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: KK6G3

Calculation Name: 2ERF-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ERF

Chain ID: A

ChEMBL ID:

UniProt ID: P07996

Base Structure: X-ray

Registration Date: 2025-10-04

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 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2422061.289182
FMO2-HF: Nuclear repulsion 2342494.255973
FMO2-HF: Total energy -79567.033209
FMO2-MP2: Total energy -79801.614197


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:7:GLY)


Summations of interaction energy for fragment #1(A:7:GLY)
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.
-158.579-152.65312.022-9.333-8.612-0.117
Interaction energy analysis for fragmet #1(A:7:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.904
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].
3A9ASP-1-0.866-0.9243.844-42.026-41.228-0.009-0.425-0.3630.000
5A11SER00.002-0.0062.110-18.223-16.7423.967-2.683-2.765-0.038
6A12VAL00.001-0.0084.078-4.463-4.231-0.001-0.046-0.1850.000
194A200VAL0-0.022-0.0204.299-1.783-1.748-0.001-0.005-0.0280.000
195A201PHE00.0250.0234.0435.4945.7220.000-0.120-0.1070.000
196A202GLY0-0.007-0.0272.008-40.983-40.0927.334-4.640-3.585-0.058
197A203THR0-0.049-0.0322.649-16.800-14.5590.733-1.403-1.571-0.021
198A204THR00.017-0.0034.5485.6125.632-0.001-0.011-0.0080.000
4A10ASN0-0.047-0.0275.673-3.053-3.0530.0000.0000.0000.000
7A13PHE00.0170.0116.2984.0784.0780.0000.0000.0000.000
8A14ASP-1-0.763-0.87010.083-19.880-19.8800.0000.0000.0000.000
9A15ILE00.0450.00912.9221.1721.1720.0000.0000.0000.000
10A16PHE00.0010.00115.9361.3611.3610.0000.0000.0000.000
11A17GLU-1-0.997-0.98814.316-19.724-19.7240.0000.0000.0000.000
12A18LEU0-0.007-0.00512.4900.9210.9210.0000.0000.0000.000
13A19THR0-0.046-0.02916.9400.8920.8920.0000.0000.0000.000
14A20GLY00.0200.01319.9570.8540.8540.0000.0000.0000.000
15A21ALA00.0230.01621.8920.7540.7540.0000.0000.0000.000
16A22ALA00.0110.00621.8670.6280.6280.0000.0000.0000.000
17A23ARG10.9050.95220.60614.59914.5990.0000.0000.0000.000
18A24LYS10.9800.99526.14810.67310.6730.0000.0000.0000.000
19A25GLY00.006-0.00228.253-0.183-0.1830.0000.0000.0000.000
20A26SER0-0.017-0.01529.8260.3390.3390.0000.0000.0000.000
21A27GLY00.0750.03729.331-0.341-0.3410.0000.0000.0000.000
22A28ARG10.8440.92026.10811.36911.3690.0000.0000.0000.000
23A29ARG10.9891.01629.3679.3929.3920.0000.0000.0000.000
24A30LEU0-0.0150.00325.213-0.280-0.2800.0000.0000.0000.000
25A31VAL0-0.083-0.05226.7700.5910.5910.0000.0000.0000.000
26A32LYS10.9810.98625.98310.28310.2830.0000.0000.0000.000
27A33GLY00.034-0.00523.4620.3360.3360.0000.0000.0000.000
28A34PRO0-0.0090.00921.1780.3450.3450.0000.0000.0000.000
29A35ASP-1-0.731-0.80617.027-17.985-17.9850.0000.0000.0000.000
30A36PRO0-0.040-0.02320.3470.5070.5070.0000.0000.0000.000
31A37SER0-0.097-0.06518.4550.2750.2750.0000.0000.0000.000
32A38SER00.008-0.00517.6310.3140.3140.0000.0000.0000.000
33A39PRO0-0.040-0.02019.7380.6960.6960.0000.0000.0000.000
34A40ALA00.0230.02221.179-0.618-0.6180.0000.0000.0000.000
35A41PHE0-0.002-0.02020.3290.7880.7880.0000.0000.0000.000
36A42ARG10.9430.97225.05110.11510.1150.0000.0000.0000.000
37A43ILE0-0.004-0.00424.9350.0950.0950.0000.0000.0000.000
38A44GLU-1-0.979-0.99328.973-9.406-9.4060.0000.0000.0000.000
39A45ASP-1-0.829-0.92531.315-9.380-9.3800.0000.0000.0000.000
40A46ALA00.0160.00727.375-0.153-0.1530.0000.0000.0000.000
41A47ASN0-0.077-0.04828.157-0.457-0.4570.0000.0000.0000.000
42A48LEU0-0.010-0.00930.083-0.110-0.1100.0000.0000.0000.000
43A49ILE0-0.0340.00724.130-0.072-0.0720.0000.0000.0000.000
44A50PRO0-0.020-0.00323.8560.0760.0760.0000.0000.0000.000
45A51PRO0-0.002-0.00223.129-0.338-0.3380.0000.0000.0000.000
46A52VAL0-0.009-0.00616.644-0.075-0.0750.0000.0000.0000.000
47A53PRO0-0.023-0.00618.9910.5010.5010.0000.0000.0000.000
48A54ASP-1-0.794-0.91219.297-13.874-13.8740.0000.0000.0000.000
49A55ASP-1-0.817-0.89818.717-17.201-17.2010.0000.0000.0000.000
50A56LYS10.8970.93214.60818.09718.0970.0000.0000.0000.000
51A57PHE0-0.016-0.00414.575-1.324-1.3240.0000.0000.0000.000
52A58GLN00.019-0.01615.5040.1480.1480.0000.0000.0000.000
53A59ASP-1-0.890-0.94211.652-23.071-23.0710.0000.0000.0000.000
54A60LEU0-0.045-0.01710.759-1.971-1.9710.0000.0000.0000.000
55A61VAL0-0.050-0.02411.459-0.944-0.9440.0000.0000.0000.000
56A62ASP-1-0.786-0.87412.214-19.526-19.5260.0000.0000.0000.000
57A63ALA00.0140.0357.233-0.557-0.5570.0000.0000.0000.000
58A64VAL0-0.018-0.0038.854-0.680-0.6800.0000.0000.0000.000
59A65ARG10.7540.85411.09719.99719.9970.0000.0000.0000.000
60A66THR0-0.099-0.0558.4401.5821.5820.0000.0000.0000.000
61A67GLU-1-0.849-0.9255.893-44.378-44.3780.0000.0000.0000.000
62A68LYS10.8840.9549.15820.24420.2440.0000.0000.0000.000
63A69GLY00.0490.01711.5591.6891.6890.0000.0000.0000.000
64A70PHE00.019-0.0059.080-0.699-0.6990.0000.0000.0000.000
65A71LEU00.0000.0237.3342.8662.8660.0000.0000.0000.000
66A72LEU0-0.046-0.0199.269-1.496-1.4960.0000.0000.0000.000
67A73LEU00.0050.0059.4601.3451.3450.0000.0000.0000.000
68A74ALA00.008-0.01013.1820.4220.4220.0000.0000.0000.000
69A75SER00.0200.02516.7270.1740.1740.0000.0000.0000.000
70A76LEU0-0.048-0.03919.5590.3790.3790.0000.0000.0000.000
71A77ARG10.8750.94122.91710.97010.9700.0000.0000.0000.000
72A78GLN0-0.0050.02026.692-0.087-0.0870.0000.0000.0000.000
73A79MET0-0.026-0.01128.5390.3150.3150.0000.0000.0000.000
74A80LYS10.9730.99032.1718.6848.6840.0000.0000.0000.000
75A81LYS10.9570.98533.7468.7328.7320.0000.0000.0000.000
76A82THR0-0.026-0.00231.5140.0730.0730.0000.0000.0000.000
77A83ARG10.8340.89230.1979.4879.4870.0000.0000.0000.000
78A84GLY00.0140.00927.9850.2090.2090.0000.0000.0000.000
79A85THR0-0.025-0.02524.264-0.430-0.4300.0000.0000.0000.000
80A86LEU0-0.018-0.00220.2500.0970.0970.0000.0000.0000.000
81A87LEU00.009-0.00116.636-0.213-0.2130.0000.0000.0000.000
82A88ALA00.0150.00321.2270.2040.2040.0000.0000.0000.000
83A89LEU0-0.0350.00518.274-0.265-0.2650.0000.0000.0000.000
84A90GLU-1-0.785-0.86822.431-11.034-11.0340.0000.0000.0000.000
85A91ARG10.9890.98825.53410.77010.7700.0000.0000.0000.000
86A92LYS10.7310.85224.45112.83912.8390.0000.0000.0000.000
87A93ASP-1-0.836-0.88429.272-9.888-9.8880.0000.0000.0000.000
88A94HIS0-0.040-0.02731.3540.2430.2430.0000.0000.0000.000
89A95SER0-0.075-0.05431.8290.0650.0650.0000.0000.0000.000
90A96GLY00.0260.00730.6880.1610.1610.0000.0000.0000.000
91A97GLN0-0.0290.00525.653-0.432-0.4320.0000.0000.0000.000
92A98VAL0-0.003-0.00822.1940.3230.3230.0000.0000.0000.000
93A99PHE00.0630.01617.532-0.179-0.1790.0000.0000.0000.000
94A100SER0-0.048-0.03122.0330.2950.2950.0000.0000.0000.000
95A101VAL00.0590.05218.253-0.023-0.0230.0000.0000.0000.000
96A102VAL0-0.021-0.02121.7310.1440.1440.0000.0000.0000.000
97A103SER00.0480.01624.040-0.031-0.0310.0000.0000.0000.000
98A104ASN00.016-0.01925.6200.7400.7400.0000.0000.0000.000
99A105GLY00.0640.01729.0960.1320.1320.0000.0000.0000.000
100A106LYS10.7800.87131.3109.2999.2990.0000.0000.0000.000
101A107ALA00.0020.01531.4960.3140.3140.0000.0000.0000.000
102A108GLY0-0.053-0.01830.6710.1320.1320.0000.0000.0000.000
103A109THR00.035-0.00827.429-0.074-0.0740.0000.0000.0000.000
104A110LEU0-0.030-0.01219.840-0.077-0.0770.0000.0000.0000.000
105A111ASP-1-0.778-0.83424.071-11.296-11.2960.0000.0000.0000.000
106A112LEU0-0.012-0.00319.860-0.558-0.5580.0000.0000.0000.000
107A113SER0-0.028-0.01323.1990.6160.6160.0000.0000.0000.000
108A114LEU00.0560.01620.237-0.592-0.5920.0000.0000.0000.000
109A115THR0-0.048-0.02624.3620.6970.6970.0000.0000.0000.000
110A116VAL00.0350.01223.947-0.183-0.1830.0000.0000.0000.000
111A117GLN0-0.007-0.01326.9500.2430.2430.0000.0000.0000.000
112A118GLY0-0.008-0.00629.9430.3180.3180.0000.0000.0000.000
113A119LYS10.9320.97830.7539.7679.7670.0000.0000.0000.000
114A120GLN00.0170.01029.207-0.232-0.2320.0000.0000.0000.000
115A121HIS10.8020.88626.57911.42711.4270.0000.0000.0000.000
116A122VAL0-0.006-0.01226.880-0.403-0.4030.0000.0000.0000.000
117A123VAL00.0160.02524.1100.3260.3260.0000.0000.0000.000
118A124SER0-0.006-0.02325.539-0.299-0.2990.0000.0000.0000.000
119A125VAL0-0.028-0.01221.3600.0060.0060.0000.0000.0000.000
120A126GLU-1-0.843-0.94524.807-10.222-10.2220.0000.0000.0000.000
121A127GLU-1-0.914-0.95126.527-10.736-10.7360.0000.0000.0000.000
122A128ALA00.0090.01424.253-0.174-0.1740.0000.0000.0000.000
123A129LEU0-0.030-0.01126.0630.0890.0890.0000.0000.0000.000
124A130LEU00.0340.01422.5820.0290.0290.0000.0000.0000.000
125A131ALA0-0.029-0.00226.4840.0660.0660.0000.0000.0000.000
126A132THR00.0410.00328.4610.5320.5320.0000.0000.0000.000
127A133GLY0-0.059-0.03030.6240.4000.4000.0000.0000.0000.000
128A134GLN0-0.027-0.02629.6600.0170.0170.0000.0000.0000.000
129A135TRP0-0.026-0.01922.818-0.029-0.0290.0000.0000.0000.000
130A136LYS10.8750.95923.08512.69012.6900.0000.0000.0000.000
131A137SER0-0.019-0.00616.876-0.304-0.3040.0000.0000.0000.000
132A138ILE0-0.018-0.01017.4850.7310.7310.0000.0000.0000.000
133A139THR00.005-0.00811.999-1.717-1.7170.0000.0000.0000.000
134A140LEU0-0.0170.00114.4020.9260.9260.0000.0000.0000.000
135A141PHE00.014-0.0039.402-1.595-1.5950.0000.0000.0000.000
136A142VAL00.008-0.00412.6492.0142.0140.0000.0000.0000.000
137A143GLN0-0.0010.00510.804-2.859-2.8590.0000.0000.0000.000
138A144GLU-1-0.844-0.92414.569-16.120-16.1200.0000.0000.0000.000
139A145ASP-1-0.875-0.93617.145-14.708-14.7080.0000.0000.0000.000
140A146ARG10.9450.99016.21617.92917.9290.0000.0000.0000.000
141A147ALA0-0.003-0.00217.210-1.256-1.2560.0000.0000.0000.000
142A148GLN0-0.011-0.01416.086-0.040-0.0400.0000.0000.0000.000
143A149LEU0-0.029-0.01216.337-1.217-1.2170.0000.0000.0000.000
144A150TYR00.0400.01114.8270.4730.4730.0000.0000.0000.000
145A151ILE0-0.037-0.02818.201-0.292-0.2920.0000.0000.0000.000
146A152ASP-1-0.807-0.90320.498-13.174-13.1740.0000.0000.0000.000
147A153CYS0-0.123-0.05314.397-0.902-0.9020.0000.0000.0000.000
148A154GLU-1-0.914-0.94020.726-12.918-12.9180.0000.0000.0000.000
149A155LYS10.8530.93622.30612.00212.0020.0000.0000.0000.000
150A156MET0-0.013-0.01019.038-1.065-1.0650.0000.0000.0000.000
151A157GLU-1-0.861-0.90921.467-11.817-11.8170.0000.0000.0000.000
152A158ASN0-0.018-0.03620.333-1.556-1.5560.0000.0000.0000.000
153A159ALA0-0.019-0.00721.6250.6750.6750.0000.0000.0000.000
154A160GLU-1-0.926-0.95521.834-12.883-12.8830.0000.0000.0000.000
155A161LEU0-0.057-0.02919.2960.3810.3810.0000.0000.0000.000
156A162ASP-1-0.829-0.90023.655-10.778-10.7780.0000.0000.0000.000
157A163VAL0-0.040-0.02823.0910.3310.3310.0000.0000.0000.000
158A164PRO00.0260.02119.211-0.388-0.3880.0000.0000.0000.000
159A165ILE00.0330.03915.0720.4140.4140.0000.0000.0000.000
160A166GLN00.012-0.02815.082-0.247-0.2470.0000.0000.0000.000
161A167SER0-0.084-0.05816.9080.4690.4690.0000.0000.0000.000
162A168VAL0-0.023-0.01119.7460.7020.7020.0000.0000.0000.000
163A169PHE0-0.0270.00115.2710.2420.2420.0000.0000.0000.000
164A170THR00.031-0.00216.885-0.770-0.7700.0000.0000.0000.000
165A171ARG10.9600.95017.94913.57313.5730.0000.0000.0000.000
166A172ASP-1-0.819-0.88119.026-12.969-12.9690.0000.0000.0000.000
167A173LEU0-0.0340.00718.7910.6340.6340.0000.0000.0000.000
168A174ALA00.0290.01219.0730.5330.5330.0000.0000.0000.000
169A175SER0-0.023-0.01321.1670.5510.5510.0000.0000.0000.000
170A176ILE00.006-0.00124.5550.5230.5230.0000.0000.0000.000
171A177ALA0-0.031-0.01422.8770.4570.4570.0000.0000.0000.000
172A178ARG10.9530.97221.95611.70511.7050.0000.0000.0000.000
173A179LEU00.0080.02716.4560.3000.3000.0000.0000.0000.000
174A180ARG10.7740.86520.60412.26212.2620.0000.0000.0000.000
175A181ILE00.0680.02618.695-0.363-0.3630.0000.0000.0000.000
176A182ALA0-0.025-0.01922.0430.6210.6210.0000.0000.0000.000
177A183LYS10.8540.92624.93211.52611.5260.0000.0000.0000.000
178A184GLY00.007-0.02026.065-0.485-0.4850.0000.0000.0000.000
179A185GLY0-0.0070.00728.3760.2710.2710.0000.0000.0000.000
180A186VAL0-0.014-0.00930.9920.1350.1350.0000.0000.0000.000
181A187ASN0-0.033-0.02834.5240.2380.2380.0000.0000.0000.000
182A188ASP-1-0.763-0.82730.261-9.795-9.7950.0000.0000.0000.000
183A189ASN00.0750.04228.956-0.673-0.6730.0000.0000.0000.000
184A190PHE0-0.037-0.01925.5060.2420.2420.0000.0000.0000.000
185A191GLN00.0290.01328.0210.1240.1240.0000.0000.0000.000
186A192GLY00.012-0.01328.6040.1040.1040.0000.0000.0000.000
187A193VAL0-0.095-0.03525.1830.1750.1750.0000.0000.0000.000
188A194LEU00.0310.02421.152-0.139-0.1390.0000.0000.0000.000
189A195GLN00.001-0.02819.0590.5470.5470.0000.0000.0000.000
190A196ASN0-0.002-0.00414.8410.0140.0140.0000.0000.0000.000
191A197VAL00.0110.01514.656-0.860-0.8600.0000.0000.0000.000
192A198ARG10.8620.91710.21223.46823.4680.0000.0000.0000.000
193A199PHE00.0170.0239.8530.6780.6780.0000.0000.0000.000
199A205PRO00.0400.0058.365-0.569-0.5690.0000.0000.0000.000
200A206GLU-1-0.935-0.95311.227-19.839-19.8390.0000.0000.0000.000
201A207ASP-1-0.816-0.8928.142-32.791-32.7910.0000.0000.0000.000
202A208ILE0-0.018-0.0067.5740.9730.9730.0000.0000.0000.000
203A209LEU00.0250.01910.7521.8671.8670.0000.0000.0000.000
204A210ARG10.8840.93713.55520.05820.0580.0000.0000.0000.000
205A211ASN0-0.039-0.0229.5082.7452.7450.0000.0000.0000.000
206A212LYS10.8470.91013.55017.47017.4700.0000.0000.0000.000
207A213GLY00.0420.02613.4650.5180.5180.0000.0000.0000.000
208A215SER-1-0.822-0.90016.805-15.034-15.0340.0000.0000.0000.000