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: XRY58

Calculation Name: 1UPQ-A-Xray28

Preferred Name:

Target Type:

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 1UPQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H4M7

Base Structure: X-ray

Registration Date: 2018-07-26

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 194
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1140013.401817
FMO2-HF: Nuclear repulsion 1088615.637116
FMO2-HF: Total energy -51397.764701
FMO2-MP2: Total energy -51544.559143


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:46:ACE)


Summations of interaction energy for fragment #1(A:46: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.
0.8272.4830.344-0.941-1.057-0.002
Interaction energy analysis for fragmet #1(A:46:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.006
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].
3A48ARG10.9580.9913.8371.7132.424-0.010-0.314-0.3870.001
4A49ARG10.8460.9036.9580.2070.2070.0000.0000.0000.000
5A50ASP-1-0.835-0.91910.118-0.261-0.2610.0000.0000.0000.000
6A51PRO0-0.0010.00513.4520.0210.0210.0000.0000.0000.000
7A52ASN0-0.030-0.01815.9740.0510.0510.0000.0000.0000.000
8A53LEU0-0.0060.01414.1130.0210.0210.0000.0000.0000.000
9A54PRO00.0520.03717.6140.0110.0110.0000.0000.0000.000
10A55VAL0-0.0120.03516.063-0.031-0.0310.0000.0000.0000.000
11A56HIS10.8020.89416.5220.2160.2160.0000.0000.0000.000
12A57ILE00.0110.00617.7010.0160.0160.0000.0000.0000.000
13A58ARG10.8510.91316.8960.0700.0700.0000.0000.0000.000
14A59GLY00.0240.01817.3100.0040.0040.0000.0000.0000.000
15A60TRP0-0.046-0.02017.5300.0080.0080.0000.0000.0000.000
16A61LEU00.0290.03115.955-0.011-0.0110.0000.0000.0000.000
17A62HIS0-0.056-0.02817.6310.0270.0270.0000.0000.0000.000
18A63LYS10.8280.90510.673-0.332-0.3320.0000.0000.0000.000
19A64GLN0-0.054-0.04716.4790.0150.0150.0000.0000.0000.000
20A65ASP-1-0.725-0.82315.6180.2200.2200.0000.0000.0000.000
21A66SER0-0.080-0.07214.177-0.012-0.0120.0000.0000.0000.000
22A67SER0-0.029-0.01516.232-0.005-0.0050.0000.0000.0000.000
23A68GLY00.0030.00018.701-0.013-0.0130.0000.0000.0000.000
24A69LEU0-0.015-0.01521.529-0.018-0.0180.0000.0000.0000.000
25A70ARG10.8740.96718.405-0.158-0.1580.0000.0000.0000.000
26A71LEU00.0590.03820.631-0.016-0.0160.0000.0000.0000.000
27A72TRP0-0.005-0.01119.6020.0080.0080.0000.0000.0000.000
28A73LYS10.9490.98516.449-0.178-0.1780.0000.0000.0000.000
29A74ARG10.8840.93517.279-0.054-0.0540.0000.0000.0000.000
30A75ARG10.7680.86113.107-0.292-0.2920.0000.0000.0000.000
31A76TRP0-0.025-0.00714.804-0.020-0.0200.0000.0000.0000.000
32A77PHE00.0540.01111.3400.0170.0170.0000.0000.0000.000
33A78VAL00.007-0.00912.368-0.004-0.0040.0000.0000.0000.000
34A79LEU0-0.0010.01111.988-0.044-0.0440.0000.0000.0000.000
35A80SER0-0.028-0.01412.4880.0240.0240.0000.0000.0000.000
36A81GLY00.0600.03512.568-0.090-0.0900.0000.0000.0000.000
37A82HIS00.0230.01813.1500.0490.0490.0000.0000.0000.000
38A83CYS0-0.010-0.0048.284-0.124-0.1240.0000.0000.0000.000
39A84LEU0-0.0040.0049.1020.0980.0980.0000.0000.0000.000
40A85PHE0-0.007-0.0166.483-0.067-0.0670.0000.0000.0000.000
41A86TYR0-0.020-0.0258.2220.0150.0150.0000.0000.0000.000
42A87TYR0-0.0100.0049.2790.0540.0540.0000.0000.0000.000
43A88LYS10.8820.92612.078-0.237-0.2370.0000.0000.0000.000
44A89ASP-1-0.795-0.89314.9240.0660.0660.0000.0000.0000.000
45A90SER00.0390.01016.430-0.002-0.0020.0000.0000.0000.000
46A91ARG10.8590.94218.144-0.073-0.0730.0000.0000.0000.000
47A92GLU-1-0.746-0.82114.352-0.102-0.1020.0000.0000.0000.000
48A93GLU-1-0.744-0.82114.2980.0070.0070.0000.0000.0000.000
49A94SER0-0.026-0.00510.5600.0660.0660.0000.0000.0000.000
50A95VAL0-0.007-0.0015.541-0.003-0.0030.0000.0000.0000.000
51A96LEU0-0.002-0.0017.4770.1740.1740.0000.0000.0000.000
52A97GLY0-0.0010.0025.0250.3210.3210.0000.0000.0000.000
53A98SER0-0.102-0.0592.862-0.6510.0410.345-0.542-0.494-0.003
54A99VAL0-0.0060.0064.7440.1150.238-0.001-0.005-0.1160.000
55A100LEU00.010-0.0016.936-0.088-0.0880.0000.0000.0000.000
56A101LEU00.0420.0048.6520.1360.1360.0000.0000.0000.000
57A102PRO00.0080.02112.0660.0550.0550.0000.0000.0000.000
58A103SER0-0.0070.00313.1890.0410.0410.0000.0000.0000.000
59A104TYR0-0.068-0.03910.1380.0310.0310.0000.0000.0000.000
60A105ASN0-0.066-0.03815.118-0.008-0.0080.0000.0000.0000.000
61A106ILE0-0.006-0.01215.9340.0180.0180.0000.0000.0000.000
62A107ARG10.8600.93119.0070.0210.0210.0000.0000.0000.000
63A108PRO00.0080.01321.9250.0090.0090.0000.0000.0000.000
64A109ASP-1-0.740-0.81523.0220.0310.0310.0000.0000.0000.000
65A110GLY00.0080.02925.5540.0010.0010.0000.0000.0000.000
66A111PRO00.0520.00829.0190.0040.0040.0000.0000.0000.000
67A112GLY00.0630.03231.6360.0020.0020.0000.0000.0000.000
68A113ALA0-0.047-0.01929.1180.0020.0020.0000.0000.0000.000
69A114PRO00.0360.03927.3080.0050.0050.0000.0000.0000.000
70A115ARG10.8150.88121.389-0.057-0.0570.0000.0000.0000.000
71A116GLY00.0170.00726.0630.0080.0080.0000.0000.0000.000
72A117ARG10.9210.96723.415-0.065-0.0650.0000.0000.0000.000
73A118ARG10.9700.99527.290-0.017-0.0170.0000.0000.0000.000
74A119PHE0-0.034-0.01725.6460.0020.0020.0000.0000.0000.000
75A120THR00.020-0.01522.355-0.001-0.0010.0000.0000.0000.000
76A121PHE0-0.009-0.01017.405-0.009-0.0090.0000.0000.0000.000
77A122THR00.0010.00118.2010.0190.0190.0000.0000.0000.000
78A123ALA0-0.013-0.00614.154-0.020-0.0200.0000.0000.0000.000
79A124GLU-1-0.837-0.89514.8460.0190.0190.0000.0000.0000.000
80A125HIS00.0420.00113.889-0.036-0.0360.0000.0000.0000.000
81A126PRO00.0590.04814.8820.0250.0250.0000.0000.0000.000
82A127GLY00.0150.02114.810-0.022-0.0220.0000.0000.0000.000
83A128MET0-0.048-0.0088.8750.0110.0110.0000.0000.0000.000
84A129ARG10.9440.9985.968-0.907-0.9070.0000.0000.0000.000
85A130THR00.0260.01411.310-0.062-0.0620.0000.0000.0000.000
86A131TYR0-0.041-0.0107.6000.1020.1020.0000.0000.0000.000
87A132VAL0-0.0100.00313.749-0.035-0.0350.0000.0000.0000.000
88A133LEU00.0030.00314.0070.0190.0190.0000.0000.0000.000
89A134ALA0-0.001-0.00418.043-0.011-0.0110.0000.0000.0000.000
90A135ALA00.0480.03220.9470.0040.0040.0000.0000.0000.000
91A136ASP-1-0.924-0.95022.7740.0370.0370.0000.0000.0000.000
92A137THR0-0.046-0.03425.702-0.002-0.0020.0000.0000.0000.000
93A138LEU00.0460.01526.739-0.002-0.0020.0000.0000.0000.000
94A139GLU-1-0.727-0.84327.759-0.034-0.0340.0000.0000.0000.000
95A140ASP-1-0.701-0.77622.908-0.009-0.0090.0000.0000.0000.000
96A141LEU00.0140.01022.788-0.005-0.0050.0000.0000.0000.000
97A142ARG10.8380.91923.5940.0350.0350.0000.0000.0000.000
98A143GLY00.016-0.00623.911-0.008-0.0080.0000.0000.0000.000
99A144TRP00.011-0.01815.373-0.021-0.0210.0000.0000.0000.000
100A145LEU00.0030.00219.657-0.014-0.0140.0000.0000.0000.000
101A146ARG10.8280.94421.5050.0770.0770.0000.0000.0000.000
102A147ALA00.0460.03218.808-0.011-0.0110.0000.0000.0000.000
103A148LEU00.0390.00714.697-0.023-0.0230.0000.0000.0000.000
104A149GLY00.002-0.00317.569-0.014-0.0140.0000.0000.0000.000
105A150ARG10.8560.91420.2320.1050.1050.0000.0000.0000.000
106A151ALA00.0200.02414.775-0.012-0.0120.0000.0000.0000.000
107A152SER0-0.087-0.03315.995-0.023-0.0230.0000.0000.0000.000
108A153ARG10.8570.95017.0230.1090.1090.0000.0000.0000.000
109A154NME00.0220.01419.473-0.020-0.0200.0000.0000.0000.000
110A1154SO4-2-1.686-1.79814.8520.6190.6190.0000.0000.0000.000
111A1155SO4-2-1.660-1.77122.440-0.248-0.2480.0000.0000.0000.000
112A1156SO4-2-1.584-1.71711.3570.8360.8360.0000.0000.0000.000
113A2002HOH0-0.002-0.00810.0090.0730.0730.0000.0000.0000.000
114A2003HOH00.0120.0168.658-0.076-0.0760.0000.0000.0000.000
115A2004HOH0-0.005-0.01715.028-0.003-0.0030.0000.0000.0000.000
116A2006HOH0-0.022-0.01918.7430.0060.0060.0000.0000.0000.000
117A2007HOH0-0.024-0.05017.352-0.013-0.0130.0000.0000.0000.000
118A2008HOH00.0130.00521.4610.0000.0000.0000.0000.0000.000
119A2009HOH00.0300.02317.8100.0010.0010.0000.0000.0000.000
120A2011HOH00.0070.04221.5820.0000.0000.0000.0000.0000.000
121A2012HOH00.0280.01522.4120.0020.0020.0000.0000.0000.000
122A2013HOH0-0.038-0.03422.5080.0040.0040.0000.0000.0000.000
123A2015HOH00.0120.01014.710-0.005-0.0050.0000.0000.0000.000
124A2016HOH00.0510.04023.6860.0020.0020.0000.0000.0000.000
125A2017HOH00.000-0.00722.482-0.001-0.0010.0000.0000.0000.000
126A2018HOH0-0.043-0.04716.4790.0000.0000.0000.0000.0000.000
127A2023HOH0-0.029-0.01524.898-0.001-0.0010.0000.0000.0000.000
128A2026HOH00.0010.00825.9190.0020.0020.0000.0000.0000.000
129A2028HOH00.0360.02221.1200.0050.0050.0000.0000.0000.000
130A2031HOH00.0280.03621.570-0.003-0.0030.0000.0000.0000.000
131A2032HOH0-0.0090.00211.741-0.016-0.0160.0000.0000.0000.000
132A2038HOH0-0.027-0.02111.243-0.049-0.0490.0000.0000.0000.000
133A2039HOH0-0.035-0.04016.2370.0020.0020.0000.0000.0000.000
134A2041HOH0-0.015-0.0019.1440.0260.0260.0000.0000.0000.000
135A2042HOH00.0630.04311.371-0.012-0.0120.0000.0000.0000.000
136A2045HOH0-0.023-0.01518.7090.0010.0010.0000.0000.0000.000
137A2046HOH0-0.021-0.02216.3780.0140.0140.0000.0000.0000.000
138A2047HOH00.0350.02419.2020.0000.0000.0000.0000.0000.000
139A2049HOH00.0170.00515.524-0.002-0.0020.0000.0000.0000.000
140A2050HOH0-0.047-0.03217.8920.0070.0070.0000.0000.0000.000
141A2051HOH00.022-0.00421.4890.0040.0040.0000.0000.0000.000
142A2053HOH0-0.070-0.05018.659-0.006-0.0060.0000.0000.0000.000
143A2055HOH0-0.011-0.01215.406-0.013-0.0130.0000.0000.0000.000
144A2056HOH0-0.045-0.03716.484-0.009-0.0090.0000.0000.0000.000
145A2058HOH0-0.052-0.04520.7080.0030.0030.0000.0000.0000.000
146A2059HOH0-0.005-0.01317.2550.0060.0060.0000.0000.0000.000
147A2060HOH0-0.038-0.02319.8440.0040.0040.0000.0000.0000.000
148A2061HOH0-0.041-0.04013.1080.0010.0010.0000.0000.0000.000
149A2062HOH00.003-0.01211.9650.0030.0030.0000.0000.0000.000
150A2063HOH00.0350.0187.741-0.031-0.0310.0000.0000.0000.000
151A2065HOH00.0500.0385.9700.0780.0780.0000.0000.0000.000
152A2066HOH00.013-0.0079.446-0.031-0.0310.0000.0000.0000.000
153A2067HOH0-0.040-0.02517.7180.0080.0080.0000.0000.0000.000
154A2069HOH00.0230.01311.9400.0070.0070.0000.0000.0000.000
155A2070HOH0-0.008-0.0237.1800.0970.0970.0000.0000.0000.000
156A2071HOH00.0470.03519.2630.0060.0060.0000.0000.0000.000
157A2072HOH0-0.002-0.02022.254-0.001-0.0010.0000.0000.0000.000
158A2073HOH0-0.006-0.01026.091-0.003-0.0030.0000.0000.0000.000
159A2074HOH0-0.033-0.02823.302-0.001-0.0010.0000.0000.0000.000
160A2075HOH00.0280.01126.4920.0000.0000.0000.0000.0000.000
161A2076HOH0-0.047-0.03329.590-0.001-0.0010.0000.0000.0000.000
162A2077HOH0-0.039-0.02731.9190.0000.0000.0000.0000.0000.000
163A2078HOH00.0220.05929.0390.0000.0000.0000.0000.0000.000
164A2080HOH00.0120.01420.014-0.007-0.0070.0000.0000.0000.000
165A2085HOH0-0.008-0.02525.8000.0000.0000.0000.0000.0000.000
166A2087HOH00.0300.00933.2050.0010.0010.0000.0000.0000.000
167A2088HOH0-0.029-0.02425.2790.0030.0030.0000.0000.0000.000
168A2089HOH0-0.043-0.05928.9690.0010.0010.0000.0000.0000.000
169A2090HOH0-0.021-0.01625.4940.0010.0010.0000.0000.0000.000
170A2091HOH0-0.035-0.03116.8380.0040.0040.0000.0000.0000.000
171A2092HOH00.0140.01617.4150.0020.0020.0000.0000.0000.000
172A2093HOH0-0.036-0.03214.0110.0010.0010.0000.0000.0000.000
173A2094HOH00.0430.03017.3120.0030.0030.0000.0000.0000.000
174A2095HOH0-0.028-0.01312.5740.0090.0090.0000.0000.0000.000
175A2096HOH0-0.030-0.03814.3740.0100.0100.0000.0000.0000.000
176A2097HOH00.0340.0183.216-0.619-0.4890.010-0.080-0.0600.000
177A2098HOH00.0270.0208.0220.0200.0200.0000.0000.0000.000
178A2100HOH00.019-0.00514.480-0.016-0.0160.0000.0000.0000.000
179A2101HOH00.0110.01916.2800.0020.0020.0000.0000.0000.000
180A2104HOH0-0.045-0.03426.7840.0000.0000.0000.0000.0000.000
181A2105HOH0-0.044-0.02424.165-0.003-0.0030.0000.0000.0000.000
182A2106HOH0-0.073-0.08122.7420.0000.0000.0000.0000.0000.000
183A2107HOH0-0.005-0.01420.700-0.004-0.0040.0000.0000.0000.000
184A2109HOH0-0.056-0.07822.771-0.003-0.0030.0000.0000.0000.000
185A2110HOH0-0.044-0.04922.107-0.002-0.0020.0000.0000.0000.000
186A2111HOH0-0.038-0.02922.866-0.001-0.0010.0000.0000.0000.000
187A2112HOH0-0.023-0.02318.338-0.011-0.0110.0000.0000.0000.000
188A2119HOH0-0.029-0.02518.378-0.012-0.0120.0000.0000.0000.000
189A2120HOH0-0.020-0.03020.821-0.005-0.0050.0000.0000.0000.000
190A2123HOH0-0.021-0.02821.701-0.007-0.0070.0000.0000.0000.000
191A2124HOH0-0.005-0.01614.804-0.018-0.0180.0000.0000.0000.000
192A2125HOH0-0.012-0.03014.361-0.013-0.0130.0000.0000.0000.000
193A2126HOH00.0260.01214.586-0.021-0.0210.0000.0000.0000.000
194A2127HOH0-0.031-0.05011.0280.0120.0120.0000.0000.0000.000