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

tag_button

FMODB ID: 64L9Z

Calculation Name: 1JEB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | carbon monoxide | acetyl group

Ligand 3-letter code: HEM | CMO | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JEB

Chain ID: A

ChEMBL ID:

UniProt ID: P02008

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 141
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1258635.683986
FMO2-HF: Nuclear repulsion 1205172.241813
FMO2-HF: Total energy -53463.442173
FMO2-MP2: Total energy -53622.646645


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:SER)


Summations of interaction energy for fragment #1(A:1: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.
3.7975.876-0.007-0.757-1.3150
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / 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].
3A3THR00.024-0.0103.8354.4055.588-0.015-0.444-0.7230.000
127A127LYS10.8360.9013.49451.43952.2030.009-0.290-0.4830.000
131A131VAL0-0.052-0.0264.075-0.702-0.570-0.001-0.023-0.1090.000
4A4LYS10.9870.9826.43822.53622.5360.0000.0000.0000.000
5A5THR00.0630.0329.5640.7540.7540.0000.0000.0000.000
6A6GLU-1-0.697-0.8016.234-46.117-46.1170.0000.0000.0000.000
7A7ARG10.8290.8906.88136.00936.0090.0000.0000.0000.000
8A8THR0-0.050-0.0319.4522.4412.4410.0000.0000.0000.000
9A9ILE00.0530.03912.4541.6191.6190.0000.0000.0000.000
10A10ILE0-0.0120.0068.3111.2771.2770.0000.0000.0000.000
11A11VAL00.021-0.00112.3611.6331.6330.0000.0000.0000.000
12A12SER0-0.033-0.03414.6101.6421.6420.0000.0000.0000.000
13A13MET0-0.032-0.00615.6371.4691.4690.0000.0000.0000.000
14A14TRP00.0420.03915.5170.8890.8890.0000.0000.0000.000
15A15ALA00.0090.02717.4460.8550.8550.0000.0000.0000.000
16A16LYS10.8510.92420.48015.04315.0430.0000.0000.0000.000
17A17ILE00.000-0.00717.0130.5870.5870.0000.0000.0000.000
18A18SER0-0.049-0.04320.7590.8090.8090.0000.0000.0000.000
19A19THR0-0.0050.00122.2100.6470.6470.0000.0000.0000.000
20A20GLN0-0.005-0.01324.4690.2900.2900.0000.0000.0000.000
21A21ALA00.0530.04122.9320.1540.1540.0000.0000.0000.000
22A22ASP-1-0.750-0.85724.007-11.088-11.0880.0000.0000.0000.000
23A23THR0-0.078-0.03026.9760.1520.1520.0000.0000.0000.000
24A24ILE00.0430.03621.0960.0720.0720.0000.0000.0000.000
25A25GLY00.0380.02123.165-0.301-0.3010.0000.0000.0000.000
26A26THR0-0.045-0.04624.0790.1610.1610.0000.0000.0000.000
27A27GLU-1-0.772-0.85825.924-11.829-11.8290.0000.0000.0000.000
28A28THR0-0.014-0.02520.612-0.219-0.2190.0000.0000.0000.000
29A29LEU0-0.020-0.00623.795-0.104-0.1040.0000.0000.0000.000
30A30GLU-1-0.915-0.95925.893-9.826-9.8260.0000.0000.0000.000
31A31ARG10.8420.90124.54412.23312.2330.0000.0000.0000.000
32A32LEU00.0430.02422.1970.0850.0850.0000.0000.0000.000
33A33PHE0-0.018-0.02525.3010.1690.1690.0000.0000.0000.000
34A34LEU0-0.039-0.01628.7030.3920.3920.0000.0000.0000.000
35A35SER0-0.036-0.02726.0230.2590.2590.0000.0000.0000.000
36A36HIS00.0200.00523.260-0.111-0.1110.0000.0000.0000.000
37A37PRO00.0090.01027.088-0.122-0.1220.0000.0000.0000.000
38A38GLN00.004-0.00224.5810.4990.4990.0000.0000.0000.000
39A39THR00.002-0.00424.2270.1430.1430.0000.0000.0000.000
40A40LYS10.9680.98226.9659.4679.4670.0000.0000.0000.000
41A41THR0-0.055-0.02929.4470.1800.1800.0000.0000.0000.000
42A42TYR00.0060.01825.5420.0040.0040.0000.0000.0000.000
43A43PHE0-0.063-0.03325.385-0.161-0.1610.0000.0000.0000.000
44A44PRO00.0270.01731.1480.2200.2200.0000.0000.0000.000
45A45HIS0-0.008-0.00130.7370.4340.4340.0000.0000.0000.000
46A46PHE0-0.052-0.03429.707-0.060-0.0600.0000.0000.0000.000
47A47ASP-1-0.809-0.90034.716-8.348-8.3480.0000.0000.0000.000
48A48LEU0-0.048-0.01831.133-0.331-0.3310.0000.0000.0000.000
49A49HIS0-0.0140.01034.389-0.150-0.1500.0000.0000.0000.000
50A50PRO00.022-0.01034.866-0.164-0.1640.0000.0000.0000.000
51A51GLY0-0.0020.00934.4790.2320.2320.0000.0000.0000.000
52A52SER0-0.027-0.01334.2850.0500.0500.0000.0000.0000.000
53A53ALA00.0430.00933.879-0.286-0.2860.0000.0000.0000.000
54A54GLN0-0.022-0.00833.027-0.082-0.0820.0000.0000.0000.000
55A55LEU00.0190.01429.363-0.415-0.4150.0000.0000.0000.000
56A56ARG10.8740.93329.0029.6769.6760.0000.0000.0000.000
57A57ALA00.004-0.00328.919-0.377-0.3770.0000.0000.0000.000
58A58HIS0-0.007-0.01324.473-0.121-0.1210.0000.0000.0000.000
59A59GLY00.0630.02224.935-0.570-0.5700.0000.0000.0000.000
60A60SER0-0.050-0.04023.977-0.670-0.6700.0000.0000.0000.000
61A61LYS10.9120.95923.68611.15511.1550.0000.0000.0000.000
62A62VAL0-0.0130.00519.699-0.634-0.6340.0000.0000.0000.000
63A63VAL00.0150.01019.233-0.954-0.9540.0000.0000.0000.000
64A64ALA0-0.0050.00119.165-0.666-0.6660.0000.0000.0000.000
65A65ALA00.0330.01817.914-0.548-0.5480.0000.0000.0000.000
66A66VAL0-0.021-0.01314.265-1.313-1.3130.0000.0000.0000.000
67A67GLY00.042-0.00214.546-1.302-1.3020.0000.0000.0000.000
68A68ASP-1-0.928-0.96515.843-16.700-16.7000.0000.0000.0000.000
69A69ALA0-0.015-0.00911.303-0.941-0.9410.0000.0000.0000.000
70A70VAL0-0.031-0.01810.898-2.407-2.4070.0000.0000.0000.000
71A71LYS10.9150.95712.36814.99714.9970.0000.0000.0000.000
72A72SER0-0.032-0.01512.3520.6750.6750.0000.0000.0000.000
73A73ILE0-0.021-0.0077.095-2.235-2.2350.0000.0000.0000.000
74A74ASP-1-0.852-0.9086.790-37.680-37.6800.0000.0000.0000.000
75A75ASP-1-0.895-0.9428.502-25.998-25.9980.0000.0000.0000.000
76A76ILE00.0080.0026.7752.0572.0570.0000.0000.0000.000
77A77GLY00.0300.01910.0851.6591.6590.0000.0000.0000.000
78A78GLY00.017-0.00411.8061.8891.8890.0000.0000.0000.000
79A79ALA0-0.067-0.02513.3961.4461.4460.0000.0000.0000.000
80A80LEU0-0.014-0.00912.5471.3771.3770.0000.0000.0000.000
81A81SER00.0440.04615.5130.8900.8900.0000.0000.0000.000
82A82LYS11.0351.01017.21913.74713.7470.0000.0000.0000.000
83A83LEU0-0.012-0.00117.9570.7550.7550.0000.0000.0000.000
84A84SER00.0180.00716.1920.4000.4000.0000.0000.0000.000
85A85GLU-1-0.907-0.94918.213-13.940-13.9400.0000.0000.0000.000
86A86LEU0-0.027-0.01321.6680.5800.5800.0000.0000.0000.000
87A87HIS0-0.036-0.05119.7990.7130.7130.0000.0000.0000.000
88A88ALA00.0190.02819.9000.3360.3360.0000.0000.0000.000
89A89TYR00.019-0.00821.9620.4340.4340.0000.0000.0000.000
90A90ILE0-0.052-0.01625.2690.5260.5260.0000.0000.0000.000
91A91LEU0-0.055-0.03724.0530.3510.3510.0000.0000.0000.000
92A92ARG10.9140.98224.32111.06311.0630.0000.0000.0000.000
93A93VAL00.0020.00121.3150.2470.2470.0000.0000.0000.000
94A94ASP-1-0.817-0.89521.285-14.662-14.6620.0000.0000.0000.000
95A95PRO00.0540.00116.774-0.423-0.4230.0000.0000.0000.000
96A96VAL0-0.0050.00817.166-1.196-1.1960.0000.0000.0000.000
97A97ASN00.0400.01718.949-0.104-0.1040.0000.0000.0000.000
98A98PHE00.0300.01815.437-0.082-0.0820.0000.0000.0000.000
99A99LYS10.8890.95712.79120.00720.0070.0000.0000.0000.000
100A100LEU0-0.0100.00816.357-0.068-0.0680.0000.0000.0000.000
101A101LEU00.0360.02117.5890.3080.3080.0000.0000.0000.000
102A102SER00.001-0.01914.048-0.392-0.3920.0000.0000.0000.000
103A103HIS00.0200.01316.058-0.555-0.5550.0000.0000.0000.000
104A104CYS0-0.052-0.01418.2060.6130.6130.0000.0000.0000.000
105A105LEU00.0110.02316.0060.4990.4990.0000.0000.0000.000
106A106LEU00.011-0.00313.6260.2520.2520.0000.0000.0000.000
107A107VAL0-0.018-0.00717.7530.4780.4780.0000.0000.0000.000
108A108THR0-0.038-0.02021.3800.7440.7440.0000.0000.0000.000
109A109LEU0-0.035-0.03016.5020.4030.4030.0000.0000.0000.000
110A110ALA0-0.025-0.00720.3810.3850.3850.0000.0000.0000.000
111A111ALA0-0.032-0.01821.6790.4840.4840.0000.0000.0000.000
112A112ARG10.8370.92123.83912.38112.3810.0000.0000.0000.000
113A113PHE0-0.010-0.01520.6750.2960.2960.0000.0000.0000.000
114A114PRO00.0370.01922.307-0.622-0.6220.0000.0000.0000.000
115A115ALA0-0.026-0.01023.761-0.098-0.0980.0000.0000.0000.000
116A116ASP-1-0.825-0.90619.601-14.708-14.7080.0000.0000.0000.000
117A117PHE0-0.028-0.01016.274-1.249-1.2490.0000.0000.0000.000
118A118THR00.0500.02117.467-0.031-0.0310.0000.0000.0000.000
119A119ALA00.0320.00716.408-0.772-0.7720.0000.0000.0000.000
120A120GLU-1-0.941-0.96913.000-21.539-21.5390.0000.0000.0000.000
121A121ALA0-0.0020.00112.475-2.302-2.3020.0000.0000.0000.000
122A122HIS00.0160.00813.273-1.652-1.6520.0000.0000.0000.000
123A123ALA00.0310.01410.135-1.130-1.1300.0000.0000.0000.000
124A124ALA0-0.028-0.0148.569-3.297-3.2970.0000.0000.0000.000
125A125TRP00.014-0.0108.619-3.131-3.1310.0000.0000.0000.000
126A126ASP-1-0.899-0.93810.636-26.077-26.0770.0000.0000.0000.000
128A128PHE0-0.024-0.0216.201-3.951-3.9510.0000.0000.0000.000
129A129LEU00.0180.0077.6430.5250.5250.0000.0000.0000.000
130A130SER00.0030.0107.4932.5032.5030.0000.0000.0000.000
132A132VAL00.0220.0117.1772.5512.5510.0000.0000.0000.000
133A133SER0-0.040-0.03410.7542.6362.6360.0000.0000.0000.000
134A134SER0-0.055-0.0028.9272.8242.8240.0000.0000.0000.000
135A135VAL00.0680.0469.6411.6081.6080.0000.0000.0000.000
136A136LEU0-0.051-0.03212.2651.9031.9030.0000.0000.0000.000
137A137THR0-0.035-0.02414.0531.2381.2380.0000.0000.0000.000
138A138GLU-1-0.863-0.93513.072-21.370-21.3700.0000.0000.0000.000
139A139LYS10.8000.89515.18617.95517.9550.0000.0000.0000.000
140A140TYR0-0.107-0.06318.1761.1101.1100.0000.0000.0000.000
141A141ARG0-0.068-0.02212.1644.7544.7540.0000.0000.0000.000