FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 6Z54Z

Calculation Name: 1EPF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EPF

Chain ID: A

ChEMBL ID:

UniProt ID: P13596

Base Structure: X-ray

Registration Date: 2025-09-02

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1771374.87648
FMO2-HF: Nuclear repulsion 1697506.204179
FMO2-HF: Total energy -73868.672301
FMO2-MP2: Total energy -74084.995222


3D Structure Molmil
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:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-156.598-150.0596.931-3.846-9.625-0.025
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.920
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].
3A3VAL00.0250.0153.036-1.0531.7970.112-1.141-1.821-0.005
4A4ASP-1-0.883-0.9415.037-22.967-22.937-0.001-0.003-0.0260.000
24A24VAL00.0420.0212.379-3.767-3.9491.814-0.345-1.287-0.004
25A25ALA0-0.068-0.0353.8713.3363.5480.001-0.043-0.1710.000
26A26GLY00.0010.0044.505-4.040-3.864-0.001-0.013-0.1620.000
29A29LYS10.8280.9194.72537.14937.239-0.001-0.003-0.0860.000
31A31LYS10.8250.8833.12027.30127.7790.032-0.077-0.4330.000
78A79VAL00.0070.0032.3450.3270.7661.527-0.385-1.581-0.002
79A80THR0-0.016-0.0113.133-5.916-4.7470.210-0.633-0.746-0.006
80A81ALA0-0.012-0.0112.6380.7421.2310.293-0.176-0.606-0.002
81A82GLU-1-0.895-0.9544.576-25.791-25.753-0.001-0.010-0.0270.000
85A86GLN0-0.008-0.0163.571-0.332-0.0810.007-0.053-0.2060.000
86A87SER0-0.036-0.0082.335-5.584-5.2182.938-1.102-2.202-0.006
87A88GLU-1-0.835-0.9053.575-21.608-21.4750.0010.138-0.2710.000
5A5ILE0-0.046-0.0258.8530.6840.6840.0000.0000.0000.000
6A6VAL0-0.0080.02912.0561.0741.0740.0000.0000.0000.000
7A7PRO0-0.041-0.03715.3800.4210.4210.0000.0000.0000.000
8A8SER00.0880.02514.7840.2810.2810.0000.0000.0000.000
9A9GLN0-0.056-0.02616.148-0.130-0.1300.0000.0000.0000.000
10A10GLY00.001-0.00319.2030.2400.2400.0000.0000.0000.000
11A11GLU-1-0.977-0.96921.931-10.436-10.4360.0000.0000.0000.000
12A12ILE00.0000.00023.362-0.050-0.0500.0000.0000.0000.000
13A13SER0-0.024-0.02127.3420.1100.1100.0000.0000.0000.000
14A14VAL0-0.009-0.00630.655-0.125-0.1250.0000.0000.0000.000
15A15GLY0-0.022-0.00131.9530.2570.2570.0000.0000.0000.000
16A16GLU-1-0.913-0.93930.478-9.190-9.1900.0000.0000.0000.000
17A17SER0-0.041-0.04226.545-0.043-0.0430.0000.0000.0000.000
18A18LYS10.8550.92822.27012.09512.0950.0000.0000.0000.000
19A19PHE00.0000.02218.5590.1280.1280.0000.0000.0000.000
20A20PHE00.002-0.01716.0340.3210.3210.0000.0000.0000.000
21A21LEU00.0310.03312.690-0.082-0.0820.0000.0000.0000.000
22A22CYS0-0.037-0.0018.457-0.646-0.6460.0000.0000.0000.000
23A23GLN00.0350.0108.675-0.120-0.1200.0000.0000.0000.000
27A27ASP-1-0.864-0.9515.408-40.006-40.0060.0000.0000.0000.000
28A28ALA0-0.043-0.0227.635-0.134-0.1340.0000.0000.0000.000
30A30ASP-1-0.917-0.9387.483-23.544-23.5440.0000.0000.0000.000
32A32ASP-1-0.846-0.8766.570-20.132-20.1320.0000.0000.0000.000
33A33ILE0-0.026-0.0165.981-3.507-3.5070.0000.0000.0000.000
34A34SER0-0.045-0.0467.8403.0793.0790.0000.0000.0000.000
35A35TRP0-0.016-0.0299.953-1.058-1.0580.0000.0000.0000.000
36A36PHE0-0.029-0.01910.7100.6680.6680.0000.0000.0000.000
37A37SER00.0360.00714.816-0.383-0.3830.0000.0000.0000.000
38A38PRO0-0.035-0.01618.058-0.289-0.2890.0000.0000.0000.000
39A39ASN0-0.058-0.03419.911-0.434-0.4340.0000.0000.0000.000
40A40GLY0-0.0010.00317.5160.2500.2500.0000.0000.0000.000
41A41GLU-1-0.899-0.92317.769-12.280-12.2800.0000.0000.0000.000
42A42LYS10.9230.96412.11818.03918.0390.0000.0000.0000.000
43A43LEU0-0.032-0.02115.8230.7080.7080.0000.0000.0000.000
44A44SER00.0120.00415.661-0.816-0.8160.0000.0000.0000.000
45A45PRO00.011-0.00215.6710.4520.4520.0000.0000.0000.000
46A46ASN0-0.050-0.03418.1691.0881.0880.0000.0000.0000.000
47A47GLN00.0120.00921.542-0.565-0.5650.0000.0000.0000.000
48A48GLN00.0160.01623.9120.6430.6430.0000.0000.0000.000
49A49ARG10.7720.83724.79310.20810.2080.0000.0000.0000.000
50A50ILE0-0.0070.00520.498-0.097-0.0970.0000.0000.0000.000
51A51SER0-0.0290.00121.325-0.145-0.1450.0000.0000.0000.000
52A52VAL00.0230.00015.062-0.499-0.4990.0000.0000.0000.000
53A53VAL0-0.023-0.01116.8770.5260.5260.0000.0000.0000.000
54A54TRP00.0200.02511.5130.2110.2110.0000.0000.0000.000
55A55ASN0-0.052-0.01713.3020.5320.5320.0000.0000.0000.000
56A56ASP-1-0.780-0.88211.063-19.895-19.8950.0000.0000.0000.000
57A57ASP-1-0.891-0.9519.750-20.339-20.3390.0000.0000.0000.000
58A58ASP-1-0.882-0.9206.637-31.832-31.8320.0000.0000.0000.000
59A59SER0-0.050-0.0547.221-1.330-1.3300.0000.0000.0000.000
60A60SER00.0290.0099.8051.6941.6940.0000.0000.0000.000
61A61THR0-0.027-0.02012.205-0.479-0.4790.0000.0000.0000.000
62A62LEU00.0240.04115.3530.6040.6040.0000.0000.0000.000
63A63THR0-0.078-0.06716.9610.3110.3110.0000.0000.0000.000
64A64ILE00.0140.03220.7520.2610.2610.0000.0000.0000.000
65A65TYR00.016-0.01123.3550.1440.1440.0000.0000.0000.000
66A66ASN0-0.053-0.03226.8530.1170.1170.0000.0000.0000.000
67A67ALA00.0260.02727.2940.0340.0340.0000.0000.0000.000
68A68ASN0-0.008-0.01528.5310.4820.4820.0000.0000.0000.000
69A69ILE00.022-0.01528.589-0.279-0.2790.0000.0000.0000.000
70A70ASP-1-0.909-0.94128.258-9.764-9.7640.0000.0000.0000.000
71A71ASP-1-0.745-0.82424.590-11.111-11.1110.0000.0000.0000.000
72A72ALA0-0.014-0.00523.625-0.544-0.5440.0000.0000.0000.000
73A73GLY00.0100.00722.4600.0170.0170.0000.0000.0000.000
74A74ILE0-0.040-0.02916.361-0.177-0.1770.0000.0000.0000.000
75A75TYR00.008-0.01015.8830.0290.0290.0000.0000.0000.000
76A76LYS10.8080.87910.49121.05921.0590.0000.0000.0000.000
77A78VAL00.001-0.0116.725-1.873-1.8730.0000.0000.0000.000
82A83ASP-1-0.964-0.9757.837-25.954-25.9540.0000.0000.0000.000
83A84GLY00.0170.0087.8722.3962.3960.0000.0000.0000.000
84A85THR0-0.050-0.0104.878-0.985-0.9850.0000.0000.0000.000
88A89ALA00.0120.0196.764-1.935-1.9350.0000.0000.0000.000
89A90THR0-0.015-0.0198.9311.7911.7910.0000.0000.0000.000
90A91VAL00.0240.02412.754-0.018-0.0180.0000.0000.0000.000
91A92ASN0-0.041-0.02115.7420.7840.7840.0000.0000.0000.000
92A93VAL00.0160.01719.3700.2250.2250.0000.0000.0000.000
93A94LYS10.9470.96921.95611.83711.8370.0000.0000.0000.000
94A95ILE00.0440.02025.6030.0110.0110.0000.0000.0000.000
95A96PHE0-0.010-0.00828.5810.3260.3260.0000.0000.0000.000
96A97GLN00.011-0.01231.4250.0900.0900.0000.0000.0000.000
97A98LYS10.9790.99934.9458.4448.4440.0000.0000.0000.000
98A99LEU00.0320.02236.7570.1260.1260.0000.0000.0000.000
99A100MET0-0.060-0.01939.1150.0700.0700.0000.0000.0000.000
100A101PHE00.005-0.00842.3550.0450.0450.0000.0000.0000.000
101A102LYS10.9250.98042.1297.0327.0320.0000.0000.0000.000
102A103ASN0-0.007-0.02044.4470.0720.0720.0000.0000.0000.000
103A104ALA00.004-0.00748.220-0.009-0.0090.0000.0000.0000.000
104A105PRO00.0010.01951.1470.0260.0260.0000.0000.0000.000
105A106THR00.0300.03053.9980.0880.0880.0000.0000.0000.000
106A107PRO00.0260.00156.879-0.035-0.0350.0000.0000.0000.000
107A108GLN0-0.056-0.03755.121-0.040-0.0400.0000.0000.0000.000
108A109GLU-1-0.928-0.95760.208-4.787-4.7870.0000.0000.0000.000
109A110PHE0-0.008-0.01159.498-0.060-0.0600.0000.0000.0000.000
110A111LYS10.9170.95865.4164.4314.4310.0000.0000.0000.000
111A112GLU-1-0.817-0.90969.119-4.318-4.3180.0000.0000.0000.000
112A113GLY0-0.058-0.03471.0650.0560.0560.0000.0000.0000.000
113A114GLU-1-0.898-0.93764.795-4.796-4.7960.0000.0000.0000.000
114A115ASP-1-0.854-0.92664.391-4.776-4.7760.0000.0000.0000.000
115A116ALA00.0310.03862.833-0.058-0.0580.0000.0000.0000.000
116A117VAL0-0.033-0.03756.677-0.043-0.0430.0000.0000.0000.000
117A118ILE0-0.0230.00456.399-0.034-0.0340.0000.0000.0000.000
118A119VAL00.000-0.00251.801-0.102-0.1020.0000.0000.0000.000
119A120CYS0-0.0210.00050.361-0.033-0.0330.0000.0000.0000.000
120A121ASP-1-0.802-0.85545.802-6.551-6.5510.0000.0000.0000.000
121A122VAL0-0.015-0.01843.873-0.099-0.0990.0000.0000.0000.000
122A123VAL0-0.033-0.01939.909-0.060-0.0600.0000.0000.0000.000
123A124SER00.001-0.03438.315-0.050-0.0500.0000.0000.0000.000
124A125SER00.0390.02733.0160.0350.0350.0000.0000.0000.000
125A126LEU0-0.036-0.00534.348-0.111-0.1110.0000.0000.0000.000
126A127PRO00.0390.01837.4980.1610.1610.0000.0000.0000.000
127A128PRO0-0.0200.01141.0260.0200.0200.0000.0000.0000.000
128A129THR0-0.052-0.03143.6720.1460.1460.0000.0000.0000.000
129A130ILE00.0200.00146.688-0.038-0.0380.0000.0000.0000.000
130A131ILE0-0.047-0.01549.6630.0900.0900.0000.0000.0000.000
131A132TRP00.0390.00853.0050.0040.0040.0000.0000.0000.000
132A133LYS10.7880.88454.1235.8705.8700.0000.0000.0000.000
133A134HIS00.0460.02858.388-0.008-0.0080.0000.0000.0000.000
134A135LYS10.9030.95161.6844.7884.7880.0000.0000.0000.000
135A136GLY00.0270.02259.2410.0320.0320.0000.0000.0000.000
136A137ARG10.9200.96559.5854.8044.8040.0000.0000.0000.000
137A138ASP-1-0.823-0.92057.322-5.511-5.5110.0000.0000.0000.000
138A139VAL00.0490.01358.5970.1150.1150.0000.0000.0000.000
139A140ILE00.0240.01558.1730.1090.1090.0000.0000.0000.000
140A141LEU0-0.101-0.05361.5820.1020.1020.0000.0000.0000.000
141A142LYS10.8060.90664.0034.9594.9590.0000.0000.0000.000
142A143LYS10.9110.95765.3264.8244.8240.0000.0000.0000.000
143A144ASP-1-0.786-0.86166.474-4.575-4.5750.0000.0000.0000.000
144A145VAL00.030-0.00565.629-0.070-0.0700.0000.0000.0000.000
145A146ARG10.6930.81165.5604.6174.6170.0000.0000.0000.000
146A147PHE0-0.036-0.01561.944-0.046-0.0460.0000.0000.0000.000
147A148ILE0-0.006-0.00158.506-0.023-0.0230.0000.0000.0000.000
148A149VAL0-0.017-0.00553.461-0.019-0.0190.0000.0000.0000.000
149A150LEU00.0090.01154.541-0.004-0.0040.0000.0000.0000.000
150A151SER00.001-0.01150.571-0.067-0.0670.0000.0000.0000.000
151A152ASN00.0140.00648.815-0.083-0.0830.0000.0000.0000.000
152A153ASN0-0.011-0.01246.748-0.031-0.0310.0000.0000.0000.000
153A154TYR00.000-0.01649.4210.1080.1080.0000.0000.0000.000
154A155LEU0-0.0080.00853.8590.0290.0290.0000.0000.0000.000
155A156GLN00.0090.00557.2420.0530.0530.0000.0000.0000.000
156A157ILE0-0.024-0.01660.2170.0060.0060.0000.0000.0000.000
157A158ARG10.8920.93863.5554.9554.9550.0000.0000.0000.000
158A159GLY00.014-0.00166.3890.0390.0390.0000.0000.0000.000
159A160ILE0-0.071-0.01864.6930.0440.0440.0000.0000.0000.000
160A161LYS10.9710.97968.4424.4954.4950.0000.0000.0000.000
161A162LYS10.9050.93769.9224.3804.3800.0000.0000.0000.000
162A163THR0-0.031-0.02970.733-0.051-0.0510.0000.0000.0000.000
163A164ASP-1-0.791-0.85766.395-4.692-4.6920.0000.0000.0000.000
164A165GLU-1-0.828-0.88965.896-4.625-4.6250.0000.0000.0000.000
165A166GLY0-0.050-0.03264.9800.0210.0210.0000.0000.0000.000
166A167THR0-0.036-0.03159.324-0.025-0.0250.0000.0000.0000.000
167A168TYR0-0.024-0.03758.3000.0190.0190.0000.0000.0000.000
168A169ARG10.7770.86653.0935.7665.7660.0000.0000.0000.000
169A171GLU-1-0.809-0.92450.067-6.098-6.0980.0000.0000.0000.000
170A172GLY00.0430.02446.3160.0210.0210.0000.0000.0000.000
171A173ARG10.9520.96445.3916.4286.4280.0000.0000.0000.000
172A174ILE00.0450.02839.0610.0410.0410.0000.0000.0000.000
173A175LEU0-0.003-0.00842.086-0.079-0.0790.0000.0000.0000.000
174A176ALA00.000-0.00839.3010.0050.0050.0000.0000.0000.000
175A177ARG10.8880.94732.4388.8418.8410.0000.0000.0000.000
176A178GLY0-0.0070.01339.681-0.001-0.0010.0000.0000.0000.000
177A179GLU-1-0.863-0.91937.100-8.234-8.2340.0000.0000.0000.000
178A180ILE0-0.026-0.02542.0420.1160.1160.0000.0000.0000.000
179A181ASN0-0.033-0.02643.0860.0760.0760.0000.0000.0000.000
180A182PHE0-0.032-0.02246.0620.0740.0740.0000.0000.0000.000
181A183LYS10.9640.98547.4106.4066.4060.0000.0000.0000.000
182A184ASP-1-0.795-0.85551.483-5.635-5.6350.0000.0000.0000.000
183A185ILE0-0.022-0.01953.548-0.036-0.0360.0000.0000.0000.000
184A186GLN00.0010.01357.2130.0190.0190.0000.0000.0000.000
185A187VAL00.0190.01360.400-0.017-0.0170.0000.0000.0000.000
186A188ILE0-0.004-0.00962.5410.0600.0600.0000.0000.0000.000
187A189VAL-1-0.836-0.90565.707-4.534-4.5340.0000.0000.0000.000