Manual

About

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

tag_button

FMODB ID: P247R

Calculation Name: 1EJ8-A-Xray41

Preferred Name:

Target Type:

Ligand Name: calcium ion

ligand 3-letter code: CA

PDB ID: 1EJ8

Chain ID: A

ChEMBL ID:

UniProt ID: P40202

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 217
LigandCharge CA+=2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1465773.788041
FMO2-HF: Nuclear repulsion 1406064.728173
FMO2-HF: Total energy -59709.059868
FMO2-MP2: Total energy -59881.963409


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:78:SER)


Summations of interaction energy for fragment #1(A:78:SER)
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.
-24.345-22.215.672-8.038-9.7810.043
Interaction energy analysis for fragmet #1(A:78:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.008
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].
3A80ALA00.0360.0223.8050.9012.947-0.035-1.047-0.9650.000
4A81VAL0-0.052-0.0386.177-0.376-0.3760.0000.0000.0000.000
5A82ALA00.0380.0349.8890.1210.1210.0000.0000.0000.000
6A83ILE00.0210.00212.818-0.061-0.0610.0000.0000.0000.000
7A84LEU0-0.050-0.01115.6830.0160.0160.0000.0000.0000.000
8A85GLU-1-0.761-0.88418.8030.0430.0430.0000.0000.0000.000
9A86THR0-0.0130.03822.203-0.013-0.0130.0000.0000.0000.000
10A87PHE00.005-0.01320.9620.0140.0140.0000.0000.0000.000
11A88GLN0-0.060-0.02726.3650.0120.0120.0000.0000.0000.000
12A89LYS10.9350.97129.578-0.008-0.0080.0000.0000.0000.000
13A90TYR00.0300.00328.582-0.004-0.0040.0000.0000.0000.000
14A91THR00.0110.00133.8780.0050.0050.0000.0000.0000.000
15A92ILE0-0.0370.00132.8500.0030.0030.0000.0000.0000.000
16A93ASP-1-0.776-0.84629.684-0.067-0.0670.0000.0000.0000.000
17A94GLN0-0.010-0.00933.3250.0130.0130.0000.0000.0000.000
18A95LYS10.8460.93128.4510.0440.0440.0000.0000.0000.000
19A96LYS10.9400.95531.2580.0040.0040.0000.0000.0000.000
20A97ASP-1-0.854-0.89630.249-0.001-0.0010.0000.0000.0000.000
21A98THR00.0330.01625.2930.0080.0080.0000.0000.0000.000
22A99ALA00.0260.01825.519-0.012-0.0120.0000.0000.0000.000
23A100VAL0-0.009-0.00320.631-0.019-0.0190.0000.0000.0000.000
24A101ARG10.7770.87022.2740.0650.0650.0000.0000.0000.000
25A102GLY00.0440.01820.130-0.025-0.0250.0000.0000.0000.000
26A103LEU0-0.053-0.00814.3220.0510.0510.0000.0000.0000.000
27A104ALA00.0260.01512.605-0.053-0.0530.0000.0000.0000.000
28A105ARG10.9610.9878.4710.4640.4640.0000.0000.0000.000
29A106ILE0-0.014-0.0055.690-0.134-0.1340.0000.0000.0000.000
30A107VAL00.009-0.0063.624-0.420-0.2490.000-0.046-0.1260.000
31A108GLN0-0.0160.0072.589-1.9350.1250.701-1.079-1.682-0.006
32A109VAL0-0.039-0.0314.042-0.0550.1630.000-0.076-0.1420.000
33A110GLY00.0020.0046.7200.8080.8080.0000.0000.0000.000
34A111GLU-1-0.873-0.9446.755-1.730-1.7300.0000.0000.0000.000
35A112ASN0-0.007-0.0167.565-0.223-0.2230.0000.0000.0000.000
36A113LYS10.9500.9837.6191.5941.5940.0000.0000.0000.000
37A114THR0-0.038-0.0045.282-0.771-0.7710.0000.0000.0000.000
38A115LEU00.0250.0127.7460.6730.6730.0000.0000.0000.000
39A116PHE0-0.007-0.0199.250-0.336-0.3360.0000.0000.0000.000
40A117ASP-1-0.831-0.90211.742-0.446-0.4460.0000.0000.0000.000
41A118ILE00.0120.00413.5400.0630.0630.0000.0000.0000.000
42A119THR0-0.035-0.02216.4650.0550.0550.0000.0000.0000.000
43A120VAL00.0180.00219.5000.0070.0070.0000.0000.0000.000
44A121ASN00.023-0.02022.313-0.004-0.0040.0000.0000.0000.000
45A122GLY00.0540.04325.2080.0100.0100.0000.0000.0000.000
46A123VAL00.0660.06025.9120.0130.0130.0000.0000.0000.000
47A124PRO00.2500.16228.7440.0000.0000.0000.0000.0000.000
48A125GLU-1-0.593-0.84931.505-0.098-0.0980.0000.0000.0000.000
49A126ALA00.1070.13730.883-0.011-0.0110.0000.0000.0000.000
50A127GLY00.0980.09230.4080.0090.0090.0000.0000.0000.000
51A128ASN00.0300.02227.639-0.006-0.0060.0000.0000.0000.000
52A129TYR0-0.014-0.01523.9590.0200.0200.0000.0000.0000.000
53A130HIS00.0240.01022.838-0.051-0.0510.0000.0000.0000.000
54A131ALA00.0290.01417.4220.0250.0250.0000.0000.0000.000
55A132SER0-0.055-0.03817.9840.0000.0000.0000.0000.0000.000
56A133ILE00.0170.02211.936-0.008-0.0080.0000.0000.0000.000
57A134HIS10.8410.89715.8530.2170.2170.0000.0000.0000.000
58A135GLU-1-0.791-0.89016.395-0.110-0.1100.0000.0000.0000.000
59A136LYS10.9010.95716.8710.0530.0530.0000.0000.0000.000
60A137GLY00.0510.02816.446-0.038-0.0380.0000.0000.0000.000
61A138ASP-1-0.816-0.88517.1280.0790.0790.0000.0000.0000.000
62A139VAL00.0190.01219.190-0.029-0.0290.0000.0000.0000.000
63A140SER0-0.018-0.01021.979-0.004-0.0040.0000.0000.0000.000
64A141LYS10.9330.96825.2280.0180.0180.0000.0000.0000.000
65A142GLY00.0110.01524.274-0.014-0.0140.0000.0000.0000.000
66A143VAL00.0420.01322.8710.0020.0020.0000.0000.0000.000
67A144GLU-1-0.861-0.92524.232-0.083-0.0830.0000.0000.0000.000
68A145SER0-0.0310.03123.6770.0030.0030.0000.0000.0000.000
69A146THR0-0.038-0.02319.9690.0010.0010.0000.0000.0000.000
70A147GLY0-0.050-0.02220.756-0.012-0.0120.0000.0000.0000.000
71A148LYS10.9420.99122.9970.0720.0720.0000.0000.0000.000
72A149VAL00.0150.02119.917-0.004-0.0040.0000.0000.0000.000
73A150TRP0-0.014-0.00511.7420.0070.0070.0000.0000.0000.000
74A151HIS00.0350.02515.032-0.010-0.0100.0000.0000.0000.000
75A152LYS10.8800.92717.0770.3840.3840.0000.0000.0000.000
76A153PHE0-0.0250.00213.012-0.034-0.0340.0000.0000.0000.000
77A154ASP-1-0.860-0.93119.077-0.370-0.3700.0000.0000.0000.000
78A155GLU-1-0.832-0.89619.536-0.585-0.5850.0000.0000.0000.000
79A156PRO0-0.0150.00621.663-0.017-0.0170.0000.0000.0000.000
80A157ILE0-0.027-0.02719.406-0.024-0.0240.0000.0000.0000.000
81A158GLU-1-0.863-0.87423.263-0.225-0.2250.0000.0000.0000.000
82A159CYS0-0.058-0.02225.459-0.008-0.0080.0000.0000.0000.000
83A160PHE00.0720.03127.7360.0190.0190.0000.0000.0000.000
84A161ASN0-0.019-0.00327.2030.0200.0200.0000.0000.0000.000
85A162GLU-1-0.338-0.42430.607-0.087-0.0870.0000.0000.0000.000
86A163SER0-0.029-0.00828.9010.0060.0060.0000.0000.0000.000
87A164ASP-1-0.849-0.92531.554-0.043-0.0430.0000.0000.0000.000
88A165LEU00.0770.03634.050-0.002-0.0020.0000.0000.0000.000
89A166GLY00.0230.02937.6550.0020.0020.0000.0000.0000.000
90A167LYS11.0891.09834.4400.0380.0380.0000.0000.0000.000
91A168ASN00.4060.13936.312-0.004-0.0040.0000.0000.0000.000
92A169LEU00.3710.26230.929-0.002-0.0020.0000.0000.0000.000
93A170TYR01.3321.34529.9180.0030.0030.0000.0000.0000.000
94A171SER0-0.032-0.01325.876-0.003-0.0030.0000.0000.0000.000
95A172GLY00.0220.00024.5920.0040.0040.0000.0000.0000.000
96A173LYS10.8420.91318.4290.3800.3800.0000.0000.0000.000
97A174THR00.0560.04518.5660.0360.0360.0000.0000.0000.000
98A175PHE00.0000.01813.902-0.046-0.0460.0000.0000.0000.000
99A176LEU00.0070.01414.7100.0690.0690.0000.0000.0000.000
100A177SER0-0.019-0.00712.274-0.207-0.2070.0000.0000.0000.000
101A178ALA00.0640.02811.4350.2080.2080.0000.0000.0000.000
102A179PRO0-0.0300.00610.925-0.349-0.3490.0000.0000.0000.000
103A180LEU00.0210.0009.7450.1990.1990.0000.0000.0000.000
104A181PRO00.0320.0306.039-0.696-0.6960.0000.0000.0000.000
105A182THR00.0620.0071.955-2.574-2.2203.618-1.729-2.243-0.001
106A183TRP0-0.008-0.0054.0611.3581.527-0.001-0.019-0.1490.000
107A184GLN0-0.025-0.0085.6240.1160.1160.0000.0000.0000.000
108A185LEU0-0.028-0.0096.4820.1180.1180.0000.0000.0000.000
109A186ILE0-0.006-0.0015.1630.1160.1160.0000.0000.0000.000
110A187GLY00.0080.0128.4350.0220.0220.0000.0000.0000.000
111A188ARG10.8800.96111.5320.1950.1950.0000.0000.0000.000
112A189SER00.0120.00513.3400.0040.0040.0000.0000.0000.000
113A190PHE00.0090.00012.812-0.060-0.0600.0000.0000.0000.000
114A191VAL00.017-0.00315.3080.0640.0640.0000.0000.0000.000
115A192ILE0-0.023-0.01018.106-0.052-0.0520.0000.0000.0000.000
116A193SER00.0300.01221.0930.0250.0250.0000.0000.0000.000
117A194LYS10.8020.88324.7530.1210.1210.0000.0000.0000.000
118A195SER0-0.0020.02628.1000.0110.0110.0000.0000.0000.000
119A196LEU0-0.058-0.02231.493-0.002-0.0020.0000.0000.0000.000
120A197ASN00.0280.02633.801-0.008-0.0080.0000.0000.0000.000
121A198HIS0-0.0140.01236.6860.0000.0000.0000.0000.0000.000
122A199PRO00.0340.02036.5810.0050.0050.0000.0000.0000.000
123A200GLU-1-0.838-0.92437.940-0.064-0.0640.0000.0000.0000.000
124A201ASN0-0.021-0.01040.1980.0070.0070.0000.0000.0000.000
125A202GLU-1-0.809-0.91934.677-0.061-0.0610.0000.0000.0000.000
126A203PRO00.0010.04836.788-0.004-0.0040.0000.0000.0000.000
127A204SER00.006-0.03638.0280.0030.0030.0000.0000.0000.000
128A205SER0-0.057-0.04034.953-0.004-0.0040.0000.0000.0000.000
129A206VAL00.0110.01731.619-0.006-0.0060.0000.0000.0000.000
130A207LYS10.9360.97432.2260.0820.0820.0000.0000.0000.000
131A208ASP-1-0.789-0.88628.297-0.153-0.1530.0000.0000.0000.000
132A209TYR0-0.033-0.04126.7850.0090.0090.0000.0000.0000.000
133A210SER00.012-0.02324.092-0.028-0.0280.0000.0000.0000.000
134A211PHE0-0.017-0.00621.1650.0230.0230.0000.0000.0000.000
135A212LEU0-0.015-0.01618.903-0.037-0.0370.0000.0000.0000.000
136A213GLY00.0570.04316.6020.0370.0370.0000.0000.0000.000
137A214VAL0-0.041-0.01713.079-0.073-0.0730.0000.0000.0000.000
138A215ILE0-0.040-0.0138.185-0.013-0.0130.0000.0000.0000.000
139A216ALA00.0100.0079.6930.1180.1180.0000.0000.0000.000
140A217ARG00.0400.0201.972-21.758-24.99511.365-3.858-4.2700.051
141A218CA+2-2.251-1.03736.0430.1730.1730.0000.0000.0000.000
142A1002HOH00.0940.01036.9460.0010.0010.0000.0000.0000.000
143A1003HOH00.071-0.01635.896-0.004-0.0040.0000.0000.0000.000
144A1004HOH0-0.075-0.07830.5360.0050.0050.0000.0000.0000.000
145A1005HOH00.083-0.01636.265-0.002-0.0020.0000.0000.0000.000
146A1006HOH0-0.005-0.00215.5210.0430.0430.0000.0000.0000.000
147A1007HOH0-0.022-0.01535.915-0.001-0.0010.0000.0000.0000.000
148A1008HOH00.0110.00033.4000.0030.0030.0000.0000.0000.000
149A1009HOH0-0.005-0.00821.3110.0060.0060.0000.0000.0000.000
150A1010HOH00.0100.01311.293-0.129-0.1290.0000.0000.0000.000
151A1011HOH0-0.018-0.01330.6780.0020.0020.0000.0000.0000.000
152A1012HOH00.0700.01636.117-0.003-0.0030.0000.0000.0000.000
153A1013HOH00.0180.01125.8700.0070.0070.0000.0000.0000.000
154A1014HOH0-0.0060.00221.560-0.005-0.0050.0000.0000.0000.000
155A1015HOH00.008-0.00329.6830.0040.0040.0000.0000.0000.000
156A1016HOH00.0220.01824.3890.0060.0060.0000.0000.0000.000
157A1017HOH0-0.024-0.02215.746-0.005-0.0050.0000.0000.0000.000
158A1018HOH00.0440.02428.720-0.004-0.0040.0000.0000.0000.000
159A1019HOH0-0.0070.00533.351-0.001-0.0010.0000.0000.0000.000
160A1020HOH0-0.0070.00114.057-0.007-0.0070.0000.0000.0000.000
161A1022HOH00.0120.00628.974-0.001-0.0010.0000.0000.0000.000
162A1023HOH0-0.010-0.03017.489-0.004-0.0040.0000.0000.0000.000
163A1024HOH00.015-0.02336.4060.0000.0000.0000.0000.0000.000
164A1025HOH0-0.008-0.00312.565-0.061-0.0610.0000.0000.0000.000
165A1028HOH00.0110.00424.152-0.005-0.0050.0000.0000.0000.000
166A1029HOH0-0.002-0.00127.3060.0070.0070.0000.0000.0000.000
167A1030HOH00.0470.02623.4580.0010.0010.0000.0000.0000.000
168A1032HOH0-0.038-0.02916.4800.0360.0360.0000.0000.0000.000
169A1033HOH0-0.002-0.00629.801-0.002-0.0020.0000.0000.0000.000
170A1035HOH0-0.028-0.03537.202-0.002-0.0020.0000.0000.0000.000
171A1036HOH00.0200.02027.940-0.004-0.0040.0000.0000.0000.000
172A1037HOH00.0290.01719.0380.0020.0020.0000.0000.0000.000
173A1038HOH0-0.022-0.01424.888-0.003-0.0030.0000.0000.0000.000
174A1039HOH0-0.006-0.00617.164-0.049-0.0490.0000.0000.0000.000
175A1040HOH0-0.049-0.04138.8380.0010.0010.0000.0000.0000.000
176A1041HOH0-0.036-0.03530.1600.0030.0030.0000.0000.0000.000
177A1044HOH0-0.009-0.02618.623-0.019-0.0190.0000.0000.0000.000
178A1045HOH0-0.012-0.02635.193-0.003-0.0030.0000.0000.0000.000
179A1047HOH0-0.0210.01218.3300.0120.0120.0000.0000.0000.000
180A1048HOH0-0.014-0.00441.0570.0010.0010.0000.0000.0000.000
181A1049HOH00.0130.01433.9470.0000.0000.0000.0000.0000.000
182A1050HOH0-0.031-0.02424.0980.0030.0030.0000.0000.0000.000
183A1051HOH0-0.002-0.01234.482-0.004-0.0040.0000.0000.0000.000
184A1053HOH00.0240.02839.2690.0000.0000.0000.0000.0000.000
185A1054HOH0-0.017-0.02436.7350.0030.0030.0000.0000.0000.000
186A1055HOH0-0.023-0.02218.6080.0210.0210.0000.0000.0000.000
187A1057HOH0-0.058-0.05623.9540.0020.0020.0000.0000.0000.000
188A1059HOH0-0.026-0.01518.171-0.007-0.0070.0000.0000.0000.000
189A1060HOH0-0.024-0.02335.942-0.002-0.0020.0000.0000.0000.000
190A1063HOH00.0200.02722.4970.0020.0020.0000.0000.0000.000
191A1064HOH0-0.013-0.03128.060-0.003-0.0030.0000.0000.0000.000
192A1065HOH0-0.061-0.05030.3560.0010.0010.0000.0000.0000.000
193A1066HOH0-0.093-0.09929.3740.0030.0030.0000.0000.0000.000
194A1067HOH0-0.046-0.03423.168-0.001-0.0010.0000.0000.0000.000
195A1068HOH0-0.017-0.0233.3741.1211.4850.024-0.184-0.204-0.001
196A1069HOH0-0.011-0.01734.2460.0000.0000.0000.0000.0000.000
197A1071HOH0-0.045-0.02624.151-0.001-0.0010.0000.0000.0000.000
198A1072HOH0-0.030-0.01821.318-0.001-0.0010.0000.0000.0000.000
199A1073HOH00.0220.04131.338-0.001-0.0010.0000.0000.0000.000
200A1074HOH0-0.042-0.02129.6410.0020.0020.0000.0000.0000.000
201A1078HOH0-0.036-0.01932.014-0.002-0.0020.0000.0000.0000.000
202A1079HOH00.0100.01232.003-0.001-0.0010.0000.0000.0000.000
203A1080HOH00.0490.03130.4810.0000.0000.0000.0000.0000.000
204A1084HOH0-0.030-0.02215.7660.0270.0270.0000.0000.0000.000
205A1085HOH00.0090.02736.4410.0020.0020.0000.0000.0000.000
206A1088HOH0-0.049-0.07125.8820.0030.0030.0000.0000.0000.000
207A1090HOH00.009-0.00125.3000.0110.0110.0000.0000.0000.000
208A1093HOH0-0.030-0.02122.246-0.001-0.0010.0000.0000.0000.000
209A1094HOH0-0.022-0.02741.683-0.001-0.0010.0000.0000.0000.000
210A1096HOH0-0.028-0.01930.3890.0030.0030.0000.0000.0000.000
211A1098HOH0-0.009-0.02228.2960.0050.0050.0000.0000.0000.000
212A1100HOH0-0.063-0.04120.8540.0060.0060.0000.0000.0000.000
213A1105HOH0-0.005-0.00715.129-0.017-0.0170.0000.0000.0000.000
214A1106HOH0-0.041-0.02541.747-0.001-0.0010.0000.0000.0000.000
215A1111HOH0-0.039-0.02911.928-0.039-0.0390.0000.0000.0000.000
216A1112HOH0-0.051-0.03327.543-0.003-0.0030.0000.0000.0000.000
217A1113HOH00.0230.02529.8610.0010.0010.0000.0000.0000.000