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: G4Q11

Calculation Name: 2VKE-A-Xray549

Preferred Name:

Target Type:

Ligand Name: tetracycline | cobalt (ii) ion

Ligand 3-letter code: TAC | CO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VKE

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACT4

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2189786.276016
FMO2-HF: Nuclear repulsion 2109175.507607
FMO2-HF: Total energy -80610.768408
FMO2-MP2: Total energy -80849.574473


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-145.774-142.40211.19-6.853-7.706-0.059
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.924
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].
3A4LEU00.0490.0233.2350.2651.7620.018-0.575-0.9410.000
7A8SER00.0590.0224.596-1.033-0.954-0.001-0.004-0.0730.000
11A12ALA0-0.002-0.0034.5131.1501.211-0.001-0.003-0.0560.000
33A34LEU0-0.010-0.0042.435-6.860-4.8261.209-1.128-2.1140.003
34A35GLY0-0.0110.0031.920-40.494-41.5939.877-4.853-3.924-0.060
35A36ILE0-0.095-0.0512.850-5.528-4.7280.088-0.290-0.598-0.002
4A5ASN0-0.0110.0046.2422.2512.2510.0000.0000.0000.000
5A6ARG11.0020.9818.47716.83216.8320.0000.0000.0000.000
6A7GLU-1-0.850-0.9179.942-23.844-23.8440.0000.0000.0000.000
8A9VAL0-0.070-0.0395.630-2.508-2.5080.0000.0000.0000.000
9A10ILE00.0090.0127.0661.1731.1730.0000.0000.0000.000
10A11ASP-1-0.796-0.8796.995-25.755-25.7550.0000.0000.0000.000
12A13ALA0-0.020-0.0226.6461.8191.8190.0000.0000.0000.000
13A14LEU00.0330.0179.9901.7001.7000.0000.0000.0000.000
14A15GLU-1-0.907-0.9458.170-29.445-29.4450.0000.0000.0000.000
15A16LEU0-0.033-0.0219.8421.1421.1420.0000.0000.0000.000
16A17LEU0-0.0240.00811.5261.2031.2030.0000.0000.0000.000
17A18ASN00.0460.01514.1361.7871.7870.0000.0000.0000.000
18A19GLU-1-0.838-0.90111.380-23.363-23.3630.0000.0000.0000.000
19A20THR0-0.104-0.07414.4391.0151.0150.0000.0000.0000.000
20A21GLY00.0750.04316.8410.7100.7100.0000.0000.0000.000
21A22ILE0-0.034-0.03517.416-0.986-0.9860.0000.0000.0000.000
22A23ASP-1-0.888-0.93019.124-13.377-13.3770.0000.0000.0000.000
23A24GLY0-0.091-0.05317.100-0.311-0.3110.0000.0000.0000.000
24A25LEU00.0490.02812.769-1.501-1.5010.0000.0000.0000.000
25A26THR0-0.023-0.02114.0380.4010.4010.0000.0000.0000.000
26A27THR00.0520.01112.275-1.242-1.2420.0000.0000.0000.000
27A28ARG10.8930.93611.26816.72216.7220.0000.0000.0000.000
28A29LYS10.9781.00411.18616.96716.9670.0000.0000.0000.000
29A30LEU00.0420.0316.909-1.848-1.8480.0000.0000.0000.000
30A31ALA0-0.023-0.0136.878-4.610-4.6100.0000.0000.0000.000
31A32GLN0-0.001-0.0116.297-4.362-4.3620.0000.0000.0000.000
32A33LYS10.7720.8965.71125.56625.5660.0000.0000.0000.000
36A37GLU-1-0.827-0.9105.560-22.088-22.0880.0000.0000.0000.000
37A38GLN00.0510.0139.0260.0450.0450.0000.0000.0000.000
38A39PRO00.0150.00111.155-0.036-0.0360.0000.0000.0000.000
39A40THR00.0240.0226.2771.5241.5240.0000.0000.0000.000
40A41LEU00.0120.0217.921-0.565-0.5650.0000.0000.0000.000
41A42TYR00.0030.0189.1741.4351.4350.0000.0000.0000.000
42A43TRP00.0090.01311.2311.2091.2090.0000.0000.0000.000
43A44HIS0-0.051-0.0348.3561.0131.0130.0000.0000.0000.000
44A45VAL0-0.008-0.01210.9331.6621.6620.0000.0000.0000.000
45A46LYS10.8500.92213.38519.72519.7250.0000.0000.0000.000
46A47ASN00.002-0.01316.6150.6180.6180.0000.0000.0000.000
47A48LYS10.8980.93316.51615.24315.2430.0000.0000.0000.000
48A49ARG10.9410.99817.57712.84312.8430.0000.0000.0000.000
49A50ALA00.0550.02017.524-0.038-0.0380.0000.0000.0000.000
50A51LEU0-0.042-0.01711.414-0.503-0.5030.0000.0000.0000.000
51A52LEU00.0100.00115.445-0.146-0.1460.0000.0000.0000.000
52A53ASP-1-0.839-0.93118.121-13.598-13.5980.0000.0000.0000.000
53A54ALA0-0.050-0.02415.2770.2150.2150.0000.0000.0000.000
54A55LEU0-0.003-0.01512.529-0.132-0.1320.0000.0000.0000.000
55A56ALA00.0160.01916.4640.2760.2760.0000.0000.0000.000
56A57VAL0-0.042-0.01019.0760.5070.5070.0000.0000.0000.000
57A58GLU-1-0.828-0.89614.070-18.394-18.3940.0000.0000.0000.000
58A59ILE0-0.028-0.01817.4090.1260.1260.0000.0000.0000.000
59A60LEU0-0.017-0.01119.0520.4570.4570.0000.0000.0000.000
60A61ALA0-0.014-0.00718.7740.3480.3480.0000.0000.0000.000
61A62ARG10.7260.82911.42220.67320.6730.0000.0000.0000.000
62A63HIS00.011-0.01018.0900.0690.0690.0000.0000.0000.000
63A64HIS00.0050.04922.3240.2470.2470.0000.0000.0000.000
64A65ASP-1-0.825-0.88425.327-10.564-10.5640.0000.0000.0000.000
65A66TYR0-0.072-0.06927.0390.1910.1910.0000.0000.0000.000
66A67SER00.009-0.00927.3700.1400.1400.0000.0000.0000.000
67A68LEU0-0.036-0.02030.0690.1290.1290.0000.0000.0000.000
68A69PRO0-0.0210.01033.436-0.016-0.0160.0000.0000.0000.000
69A70ALA00.0320.01337.034-0.041-0.0410.0000.0000.0000.000
70A71ALA0-0.014-0.02438.3600.1590.1590.0000.0000.0000.000
71A72GLY0-0.008-0.00441.4630.0950.0950.0000.0000.0000.000
72A73GLU-1-0.790-0.83138.233-7.935-7.9350.0000.0000.0000.000
73A74SER00.015-0.00442.454-0.026-0.0260.0000.0000.0000.000
74A75TRP00.0640.01541.615-0.241-0.2410.0000.0000.0000.000
75A76GLN0-0.012-0.01141.060-0.270-0.2700.0000.0000.0000.000
76A77SER0-0.078-0.05740.043-0.103-0.1030.0000.0000.0000.000
77A78PHE00.0350.02633.868-0.147-0.1470.0000.0000.0000.000
78A79LEU0-0.005-0.00936.379-0.253-0.2530.0000.0000.0000.000
79A80ARG10.8560.89036.3817.1407.1400.0000.0000.0000.000
80A81ASN0-0.021-0.01734.873-0.246-0.2460.0000.0000.0000.000
81A82ASN00.0210.00831.728-0.504-0.5040.0000.0000.0000.000
82A83ALA00.0190.00631.439-0.339-0.3390.0000.0000.0000.000
83A84MET0-0.012-0.01031.775-0.216-0.2160.0000.0000.0000.000
84A85SER0-0.061-0.03328.217-0.326-0.3260.0000.0000.0000.000
85A86PHE0-0.0030.00426.447-0.403-0.4030.0000.0000.0000.000
86A87ARG10.8430.90427.0119.0379.0370.0000.0000.0000.000
87A88ARG10.8620.91526.1119.8699.8690.0000.0000.0000.000
88A89ALA0-0.015-0.00623.309-0.454-0.4540.0000.0000.0000.000
89A90LEU0-0.026-0.01822.383-0.617-0.6170.0000.0000.0000.000
90A91LEU00.0090.00623.141-0.360-0.3600.0000.0000.0000.000
91A92ARG10.7490.90418.93612.81612.8160.0000.0000.0000.000
92A93TYR00.001-0.01515.058-1.054-1.0540.0000.0000.0000.000
93A94ARG10.9670.99418.49014.85614.8560.0000.0000.0000.000
94A95ASP-1-0.808-0.90419.367-14.077-14.0770.0000.0000.0000.000
95A96GLY00.0260.01520.623-0.025-0.0250.0000.0000.0000.000
96A97ALA00.0180.01121.5170.0510.0510.0000.0000.0000.000
97A98LYS10.8360.90123.39211.77311.7730.0000.0000.0000.000
98A99VAL0-0.071-0.03618.450-0.024-0.0240.0000.0000.0000.000
99A100HIS00.0820.05021.611-0.404-0.4040.0000.0000.0000.000
100A101LEU0-0.0140.01524.2400.4060.4060.0000.0000.0000.000
101A102GLY0-0.059-0.03326.261-0.225-0.2250.0000.0000.0000.000
102A103THR0-0.061-0.03523.4440.1860.1860.0000.0000.0000.000
103A104ARG10.9000.93726.64510.06410.0640.0000.0000.0000.000
104A105PRO00.0270.01526.573-0.365-0.3650.0000.0000.0000.000
105A106ASP-1-0.804-0.91122.892-13.201-13.2010.0000.0000.0000.000
106A107GLU-1-0.939-0.96923.738-12.310-12.3100.0000.0000.0000.000
107A108LYS10.8630.92421.33613.64413.6440.0000.0000.0000.000
108A109GLN00.0280.01123.4090.3390.3390.0000.0000.0000.000
109A110TYR0-0.0130.00827.0450.3960.3960.0000.0000.0000.000
110A111ASP-1-0.855-0.92430.363-9.698-9.6980.0000.0000.0000.000
111A112THR0-0.038-0.00229.2180.2510.2510.0000.0000.0000.000
112A113VAL00.009-0.01529.9450.2690.2690.0000.0000.0000.000
113A114GLU-1-0.928-0.95132.672-7.977-7.9770.0000.0000.0000.000
114A115THR0-0.040-0.03534.6530.3680.3680.0000.0000.0000.000
115A116GLN0-0.045-0.02931.2570.2750.2750.0000.0000.0000.000
116A117LEU0-0.008-0.00836.1710.2620.2620.0000.0000.0000.000
117A118ARG10.8630.92738.6857.6197.6190.0000.0000.0000.000
118A119PHE00.0500.04039.1780.2260.2260.0000.0000.0000.000
119A120MET0-0.0170.00239.8530.1780.1780.0000.0000.0000.000
120A121THR0-0.101-0.05742.4410.1830.1830.0000.0000.0000.000
121A122GLU-1-0.863-0.92443.025-7.039-7.0390.0000.0000.0000.000
122A123ASN0-0.080-0.05043.7080.2180.2180.0000.0000.0000.000
123A124GLY0-0.0020.00746.6520.0870.0870.0000.0000.0000.000
124A125PHE00.0090.00645.1110.0830.0830.0000.0000.0000.000
125A126SER0-0.018-0.03147.152-0.060-0.0600.0000.0000.0000.000
126A127LEU00.0450.00640.623-0.086-0.0860.0000.0000.0000.000
127A128ARG10.9120.95942.5616.6046.6040.0000.0000.0000.000
128A129ASP-1-0.800-0.88343.296-6.670-6.6700.0000.0000.0000.000
129A130GLY00.0340.02042.431-0.068-0.0680.0000.0000.0000.000
130A131LEU0-0.0030.00436.991-0.186-0.1860.0000.0000.0000.000
131A132TYR0-0.023-0.01438.859-0.122-0.1220.0000.0000.0000.000
132A133ALA00.0400.03040.372-0.099-0.0990.0000.0000.0000.000
133A134ILE00.0460.01934.851-0.122-0.1220.0000.0000.0000.000
134A135SER0-0.069-0.03435.628-0.304-0.3040.0000.0000.0000.000
135A136ALA0-0.011-0.00436.086-0.161-0.1610.0000.0000.0000.000
136A137VAL00.0330.01534.819-0.068-0.0680.0000.0000.0000.000
137A138SER0-0.026-0.01131.927-0.266-0.2660.0000.0000.0000.000
138A139HIS00.006-0.01932.422-0.359-0.3590.0000.0000.0000.000
139A140PHE0-0.0250.01334.332-0.075-0.0750.0000.0000.0000.000
140A141THR0-0.020-0.02330.312-0.033-0.0330.0000.0000.0000.000
141A142LEU0-0.051-0.02227.570-0.237-0.2370.0000.0000.0000.000
142A143GLY00.0000.00030.507-0.181-0.1810.0000.0000.0000.000
143A144ALA00.0320.01532.882-0.045-0.0450.0000.0000.0000.000
144A145VAL00.007-0.00226.551-0.078-0.0780.0000.0000.0000.000
145A146LEU0-0.046-0.02527.324-0.309-0.3090.0000.0000.0000.000
146A147GLU-1-0.923-0.95529.419-8.767-8.7670.0000.0000.0000.000
147A148GLN00.0360.03329.3970.0400.0400.0000.0000.0000.000
148A149GLN0-0.022-0.01623.252-0.115-0.1150.0000.0000.0000.000
149A150GLU-1-0.832-0.93026.179-11.542-11.5420.0000.0000.0000.000
150A151HIS0-0.0140.00428.929-0.046-0.0460.0000.0000.0000.000
151A152THR0-0.052-0.03626.8270.0650.0650.0000.0000.0000.000
152A153ALA0-0.025-0.00725.966-0.161-0.1610.0000.0000.0000.000
153A154ALA0-0.051-0.01027.5460.0040.0040.0000.0000.0000.000
154A155LEU00.0360.00230.0180.4210.4210.0000.0000.0000.000
155A156THR0-0.080-0.03328.022-0.550-0.5500.0000.0000.0000.000
156A157ASP-1-0.878-0.93026.374-11.308-11.3080.0000.0000.0000.000
157A158ARG10.8120.90229.7339.4229.4220.0000.0000.0000.000
158A159PRO0-0.021-0.00433.305-0.065-0.0650.0000.0000.0000.000
159A160ALA00.0450.01836.1240.0230.0230.0000.0000.0000.000
160A161ALA0-0.034-0.02438.4600.0730.0730.0000.0000.0000.000
161A162PRO00.0090.00642.295-0.056-0.0560.0000.0000.0000.000
162A163ASP-1-0.882-0.94644.987-6.623-6.6230.0000.0000.0000.000
163A164GLU-1-0.954-0.98046.695-5.876-5.8760.0000.0000.0000.000
164A165ASN0-0.021-0.00549.8510.0230.0230.0000.0000.0000.000
165A166LEU0-0.023-0.00545.5430.0380.0380.0000.0000.0000.000
166A167PRO00.0160.00649.7860.1140.1140.0000.0000.0000.000
167A168PRO00.002-0.01550.751-0.105-0.1050.0000.0000.0000.000
168A169LEU00.0610.01950.690-0.076-0.0760.0000.0000.0000.000
169A170LEU0-0.0150.01044.930-0.082-0.0820.0000.0000.0000.000
170A171ARG10.9190.96646.0856.0206.0200.0000.0000.0000.000
171A172GLU-1-0.934-0.95946.154-6.237-6.2370.0000.0000.0000.000
172A173ALA00.000-0.01145.008-0.114-0.1140.0000.0000.0000.000
173A174LEU0-0.010-0.00540.901-0.139-0.1390.0000.0000.0000.000
174A175GLN00.011-0.00141.378-0.087-0.0870.0000.0000.0000.000
175A176ILE0-0.027-0.00942.166-0.098-0.0980.0000.0000.0000.000
176A177MET0-0.027-0.00936.971-0.077-0.0770.0000.0000.0000.000
177A178ASP-1-0.912-0.94137.234-8.299-8.2990.0000.0000.0000.000
178A179SER0-0.109-0.06238.2710.0080.0080.0000.0000.0000.000
179A180ASP-1-0.851-0.93536.801-8.124-8.1240.0000.0000.0000.000
180A181ASP-1-0.837-0.91031.484-9.330-9.3300.0000.0000.0000.000
181A182GLY00.0410.02132.821-0.233-0.2330.0000.0000.0000.000
182A183GLU-1-0.968-0.98733.627-8.899-8.8990.0000.0000.0000.000
183A184GLN0-0.018-0.02235.6160.2870.2870.0000.0000.0000.000
184A185ALA00.0020.00538.2740.1650.1650.0000.0000.0000.000
185A186PHE0-0.008-0.01233.8360.0600.0600.0000.0000.0000.000
186A187LEU00.029-0.00536.4780.1080.1080.0000.0000.0000.000
187A188HIS00.0020.00939.1600.0820.0820.0000.0000.0000.000
188A189GLY00.0280.02040.9040.1600.1600.0000.0000.0000.000
189A190LEU0-0.018-0.00136.6360.0760.0760.0000.0000.0000.000
190A191GLU-1-0.782-0.86040.104-7.170-7.1700.0000.0000.0000.000
191A192SER0-0.044-0.02643.4180.2050.2050.0000.0000.0000.000
192A193LEU0-0.044-0.00739.3790.1190.1190.0000.0000.0000.000
193A194ILE0-0.019-0.00839.6410.0830.0830.0000.0000.0000.000
194A195ARG10.8520.91243.7406.3106.3100.0000.0000.0000.000
195A196GLY00.0390.01746.6390.1470.1470.0000.0000.0000.000
196A197PHE00.003-0.00940.9260.0760.0760.0000.0000.0000.000
197A198GLU-1-0.805-0.87946.695-6.235-6.2350.0000.0000.0000.000
198A199VAL0-0.0130.01649.0870.1210.1210.0000.0000.0000.000
199A200GLN00.0100.01049.0270.1090.1090.0000.0000.0000.000
200A201LEU0-0.052-0.02247.9490.0770.0770.0000.0000.0000.000
201A202THR0-0.068-0.06450.8360.1200.1200.0000.0000.0000.000
202A203ALA00.0280.03354.1010.1130.1130.0000.0000.0000.000
203A204LEU0-0.029-0.02154.4420.1370.1370.0000.0000.0000.000
204A205LEU0-0.042-0.02256.138-0.031-0.0310.0000.0000.0000.000
205A206GLN0-0.061-0.02458.9780.1280.1280.0000.0000.0000.000
206A207ILE0-0.044-0.02558.677-0.069-0.0690.0000.0000.0000.000
207A208VAL-1-0.931-0.95255.005-5.490-5.4900.0000.0000.0000.000