.0000.0000.0000.000
184A321HOH0-0.031-0.03340.124-0.001-0.0010.0000.0000.0000.000
185A323HOH0-0.041-0.0336.4670.0080.0080.0000.0000.0000.000
186A326HOH0-0.053-0.03036.6570.0010.0010.0000.0000.0000.000
187A328HOH0-0.028-0.03338.7780.0010.0010.0000.0000.0000.000
188A329HOH0-0.040-0.03833.7170.0020.0020.0000.0000.0000.000
189A330HOH00.0290.02716.285-0.022-0.0220.0000.0000.0000.000
190A332HOH0-0.024-0.01935.7580.0020.0020.0000.0000.0000.000
191A333HOH0-0.031-0.02031.214-0.002-0.0020.0000.0000.0000.000
192A335HOH0-0.046-0.05029.601-0.001-0.0010.0000.0000.0000.000
193A336HOH0-0.017-0.0199.5580.0180.0180.0000.0000.0000.000
194A344HOH00.0090.02819.2370.0040.0040.0000.0000.0000.000
195B11HOH0-0.007-0.00613.684-0.004-0.0040.0000.0000.0000.000
196B42HOH0-0.039-0.01817.5960.0000.0000.0000.0000.0000.000