Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: XY962

Calculation Name: 2HX0-A-Xray42

Preferred Name:

Target Type:

Ligand Name: magnesium ion

ligand 3-letter code: MG

PDB ID: 2HX0

Chain ID: A

ChEMBL ID:

UniProt ID: Q57K43

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 214
LigandCharge MG2=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1346267.122097
FMO2-HF: Nuclear repulsion 1287483.429652
FMO2-HF: Total energy -58783.692445
FMO2-MP2: Total energy -58951.011222


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:4:ACE)


Summations of interaction energy for fragment #1(A:4: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.
0.8621.9730.007-0.505-0.6130
Interaction energy analysis for fragmet #1(A:4:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.001
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].
3A6HIS00.0580.0283.8450.7171.553-0.012-0.411-0.4120.000
4A7ASN0-0.052-0.0387.0330.0700.0700.0000.0000.0000.000
5A8ALA00.0690.0288.8960.1480.1480.0000.0000.0000.000
6A9SER0-0.004-0.0259.2950.0660.0660.0000.0000.0000.000
7A10THR0-0.0120.03211.831-0.010-0.0100.0000.0000.0000.000
8A11ALA00.0750.03114.981-0.002-0.0020.0000.0000.0000.000
9A12ARG10.8670.93617.423-0.068-0.0680.0000.0000.0000.000
10A13PHE00.000-0.01020.238-0.007-0.0070.0000.0000.0000.000
11A14TYR00.0000.01621.1690.0110.0110.0000.0000.0000.000
12A15ALA00.0210.01926.009-0.007-0.0070.0000.0000.0000.000
13A16LEU0-0.032-0.01228.2240.0040.0040.0000.0000.0000.000
14A17ARG10.9100.93831.836-0.002-0.0020.0000.0000.0000.000
15A18LEU0-0.038-0.00332.4930.0020.0020.0000.0000.0000.000
16A19LEU0-0.003-0.02436.170-0.001-0.0010.0000.0000.0000.000
17A20PRO0-0.002-0.00639.819-0.001-0.0010.0000.0000.0000.000
18A21GLY00.0210.01642.4540.0020.0020.0000.0000.0000.000
19A22GLN00.0090.02537.140-0.001-0.0010.0000.0000.0000.000
20A23GLU-1-0.636-0.78934.661-0.015-0.0150.0000.0000.0000.000
21A24VAL00.021-0.00931.6420.0020.0020.0000.0000.0000.000
22A25PHE0-0.013-0.00328.7900.0010.0010.0000.0000.0000.000
23A26SER0-0.026-0.02530.0850.0030.0030.0000.0000.0000.000
24A27GLN00.0300.02231.1700.0050.0050.0000.0000.0000.000
25A28LEU00.0120.01227.2190.0030.0030.0000.0000.0000.000
26A29HIS00.0220.02025.0590.0040.0040.0000.0000.0000.000
27A30ALA00.0150.01026.6340.0060.0060.0000.0000.0000.000
28A31PHE00.0280.01325.2240.0070.0070.0000.0000.0000.000
29A32VAL0-0.006-0.00421.4760.0070.0070.0000.0000.0000.000
30A33GLN00.0200.00122.8450.0080.0080.0000.0000.0000.000
31A34GLN0-0.0050.02224.6420.0050.0050.0000.0000.0000.000
32A35ASN0-0.044-0.02922.7670.0130.0130.0000.0000.0000.000
33A36GLN0-0.051-0.02519.5920.0170.0170.0000.0000.0000.000
34A37LEU0-0.054-0.00818.5750.0130.0130.0000.0000.0000.000
35A38ARG10.8860.91914.177-0.099-0.0990.0000.0000.0000.000
36A39ALA0-0.004-0.00113.312-0.020-0.0200.0000.0000.0000.000
37A40ALA00.0440.03915.435-0.001-0.0010.0000.0000.0000.000
38A41TRP00.003-0.00918.184-0.017-0.0170.0000.0000.0000.000
39A42ILE0-0.0120.00821.2440.0110.0110.0000.0000.0000.000
40A43ALA0-0.0100.00223.639-0.008-0.0080.0000.0000.0000.000
41A44GLY00.0240.00925.292-0.002-0.0020.0000.0000.0000.000
42A45CYS0-0.059-0.02229.0650.0040.0040.0000.0000.0000.000
43A46THR00.0890.06431.855-0.003-0.0030.0000.0000.0000.000
44A47GLY00.0470.02535.6370.0030.0030.0000.0000.0000.000
45A48SER00.0260.03938.306-0.001-0.0010.0000.0000.0000.000
46A49LEU0-0.012-0.00736.8470.0010.0010.0000.0000.0000.000
47A50THR0-0.007-0.00241.1280.0000.0000.0000.0000.0000.000
48A51ASP-1-0.790-0.87441.690-0.013-0.0130.0000.0000.0000.000
49A52VAL0-0.001-0.01438.263-0.001-0.0010.0000.0000.0000.000
50A53ALA00.0320.01136.8420.0000.0000.0000.0000.0000.000
51A54LEU0-0.016-0.01635.131-0.002-0.0020.0000.0000.0000.000
52A55ARG10.9280.98529.4980.0530.0530.0000.0000.0000.000
53A56TYR00.0280.01034.670-0.004-0.0040.0000.0000.0000.000
54A57ALA00.0380.00134.174-0.001-0.0010.0000.0000.0000.000
55A58GLY00.006-0.00133.9060.0020.0020.0000.0000.0000.000
56A59GLN0-0.0540.00035.3180.0050.0050.0000.0000.0000.000
57A60GLU-1-0.878-0.93134.564-0.046-0.0460.0000.0000.0000.000
58A61ALA00.0140.00236.7520.0010.0010.0000.0000.0000.000
59A62THR00.011-0.00136.975-0.003-0.0030.0000.0000.0000.000
60A63THR0-0.035-0.01038.7170.0020.0020.0000.0000.0000.000
61A64SER00.0170.01140.3790.0000.0000.0000.0000.0000.000
62A65LEU0-0.039-0.02142.3060.0010.0010.0000.0000.0000.000
63A66THR00.0330.00843.7370.0000.0000.0000.0000.0000.000
64A67GLY0-0.048-0.02546.0700.0000.0000.0000.0000.0000.000
65A68THR0-0.045-0.01946.3730.0010.0010.0000.0000.0000.000
66A69PHE00.0160.00641.893-0.001-0.0010.0000.0000.0000.000
67A70GLU-1-0.808-0.89141.311-0.016-0.0160.0000.0000.0000.000
68A71VAL0-0.007-0.01934.619-0.002-0.0020.0000.0000.0000.000
69A72ILE0-0.013-0.00736.2180.0000.0000.0000.0000.0000.000
70A73SER0-0.017-0.01831.755-0.003-0.0030.0000.0000.0000.000
71A74LEU00.0200.00829.0080.0010.0010.0000.0000.0000.000
72A75ASN0-0.023-0.01626.445-0.002-0.0020.0000.0000.0000.000
73A76GLY00.0540.00923.7750.0010.0010.0000.0000.0000.000
74A77THR0-0.026-0.00218.5830.0020.0020.0000.0000.0000.000
75A78LEU00.009-0.00720.1400.0040.0040.0000.0000.0000.000
76A79GLU-1-0.827-0.88717.173-0.067-0.0670.0000.0000.0000.000
77A80LEU00.018-0.00618.3070.0000.0000.0000.0000.0000.000
78A81THR0-0.030-0.00919.8400.0040.0040.0000.0000.0000.000
79A82GLY00.0520.03721.236-0.005-0.0050.0000.0000.0000.000
80A83GLU-1-0.767-0.87721.790-0.030-0.0300.0000.0000.0000.000
81A84HIS-10.076-0.19322.745-0.093-0.0930.0000.0000.0000.000
82A85LEU00.0060.01724.363-0.005-0.0050.0000.0000.0000.000
83A86HIS00.179-0.00227.0600.0010.0010.0000.0000.0000.000
84A87LEU00.0300.01329.8830.0010.0010.0000.0000.0000.000
85A88ALA0-0.0070.00533.060-0.001-0.0010.0000.0000.0000.000
86A89VAL00.0060.00435.9250.0020.0020.0000.0000.0000.000
87A90SER00.0120.01739.171-0.001-0.0010.0000.0000.0000.000
88A91ASP-1-0.694-0.84742.495-0.022-0.0220.0000.0000.0000.000
89A92PRO0-0.004-0.01745.9660.0000.0000.0000.0000.0000.000
90A93TYR0-0.0310.00248.7670.0010.0010.0000.0000.0000.000
91A94GLY00.0070.01446.021-0.001-0.0010.0000.0000.0000.000
92A95VAL0-0.038-0.00344.920-0.002-0.0020.0000.0000.0000.000
93A96MET00.0230.01437.7200.0000.0000.0000.0000.0000.000
94A97LEU00.0020.01940.3860.0000.0000.0000.0000.0000.000
95A98GLY00.0290.00836.2880.0000.0000.0000.0000.0000.000
96A99GLY0-0.034-0.01534.3210.0000.0000.0000.0000.0000.000
97A100HIS00.2320.03227.197-0.007-0.0070.0000.0000.0000.000
98A101MET00.0030.02930.0510.0040.0040.0000.0000.0000.000
99A102MET00.0060.01431.060-0.004-0.0040.0000.0000.0000.000
100A103PRO00.0310.01632.2060.0010.0010.0000.0000.0000.000
101A104GLY00.0520.05034.5080.0000.0000.0000.0000.0000.000
102A105CYS0-0.0520.02035.5010.0000.0000.0000.0000.0000.000
103A106THR0-0.012-0.02237.2250.0010.0010.0000.0000.0000.000
104A107VAL0-0.0040.00537.410-0.001-0.0010.0000.0000.0000.000
105A108ARG10.8470.95539.9560.0160.0160.0000.0000.0000.000
106A109THR0-0.010-0.02242.7550.0020.0020.0000.0000.0000.000
107A110THR00.020-0.00439.0480.0030.0030.0000.0000.0000.000
108A111LEU00.0300.01933.201-0.002-0.0020.0000.0000.0000.000
109A112GLU-1-0.971-0.96634.442-0.009-0.0090.0000.0000.0000.000
110A113LEU00.004-0.01329.013-0.004-0.0040.0000.0000.0000.000
111A114VAL00.0400.01926.0310.0050.0050.0000.0000.0000.000
112A115ILE0-0.028-0.01722.560-0.007-0.0070.0000.0000.0000.000
113A116GLY00.0250.01621.0270.0090.0090.0000.0000.0000.000
114A117GLU-1-0.677-0.82816.5210.0330.0330.0000.0000.0000.000
115A118LEU00.018-0.00113.2380.0070.0070.0000.0000.0000.000
116A119PRO0-0.038-0.02712.9780.0090.0090.0000.0000.0000.000
117A120ALA00.0290.0308.4400.0710.0710.0000.0000.0000.000
118A121LEU0-0.026-0.0077.7130.0250.0250.0000.0000.0000.000
119A122THR00.0110.0109.5920.0770.0770.0000.0000.0000.000
120A123PHE0-0.0130.00011.097-0.075-0.0750.0000.0000.0000.000
121A124SER0-0.020-0.01312.9750.0370.0370.0000.0000.0000.000
122A125ARG10.8340.89415.4600.0660.0660.0000.0000.0000.000
123A126GLN00.0140.01214.4680.0230.0230.0000.0000.0000.000
124A127PRO00.0480.05617.879-0.016-0.0160.0000.0000.0000.000
125A128CYS0-0.0780.04019.549-0.024-0.0240.0000.0000.0000.000
126A129ALA00.025-0.00620.9160.0150.0150.0000.0000.0000.000
127A130ILE0-0.033-0.02820.7420.0080.0080.0000.0000.0000.000
128A131SER00.004-0.05023.6720.0090.0090.0000.0000.0000.000
129A132GLY00.0380.02824.7720.0100.0100.0000.0000.0000.000
130A133TYR0-0.030-0.01224.7020.0110.0110.0000.0000.0000.000
131A134ASP-1-0.827-0.91121.133-0.086-0.0860.0000.0000.0000.000
132A135GLU-1-0.788-0.86419.234-0.121-0.1210.0000.0000.0000.000
133A136LEU0-0.009-0.01215.291-0.001-0.0010.0000.0000.0000.000
134A137HIS00.0050.01910.045-0.053-0.0530.0000.0000.0000.000
135A138ILE0-0.015-0.0349.3740.0540.0540.0000.0000.0000.000
136A139SER0-0.024-0.0166.810-0.143-0.1430.0000.0000.0000.000
137A140SER00.007-0.0023.4880.1330.3040.014-0.053-0.1320.000
138A141ARG10.7600.8795.482-0.096-0.0960.0000.0000.0000.000
139A142LEU0-0.039-0.0216.335-0.054-0.0540.0000.0000.0000.000
140A143NME00.0150.0123.564-0.156-0.0520.005-0.041-0.0690.000
141A201MG220.2841.07428.0340.1520.1520.0000.0000.0000.000
142A202HOH0-0.032-0.03444.3010.0000.0000.0000.0000.0000.000
143A203HOH0-0.015-0.01924.717-0.003-0.0030.0000.0000.0000.000
144A204HOH0-0.021-0.01838.973-0.001-0.0010.0000.0000.0000.000
145A205HOH0-0.031-0.01920.4070.0000.0000.0000.0000.0000.000
146A206HOH0-0.013-0.01720.440-0.008-0.0080.0000.0000.0000.000
147A207HOH0-0.036-0.02242.519-0.001-0.0010.0000.0000.0000.000
148A208HOH0-0.030-0.03043.4380.0000.0000.0000.0000.0000.000
149A210HOH0-0.018-0.01843.6030.0000.0000.0000.0000.0000.000
150A211HOH0-0.038-0.02230.2810.0000.0000.0000.0000.0000.000
151A215HOH0-0.028-0.01548.7150.0000.0000.0000.0000.0000.000
152A216HOH00.0270.01815.6370.0120.0120.0000.0000.0000.000
153A217HOH00.0090.01711.2350.0120.0120.0000.0000.0000.000
154A218HOH0-0.015-0.01145.698-0.001-0.0010.0000.0000.0000.000
155A221HOH0-0.019-0.02434.1060.0000.0000.0000.0000.0000.000
156A224HOH0-0.010-0.01443.4310.0010.0010.0000.0000.0000.000
157A226HOH0-0.013-0.01427.906-0.003-0.0030.0000.0000.0000.000
158A227HOH0-0.030-0.02219.0490.0070.0070.0000.0000.0000.000
159A228HOH0-0.021-0.02034.6850.0010.0010.0000.0000.0000.000
160A229HOH0-0.002-0.00311.752-0.033-0.0330.0000.0000.0000.000
161A230HOH0-0.039-0.02750.8420.0000.0000.0000.0000.0000.000
162A232HOH0-0.025-0.03318.5410.0060.0060.0000.0000.0000.000
163A233HOH00.003-0.01116.6290.0080.0080.0000.0000.0000.000
164A234HOH0-0.030-0.01748.9080.0000.0000.0000.0000.0000.000
165A237HOH00.009-0.00211.908-0.012-0.0120.0000.0000.0000.000
166A238HOH0-0.046-0.03030.7920.0010.0010.0000.0000.0000.000
167A239HOH0-0.029-0.01912.660-0.015-0.0150.0000.0000.0000.000
168A240HOH0-0.003-0.00914.8270.0130.0130.0000.0000.0000.000
169A241HOH0-0.028-0.02330.7270.0000.0000.0000.0000.0000.000
170A242HOH0-0.010-0.00221.840-0.001-0.0010.0000.0000.0000.000
171A243HOH0-0.024-0.02045.8060.0000.0000.0000.0000.0000.000
172A244HOH00.0080.01014.279-0.030-0.0300.0000.0000.0000.000
173A245HOH00.0220.00540.5610.0000.0000.0000.0000.0000.000
174A246HOH0-0.033-0.01942.9980.0000.0000.0000.0000.0000.000
175A248HOH00.0270.01739.144-0.001-0.0010.0000.0000.0000.000
176A251HOH0-0.027-0.01330.884-0.002-0.0020.0000.0000.0000.000
177A252HOH0-0.039-0.02228.544-0.001-0.0010.0000.0000.0000.000
178A253HOH0-0.031-0.01924.5780.0050.0050.0000.0000.0000.000
179A255HOH0-0.018-0.01223.8930.0010.0010.0000.0000.0000.000
180A256HOH00.0180.01318.8870.0100.0100.0000.0000.0000.000
181A259HOH0-0.0060.00027.1340.0010.0010.0000.0000.0000.000
182A260HOH00.004-0.01525.2910.0020.0020.0000.0000.0000.000
183A262HOH0-0.062-0.04445.4990.0010.0010.0000.0000.0000.000
184A263HOH0-0.042-0.02616.372-0.008-0.0080.0000.0000.0000.000
185A267HOH00.0040.00944.7170.0000.0000.0000.0000.0000.000
186A268HOH00.013-0.01617.9310.0040.0040.0000.0000.0000.000
187A269HOH0-0.030-0.01735.1520.0010.0010.0000.0000.0000.000
188A270HOH00.0140.00331.375-0.001-0.0010.0000.0000.0000.000
189A271HOH00.0400.02218.512-0.005-0.0050.0000.0000.0000.000
190A273HOH0-0.036-0.03535.0660.0000.0000.0000.0000.0000.000
191A275HOH0-0.047-0.02341.0600.0000.0000.0000.0000.0000.000
192A276HOH0-0.0020.0015.3240.3020.3020.0000.0000.0000.000
193A279HOH0-0.029-0.03132.796-0.002-0.0020.0000.0000.0000.000
194A281HOH0-0.013-0.00642.0590.0000.0000.0000.0000.0000.000
195A283HOH0-0.032-0.02122.252-0.004-0.0040.0000.0000.0000.000
196A284HOH0-0.041-0.01923.0490.0030.0030.0000.0000.0000.000
197A285HOH0-0.016-0.01023.1260.0020.0020.0000.0000.0000.000
198A286HOH0-0.022-0.02434.367-0.001-0.0010.0000.0000.0000.000
199A289HOH00.0500.03433.025-0.001-0.0010.0000.0000.0000.000
200A290HOH0-0.038-0.02324.033-0.001-0.0010.0000.0000.0000.000
201A291HOH0-0.035-0.02342.3200.0000.0000.0000.0000.0000.000
202A296HOH0-0.031-0.01627.7490.0010.0010.0000.0000.0000.000
203A297HOH00.004-0.00132.975-0.001-0.0010.0000.0000.0000.000
204A301HOH0-0.0020.00722.9300.0000.0000.0000.0000.0000.000
205A302HOH0-0.037-0.0216.7590.0620.0620.0000.0000.0000.000
206A303HOH0-0.015-0.01417.359-0.014-0.0140.0000.0000.0000.000
207A306HOH0-0.059-0.03723.2740.0020.0020.0000.0000.0000.000
208A307HOH0-0.040-0.02326.6890.0010.0010.0000.0000.0000.000
209A308HOH0-0.036-0.02227.093-0.001-0.0010.0000.0000.0000.000
210A312HOH0-0.023-0.01919.7360.0030.0030.0000.0000.0000.000
211A313HOH0-0.0070.00441.6910.0000.0000.0000.0000.0000.000
212A314HOH0-0.030-0.02225.3560.0000.0000.0000.0000.0000.000
213A317HOH0-0.050-0.06236.9020.0000.0000.0000.0000.0000.000
214A319HOH0-0.023-0.03240.3500.0000.0000.0000.0000.0000.000