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: XYV72

Calculation Name: 1M1F-A-Xray18

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 1M1F

Chain ID: A

ChEMBL ID:

UniProt ID: P13976

Base Structure: X-ray

Registration Date: 2018-06-04

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 203
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1043771.596601
FMO2-HF: Nuclear repulsion 994948.218429
FMO2-HF: Total energy -48823.378172
FMO2-MP2: Total energy -48962.703128


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.
-21.219-39.65467.87-20.879-28.549-0.059
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 : -0.056 / q_NPA : 0.003
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].
3A3ARG10.8830.9233.783-0.9010.975-0.030-0.809-1.0370.001
4A4GLY00.0290.0036.325-0.471-0.4710.0000.0000.0000.000
5A5GLU-1-0.822-0.8922.730-9.433-5.4771.204-2.559-2.602-0.026
6A6ILE00.0280.0136.3360.7040.7040.0000.0000.0000.000
7A7TRP0-0.033-0.0442.670-2.836-0.4941.028-0.870-2.499-0.005
8A8LEU0-0.0060.0087.3700.1430.1430.0000.0000.0000.000
9A9VAL0-0.007-0.0097.184-0.159-0.1590.0000.0000.0000.000
10A10SER00.0730.0579.5110.0860.0860.0000.0000.0000.000
11A11LEU0-0.001-0.00710.9040.0540.0540.0000.0000.0000.000
12A12ASP-1-0.789-0.85013.2500.1490.1490.0000.0000.0000.000
13A13PRO0-0.001-0.01715.246-0.004-0.0040.0000.0000.0000.000
14A14THR00.004-0.00817.1860.0250.0250.0000.0000.0000.000
15A15ALA00.0130.00919.608-0.029-0.0290.0000.0000.0000.000
16A16GLY00.0600.02622.6130.0150.0150.0000.0000.0000.000
17A17HIS00.0250.01624.407-0.004-0.0040.0000.0000.0000.000
18A18GLU-1-0.823-0.87818.8460.2780.2780.0000.0000.0000.000
19A19GLN0-0.020-0.00916.662-0.053-0.0530.0000.0000.0000.000
20A20GLN0-0.0060.00817.3410.0120.0120.0000.0000.0000.000
21A21GLY00.0400.02217.2570.0090.0090.0000.0000.0000.000
22A22THR0-0.035-0.03212.8460.0280.0280.0000.0000.0000.000
23A23ARG10.7760.88112.814-0.222-0.2220.0000.0000.0000.000
24A24PRO0-0.001-0.00311.1180.0340.0340.0000.0000.0000.000
25A25VAL0-0.0020.0067.3030.0400.0400.0000.0000.0000.000
26A26LEU00.0050.0028.641-0.001-0.0010.0000.0000.0000.000
27A27ILE0-0.026-0.0132.37910.369-11.72633.706-5.510-6.100-0.013
28A28VAL00.0580.0266.098-0.794-0.807-0.001-0.0040.0180.000
29A29THR0-0.013-0.0075.223-0.599-0.5990.0000.0000.0000.000
30A30PRO00.0220.0085.166-0.0580.011-0.001-0.005-0.0610.000
31A31ALA00.0360.0193.8390.2390.6570.002-0.162-0.2580.000
32A32ALA00.012-0.0094.9081.2591.408-0.001-0.013-0.1350.000
33A33PHE00.0410.0206.352-0.032-0.0320.0000.0000.0000.000
34A34ASN00.0100.0131.980-0.529-0.4896.227-2.189-4.077-0.007
35A35ARG10.8550.9114.275-2.215-1.901-0.001-0.033-0.2800.000
36A36VAL0-0.009-0.0065.529-0.686-0.6860.0000.0000.0000.000
37A37THR00.0450.0187.352-0.192-0.1920.0000.0000.0000.000
38A38ARG10.8470.9594.777-0.955-0.838-0.001-0.003-0.1120.000
39A39LEU00.0070.0165.249-0.442-0.4420.0000.0000.0000.000
40A40PRO00.0120.0222.289-0.882-1.3924.289-0.838-2.9410.003
41A41VAL00.0460.0195.107-1.217-1.1100.000-0.049-0.0590.000
42A42VAL0-0.035-0.0195.6630.3890.504-0.001-0.007-0.1060.000
43A43VAL00.0380.0268.271-0.281-0.2810.0000.0000.0000.000
44A44PRO00.0030.01811.2850.0190.0190.0000.0000.0000.000
45A45VAL00.0150.01712.957-0.042-0.0420.0000.0000.0000.000
46A46THR0-0.0160.00815.371-0.025-0.0250.0000.0000.0000.000
47A47SER00.0740.03118.950-0.004-0.0040.0000.0000.0000.000
48A48GLY0-0.004-0.00422.1440.0070.0070.0000.0000.0000.000
49A49GLY00.0450.00424.551-0.009-0.0090.0000.0000.0000.000
50A50ASN0-0.061-0.02924.1600.0090.0090.0000.0000.0000.000
51A51PHE00.0140.02124.708-0.006-0.0060.0000.0000.0000.000
52A52ALA00.0080.00824.802-0.001-0.0010.0000.0000.0000.000
53A53ARG10.9380.96225.334-0.045-0.0450.0000.0000.0000.000
54A54THR0-0.028-0.03722.8760.0130.0130.0000.0000.0000.000
55A55ALA0-0.0050.00924.329-0.013-0.0130.0000.0000.0000.000
56A56GLY00.0590.04324.7500.0130.0130.0000.0000.0000.000
57A57PHE00.0490.02020.3160.0010.0010.0000.0000.0000.000
58A58ALA0-0.0160.01419.7380.0320.0320.0000.0000.0000.000
59A59VAL00.0340.00718.140-0.028-0.0280.0000.0000.0000.000
60A60SER0-0.009-0.00119.1340.0050.0050.0000.0000.0000.000
61A61LEU00.0290.01415.191-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.801-0.84519.014-0.041-0.0410.0000.0000.0000.000
63A63GLY00.0100.01522.3380.0060.0060.0000.0000.0000.000
64A64VAL0-0.0120.01917.667-0.007-0.0070.0000.0000.0000.000
65A65GLY00.0680.05718.915-0.026-0.0260.0000.0000.0000.000
66A66ILE0-0.055-0.00614.523-0.044-0.0440.0000.0000.0000.000
67A67ARG10.9210.95412.9180.4200.4200.0000.0000.0000.000
68A68THR0-0.044-0.02413.6870.0330.0330.0000.0000.0000.000
69A69THR00.0240.04716.2840.0170.0170.0000.0000.0000.000
70A70GLY00.0230.01518.3950.0220.0220.0000.0000.0000.000
71A71VAL0-0.018-0.01219.399-0.008-0.0080.0000.0000.0000.000
72A72VAL00.019-0.00413.8750.0230.0230.0000.0000.0000.000
73A73ARG10.7960.86016.068-0.264-0.2640.0000.0000.0000.000
74A74CYS0-0.013-0.00915.6810.0700.0700.0000.0000.0000.000
75A75ASP-1-0.725-0.82816.7710.3280.3280.0000.0000.0000.000
76A76GLN0-0.022-0.01516.4960.0090.0090.0000.0000.0000.000
77A77PRO00.0130.00312.7440.0680.0680.0000.0000.0000.000
78A78ARG10.8660.92111.269-0.572-0.5720.0000.0000.0000.000
79A79THR00.0170.0148.6730.2840.2840.0000.0000.0000.000
80A80ILE0-0.009-0.0015.712-0.373-0.3730.0000.0000.0000.000
81A81ASP-1-0.733-0.8465.5670.3350.3350.0000.0000.0000.000
82A82MET00.0360.0152.180-1.169-0.5931.941-0.531-1.985-0.001
83A83LYS10.8960.9384.5220.0930.196-0.001-0.008-0.0930.000
84A84ALA0-0.057-0.0336.1130.0830.0830.0000.0000.0000.000
85A85ARG10.8400.9147.902-0.256-0.2560.0000.0000.0000.000
86A86GLY00.0310.0358.2350.0410.0410.0000.0000.0000.000
87A87GLY0-0.026-0.0195.8700.0630.0630.0000.0000.0000.000
88A88LYS10.9310.9706.5080.1010.1010.0000.0000.0000.000
89A89ARG10.9230.9674.6392.1432.301-0.001-0.007-0.1500.000
90A90LEU0-0.035-0.0237.1120.0020.0020.0000.0000.0000.000
91A91GLU-1-0.746-0.8518.986-0.291-0.2910.0000.0000.0000.000
92A92ARG10.8930.9477.4780.9110.9110.0000.0000.0000.000
93A93VAL0-0.0060.0139.7070.0460.0460.0000.0000.0000.000
94A94PRO00.0600.02012.203-0.067-0.0670.0000.0000.0000.000
95A95GLU-1-0.787-0.89311.909-0.171-0.1710.0000.0000.0000.000
96A96THR00.012-0.01015.0910.0480.0480.0000.0000.0000.000
97A97ILE00.0320.03214.5580.0400.0400.0000.0000.0000.000
98A98MET0-0.0070.01610.8540.0720.0720.0000.0000.0000.000
99A99ASN00.0760.02714.0730.0980.0980.0000.0000.0000.000
100A100GLU-1-0.745-0.77816.6660.1350.1350.0000.0000.0000.000
101A101VAL00.029-0.00113.1360.0210.0210.0000.0000.0000.000
102A102LEU0-0.033-0.01811.7760.0510.0510.0000.0000.0000.000
103A103GLY00.0250.02215.6430.0050.0050.0000.0000.0000.000
104A104ARG10.8180.88718.453-0.188-0.1880.0000.0000.0000.000
105A105LEU00.0190.01113.3500.0050.0050.0000.0000.0000.000
106A106SER00.0060.01217.6310.0090.0090.0000.0000.0000.000
107A107THR0-0.083-0.03519.600-0.019-0.0190.0000.0000.0000.000
108A108ILE0-0.019-0.00918.537-0.018-0.0180.0000.0000.0000.000
109A109LEU0-0.081-0.03115.3570.0210.0210.0000.0000.0000.000
110A110THR-1-0.895-0.91819.0850.2890.2890.0000.0000.0000.000
111A111HOH0-0.0020.00020.191-0.013-0.0130.0000.0000.0000.000
112A112HOH0-0.051-0.04321.581-0.006-0.0060.0000.0000.0000.000
113A113HOH0-0.011-0.00710.5660.0400.0400.0000.0000.0000.000
114A114HOH00.0140.0116.2090.1890.1890.0000.0000.0000.000
115A115HOH00.003-0.00122.538-0.002-0.0020.0000.0000.0000.000
116A116HOH00.0570.03325.4950.0010.0010.0000.0000.0000.000
117A117HOH0-0.027-0.02022.068-0.009-0.0090.0000.0000.0000.000
118A118HOH0-0.010-0.00920.532-0.003-0.0030.0000.0000.0000.000
119A119HOH0-0.037-0.03018.937-0.008-0.0080.0000.0000.0000.000
120A122HOH00.0280.0176.5730.1450.1450.0000.0000.0000.000
121A124HOH0-0.034-0.02518.478-0.010-0.0100.0000.0000.0000.000
122A126HOH00.0270.02327.2580.0050.0050.0000.0000.0000.000
123A129HOH00.0530.0258.0060.1400.1400.0000.0000.0000.000
124A130HOH00.0340.05216.6430.0000.0000.0000.0000.0000.000
125A131HOH0-0.011-0.00512.4160.0260.0260.0000.0000.0000.000
126A132HOH0-0.041-0.03215.637-0.013-0.0130.0000.0000.0000.000
127A133HOH0-0.019-0.01610.1870.0290.0290.0000.0000.0000.000
128A134HOH00.0070.00717.6770.0100.0100.0000.0000.0000.000
129A136HOH0-0.022-0.02018.9710.0060.0060.0000.0000.0000.000
130A137HOH0-0.007-0.01316.3420.0260.0260.0000.0000.0000.000
131A140HOH0-0.056-0.04124.948-0.004-0.0040.0000.0000.0000.000
132A141HOH0-0.016-0.00911.378-0.034-0.0340.0000.0000.0000.000
133A143HOH00.0380.04621.040-0.005-0.0050.0000.0000.0000.000
134A144HOH0-0.039-0.03916.682-0.005-0.0050.0000.0000.0000.000
135A147HOH0-0.033-0.02519.922-0.003-0.0030.0000.0000.0000.000
136A149HOH0-0.024-0.01620.9190.0010.0010.0000.0000.0000.000
137A152HOH00.0220.01726.1170.0050.0050.0000.0000.0000.000
138A153HOH0-0.046-0.0402.432-1.729-0.1371.547-1.811-1.328-0.017
139A154HOH0-0.005-0.00922.3490.0010.0010.0000.0000.0000.000
140A155HOH0-0.028-0.03918.847-0.005-0.0050.0000.0000.0000.000
141A157HOH00.0140.01711.605-0.023-0.0230.0000.0000.0000.000
142A159HOH0-0.020-0.01816.9200.0140.0140.0000.0000.0000.000
143A160HOH0-0.015-0.0281.906-10.630-16.68612.283-3.951-2.2760.023
144A162HOH0-0.031-0.02027.831-0.005-0.0050.0000.0000.0000.000
145A164HOH0-0.023-0.01815.9230.0040.0040.0000.0000.0000.000
146A165HOH00.003-0.0033.480-0.769-0.3920.025-0.214-0.188-0.002
147A166HOH00.0290.01818.5480.0090.0090.0000.0000.0000.000
148A167HOH0-0.010-0.01414.7110.0070.0070.0000.0000.0000.000
149A169HOH0-0.042-0.02214.545-0.005-0.0050.0000.0000.0000.000
150A170HOH0-0.0080.00021.7490.0100.0100.0000.0000.0000.000
151A172HOH00.0230.01415.3660.0070.0070.0000.0000.0000.000
152A176HOH0-0.056-0.07019.690-0.009-0.0090.0000.0000.0000.000
153A179HOH0-0.009-0.0039.090-0.066-0.0660.0000.0000.0000.000
154A184HOH0-0.039-0.02320.3020.0060.0060.0000.0000.0000.000
155A187HOH0-0.002-0.00219.724-0.008-0.0080.0000.0000.0000.000
156A188HOH0-0.036-0.02725.163-0.005-0.0050.0000.0000.0000.000
157A189HOH0-0.037-0.0195.704-0.139-0.1390.0000.0000.0000.000
158A193HOH0-0.020-0.02523.7370.0010.0010.0000.0000.0000.000
159A194HOH0-0.005-0.01018.9280.0040.0040.0000.0000.0000.000
160A197HOH0-0.077-0.06826.4370.0020.0020.0000.0000.0000.000
161A198HOH00.003-0.00621.484-0.008-0.0080.0000.0000.0000.000
162A199HOH0-0.006-0.00123.943-0.006-0.0060.0000.0000.0000.000
163A202HOH00.0280.02011.9970.0480.0480.0000.0000.0000.000
164A204HOH00.0230.01526.1710.0060.0060.0000.0000.0000.000
165A208HOH0-0.006-0.00523.2840.0040.0040.0000.0000.0000.000
166A213HOH00.0160.00114.500-0.008-0.0080.0000.0000.0000.000
167A214HOH0-0.002-0.01728.970-0.002-0.0020.0000.0000.0000.000
168A215HOH0-0.020-0.0217.431-0.081-0.0810.0000.0000.0000.000
169A217HOH00.0310.02110.7510.0770.0770.0000.0000.0000.000
170A218HOH00.0390.02822.339-0.003-0.0030.0000.0000.0000.000
171A219HOH0-0.048-0.04723.309-0.003-0.0030.0000.0000.0000.000
172A224HOH00.0120.00722.986-0.001-0.0010.0000.0000.0000.000
173A226HOH0-0.032-0.02010.837-0.036-0.0360.0000.0000.0000.000
174A227HOH0-0.063-0.05316.4920.0040.0040.0000.0000.0000.000
175A228HOH00.0160.02127.533-0.005-0.0050.0000.0000.0000.000
176A245HOH0-0.026-0.03113.2040.0270.0270.0000.0000.0000.000
177A248HOH0-0.013-0.00922.3980.0070.0070.0000.0000.0000.000
178A251HOH00.0360.03131.3210.0010.0010.0000.0000.0000.000
179A256HOH0-0.031-0.03123.8230.0000.0000.0000.0000.0000.000
180A258HOH0-0.011-0.00323.478-0.005-0.0050.0000.0000.0000.000
181A259HOH0-0.088-0.09216.4770.0020.0020.0000.0000.0000.000
182A264HOH00.0120.00221.4090.0060.0060.0000.0000.0000.000
183A265HOH0-0.036-0.03125.1420.0020.0020.0000.0000.0000.000
184A270HOH0-0.0070.00120.3340.0090.0090.0000.0000.0000.000
185A279HOH0-0.030-0.03821.6490.0010.0010.0000.0000.0000.000
186A284HOH0-0.035-0.04124.3600.0010.0010.0000.0000.0000.000
187A302HOH0-0.030-0.02719.6010.0100.0100.0000.0000.0000.000
188A303HOH0-0.027-0.0426.558-0.021-0.0210.0000.0000.0000.000
189A305HOH00.0030.01410.710-0.022-0.0220.0000.0000.0000.000
190A307HOH0-0.046-0.03325.154-0.006-0.0060.0000.0000.0000.000
191A309HOH00.0200.0168.0220.1110.1110.0000.0000.0000.000
192A310HOH0-0.020-0.0179.056-0.069-0.0690.0000.0000.0000.000
193A313HOH00.002-0.00622.1190.0010.0010.0000.0000.0000.000
194A320HOH0-0.029-0.01920.2270.0000.0000.0000.0000.0000.000
195A327HOH00.0230.0284.434-0.506-0.473-0.001-0.005-0.0270.000
196A328HOH00.0180.02726.6920.0020.0020.0000.0000.0000.000
197A331HOH00.0310.02221.0520.0090.0090.0000.0000.0000.000
198A339HOH0-0.012-0.0082.056-0.927-3.0305.657-1.301-2.253-0.015
199A347HOH0-0.025-0.0289.036-0.035-0.0350.0000.0000.0000.000
200A355HOH00.0110.01811.4220.0020.0020.0000.0000.0000.000
201A357HOH0-0.011-0.01321.8990.0020.0020.0000.0000.0000.000
202B112HOH0-0.022-0.0158.726-0.132-0.1320.0000.0000.0000.000
203B148HOH0-0.023-0.01218.1390.0060.0060.0000.0000.0000.000