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: RM348

Calculation Name: 1COT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1COT

Chain ID: A

ChEMBL ID:

UniProt ID: P00096

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 121
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -960102.529615
FMO2-HF: Nuclear repulsion 913244.702893
FMO2-HF: Total energy -46857.826721
FMO2-MP2: Total energy -46991.890593


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
-13.627-11.603-0.027-0.823-1.1740
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.062
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].
3A4ASP-1-0.803-0.8793.82811.26213.236-0.026-0.784-1.1640.000
108A109ALA00.0410.0134.1960.1450.195-0.001-0.039-0.0100.000
4A5ALA00.1040.0486.310-2.141-2.1410.0000.0000.0000.000
5A6ALA00.0420.0259.373-0.745-0.7450.0000.0000.0000.000
6A7LYS10.7580.8556.593-10.462-10.4620.0000.0000.0000.000
7A8GLY00.0220.00310.364-0.693-0.6930.0000.0000.0000.000
8A9GLU-1-0.883-0.93611.7350.5040.5040.0000.0000.0000.000
9A10LYS10.8760.93513.845-2.780-2.7800.0000.0000.0000.000
10A11GLU-1-0.811-0.88212.2780.1940.1940.0000.0000.0000.000
11A12PHE00.0760.03115.352-0.198-0.1980.0000.0000.0000.000
12A13ASN0-0.059-0.03517.036-0.105-0.1050.0000.0000.0000.000
13A14LYS10.8130.89516.610-0.141-0.1410.0000.0000.0000.000
14A15CYS00.0120.02216.261-0.068-0.0680.0000.0000.0000.000
15A16LYS10.9430.98019.810-0.163-0.1630.0000.0000.0000.000
16A17ALA0-0.0040.00322.4170.0510.0510.0000.0000.0000.000
17A18CYS0-0.068-0.04023.3510.0160.0160.0000.0000.0000.000
18A19HIS0-0.046-0.02220.948-0.066-0.0660.0000.0000.0000.000
19A20MET00.0010.00323.0050.1100.1100.0000.0000.0000.000
20A21ILE00.0060.01117.033-0.146-0.1460.0000.0000.0000.000
21A22GLN0-0.048-0.04221.2840.1080.1080.0000.0000.0000.000
22A23ALA00.0690.04923.375-0.110-0.1100.0000.0000.0000.000
23A24PRO00.004-0.01823.7180.0270.0270.0000.0000.0000.000
24A25ASP-1-0.828-0.87726.839-0.198-0.1980.0000.0000.0000.000
25A26GLY0-0.021-0.00128.3510.0350.0350.0000.0000.0000.000
26A27THR0-0.082-0.06825.4610.0590.0590.0000.0000.0000.000
27A28ASP-1-0.869-0.92725.604-0.232-0.2320.0000.0000.0000.000
28A29ILE0-0.0070.00819.5540.0800.0800.0000.0000.0000.000
29A30ILE0-0.041-0.02418.8870.1120.1120.0000.0000.0000.000
30A31LYS10.8840.93622.231-0.024-0.0240.0000.0000.0000.000
31A32GLY00.002-0.01324.7000.0480.0480.0000.0000.0000.000
32A33GLY0-0.042-0.00525.6570.0110.0110.0000.0000.0000.000
33A34LYS10.9530.96626.2310.3650.3650.0000.0000.0000.000
34A35THR0-0.028-0.00826.8880.0140.0140.0000.0000.0000.000
35A36GLY0-0.018-0.01423.973-0.042-0.0420.0000.0000.0000.000
36A37PRO0-0.053-0.01622.2830.0610.0610.0000.0000.0000.000
37A38ASN00.0420.01622.505-0.045-0.0450.0000.0000.0000.000
38A39LEU0-0.034-0.02017.161-0.126-0.1260.0000.0000.0000.000
39A40TYR00.0530.02617.519-0.131-0.1310.0000.0000.0000.000
40A41GLY00.008-0.00217.615-0.024-0.0240.0000.0000.0000.000
41A42VAL0-0.040-0.01414.786-0.053-0.0530.0000.0000.0000.000
42A43VAL0-0.010-0.01510.877-0.225-0.2250.0000.0000.0000.000
43A44GLY00.0640.03713.9170.2790.2790.0000.0000.0000.000
44A45ARG10.8090.91016.0571.6011.6010.0000.0000.0000.000
45A46LYS10.8940.96018.6321.2111.2110.0000.0000.0000.000
46A47ILE00.0020.01418.0440.0800.0800.0000.0000.0000.000
47A48ALA0-0.057-0.04421.4370.1380.1380.0000.0000.0000.000
48A49SER0-0.017-0.02422.6120.1200.1200.0000.0000.0000.000
49A50GLU-1-0.854-0.92324.364-0.847-0.8470.0000.0000.0000.000
50A51GLU-1-0.878-0.94226.158-0.571-0.5710.0000.0000.0000.000
51A52GLY0-0.009-0.00529.8130.0310.0310.0000.0000.0000.000
52A53PHE0-0.043-0.01826.8750.0280.0280.0000.0000.0000.000
53A54LYS10.9410.97729.6140.4980.4980.0000.0000.0000.000
54A55TYR00.0830.04923.2170.0190.0190.0000.0000.0000.000
55A56GLY0-0.035-0.01727.6080.0750.0750.0000.0000.0000.000
56A57GLU-1-0.872-0.95128.437-0.843-0.8430.0000.0000.0000.000
57A58GLY00.0070.01427.565-0.028-0.0280.0000.0000.0000.000
58A59ILE0-0.005-0.00721.072-0.063-0.0630.0000.0000.0000.000
59A60LEU0-0.005-0.00125.186-0.063-0.0630.0000.0000.0000.000
60A61GLU-1-0.796-0.89327.906-1.072-1.0720.0000.0000.0000.000
61A62VAL0-0.037-0.00921.496-0.033-0.0330.0000.0000.0000.000
62A63ALA0-0.0010.00124.386-0.067-0.0670.0000.0000.0000.000
63A64GLU-1-0.974-0.98125.288-0.894-0.8940.0000.0000.0000.000
64A65LYS10.8250.88326.9311.1401.1400.0000.0000.0000.000
65A66ASN0-0.059-0.02222.827-0.083-0.0830.0000.0000.0000.000
66A67PRO0-0.024-0.01124.142-0.061-0.0610.0000.0000.0000.000
67A68ASP-1-0.919-0.97423.128-1.693-1.6930.0000.0000.0000.000
68A69LEU0-0.0090.01517.492-0.104-0.1040.0000.0000.0000.000
69A70THR0-0.020-0.01817.2810.0710.0710.0000.0000.0000.000
70A71TRP0-0.018-0.01114.345-0.287-0.2870.0000.0000.0000.000
71A72THR00.0380.01011.108-0.498-0.4980.0000.0000.0000.000
72A73GLU-1-0.868-0.9606.494-10.232-10.2320.0000.0000.0000.000
73A74ALA0-0.026-0.0128.564-0.518-0.5180.0000.0000.0000.000
74A75ASP-1-0.806-0.8849.285-3.633-3.6330.0000.0000.0000.000
75A76LEU0-0.0070.00110.9070.5320.5320.0000.0000.0000.000
76A77ILE0-0.005-0.0075.8460.4540.4540.0000.0000.0000.000
77A78GLU-1-0.836-0.89310.392-2.695-2.6950.0000.0000.0000.000
78A79TYR00.0150.00213.1330.6740.6740.0000.0000.0000.000
79A80VAL0-0.033-0.03212.6100.4670.4670.0000.0000.0000.000
80A81THR0-0.044-0.01312.7550.3450.3450.0000.0000.0000.000
81A82ASP-1-0.873-0.97415.151-0.987-0.9870.0000.0000.0000.000
82A83PRO00.0400.03618.777-0.072-0.0720.0000.0000.0000.000
83A84LYS10.7960.91020.4831.0621.0620.0000.0000.0000.000
84A85PRO0-0.021-0.01719.8790.0480.0480.0000.0000.0000.000
85A86TRP00.0600.03415.8540.1950.1950.0000.0000.0000.000
86A87LEU00.0230.00220.0530.0190.0190.0000.0000.0000.000
87A88VAL0-0.057-0.00223.2530.0690.0690.0000.0000.0000.000
88A89LYS10.8150.88916.6583.0723.0720.0000.0000.0000.000
89A90MET0-0.0070.00519.973-0.045-0.0450.0000.0000.0000.000
90A91THR0-0.037-0.03623.0540.0970.0970.0000.0000.0000.000
91A92ASP-1-0.903-0.93926.602-1.191-1.1910.0000.0000.0000.000
92A93ASP-1-0.838-0.90928.508-0.813-0.8130.0000.0000.0000.000
93A94LYS10.9500.96328.8510.7240.7240.0000.0000.0000.000
94A95GLY0-0.046-0.03630.1240.0060.0060.0000.0000.0000.000
95A96ALA00.0190.03227.2440.0280.0280.0000.0000.0000.000
96A97LYS10.9330.95828.1080.6850.6850.0000.0000.0000.000
97A98THR00.0600.02523.756-0.043-0.0430.0000.0000.0000.000
98A99LYS10.8540.90225.9140.8210.8210.0000.0000.0000.000
99A100MET0-0.0210.02018.0080.0870.0870.0000.0000.0000.000
100A101THR00.0360.00523.525-0.088-0.0880.0000.0000.0000.000
101A102PHE0-0.014-0.01018.2360.0510.0510.0000.0000.0000.000
102A103LYS10.9100.96318.7480.9170.9170.0000.0000.0000.000
103A104MET0-0.064-0.01213.0440.1340.1340.0000.0000.0000.000
104A105GLY00.0310.00814.113-0.381-0.3810.0000.0000.0000.000
105A106LYS10.9210.96311.832-0.334-0.3340.0000.0000.0000.000
106A107ASN0-0.027-0.0389.3420.0590.0590.0000.0000.0000.000
107A108GLN00.0730.0289.146-0.006-0.0060.0000.0000.0000.000
109A110ASP-1-0.846-0.9136.2793.2183.2180.0000.0000.0000.000
110A111VAL0-0.019-0.0267.9880.3510.3510.0000.0000.0000.000
111A112VAL0-0.043-0.0047.8200.5400.5400.0000.0000.0000.000
112A113ALA00.0870.0545.7740.3790.3790.0000.0000.0000.000
113A114PHE0-0.042-0.0277.6891.1811.1810.0000.0000.0000.000
114A115LEU0-0.017-0.00111.1930.3450.3450.0000.0000.0000.000
115A116ALA00.0330.0309.0110.3410.3410.0000.0000.0000.000
116A117GLN0-0.041-0.01910.9990.8630.8630.0000.0000.0000.000
117A118ASN0-0.079-0.04612.5470.3850.3850.0000.0000.0000.000
118A119SER0-0.022-0.03413.7990.0040.0040.0000.0000.0000.000
119A120PRO0-0.024-0.00615.032-0.195-0.1950.0000.0000.0000.000
120A121ASP-1-0.950-0.97216.852-0.701-0.7010.0000.0000.0000.000
121A122ALA-1-0.977-0.97014.246-2.214-2.2140.0000.0000.0000.000