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: 2RJKR

Calculation Name: 3CI4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cob(ii)inamide | adenosine-5'-triphosphate | magnesium ion | potassium ion

Ligand 3-letter code: CBY | ATP | MG | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3CI4

Chain ID: A

ChEMBL ID:

UniProt ID: Q50EJ2

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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2054368.055584
FMO2-HF: Nuclear repulsion 1979233.241178
FMO2-HF: Total energy -75134.814406
FMO2-MP2: Total energy -75357.48436


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:VAL)


Summations of interaction energy for fragment #1(A:1:VAL)
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.
-38.539-36.4390.02-0.694-1.427-0.002
Interaction energy analysis for fragmet #1(A:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.926
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].
3A3ILE00.0790.0393.3071.6243.6180.021-0.686-1.330-0.002
4A4TYR00.0130.0134.9004.5214.627-0.001-0.008-0.0970.000
5A5THR00.028-0.0027.532-0.160-0.1600.0000.0000.0000.000
6A6LYS10.9860.9999.59324.21524.2150.0000.0000.0000.000
7A7ASN0-0.013-0.00511.8682.3682.3680.0000.0000.0000.000
8A8GLY00.0370.02514.2701.0731.0730.0000.0000.0000.000
9A9ASP-1-0.921-0.96015.200-19.054-19.0540.0000.0000.0000.000
10A10LYS10.8590.92717.56014.38514.3850.0000.0000.0000.000
11A11GLY00.0350.01419.9300.5680.5680.0000.0000.0000.000
12A12GLN00.0220.02320.3010.1630.1630.0000.0000.0000.000
13A13THR0-0.011-0.02216.258-1.434-1.4340.0000.0000.0000.000
14A14ARG10.7890.88614.83516.36116.3610.0000.0000.0000.000
15A15ILE00.0230.03717.132-0.282-0.2820.0000.0000.0000.000
16A16ILE0-0.0060.00217.165-0.789-0.7890.0000.0000.0000.000
17A17GLY00.0600.03818.8220.6260.6260.0000.0000.0000.000
18A18LYS0-0.013-0.02419.086-0.939-0.9390.0000.0000.0000.000
19A19GLN00.0290.02921.257-0.327-0.3270.0000.0000.0000.000
20A20ILE0-0.063-0.02219.122-0.715-0.7150.0000.0000.0000.000
21A21LEU00.0590.04321.2600.5140.5140.0000.0000.0000.000
22A22TYR00.009-0.01721.624-0.740-0.7400.0000.0000.0000.000
23A23LYS10.9000.93015.66516.98816.9880.0000.0000.0000.000
24A24ASN0-0.038-0.01421.441-0.252-0.2520.0000.0000.0000.000
25A25ASP-1-0.843-0.91324.225-10.792-10.7920.0000.0000.0000.000
26A26PRO00.0770.03825.154-0.381-0.3810.0000.0000.0000.000
27A27ARG10.8990.95223.51311.06111.0610.0000.0000.0000.000
28A28VAL0-0.039-0.02719.485-0.374-0.3740.0000.0000.0000.000
29A29ALA0-0.024-0.00621.568-0.324-0.3240.0000.0000.0000.000
30A30ALA00.000-0.00223.976-0.065-0.0650.0000.0000.0000.000
31A31TYR00.0250.01017.3300.0840.0840.0000.0000.0000.000
32A32GLY00.0110.01219.740-0.429-0.4290.0000.0000.0000.000
33A33GLU-1-0.834-0.92320.774-11.002-11.0020.0000.0000.0000.000
34A34VAL0-0.015-0.00821.5780.2120.2120.0000.0000.0000.000
35A35ASP-1-0.914-0.94616.477-16.374-16.3740.0000.0000.0000.000
36A36GLU-1-0.823-0.86419.790-11.863-11.8630.0000.0000.0000.000
37A37LEU0-0.020-0.01321.7050.1660.1660.0000.0000.0000.000
38A38ASN00.0250.01218.4450.4970.4970.0000.0000.0000.000
39A39SER0-0.011-0.01518.491-0.254-0.2540.0000.0000.0000.000
40A40TRP0-0.040-0.03220.2610.0900.0900.0000.0000.0000.000
41A41VAL0-0.0120.00923.6300.4420.4420.0000.0000.0000.000
42A42GLY00.0410.03221.0260.2220.2220.0000.0000.0000.000
43A43TYR0-0.046-0.02222.0770.1440.1440.0000.0000.0000.000
44A44THR0-0.015-0.01824.0500.4710.4710.0000.0000.0000.000
45A45LYS10.8410.90123.61412.02712.0270.0000.0000.0000.000
46A46SER0-0.111-0.07023.4370.1360.1360.0000.0000.0000.000
47A47LEU0-0.032-0.01525.4350.2050.2050.0000.0000.0000.000
48A48ILE0-0.060-0.00528.6330.4020.4020.0000.0000.0000.000
49A49ASN0-0.025-0.01930.206-0.059-0.0590.0000.0000.0000.000
50A50SER0-0.028-0.03532.999-0.080-0.0800.0000.0000.0000.000
51A51HIS0-0.0100.00835.630-0.099-0.0990.0000.0000.0000.000
52A52THR00.0690.01334.023-0.036-0.0360.0000.0000.0000.000
53A53GLN0-0.014-0.00130.108-0.394-0.3940.0000.0000.0000.000
54A54VAL00.002-0.00432.248-0.235-0.2350.0000.0000.0000.000
55A55LEU00.0330.02031.832-0.070-0.0700.0000.0000.0000.000
56A56SER0-0.0160.00028.026-0.447-0.4470.0000.0000.0000.000
57A57ASN00.013-0.00726.951-0.599-0.5990.0000.0000.0000.000
58A58GLU-1-0.713-0.79426.913-9.122-9.1220.0000.0000.0000.000
59A59LEU00.0380.01526.430-0.131-0.1310.0000.0000.0000.000
60A60GLU-1-0.864-0.92321.654-12.895-12.8950.0000.0000.0000.000
61A61GLU-1-0.909-0.95522.829-11.441-11.4410.0000.0000.0000.000
62A62ILE0-0.020-0.01624.500-0.187-0.1870.0000.0000.0000.000
63A63GLN0-0.031-0.01819.451-0.031-0.0310.0000.0000.0000.000
64A64GLN0-0.0160.00219.151-0.902-0.9020.0000.0000.0000.000
65A65LEU00.0070.00321.267-0.166-0.1660.0000.0000.0000.000
66A66LEU00.0110.00922.1980.1520.1520.0000.0000.0000.000
67A67PHE00.0000.00114.832-0.355-0.3550.0000.0000.0000.000
68A68ASP-1-0.845-0.90019.467-12.730-12.7300.0000.0000.0000.000
69A69CYS0-0.060-0.03221.9940.3170.3170.0000.0000.0000.000
70A70GLY00.0160.00120.4170.1660.1660.0000.0000.0000.000
71A71HIS0-0.046-0.03418.354-0.587-0.5870.0000.0000.0000.000
72A72ASP-1-0.711-0.83520.385-11.394-11.3940.0000.0000.0000.000
73A73LEU0-0.0130.00323.5140.3040.3040.0000.0000.0000.000
74A74ALA0-0.007-0.00919.3320.1400.1400.0000.0000.0000.000
75A75THR0-0.027-0.02321.399-0.432-0.4320.0000.0000.0000.000
76A76PRO0-0.039-0.01722.8950.4190.4190.0000.0000.0000.000
77A77ALA00.002-0.00526.115-0.066-0.0660.0000.0000.0000.000
78A78ASP-1-0.918-0.95528.844-9.917-9.9170.0000.0000.0000.000
79A79ASP-1-0.853-0.92223.565-12.509-12.5090.0000.0000.0000.000
80A80GLU-1-0.942-0.97526.384-10.351-10.3510.0000.0000.0000.000
81A81ARG10.8910.94717.90014.30614.3060.0000.0000.0000.000
82A82HIS0-0.110-0.05719.285-1.138-1.1380.0000.0000.0000.000
83A83SER00.011-0.00423.2970.5510.5510.0000.0000.0000.000
84A84PHE0-0.041-0.01424.464-0.344-0.3440.0000.0000.0000.000
85A85LYS10.8250.89221.70112.48712.4870.0000.0000.0000.000
86A86PHE0-0.046-0.01825.6220.0830.0830.0000.0000.0000.000
87A87LYS10.8440.91627.0858.6088.6080.0000.0000.0000.000
88A88GLN0-0.003-0.00830.721-0.088-0.0880.0000.0000.0000.000
89A89GLU-1-0.835-0.89832.645-8.032-8.0320.0000.0000.0000.000
90A90GLN00.0200.01431.9750.0970.0970.0000.0000.0000.000
91A91PRO00.0180.01029.4200.0790.0790.0000.0000.0000.000
92A92THR00.001-0.02731.518-0.058-0.0580.0000.0000.0000.000
93A93VAL00.0270.01034.3250.1150.1150.0000.0000.0000.000
94A94TRP0-0.046-0.01329.3230.1280.1280.0000.0000.0000.000
95A95LEU0-0.028-0.01131.1110.0200.0200.0000.0000.0000.000
96A96GLU-1-0.828-0.90134.982-7.548-7.5480.0000.0000.0000.000
97A97GLU-1-0.890-0.93938.030-7.209-7.2090.0000.0000.0000.000
98A98LYS10.8330.91033.1978.6908.6900.0000.0000.0000.000
99A99ILE0-0.028-0.00437.0270.0600.0600.0000.0000.0000.000
100A100ASP-1-0.895-0.92939.759-6.811-6.8110.0000.0000.0000.000
101A101ASN0-0.061-0.03640.4640.0670.0670.0000.0000.0000.000
102A102TYR0-0.064-0.08134.8830.1300.1300.0000.0000.0000.000
103A103THR0-0.052-0.04641.3650.0670.0670.0000.0000.0000.000
104A104GLN0-0.073-0.02544.1800.0770.0770.0000.0000.0000.000
105A105VAL0-0.0060.00543.0440.1320.1320.0000.0000.0000.000
106A106VAL0-0.036-0.00142.8820.0610.0610.0000.0000.0000.000
107A107PRO0-0.007-0.00946.1390.1190.1190.0000.0000.0000.000
108A108ALA00.0580.03548.467-0.104-0.1040.0000.0000.0000.000
109A109VAL0-0.045-0.03047.3180.0800.0800.0000.0000.0000.000
110A110LYS00.0290.01749.982-0.011-0.0110.0000.0000.0000.000
111A111LYS10.8030.88950.7585.5975.5970.0000.0000.0000.000
112A112PHE00.0390.01545.129-0.075-0.0750.0000.0000.0000.000
113A113ILE00.0230.01341.8260.1150.1150.0000.0000.0000.000
114A114LEU0-0.057-0.03743.857-0.087-0.0870.0000.0000.0000.000
115A115PRO0-0.044-0.02538.210-0.033-0.0330.0000.0000.0000.000
116A116GLY00.0190.00238.413-0.158-0.1580.0000.0000.0000.000
117A117GLY00.0000.01539.4930.0900.0900.0000.0000.0000.000
118A118THR00.0770.04037.409-0.142-0.1420.0000.0000.0000.000
119A119GLN0-0.007-0.00531.399-0.292-0.2920.0000.0000.0000.000
120A120LEU00.0690.04230.847-0.150-0.1500.0000.0000.0000.000
121A121ALA00.0440.02733.418-0.144-0.1440.0000.0000.0000.000
122A122SER0-0.057-0.04634.9760.0560.0560.0000.0000.0000.000
123A123ALA00.0210.01629.782-0.060-0.0600.0000.0000.0000.000
124A124LEU00.0400.04330.884-0.235-0.2350.0000.0000.0000.000
125A125HIS00.0480.02632.647-0.070-0.0700.0000.0000.0000.000
126A126VAL0-0.0190.00129.2640.0510.0510.0000.0000.0000.000
127A127ALA00.0530.03728.961-0.102-0.1020.0000.0000.0000.000
128A128ARG10.9050.96429.9178.0218.0210.0000.0000.0000.000
129A129THR0-0.118-0.07232.3020.0930.0930.0000.0000.0000.000
130A130ILE00.0070.00625.9310.0870.0870.0000.0000.0000.000
131A131THR00.019-0.00128.967-0.186-0.1860.0000.0000.0000.000
132A132ARG10.9530.96729.9148.0768.0760.0000.0000.0000.000
133A133ARG10.6400.78725.76311.11411.1140.0000.0000.0000.000
134A134ALA00.0670.02026.7830.0180.0180.0000.0000.0000.000
135A135GLU-1-0.890-0.95228.366-8.517-8.5170.0000.0000.0000.000
136A136ARG10.8850.94131.5888.9198.9190.0000.0000.0000.000
137A137GLN0-0.0150.00926.8980.2520.2520.0000.0000.0000.000
138A138ILE00.0400.01927.313-0.043-0.0430.0000.0000.0000.000
139A139VAL0-0.020-0.01430.0640.1500.1500.0000.0000.0000.000
140A140GLN0-0.044-0.02931.4900.3890.3890.0000.0000.0000.000
141A141LEU00.0310.02126.9370.1020.1020.0000.0000.0000.000
142A142MET0-0.0200.00730.8910.1190.1190.0000.0000.0000.000
143A143ARG10.8400.92433.5708.1438.1430.0000.0000.0000.000
144A144GLU-1-0.981-0.97632.525-9.030-9.0300.0000.0000.0000.000
145A145GLU-1-0.909-0.96129.492-9.700-9.7000.0000.0000.0000.000
146A146GLN0-0.049-0.01932.005-0.005-0.0050.0000.0000.0000.000
147A147ILE00.000-0.00828.917-0.373-0.3730.0000.0000.0000.000
148A148ASN0-0.028-0.02527.9610.6150.6150.0000.0000.0000.000
149A149GLN00.030-0.01130.324-0.058-0.0580.0000.0000.0000.000
150A150ASP-1-0.802-0.89831.268-8.714-8.7140.0000.0000.0000.000
151A151VAL00.0110.00226.7310.0240.0240.0000.0000.0000.000
152A152LEU00.0030.00529.578-0.034-0.0340.0000.0000.0000.000
153A153ILE0-0.041-0.02232.3380.1510.1510.0000.0000.0000.000
154A154PHE00.0280.00627.2830.1240.1240.0000.0000.0000.000
155A155ILE00.003-0.00826.7800.0450.0450.0000.0000.0000.000
156A156ASN0-0.0100.00530.9530.1060.1060.0000.0000.0000.000
157A157ARG10.8630.92034.5487.9577.9570.0000.0000.0000.000
158A158LEU00.0290.02127.8560.0800.0800.0000.0000.0000.000
159A159SER0-0.072-0.03632.4580.0560.0560.0000.0000.0000.000
160A160ASP-1-0.875-0.93834.349-7.637-7.6370.0000.0000.0000.000
161A161TYR0-0.039-0.05031.1470.0400.0400.0000.0000.0000.000
162A162PHE00.016-0.00728.0360.0540.0540.0000.0000.0000.000
163A163PHE0-0.034-0.01934.2380.0700.0700.0000.0000.0000.000
164A164ALA00.0310.01737.9100.1050.1050.0000.0000.0000.000
165A165ALA00.0400.01434.4850.1050.1050.0000.0000.0000.000
166A166ALA0-0.016-0.00536.243-0.008-0.0080.0000.0000.0000.000
167A167ARG10.7780.87037.2456.8966.8960.0000.0000.0000.000
168A168TYR00.0330.01937.3450.1840.1840.0000.0000.0000.000
169A169ALA00.0220.00135.8410.0500.0500.0000.0000.0000.000
170A170ASN0-0.023-0.03237.882-0.069-0.0690.0000.0000.0000.000
171A171TYR00.0040.00140.9870.0850.0850.0000.0000.0000.000
172A172LEU0-0.041-0.01037.7100.1260.1260.0000.0000.0000.000
173A173GLU-1-0.913-0.95537.039-8.097-8.0970.0000.0000.0000.000
174A174GLN0-0.078-0.03041.6000.2150.2150.0000.0000.0000.000
175A175GLN0-0.060-0.01642.2900.0910.0910.0000.0000.0000.000
176A176PRO0-0.014-0.00444.617-0.023-0.0230.0000.0000.0000.000
177A177ASP-1-0.756-0.85843.248-7.134-7.1340.0000.0000.0000.000
178A178MET0-0.010-0.00445.7070.2150.2150.0000.0000.0000.000
179A179LEU00.0360.01546.755-0.099-0.0990.0000.0000.0000.000
180A180TYR0-0.003-0.01047.4780.0430.0430.0000.0000.0000.000
181A181ARG10.9580.96649.2966.0076.0070.0000.0000.0000.000
182A182ASN0-0.021-0.00352.1540.1580.1580.0000.0000.0000.000
183A183SER0-0.041-0.01850.578-0.041-0.0410.0000.0000.0000.000
184A184LYS10.9560.97052.2585.6395.6390.0000.0000.0000.000
185A185ASP-1-0.814-0.88152.665-5.666-5.6660.0000.0000.0000.000
186A186VAL0-0.090-0.05948.7440.0710.0710.0000.0000.0000.000
187A187PHE-1-0.865-0.89945.014-6.153-6.1530.0000.0000.0000.000