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: QLKVY

Calculation Name: 2EHD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cobalt (ii) ion

Ligand 3-letter code: CO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EHD

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SK86

Base Structure: X-ray

Registration Date: 2025-10-05

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2190899.124032
FMO2-HF: Nuclear repulsion 2114794.819976
FMO2-HF: Total energy -76104.304056
FMO2-MP2: Total energy -76326.125211


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:4:MET)


Summations of interaction energy for fragment #1(A:4:MET)
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.
-91.855-88.3940.331-1.429-2.361-0.006
Interaction energy analysis for fragmet #1(A:4:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.856 / q_NPA : 0.910
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].
3A6GLY00.0830.0353.8774.7496.662-0.019-0.883-1.011-0.002
4A7ALA0-0.0050.0265.370-0.823-0.750-0.001-0.004-0.0670.000
27A30TYR0-0.117-0.0814.185-12.634-12.570-0.001-0.039-0.0230.000
28A31ARG10.8190.9243.74545.48846.6870.352-0.441-1.110-0.004
75A78GLU-1-0.863-0.9434.151-41.741-41.5290.000-0.062-0.1500.000
5A8VAL00.0120.0187.7701.7911.7910.0000.0000.0000.000
6A9LEU00.0390.03410.9460.4560.4560.0000.0000.0000.000
7A10ILE00.0170.00713.7920.4170.4170.0000.0000.0000.000
8A11THR00.0590.03817.0540.5600.5600.0000.0000.0000.000
9A12GLY0-0.001-0.00420.8430.1810.1810.0000.0000.0000.000
10A13ALA0-0.014-0.01018.6090.2330.2330.0000.0000.0000.000
11A14SER00.0480.02720.498-0.210-0.2100.0000.0000.0000.000
12A15ARG10.9360.97123.00211.53411.5340.0000.0000.0000.000
13A16GLY00.0060.01724.234-0.101-0.1010.0000.0000.0000.000
14A17ILE00.0520.02721.777-0.419-0.4190.0000.0000.0000.000
15A18GLY00.0370.03620.154-0.791-0.7910.0000.0000.0000.000
16A19GLU-1-0.804-0.88618.864-14.041-14.0410.0000.0000.0000.000
17A20ALA00.0110.00318.617-0.762-0.7620.0000.0000.0000.000
18A21THR0-0.009-0.03215.624-0.880-0.8800.0000.0000.0000.000
19A22ALA0-0.014-0.00814.696-1.498-1.4980.0000.0000.0000.000
20A23ARG10.7830.83913.70113.65913.6590.0000.0000.0000.000
21A24LEU0-0.037-0.00813.997-1.110-1.1100.0000.0000.0000.000
22A25LEU00.001-0.01510.697-1.591-1.5910.0000.0000.0000.000
23A26HIS0-0.010-0.0019.234-3.353-3.3530.0000.0000.0000.000
24A27ALA00.0300.0179.221-2.597-2.5970.0000.0000.0000.000
25A28LYS10.8720.9489.21522.58122.5810.0000.0000.0000.000
26A29GLY00.0250.0105.300-3.699-3.6990.0000.0000.0000.000
29A32VAL00.0280.0027.7301.1211.1210.0000.0000.0000.000
30A33GLY00.0710.02211.2720.7930.7930.0000.0000.0000.000
31A34LEU0-0.033-0.02914.2080.5370.5370.0000.0000.0000.000
32A35MET00.0450.03217.5020.5610.5610.0000.0000.0000.000
33A36ALA0-0.067-0.04820.4150.2260.2260.0000.0000.0000.000
34A37ARG10.9730.99423.73110.04110.0410.0000.0000.0000.000
35A38ASP-1-0.927-0.95627.098-10.541-10.5410.0000.0000.0000.000
36A39GLU-1-0.841-0.94026.122-11.362-11.3620.0000.0000.0000.000
37A40LYS10.9520.99426.0929.3649.3640.0000.0000.0000.000
38A41ARG10.8120.87525.37211.52911.5290.0000.0000.0000.000
39A42LEU0-0.0140.00719.966-0.422-0.4220.0000.0000.0000.000
40A43GLN0-0.003-0.00721.634-0.402-0.4020.0000.0000.0000.000
41A44ALA0-0.028-0.00722.765-0.265-0.2650.0000.0000.0000.000
42A45LEU00.0030.00018.326-0.282-0.2820.0000.0000.0000.000
43A46ALA0-0.012-0.01717.818-0.862-0.8620.0000.0000.0000.000
44A47ALA0-0.0110.00718.082-0.526-0.5260.0000.0000.0000.000
45A48GLU-1-0.828-0.86018.267-15.537-15.5370.0000.0000.0000.000
46A49LEU0-0.059-0.03014.002-0.758-0.7580.0000.0000.0000.000
47A50GLU-1-0.887-0.94314.208-18.292-18.2920.0000.0000.0000.000
48A51GLY0-0.012-0.00411.312-1.856-1.8560.0000.0000.0000.000
49A52ALA0-0.060-0.02111.373-1.651-1.6510.0000.0000.0000.000
50A53LEU00.0170.00812.9781.1161.1160.0000.0000.0000.000
51A54PRO0-0.021-0.01115.0800.3130.3130.0000.0000.0000.000
52A55LEU0-0.017-0.01116.3790.2770.2770.0000.0000.0000.000
53A56PRO00.0180.00420.3060.1950.1950.0000.0000.0000.000
54A57GLY00.0470.02224.0350.0800.0800.0000.0000.0000.000
55A58ASP-1-0.857-0.91625.936-10.177-10.1770.0000.0000.0000.000
56A59VAL0-0.0080.00523.996-0.128-0.1280.0000.0000.0000.000
57A60ARG10.8430.89126.1339.5199.5190.0000.0000.0000.000
58A61GLU-1-0.915-0.94328.177-9.593-9.5930.0000.0000.0000.000
59A62GLU-1-0.845-0.91126.081-11.279-11.2790.0000.0000.0000.000
60A63GLY00.008-0.00325.144-0.343-0.3430.0000.0000.0000.000
61A64ASP-1-0.772-0.88124.583-11.790-11.7900.0000.0000.0000.000
62A65TRP0-0.032-0.00219.336-1.059-1.0590.0000.0000.0000.000
63A66ALA00.0070.01220.291-0.700-0.7000.0000.0000.0000.000
64A67ARG10.8500.90920.01311.00411.0040.0000.0000.0000.000
65A68ALA00.0040.00418.823-0.602-0.6020.0000.0000.0000.000
66A69VAL0-0.015-0.01514.851-1.123-1.1230.0000.0000.0000.000
67A70ALA00.0120.01114.813-0.995-0.9950.0000.0000.0000.000
68A71ALA00.0530.02315.305-0.695-0.6950.0000.0000.0000.000
69A72MET0-0.058-0.00411.044-0.992-0.9920.0000.0000.0000.000
70A73GLU-1-0.807-0.87610.532-20.383-20.3830.0000.0000.0000.000
71A74GLU-1-0.989-0.98310.940-17.137-17.1370.0000.0000.0000.000
72A75ALA0-0.023-0.00212.064-0.585-0.5850.0000.0000.0000.000
73A76PHE0-0.032-0.0447.459-2.748-2.7480.0000.0000.0000.000
74A77GLY00.0170.0186.491-3.990-3.9900.0000.0000.0000.000
76A79LEU0-0.0050.0007.830-0.196-0.1960.0000.0000.0000.000
77A80SER0-0.085-0.0537.130-0.880-0.8800.0000.0000.0000.000
78A81ALA00.020-0.0129.1831.0871.0870.0000.0000.0000.000
79A82LEU0-0.0160.01012.592-0.215-0.2150.0000.0000.0000.000
80A83VAL0-0.0120.00015.1450.3080.3080.0000.0000.0000.000
81A84ASN00.008-0.00317.7360.2620.2620.0000.0000.0000.000
82A85ASN0-0.015-0.03021.1330.5480.5480.0000.0000.0000.000
83A86ALA0-0.054-0.01222.7690.5380.5380.0000.0000.0000.000
84A87GLY00.0480.01625.2730.2210.2210.0000.0000.0000.000
85A88VAL0-0.078-0.03528.695-0.005-0.0050.0000.0000.0000.000
86A89GLY00.0500.00532.148-0.003-0.0030.0000.0000.0000.000
87A90VAL00.0000.00835.6540.0240.0240.0000.0000.0000.000
88A91MET0-0.019-0.00736.7070.0240.0240.0000.0000.0000.000
89A92LYS10.9040.93341.5037.2037.2030.0000.0000.0000.000
90A93PRO0-0.008-0.00444.885-0.107-0.1070.0000.0000.0000.000
91A94VAL00.0280.00645.133-0.029-0.0290.0000.0000.0000.000
92A95HIS0-0.001-0.00146.858-0.108-0.1080.0000.0000.0000.000
93A96GLU-1-0.930-0.97348.582-6.242-6.2420.0000.0000.0000.000
94A97LEU0-0.093-0.02442.036-0.082-0.0820.0000.0000.0000.000
95A98THR00.022-0.00944.4710.0480.0480.0000.0000.0000.000
96A99LEU00.007-0.01442.543-0.169-0.1690.0000.0000.0000.000
97A100GLU-1-0.922-0.95540.732-7.747-7.7470.0000.0000.0000.000
98A101GLU-1-0.754-0.84339.615-7.518-7.5180.0000.0000.0000.000
99A102TRP00.012-0.00138.835-0.218-0.2180.0000.0000.0000.000
100A103ARG10.9770.98737.5487.4987.4980.0000.0000.0000.000
101A104LEU00.0110.02334.212-0.290-0.2900.0000.0000.0000.000
102A105VAL0-0.0210.00633.885-0.351-0.3510.0000.0000.0000.000
103A106LEU0-0.018-0.01833.162-0.335-0.3350.0000.0000.0000.000
104A107ASP-1-0.841-0.92132.590-9.280-9.2800.0000.0000.0000.000
105A108THR0-0.082-0.06029.003-0.410-0.4100.0000.0000.0000.000
106A109ASN0-0.044-0.02928.262-0.606-0.6060.0000.0000.0000.000
107A110LEU0-0.042-0.00428.636-0.251-0.2510.0000.0000.0000.000
108A111THR0-0.004-0.01328.974-0.264-0.2640.0000.0000.0000.000
109A112GLY00.0550.02327.205-0.205-0.2050.0000.0000.0000.000
110A113ALA00.0000.00724.428-0.490-0.4900.0000.0000.0000.000
111A114PHE00.008-0.00524.161-0.446-0.4460.0000.0000.0000.000
112A115LEU0-0.026-0.00924.664-0.296-0.2960.0000.0000.0000.000
113A116GLY00.0670.00621.267-0.354-0.3540.0000.0000.0000.000
114A117ILE0-0.026-0.02519.997-0.693-0.6930.0000.0000.0000.000
115A118ARG10.8880.95620.38910.71610.7160.0000.0000.0000.000
116A119HIS0-0.067-0.05619.877-0.323-0.3230.0000.0000.0000.000
117A120ALA00.0400.02015.951-0.570-0.5700.0000.0000.0000.000
118A121VAL00.0130.01215.436-0.885-0.8850.0000.0000.0000.000
119A122PRO0-0.015-0.01816.003-0.552-0.5520.0000.0000.0000.000
120A123ALA00.0190.02212.532-0.149-0.1490.0000.0000.0000.000
121A124LEU0-0.047-0.01911.598-1.211-1.2110.0000.0000.0000.000
122A125LEU0-0.014-0.00711.937-0.695-0.6950.0000.0000.0000.000
123A126ARG10.7850.86411.81916.93916.9390.0000.0000.0000.000
124A127ARG10.8240.9225.68630.36030.3600.0000.0000.0000.000
125A128GLY00.0000.0108.990-1.232-1.2320.0000.0000.0000.000
126A129GLY00.0410.01811.6660.5890.5890.0000.0000.0000.000
127A130GLY0-0.014-0.00710.671-2.237-2.2370.0000.0000.0000.000
128A131THR0-0.047-0.01212.3621.2691.2690.0000.0000.0000.000
129A132ILE00.0160.01814.736-0.688-0.6880.0000.0000.0000.000
130A133VAL00.0120.00916.3150.6560.6560.0000.0000.0000.000
131A134ASN0-0.018-0.01519.037-0.080-0.0800.0000.0000.0000.000
132A135VAL00.0110.01521.8500.1780.1780.0000.0000.0000.000
133A136GLY00.0560.01824.2060.4490.4490.0000.0000.0000.000
134A137SER0-0.067-0.04127.8280.0100.0100.0000.0000.0000.000
135A138LEU00.015-0.01127.691-0.057-0.0570.0000.0000.0000.000
136A139ALA0-0.018-0.00431.3550.1440.1440.0000.0000.0000.000
137A140GLY00.0920.07033.2620.2650.2650.0000.0000.0000.000
138A141LYS10.8470.90732.3869.4109.4100.0000.0000.0000.000
139A142ASN00.0150.02835.8910.1910.1910.0000.0000.0000.000
140A143PRO0-0.0090.00539.070-0.119-0.1190.0000.0000.0000.000
141A144PHE00.0340.01137.1870.1230.1230.0000.0000.0000.000
142A145LYS10.9630.97342.6936.6326.6320.0000.0000.0000.000
143A146GLY00.0170.01043.792-0.085-0.0850.0000.0000.0000.000
144A147GLY00.0550.02040.098-0.099-0.0990.0000.0000.0000.000
145A148ALA0-0.0080.01139.501-0.192-0.1920.0000.0000.0000.000
146A149ALA00.0690.03238.546-0.093-0.0930.0000.0000.0000.000
147A150TYR00.0290.02431.010-0.224-0.2240.0000.0000.0000.000
148A151ASN0-0.020-0.01935.055-0.073-0.0730.0000.0000.0000.000
149A152ALA00.0430.02236.218-0.171-0.1710.0000.0000.0000.000
150A153SER0-0.018-0.00932.748-0.243-0.2430.0000.0000.0000.000
151A154LYS10.8860.92927.63711.03311.0330.0000.0000.0000.000
152A155PHE0-0.041-0.02032.169-0.193-0.1930.0000.0000.0000.000
153A156GLY00.0360.01633.563-0.093-0.0930.0000.0000.0000.000
154A157LEU0-0.017-0.01226.075-0.115-0.1150.0000.0000.0000.000
155A158LEU00.0210.01028.688-0.326-0.3260.0000.0000.0000.000
156A159GLY0-0.0080.01130.282-0.066-0.0660.0000.0000.0000.000
157A160LEU0-0.020-0.00826.519-0.055-0.0550.0000.0000.0000.000
158A161ALA0-0.003-0.00425.672-0.227-0.2270.0000.0000.0000.000
159A162GLY00.0130.00326.019-0.307-0.3070.0000.0000.0000.000
160A163ALA0-0.015-0.00228.305-0.009-0.0090.0000.0000.0000.000
161A164ALA00.0680.03223.540-0.176-0.1760.0000.0000.0000.000
162A165MET0-0.058-0.02723.166-0.434-0.4340.0000.0000.0000.000
163A166LEU0-0.076-0.04524.026-0.155-0.1550.0000.0000.0000.000
164A167ASP-1-0.917-0.95724.938-10.928-10.9280.0000.0000.0000.000
165A168LEU0-0.031-0.02619.875-0.199-0.1990.0000.0000.0000.000
166A169ARG10.9530.98919.85411.17311.1730.0000.0000.0000.000
167A170GLU-1-0.957-0.97520.243-11.887-11.8870.0000.0000.0000.000
168A171ALA0-0.016-0.00418.494-0.249-0.2490.0000.0000.0000.000
169A172ASN0-0.011-0.00812.731-0.713-0.7130.0000.0000.0000.000
170A173VAL00.0030.00414.821-1.407-1.4070.0000.0000.0000.000
171A174ARG10.8660.93011.60721.75421.7540.0000.0000.0000.000
172A175VAL0-0.0080.00517.975-0.604-0.6040.0000.0000.0000.000
173A176VAL0-0.004-0.01518.6260.4240.4240.0000.0000.0000.000
174A177ASN0-0.011-0.01021.408-0.636-0.6360.0000.0000.0000.000
175A178VAL00.0190.00320.553-0.107-0.1070.0000.0000.0000.000
176A179LEU00.0170.00523.8750.1810.1810.0000.0000.0000.000
177A180PRO0-0.052-0.04126.489-0.008-0.0080.0000.0000.0000.000
178A181GLY-1-0.876-0.92628.124-9.725-9.7250.0000.0000.0000.000
179A198LEU10.8440.91929.08310.65610.6560.0000.0000.0000.000
180A199LYS10.9500.98226.43710.89710.8970.0000.0000.0000.000
181A200PRO00.001-0.00523.997-0.200-0.2000.0000.0000.0000.000
182A201GLU-1-0.826-0.93421.474-13.569-13.5690.0000.0000.0000.000
183A202ASP-1-0.849-0.92121.294-12.577-12.5770.0000.0000.0000.000
184A203VAL00.002-0.00522.476-0.348-0.3480.0000.0000.0000.000
185A204ALA00.0070.01718.115-0.532-0.5320.0000.0000.0000.000
186A205GLN0-0.016-0.02017.309-1.526-1.5260.0000.0000.0000.000
187A206ALA00.0090.01618.129-0.651-0.6510.0000.0000.0000.000
188A207VAL00.0120.00315.824-0.319-0.3190.0000.0000.0000.000
189A208LEU0-0.0080.00011.819-1.004-1.0040.0000.0000.0000.000
190A209PHE0-0.023-0.02314.419-0.941-0.9410.0000.0000.0000.000
191A210ALA00.0250.00716.671-0.242-0.2420.0000.0000.0000.000
192A211LEU0-0.049-0.02611.727-0.085-0.0850.0000.0000.0000.000
193A212GLU-1-0.848-0.8999.701-32.022-32.0220.0000.0000.0000.000
194A213MET0-0.048-0.01512.7640.3330.3330.0000.0000.0000.000
195A214PRO0-0.0160.00715.6910.4000.4000.0000.0000.0000.000
196A215GLY00.0360.03413.3890.1630.1630.0000.0000.0000.000
197A216HIS0-0.042-0.05014.2500.1250.1250.0000.0000.0000.000
198A217ALA0-0.038-0.03116.9410.8570.8570.0000.0000.0000.000
199A218MET00.0200.01818.8400.7860.7860.0000.0000.0000.000
200A219VAL0-0.029-0.00620.4790.5640.5640.0000.0000.0000.000
201A220SER00.0360.00820.982-0.580-0.5800.0000.0000.0000.000
202A221GLU-1-0.892-0.94023.427-11.133-11.1330.0000.0000.0000.000
203A222ILE0-0.021-0.00420.560-0.069-0.0690.0000.0000.0000.000
204A223GLU-1-0.933-0.95724.992-10.100-10.1000.0000.0000.0000.000
205A224LEU0-0.068-0.02924.177-0.267-0.2670.0000.0000.0000.000
206A225ARG10.9360.96728.27410.55210.5520.0000.0000.0000.000
207A226PRO-1-0.855-0.92930.882-9.893-9.8930.0000.0000.0000.000