FMO DATABASE

FMODB ID: LQ989

Calculation Name: 1MJ4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | sulfate ion | glycerol

Ligand 3-letter code: HEM | SO4 | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MJ4

Chain ID: A

ChEMBL ID:

UniProt ID: P51687

Base Structure: X-ray

Registration Date: 2025-10-03

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-502700.028541
FMO2-HF: Nuclear repulsion	472205.281065
FMO2-HF: Total energy	-30494.747476
FMO2-MP2: Total energy	-30585.443685

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-104.345	-102.681	-0.017	-0.725	-0.922	-0.003

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.890

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 ES EX CT+mix DI(MP2)

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].
3	A	5	HIS	0	0.005	0.027	3.828	1.041	2.705	-0.017	-0.725	-0.922	-0.003
4	A	6	ILE	0	-0.012	-0.007	6.345	0.804	0.804	0.000	0.000	0.000	0.000
5	A	7	TYR	0	-0.015	0.002	9.047	1.446	1.446	0.000	0.000	0.000	0.000
6	A	8	THR	0	-0.021	-0.036	12.686	0.666	0.666	0.000	0.000	0.000	0.000
7	A	9	LYS	1	0.971	0.964	15.850	16.453	16.453	0.000	0.000	0.000	0.000
8	A	10	GLU	-1	-0.911	-0.940	18.902	-12.556	-12.556	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.823	-0.879	14.418	-19.566	-19.566	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.007	-0.001	16.275	0.323	0.323	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.039	-0.032	18.817	0.639	0.639	0.000	0.000	0.000	0.000
12	A	14	SER	0	-0.051	-0.037	20.783	0.522	0.522	0.000	0.000	0.000	0.000
13	A	15	HIS	1	0.823	0.927	18.725	15.893	15.893	0.000	0.000	0.000	0.000
14	A	16	THR	0	0.047	0.015	22.296	-0.091	-0.091	0.000	0.000	0.000	0.000
15	A	17	SER	0	0.011	0.004	25.574	0.364	0.364	0.000	0.000	0.000	0.000
16	A	18	PRO	0	0.045	-0.009	25.398	-0.410	-0.410	0.000	0.000	0.000	0.000
17	A	19	GLU	-1	-0.983	-0.970	25.423	-11.005	-11.005	0.000	0.000	0.000	0.000
18	A	20	THR	0	-0.062	-0.024	22.565	-0.499	-0.499	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.030	0.051	21.031	-0.852	-0.852	0.000	0.000	0.000	0.000
20	A	22	ILE	0	-0.036	-0.037	22.101	0.163	0.163	0.000	0.000	0.000	0.000
21	A	23	TRP	0	-0.016	-0.024	15.375	-0.697	-0.697	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.027	-0.005	19.526	0.863	0.863	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.012	-0.012	17.032	-1.020	-1.020	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.014	-0.017	17.228	1.339	1.339	0.000	0.000	0.000	0.000
25	A	27	GLY	0	-0.019	-0.004	16.437	-1.227	-1.227	0.000	0.000	0.000	0.000
26	A	28	SER	0	-0.025	-0.020	12.591	1.123	1.123	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.862	-0.911	11.613	-26.896	-26.896	0.000	0.000	0.000	0.000
28	A	30	VAL	0	0.002	-0.005	12.906	2.141	2.141	0.000	0.000	0.000	0.000
29	A	31	PHE	0	-0.013	-0.017	13.795	-1.488	-1.488	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.783	-0.862	16.503	-15.127	-15.127	0.000	0.000	0.000	0.000
31	A	33	VAL	0	-0.006	-0.022	18.456	0.050	0.050	0.000	0.000	0.000	0.000
32	A	34	THR	0	0.005	-0.016	21.681	0.934	0.934	0.000	0.000	0.000	0.000
33	A	35	GLU	-1	-0.907	-0.961	22.345	-12.297	-12.297	0.000	0.000	0.000	0.000
34	A	36	PHE	0	-0.035	-0.018	23.522	0.398	0.398	0.000	0.000	0.000	0.000
35	A	37	VAL	0	0.001	0.007	25.344	0.504	0.504	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.885	-0.967	27.598	-9.972	-9.972	0.000	0.000	0.000	0.000
37	A	39	LEU	0	-0.076	-0.031	28.072	0.414	0.414	0.000	0.000	0.000	0.000
38	A	40	HIS	0	0.014	0.026	27.736	-0.267	-0.267	0.000	0.000	0.000	0.000
39	A	41	PRO	0	-0.004	-0.020	29.888	0.415	0.415	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.057	-0.031	32.848	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.008	0.017	33.927	0.258	0.258	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.075	0.040	30.972	-0.143	-0.143	0.000	0.000	0.000	0.000
43	A	45	SER	0	-0.039	-0.024	31.278	-0.283	-0.283	0.000	0.000	0.000	0.000
44	A	46	LYS	1	0.927	0.950	32.517	9.061	9.061	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.002	0.017	25.495	-0.061	-0.061	0.000	0.000	0.000	0.000
46	A	48	MET	0	0.029	0.002	27.693	-0.402	-0.402	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.075	-0.025	29.315	0.021	0.021	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.023	-0.006	25.501	0.053	0.053	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.004	0.006	24.720	-0.609	-0.609	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.024	0.022	22.076	0.383	0.383	0.000	0.000	0.000	0.000
51	A	53	GLY	0	0.010	-0.001	22.349	-0.223	-0.223	0.000	0.000	0.000	0.000
52	A	54	PRO	0	-0.047	-0.009	21.717	-0.540	-0.540	0.000	0.000	0.000	0.000
53	A	55	LEU	0	0.078	0.023	20.886	0.792	0.792	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.826	-0.914	20.960	-14.357	-14.357	0.000	0.000	0.000	0.000
55	A	57	PRO	0	-0.042	-0.024	25.036	0.501	0.501	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.029	0.017	27.205	0.572	0.572	0.000	0.000	0.000	0.000
57	A	59	TRP	0	0.003	-0.034	22.135	0.281	0.281	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.021	0.000	27.914	0.200	0.200	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.023	0.000	29.786	0.361	0.361	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.039	-0.007	30.719	0.363	0.363	0.000	0.000	0.000	0.000
61	A	63	ALA	0	0.109	0.049	29.906	-0.345	-0.345	0.000	0.000	0.000	0.000
62	A	64	VAL	0	0.011	0.012	29.999	-0.187	-0.187	0.000	0.000	0.000	0.000
63	A	65	HIS	1	0.863	0.931	25.769	11.247	11.247	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.018	0.008	25.275	-1.018	-1.018	0.000	0.000	0.000	0.000
65	A	67	GLN	0	0.012	0.003	25.992	0.357	0.357	0.000	0.000	0.000	0.000
66	A	68	SER	0	0.030	0.006	22.846	-0.272	-0.272	0.000	0.000	0.000	0.000
67	A	69	HIS	0	0.034	0.014	22.135	-0.883	-0.883	0.000	0.000	0.000	0.000
68	A	70	VAL	0	0.005	0.011	23.040	-0.295	-0.295	0.000	0.000	0.000	0.000
69	A	71	ARG	1	0.841	0.914	19.393	13.850	13.850	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.832	-0.912	16.868	-19.287	-19.287	0.000	0.000	0.000	0.000
71	A	73	LEU	0	-0.036	-0.005	18.536	-0.552	-0.552	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.027	-0.017	17.843	-0.088	-0.088	0.000	0.000	0.000	0.000
73	A	75	ALA	0	0.018	0.006	14.458	-0.678	-0.678	0.000	0.000	0.000	0.000
74	A	76	GLN	0	-0.093	-0.050	14.511	-1.472	-1.472	0.000	0.000	0.000	0.000
75	A	77	TYR	0	-0.014	-0.004	16.135	0.080	0.080	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.739	0.854	8.660	32.508	32.508	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.015	0.009	11.814	-1.316	-1.316	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.044	-0.023	8.847	-2.577	-2.577	0.000	0.000	0.000	0.000
79	A	81	GLU	-1	-0.886	-0.942	7.700	-38.281	-38.281	0.000	0.000	0.000	0.000
80	A	82	LEU	-1	-0.921	-0.955	10.570	-23.856	-23.856	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)