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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: XVQ41

Calculation Name: 3FIA-A-Xray26

Preferred Name:

Target Type:

Ligand Name: calcium ion

ligand 3-letter code: CA

PDB ID: 3FIA

Chain ID: A

ChEMBL ID:

UniProt ID: Q15811

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 181
LigandCharge CA+=2,SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -923961.346821
FMO2-HF: Nuclear repulsion 877858.047154
FMO2-HF: Total energy -46103.299667
FMO2-MP2: Total energy -46231.341862


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:5:ACE)


Summations of interaction energy for fragment #1(A:5: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.
1.3693.3561.852-1.858-1.978-0.008
Interaction energy analysis for fragmet #1(A:5:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.064 / q_NPA : 0.028
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].
3A7PRO00.0170.0273.8480.8401.741-0.012-0.445-0.4430.001
4A8PHE00.0040.0096.8360.3090.3090.0000.0000.0000.000
5A9GLY00.0040.0145.4040.1680.1680.0000.0000.0000.000
6A10GLY00.0200.0144.2070.2860.378-0.001-0.012-0.0780.000
7A11SER00.0300.0045.155-0.024-0.010-0.001-0.005-0.0080.000
8A12LEU00.023-0.0047.3860.2360.2360.0000.0000.0000.000
9A13ASP-1-0.793-0.8758.915-0.295-0.2950.0000.0000.0000.000
10A14THR0-0.0380.0065.065-0.055-0.0550.0000.0000.0000.000
11A15TRP00.049-0.0037.5780.1140.1140.0000.0000.0000.000
12A16ALA00.0090.02310.6730.0300.0300.0000.0000.0000.000
13A17ILE0-0.0530.00112.8600.0170.0170.0000.0000.0000.000
14A18THR00.0340.00413.872-0.002-0.0020.0000.0000.0000.000
15A19VAL00.0600.01416.6180.0180.0180.0000.0000.0000.000
16A20GLU-1-0.925-0.94317.683-0.016-0.0160.0000.0000.0000.000
17A21GLU-1-0.794-0.89712.6940.0450.0450.0000.0000.0000.000
18A22ARG10.8440.89817.5330.0060.0060.0000.0000.0000.000
19A23ALA00.0260.02720.4350.0070.0070.0000.0000.0000.000
20A24LYS10.9660.97417.376-0.068-0.0680.0000.0000.0000.000
21A25HIS0-0.0220.00316.535-0.003-0.0030.0000.0000.0000.000
22A26ASP-1-0.700-0.82621.6470.0210.0210.0000.0000.0000.000
23A27GLN0-0.014-0.00424.7140.0030.0030.0000.0000.0000.000
24A28GLN0-0.012-0.00622.2580.0050.0050.0000.0000.0000.000
25A29PHE00.0050.01725.2550.0000.0000.0000.0000.0000.000
26A30HIS00.0520.06126.851-0.001-0.0010.0000.0000.0000.000
27A31SER0-0.088-0.04627.7870.0000.0000.0000.0000.0000.000
28A32LEU0-0.016-0.00426.5100.0010.0010.0000.0000.0000.000
29A33LYS10.8940.95030.700-0.033-0.0330.0000.0000.0000.000
30A34PRO00.0280.03430.465-0.001-0.0010.0000.0000.0000.000
31A35ILE00.0050.01033.206-0.003-0.0030.0000.0000.0000.000
32A36SER0-0.032-0.02835.892-0.001-0.0010.0000.0000.0000.000
33A37GLY00.0290.02932.656-0.001-0.0010.0000.0000.0000.000
34A38PHE00.2450.21831.2260.0010.0010.0000.0000.0000.000
35A39ILE0-0.0130.01926.813-0.001-0.0010.0000.0000.0000.000
36A40THR00.0470.01230.8630.0010.0010.0000.0000.0000.000
37A41GLY00.0500.01228.7860.0040.0040.0000.0000.0000.000
38A42ASP-1-0.902-0.92628.6680.0620.0620.0000.0000.0000.000
39A43GLN00.0950.06229.9580.0040.0040.0000.0000.0000.000
40A44ALA00.0250.01325.4750.0050.0050.0000.0000.0000.000
41A45ARG10.8840.94725.016-0.069-0.0690.0000.0000.0000.000
42A46ASN0-0.007-0.00525.6410.0100.0100.0000.0000.0000.000
43A47PHE00.0200.02122.8150.0060.0060.0000.0000.0000.000
44A48PHE00.040-0.00121.3080.0090.0090.0000.0000.0000.000
45A49PHE00.0120.01321.7170.0180.0180.0000.0000.0000.000
46A50GLN00.0070.02823.7670.0020.0020.0000.0000.0000.000
47A51SER0-0.009-0.01118.2870.0100.0100.0000.0000.0000.000
48A52GLY00.0150.01619.1170.0180.0180.0000.0000.0000.000
49A53LEU0-0.0250.00114.5420.0140.0140.0000.0000.0000.000
50A54PRO00.0390.01217.455-0.028-0.0280.0000.0000.0000.000
51A55GLN00.0490.02320.3050.0060.0060.0000.0000.0000.000
52A56PRO00.013-0.00320.791-0.002-0.0020.0000.0000.0000.000
53A57VAL00.0130.00715.6000.0000.0000.0000.0000.0000.000
54A58LEU00.0050.01018.326-0.003-0.0030.0000.0000.0000.000
55A59ALA0-0.0150.00720.141-0.014-0.0140.0000.0000.0000.000
56A60GLN00.0120.00515.993-0.002-0.0020.0000.0000.0000.000
57A61ILE0-0.002-0.00615.171-0.010-0.0100.0000.0000.0000.000
58A62TRP00.6490.62018.490-0.014-0.0140.0000.0000.0000.000
59A63ALA00.0300.01521.951-0.011-0.0110.0000.0000.0000.000
60A64LEU0-0.0150.01515.669-0.013-0.0130.0000.0000.0000.000
61A65ALA00.1270.06619.580-0.014-0.0140.0000.0000.0000.000
62A66ASP-1-0.049-0.35520.8610.0390.0390.0000.0000.0000.000
63A67MET00.5970.56922.121-0.004-0.0040.0000.0000.0000.000
64A68ASN00.5230.34924.4930.0010.0010.0000.0000.0000.000
65A69ASN00.4210.40726.6780.0030.0030.0000.0000.0000.000
66A70ASP-1-0.176-0.56928.7330.0360.0360.0000.0000.0000.000
67A71GLY00.2900.23829.651-0.001-0.0010.0000.0000.0000.000
68A72ARG11.6351.50930.400-0.026-0.0260.0000.0000.0000.000
69A73MET00.3490.25722.9440.0030.0030.0000.0000.0000.000
70A74ASP-1-0.491-0.58926.8550.0260.0260.0000.0000.0000.000
71A75GLN00.0240.03425.5470.0010.0010.0000.0000.0000.000
72A76VAL00.0490.02822.8570.0050.0050.0000.0000.0000.000
73A77GLU-1-0.436-0.81822.0090.0490.0490.0000.0000.0000.000
74A78PHE00.1090.10521.5190.0150.0150.0000.0000.0000.000
75A79SER0-0.053-0.04019.3110.0090.0090.0000.0000.0000.000
76A80ILE00.0320.00517.1080.0130.0130.0000.0000.0000.000
77A81ALA00.0240.00916.5470.0250.0250.0000.0000.0000.000
78A82MET0-0.033-0.01016.9480.0350.0350.0000.0000.0000.000
79A83LYS10.7840.90510.605-0.014-0.0140.0000.0000.0000.000
80A84LEU00.000-0.01012.4220.0590.0590.0000.0000.0000.000
81A85ILE00.0050.00012.6640.0690.0690.0000.0000.0000.000
82A86LYS10.8230.92510.733-0.088-0.0880.0000.0000.0000.000
83A87LEU00.0180.0126.9420.0880.0880.0000.0000.0000.000
84A88LYS10.9050.9598.628-0.305-0.3050.0000.0000.0000.000
85A89LEU0-0.041-0.03211.0440.0580.0580.0000.0000.0000.000
86A90GLN0-0.060-0.0176.8020.0760.0760.0000.0000.0000.000
87A91GLY00.0060.0217.2250.3270.3270.0000.0000.0000.000
88A92TYR0-0.036-0.0302.281-0.0960.6591.859-1.303-1.311-0.009
89A93GLN0-0.048-0.0296.715-0.392-0.3920.0000.0000.0000.000
90A94LEU0-0.010-0.0049.248-0.029-0.0290.0000.0000.0000.000
91A95PRO00.0210.02911.447-0.015-0.0150.0000.0000.0000.000
92A96SER00.0620.04213.160-0.005-0.0050.0000.0000.0000.000
93A97ALA00.0040.00216.183-0.013-0.0130.0000.0000.0000.000
94A98LEU00.0370.01815.9430.0060.0060.0000.0000.0000.000
95A99PRO00.0590.02912.521-0.020-0.0200.0000.0000.0000.000
96A100PRO0-0.006-0.01915.4440.0010.0010.0000.0000.0000.000
97A101VAL00.0570.04113.1560.0080.0080.0000.0000.0000.000
98A102MET0-0.0150.01013.7810.0090.0090.0000.0000.0000.000
99A103LYS10.9090.96516.4380.0000.0000.0000.0000.0000.000
100A104NME00.0040.03119.3540.0020.0020.0000.0000.0000.000
101A201CA+2-4.580-2.75128.336-0.086-0.0860.0000.0000.0000.000
102A301SO4-2-1.739-1.8498.5850.0870.0870.0000.0000.0000.000
103A401HOH00.005-0.01130.1500.0000.0000.0000.0000.0000.000
104A402HOH0-0.029-0.02823.6170.0040.0040.0000.0000.0000.000
105A403HOH00.075-0.02429.9530.0020.0020.0000.0000.0000.000
106A404HOH0-0.010-0.01427.1410.0000.0000.0000.0000.0000.000
107A405HOH0-0.008-0.00625.044-0.002-0.0020.0000.0000.0000.000
108A406HOH0-0.005-0.00828.2390.0000.0000.0000.0000.0000.000
109A407HOH0-0.0020.01024.3080.0010.0010.0000.0000.0000.000
110A408HOH00.0410.02919.498-0.002-0.0020.0000.0000.0000.000
111A409HOH0-0.053-0.0318.530-0.036-0.0360.0000.0000.0000.000
112A410HOH0-0.009-0.00821.285-0.001-0.0010.0000.0000.0000.000
113A411HOH00.0610.01729.4310.0010.0010.0000.0000.0000.000
114A412HOH0-0.047-0.03922.557-0.003-0.0030.0000.0000.0000.000
115A413HOH00.0120.0264.4210.1880.2340.000-0.012-0.0330.000
116A415HOH00.0030.00333.2460.0000.0000.0000.0000.0000.000
117A416HOH00.0420.01227.114-0.002-0.0020.0000.0000.0000.000
118A417HOH0-0.023-0.01129.4830.0010.0010.0000.0000.0000.000
119A420HOH0-0.025-0.02323.9570.0010.0010.0000.0000.0000.000
120A421HOH0-0.039-0.0299.765-0.001-0.0010.0000.0000.0000.000
121A422HOH0-0.031-0.02119.3150.0070.0070.0000.0000.0000.000
122A423HOH0-0.029-0.03922.4360.0040.0040.0000.0000.0000.000
123A424HOH00.0150.01612.9070.0210.0210.0000.0000.0000.000
124A425HOH0-0.033-0.02413.3200.0050.0050.0000.0000.0000.000
125A426HOH0-0.005-0.00730.4350.0030.0030.0000.0000.0000.000
126A428HOH0-0.054-0.04627.000-0.002-0.0020.0000.0000.0000.000
127A429HOH00.0270.02240.8960.0000.0000.0000.0000.0000.000
128A430HOH00.0260.0195.8120.0080.0080.0000.0000.0000.000
129A431HOH00.0290.01434.246-0.001-0.0010.0000.0000.0000.000
130A433HOH0-0.011-0.0059.9550.0420.0420.0000.0000.0000.000
131A435HOH0-0.005-0.01623.6460.0020.0020.0000.0000.0000.000
132A440HOH0-0.041-0.03034.466-0.001-0.0010.0000.0000.0000.000
133A441HOH0-0.024-0.00719.991-0.006-0.0060.0000.0000.0000.000
134A442HOH0-0.005-0.01216.9420.0030.0030.0000.0000.0000.000
135A443HOH0-0.007-0.0098.336-0.021-0.0210.0000.0000.0000.000
136A444HOH0-0.045-0.02828.293-0.001-0.0010.0000.0000.0000.000
137A445HOH0-0.035-0.02111.6680.0100.0100.0000.0000.0000.000
138A447HOH0-0.020-0.0153.518-0.195-0.1260.004-0.033-0.0400.000
139A448HOH0-0.0150.00421.8180.0000.0000.0000.0000.0000.000
140A449HOH0-0.062-0.04022.7240.0020.0020.0000.0000.0000.000
141A450HOH0-0.055-0.04412.8390.0150.0150.0000.0000.0000.000
142A451HOH0-0.034-0.02429.483-0.003-0.0030.0000.0000.0000.000
143A453HOH00.0300.02414.439-0.009-0.0090.0000.0000.0000.000
144A456HOH0-0.029-0.03410.937-0.003-0.0030.0000.0000.0000.000
145A457HOH0-0.077-0.08126.3480.0000.0000.0000.0000.0000.000
146A458HOH00.0210.01836.5070.0000.0000.0000.0000.0000.000
147A460HOH0-0.023-0.0297.821-0.017-0.0170.0000.0000.0000.000
148A461HOH0-0.015-0.02733.2480.0010.0010.0000.0000.0000.000
149A462HOH0-0.012-0.01328.250-0.001-0.0010.0000.0000.0000.000
150A463HOH0-0.030-0.01520.1290.0010.0010.0000.0000.0000.000
151A464HOH0-0.009-0.00826.5820.0020.0020.0000.0000.0000.000
152A465HOH0-0.021-0.0348.128-0.006-0.0060.0000.0000.0000.000
153A468HOH0-0.043-0.0373.9240.2820.3920.003-0.048-0.0650.000
154A469HOH0-0.031-0.05932.9480.0000.0000.0000.0000.0000.000
155A470HOH0-0.023-0.01825.539-0.001-0.0010.0000.0000.0000.000
156A471HOH0-0.016-0.01513.928-0.006-0.0060.0000.0000.0000.000
157A473HOH0-0.007-0.01135.8130.0000.0000.0000.0000.0000.000
158A476HOH00.0750.0665.888-0.177-0.1770.0000.0000.0000.000
159A479HOH0-0.016-0.01033.4440.0010.0010.0000.0000.0000.000
160A480HOH0-0.052-0.06219.423-0.004-0.0040.0000.0000.0000.000
161A481HOH0-0.041-0.02830.2280.0000.0000.0000.0000.0000.000
162A483HOH00.007-0.00315.9140.0180.0180.0000.0000.0000.000
163A485HOH0-0.029-0.04316.3300.0000.0000.0000.0000.0000.000
164A488HOH0-0.046-0.03935.0180.0010.0010.0000.0000.0000.000
165A489HOH0-0.040-0.03135.491-0.001-0.0010.0000.0000.0000.000
166A491HOH0-0.039-0.02422.149-0.006-0.0060.0000.0000.0000.000
167A492HOH0-0.034-0.02031.0310.0000.0000.0000.0000.0000.000
168A494HOH0-0.016-0.0159.913-0.080-0.0800.0000.0000.0000.000
169A503HOH0-0.023-0.0176.206-0.013-0.0130.0000.0000.0000.000
170A504HOH0-0.018-0.01123.436-0.001-0.0010.0000.0000.0000.000
171A506HOH0-0.019-0.01731.811-0.001-0.0010.0000.0000.0000.000
172A508HOH0-0.022-0.01734.572-0.001-0.0010.0000.0000.0000.000
173A510HOH0-0.009-0.02020.8140.0020.0020.0000.0000.0000.000
174A511HOH00.0230.01127.0120.0010.0010.0000.0000.0000.000
175A525HOH0-0.023-0.01733.458-0.001-0.0010.0000.0000.0000.000
176A528HOH0-0.023-0.01918.972-0.002-0.0020.0000.0000.0000.000
177A529HOH00.0430.04213.7740.0000.0000.0000.0000.0000.000
178A531HOH0-0.0090.01821.060-0.004-0.0040.0000.0000.0000.000
179A532HOH00.0260.01831.7230.0020.0020.0000.0000.0000.000
180A533HOH0-0.014-0.0196.750-0.122-0.1220.0000.0000.0000.000
181A540HOH00.0150.0059.930-0.077-0.0770.0000.0000.0000.000