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: P8N9Y

Calculation Name: 4QBO-A-Xray29

Preferred Name:

Target Type:

Ligand Name: magnesium ion

ligand 3-letter code: MG

PDB ID: 4QBO

Chain ID: A

ChEMBL ID:

UniProt ID: A7J283

Base Structure: X-ray

Registration Date: 2018-09-06

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 218
LigandCharge MG2=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -939200.894289
FMO2-HF: Nuclear repulsion 892342.446324
FMO2-HF: Total energy -46858.447964
FMO2-MP2: Total energy -46988.360028


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:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
-16.028-108.959161.111-66.531-1.650.06
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.109
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].
3A1MET0-0.0190.0123.673-4.171-0.879-0.014-2.010-1.2690.007
4A2ARG10.9100.9765.746-1.172-1.200-0.001-0.0040.0340.000
5A3THR00.0050.0147.3620.2340.2340.0000.0000.0000.000
6A4GLU-1-0.537-0.8579.6240.1280.1280.0000.0000.0000.000
7A5LYS10.9690.99312.6180.0860.0860.0000.0000.0000.000
8A6ASP-1-0.770-0.87710.0570.0780.0780.0000.0000.0000.000
9A7ILE0-0.0060.01013.466-0.019-0.0190.0000.0000.0000.000
10A8GLU-1-0.742-0.78715.7050.0360.0360.0000.0000.0000.000
11A9ASN0-0.038-0.03215.481-0.017-0.0170.0000.0000.0000.000
12A10TYR0-0.046-0.01917.272-0.020-0.0200.0000.0000.0000.000
13A11LEU00.0470.02119.085-0.012-0.0120.0000.0000.0000.000
14A12LYS10.8790.93021.083-0.016-0.0160.0000.0000.0000.000
15A13LYS10.8590.94820.537-0.048-0.0480.0000.0000.0000.000
16A14LYS10.8990.96022.317-0.101-0.1010.0000.0000.0000.000
17A15THR00.0180.01324.9770.0030.0030.0000.0000.0000.000
18A16LYS10.8990.96927.588-0.075-0.0750.0000.0000.0000.000
19A17GLY00.0670.03731.0750.0010.0010.0000.0000.0000.000
20A18LEU0-0.069-0.02530.665-0.004-0.0040.0000.0000.0000.000
21A19CYS00.0040.00124.7850.0080.0080.0000.0000.0000.000
22A20LEU0-0.0100.00826.668-0.006-0.0060.0000.0000.0000.000
23A21LYS10.9330.96723.0050.0110.0110.0000.0000.0000.000
24A22PHE00.0310.02126.182-0.006-0.0060.0000.0000.0000.000
25A23THR0-0.025-0.02126.6590.0010.0010.0000.0000.0000.000
26A24SER00.0180.01328.761-0.004-0.0040.0000.0000.0000.000
27A25PRO00.0220.00431.7730.0020.0020.0000.0000.0000.000
28A26GLY00.0440.02732.3620.0010.0010.0000.0000.0000.000
29A27THR0-0.038-0.01431.5150.0030.0030.0000.0000.0000.000
30A28ILE0-0.022-0.01627.4310.0020.0020.0000.0000.0000.000
31A29GLY00.0050.00025.7730.0030.0030.0000.0000.0000.000
32A30VAL00.0150.01826.8420.0100.0100.0000.0000.0000.000
33A31PRO00.0270.00725.1440.0030.0030.0000.0000.0000.000
34A32ASP-1-0.509-0.79020.5400.1130.1130.0000.0000.0000.000
35A33ARG10.8380.93721.533-0.059-0.0590.0000.0000.0000.000
36A34ILE00.0320.02025.7510.0070.0070.0000.0000.0000.000
37A35VAL0-0.040-0.01727.313-0.006-0.0060.0000.0000.0000.000
38A36VAL00.0130.00829.8170.0000.0000.0000.0000.0000.000
39A37MET0-0.007-0.00230.819-0.001-0.0010.0000.0000.0000.000
40A38ASN00.0040.00034.887-0.004-0.0040.0000.0000.0000.000
41A39THR00.0020.00135.446-0.003-0.0030.0000.0000.0000.000
42A40GLY00.0420.01636.7770.0010.0010.0000.0000.0000.000
43A41THR0-0.046-0.00933.476-0.002-0.0020.0000.0000.0000.000
44A42PHE00.0180.00530.6620.0020.0020.0000.0000.0000.000
45A43PHE0-0.034-0.01128.813-0.001-0.0010.0000.0000.0000.000
46A44VAL00.0480.01322.9270.0100.0100.0000.0000.0000.000
47A45GLU-1-0.541-0.82020.8370.1290.1290.0000.0000.0000.000
48A46VAL00.1670.15316.7460.0230.0230.0000.0000.0000.000
49A47LYS10.9180.88416.381-0.252-0.2520.0000.0000.0000.000
50A48ALA00.004-0.00110.7990.0100.0100.0000.0000.0000.000
51A49PRO00.0130.01410.483-0.066-0.0660.0000.0000.0000.000
52A50GLY00.0430.03812.2140.1230.1230.0000.0000.0000.000
53A51LYS10.8390.92912.275-0.561-0.5610.0000.0000.0000.000
54A52LYS11.0421.01515.712-0.306-0.3060.0000.0000.0000.000
55A53PRO00.0260.02219.298-0.004-0.0040.0000.0000.0000.000
56A54ARG10.9470.95819.185-0.120-0.1200.0000.0000.0000.000
57A55PRO00.0530.02622.589-0.007-0.0070.0000.0000.0000.000
58A56SER00.0510.02725.574-0.002-0.0020.0000.0000.0000.000
59A57GLN00.0110.00721.3080.0110.0110.0000.0000.0000.000
60A58VAL00.0120.01325.289-0.004-0.0040.0000.0000.0000.000
61A59ALA0-0.016-0.00827.614-0.005-0.0050.0000.0000.0000.000
62A60MET00.0290.02628.934-0.007-0.0070.0000.0000.0000.000
63A61HIS0-0.013-0.02225.6430.0090.0090.0000.0000.0000.000
64A62LYS10.8990.94530.281-0.099-0.0990.0000.0000.0000.000
65A63LYS10.9580.99333.210-0.060-0.0600.0000.0000.0000.000
66A64ILE0-0.019-0.00130.819-0.004-0.0040.0000.0000.0000.000
67A65LYS10.9230.96429.792-0.117-0.1170.0000.0000.0000.000
68A66GLU-1-0.937-0.90735.4940.0610.0610.0000.0000.0000.000
69A67ALA00.0100.02037.971-0.004-0.0040.0000.0000.0000.000
70A68GLY00.0460.03238.405-0.003-0.0030.0000.0000.0000.000
71A69GLN0-0.0340.00235.1190.0030.0030.0000.0000.0000.000
72A70HIS0-0.0030.00730.2540.0050.0050.0000.0000.0000.000
73A71VAL0-0.011-0.01026.768-0.005-0.0050.0000.0000.0000.000
74A72TRP0-0.0190.00725.6230.0070.0070.0000.0000.0000.000
75A73VAL0-0.039-0.03320.828-0.003-0.0030.0000.0000.0000.000
76A74VAL00.0040.01119.5830.0090.0090.0000.0000.0000.000
77A75ASP-1-0.788-0.86015.8240.4420.4420.0000.0000.0000.000
78A76SER00.025-0.00115.0970.0830.0830.0000.0000.0000.000
79A77TYR00.000-0.01514.219-0.028-0.0280.0000.0000.0000.000
80A78GLU-1-0.884-0.93718.0260.2570.2570.0000.0000.0000.000
81A79SER00.040-0.00418.994-0.039-0.0390.0000.0000.0000.000
82A80VAL0-0.022-0.01319.587-0.029-0.0290.0000.0000.0000.000
83A81ASP-1-0.755-0.86022.0480.1530.1530.0000.0000.0000.000
84A82MET00.0290.03222.633-0.019-0.0190.0000.0000.0000.000
85A83ALA0-0.0040.00925.013-0.013-0.0130.0000.0000.0000.000
86A84LEU0-0.034-0.02225.124-0.013-0.0130.0000.0000.0000.000
87A85LYS10.9300.97328.083-0.099-0.0990.0000.0000.0000.000
88A86GLU-1-0.807-0.88729.7280.1130.1130.0000.0000.0000.000
89A87MET0-0.032-0.00527.387-0.009-0.0090.0000.0000.0000.000
90A88GLU-1-0.907-0.92430.9250.0710.0710.0000.0000.0000.000
91A89ASN0-0.070-0.04134.140-0.002-0.0020.0000.0000.0000.000
92A90TRP-1-0.860-0.89733.8610.0630.0630.0000.0000.0000.000
93A101MG220.2531.40619.050-0.325-0.3250.0000.0000.0000.000
94A201HOH0-0.011-0.02132.2490.0010.0010.0000.0000.0000.000
95A202HOH0-0.032-0.02824.3100.0050.0050.0000.0000.0000.000
96A203HOH0-0.018-0.02034.7170.0020.0020.0000.0000.0000.000
97A204HOH0-0.014-0.00134.4140.0010.0010.0000.0000.0000.000
98A205HOH00.0500.02116.435-0.005-0.0050.0000.0000.0000.000
99A206HOH0-0.031-0.03225.3930.0030.0030.0000.0000.0000.000
100A207HOH0-0.002-0.01730.4380.0030.0030.0000.0000.0000.000
101A208HOH0-0.039-0.02929.2440.0030.0030.0000.0000.0000.000
102A209HOH0-0.017-0.01317.3420.0030.0030.0000.0000.0000.000
103A210HOH0-0.057-0.04238.266-0.001-0.0010.0000.0000.0000.000
104A211HOH0-0.011-0.02133.9910.0000.0000.0000.0000.0000.000
105A212HOH0-0.028-0.02315.218-0.004-0.0040.0000.0000.0000.000
106A213HOH00.0200.01111.4630.0030.0030.0000.0000.0000.000
107A214HOH0-0.010-0.00813.9530.0100.0100.0000.0000.0000.000
108A215HOH00.0150.01228.3230.0010.0010.0000.0000.0000.000
109A216HOH0-0.036-0.02526.284-0.005-0.0050.0000.0000.0000.000
110A217HOH00.041-0.02517.0680.0010.0010.0000.0000.0000.000
111A218HOH0-0.077-0.06629.761-0.001-0.0010.0000.0000.0000.000
112A219HOH00.034-0.03821.799-0.001-0.0010.0000.0000.0000.000
113A220HOH0-0.008-0.00225.132-0.001-0.0010.0000.0000.0000.000
114A221HOH00.030-0.00227.1090.0020.0020.0000.0000.0000.000
115A222HOH0-0.021-0.01920.608-0.008-0.0080.0000.0000.0000.000
116A223HOH00.0240.0019.783-0.041-0.0410.0000.0000.0000.000
117A224HOH0-0.028-0.01923.1250.0020.0020.0000.0000.0000.000
118A225HOH00.0520.03216.831-0.008-0.0080.0000.0000.0000.000
119A226HOH00.0150.01429.0760.0010.0010.0000.0000.0000.000
120A227HOH00.0220.00734.1970.0010.0010.0000.0000.0000.000
121A228HOH00.0320.01411.6620.0100.0100.0000.0000.0000.000
122A229HOH0-0.019-0.02328.743-0.002-0.0020.0000.0000.0000.000
123A231HOH0-0.0140.01023.6800.0030.0030.0000.0000.0000.000
124A232HOH0-0.042-0.03010.008-0.061-0.0610.0000.0000.0000.000
125A233HOH0-0.055-0.07623.759-0.008-0.0080.0000.0000.0000.000
126A234HOH00.006-0.0117.337-0.253-0.2530.0000.0000.0000.000
127A235HOH0-0.029-0.0233.9820.9911.1020.000-0.042-0.0690.000
128A236HOH0-0.001-0.00127.1140.0000.0000.0000.0000.0000.000
129A237HOH00.0070.01424.6930.0020.0020.0000.0000.0000.000
130A238HOH0-0.020-0.02636.8560.0010.0010.0000.0000.0000.000
131A239HOH0-0.056-0.04441.329-0.001-0.0010.0000.0000.0000.000
132A240HOH00.0190.01227.805-0.002-0.0020.0000.0000.0000.000
133A241HOH0-0.008-0.02723.1510.0070.0070.0000.0000.0000.000
134A242HOH0-0.024-0.01913.8350.0100.0100.0000.0000.0000.000
135A243HOH0-0.0020.00124.6890.0020.0020.0000.0000.0000.000
136A244HOH0-0.023-0.04439.159-0.001-0.0010.0000.0000.0000.000
137A245HOH00.0560.07824.3170.0040.0040.0000.0000.0000.000
138A246HOH00.0330.00830.7800.0010.0010.0000.0000.0000.000
139A247HOH00.0520.02828.3520.0010.0010.0000.0000.0000.000
140A248HOH00.0370.04831.1040.0010.0010.0000.0000.0000.000
141A249HOH0-0.074-0.06226.421-0.004-0.0040.0000.0000.0000.000
142A250HOH00.010-0.00338.3100.0010.0010.0000.0000.0000.000
143A251HOH00.0900.05618.5460.0110.0110.0000.0000.0000.000
144A252HOH0-0.024-0.01742.3940.0000.0000.0000.0000.0000.000
145A253HOH00.0180.00226.931-0.003-0.0030.0000.0000.0000.000
146A255HOH0-0.038-0.06517.941-0.001-0.0010.0000.0000.0000.000
147A256HOH00.0660.04233.0800.0020.0020.0000.0000.0000.000
148A257HOH0-0.070-0.04939.474-0.002-0.0020.0000.0000.0000.000
149A258HOH00.0280.01134.1130.0010.0010.0000.0000.0000.000
150A259HOH0-0.009-0.00927.1560.0020.0020.0000.0000.0000.000
151A260HOH00.0280.01423.7000.0020.0020.0000.0000.0000.000
152A261HOH00.0180.00727.3230.0040.0040.0000.0000.0000.000
153A262HOH00.0140.02236.9540.0020.0020.0000.0000.0000.000
154A263HOH00.0110.02136.260-0.002-0.0020.0000.0000.0000.000
155A264HOH00.0540.02025.1000.0020.0020.0000.0000.0000.000
156A265HOH0-0.023-0.01934.7310.0000.0000.0000.0000.0000.000
157A267HOH00.0320.02818.4420.0130.0130.0000.0000.0000.000
158A268HOH00.0100.00430.3740.0000.0000.0000.0000.0000.000
159A269HOH00.0090.00127.084-0.004-0.0040.0000.0000.0000.000
160A271HOH0-0.059-0.03419.398-0.006-0.0060.0000.0000.0000.000
161A273HOH0-0.005-0.01135.6260.0020.0020.0000.0000.0000.000
162A274HOH0-0.037-0.02423.140-0.001-0.0010.0000.0000.0000.000
163A275HOH0-0.025-0.01142.2400.0000.0000.0000.0000.0000.000
164A277HOH0-0.028-0.03616.424-0.012-0.0120.0000.0000.0000.000
165A278HOH0-0.008-0.03322.069-0.005-0.0050.0000.0000.0000.000
166A280HOH0-0.018-0.02023.1230.0030.0030.0000.0000.0000.000
167A281HOH00.000-0.00516.6510.0170.0170.0000.0000.0000.000
168A287HOH00.0280.02230.0410.0010.0010.0000.0000.0000.000
169A289HOH00.0390.03039.463-0.002-0.0020.0000.0000.0000.000
170A290HOH0-0.0020.00620.3210.0090.0090.0000.0000.0000.000
171A293HOH00.0010.00416.9290.0050.0050.0000.0000.0000.000
172A295HOH00.0340.03528.179-0.001-0.0010.0000.0000.0000.000
173A298HOH0-0.005-0.00437.4500.0000.0000.0000.0000.0000.000
174A299HOH0-0.0020.00319.941-0.001-0.0010.0000.0000.0000.000
175A300HOH00.002-0.00238.572-0.002-0.0020.0000.0000.0000.000
176A301HOH0-0.025-0.0385.1370.3230.350-0.001-0.003-0.0240.000
177A302HOH00.0070.00737.206-0.002-0.0020.0000.0000.0000.000
178A303HOH0-0.084-0.07322.781-0.003-0.0030.0000.0000.0000.000
179A304HOH00.0250.01415.174-0.013-0.0130.0000.0000.0000.000
180A305HOH00.0110.01637.186-0.001-0.0010.0000.0000.0000.000
181A306HOH00.0020.00535.8830.0020.0020.0000.0000.0000.000
182A307HOH0-0.028-0.01325.948-0.001-0.0010.0000.0000.0000.000
183A308HOH0-0.006-0.02120.608-0.007-0.0070.0000.0000.0000.000
184A309HOH00.0140.00426.437-0.004-0.0040.0000.0000.0000.000
185A310HOH0-0.046-0.04140.0680.0000.0000.0000.0000.0000.000
186A311HOH00.0690.06512.3820.0500.0500.0000.0000.0000.000
187A313HOH00.0380.0444.085-0.420-0.3500.001-0.036-0.0350.000
188A315HOH0-0.007-0.00342.529-0.001-0.0010.0000.0000.0000.000
189A316HOH0-0.026-0.06419.682-0.009-0.0090.0000.0000.0000.000
190A318HOH0-0.020-0.04235.115-0.002-0.0020.0000.0000.0000.000
191A319HOH0-0.019-0.02218.193-0.001-0.0010.0000.0000.0000.000
192A321HOH00.0350.02024.771-0.005-0.0050.0000.0000.0000.000
193A322HOH00.0340.02320.2790.0100.0100.0000.0000.0000.000
194A323HOH0-0.061-0.0379.4160.1040.1040.0000.0000.0000.000
195A324HOH0-0.068-0.08627.5180.0030.0030.0000.0000.0000.000
196A325HOH0-0.0030.00736.9450.0000.0000.0000.0000.0000.000
197A327HOH0-0.035-0.01518.522-0.007-0.0070.0000.0000.0000.000
198A328HOH0-0.0160.01438.8040.0010.0010.0000.0000.0000.000
199A330HOH0-0.030-0.01717.224-0.012-0.0120.0000.0000.0000.000
200A331HOH0-0.010-0.02312.054-0.011-0.0110.0000.0000.0000.000
201A333HOH00.014-0.00933.0710.0010.0010.0000.0000.0000.000
202A334HOH00.0120.00535.1210.0020.0020.0000.0000.0000.000
203A335HOH0-0.024-0.02238.8450.0000.0000.0000.0000.0000.000
204A337HOH0-0.019-0.01134.793-0.001-0.0010.0000.0000.0000.000
205A338HOH00.0280.02413.5920.0090.0090.0000.0000.0000.000
206A339HOH0-0.029-0.1121.277-11.083-107.486161.126-64.436-0.2870.053
207A340HOH0-0.065-0.06017.743-0.010-0.0100.0000.0000.0000.000
208A341HOH0-0.015-0.00728.5180.0000.0000.0000.0000.0000.000
209A342HOH00.0240.00139.9320.0000.0000.0000.0000.0000.000
210A344HOH00.000-0.00316.3350.0080.0080.0000.0000.0000.000
211A345HOH00.0310.01732.3450.0020.0020.0000.0000.0000.000
212A347HOH00.0400.02014.796-0.014-0.0140.0000.0000.0000.000
213A348HOH0-0.027-0.02224.931-0.006-0.0060.0000.0000.0000.000
214A349HOH00.0090.00538.2370.0000.0000.0000.0000.0000.000
215A351HOH00.0390.06228.078-0.002-0.0020.0000.0000.0000.000
216A353HOH00.0170.00320.5690.0120.0120.0000.0000.0000.000
217A354HOH00.0200.00217.4870.0020.0020.0000.0000.0000.000
218A355HOH00.0760.09120.388-0.008-0.0080.0000.0000.0000.000