FMO DATABASE

FMODB ID: RM4R8

Calculation Name: 4PXH-D-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | s-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] 1h-imidazole-4-carbothioate

Ligand 3-letter code: HEM | KH4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PXH

Chain ID: D

ChEMBL ID:

UniProt ID: F2YRY5

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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-483569.055635
FMO2-HF: Nuclear repulsion	454331.844303
FMO2-HF: Total energy	-29237.211332
FMO2-MP2: Total energy	-29324.823552

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:6:ARG)

Summations of interaction energy for fragment #1(A:6:ARG)

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.
-545.339	-538.361	55.984	-30.339	-32.626	-0.361

Interaction energy analysis for fragmet #1(A:6:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.522 / q_NPA : 1.722

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	8	PRO	0	-0.010	-0.003	1.946	-31.016	-30.048	9.057	-4.440	-5.586	-0.059
4	A	9	ARG	1	0.934	0.963	2.512	106.027	110.050	1.598	-1.598	-4.024	0.009
5	A	10	ASN	0	0.003	0.006	4.400	9.561	9.659	0.000	-0.020	-0.079	0.000
8	A	13	GLU	-1	-0.730	-0.854	1.789	-166.953	-171.102	19.999	-8.622	-7.228	-0.123
25	A	30	ASP	-1	-0.852	-0.925	1.953	-175.110	-172.676	7.673	-5.825	-4.282	-0.074
26	A	31	VAL	0	0.016	-0.012	2.705	10.227	11.212	3.149	-1.024	-3.110	0.002
27	A	32	GLU	-1	-0.854	-0.924	1.795	-157.326	-155.381	13.917	-8.435	-7.427	-0.115
28	A	33	ALA	0	-0.032	-0.003	4.990	10.429	10.498	-0.001	-0.004	-0.064	0.000
67	A	72	ALA	0	0.023	0.005	2.498	0.919	1.412	0.592	-0.341	-0.744	-0.001
68	A	73	GLY	0	-0.012	-0.011	4.033	6.247	6.359	0.000	-0.030	-0.082	0.000
6	A	11	GLU	-1	-0.878	-0.946	6.848	-43.638	-43.638	0.000	0.000	0.000	0.000
7	A	12	THR	0	0.024	0.030	8.257	0.552	0.552	0.000	0.000	0.000	0.000
9	A	14	SER	0	-0.037	-0.015	5.836	-0.398	-0.398	0.000	0.000	0.000	0.000
10	A	15	ARG	1	0.853	0.904	7.980	38.576	38.576	0.000	0.000	0.000	0.000
11	A	16	LEU	0	0.033	0.017	8.349	2.173	2.173	0.000	0.000	0.000	0.000
12	A	17	ARG	1	0.848	0.918	5.698	76.884	76.884	0.000	0.000	0.000	0.000
13	A	18	ARG	1	0.937	0.983	9.480	47.749	47.749	0.000	0.000	0.000	0.000
14	A	19	ILE	0	0.006	0.011	12.866	2.717	2.717	0.000	0.000	0.000	0.000
15	A	20	PHE	0	0.004	-0.017	11.018	1.991	1.991	0.000	0.000	0.000	0.000
16	A	21	GLU	-1	-0.804	-0.888	9.590	-53.325	-53.325	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.859	-0.925	13.157	-32.295	-32.295	0.000	0.000	0.000	0.000
18	A	23	VAL	0	-0.095	-0.038	16.169	2.890	2.890	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.037	-0.034	12.382	2.061	2.061	0.000	0.000	0.000	0.000
20	A	25	HIS	0	-0.098	-0.034	16.074	1.556	1.556	0.000	0.000	0.000	0.000
21	A	26	SER	0	-0.044	-0.026	10.987	1.935	1.935	0.000	0.000	0.000	0.000
22	A	27	GLU	-1	-0.925	-0.972	12.518	-38.067	-38.067	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.958	-0.972	5.999	-78.171	-78.171	0.000	0.000	0.000	0.000
24	A	29	VAL	0	-0.020	-0.005	7.205	5.156	5.156	0.000	0.000	0.000	0.000
29	A	34	ASN	0	0.032	0.012	8.196	2.403	2.403	0.000	0.000	0.000	0.000
30	A	35	PHE	0	0.033	0.000	11.595	2.073	2.073	0.000	0.000	0.000	0.000
31	A	36	PHE	0	-0.029	-0.020	13.796	1.968	1.968	0.000	0.000	0.000	0.000
32	A	37	GLU	-1	-0.972	-0.975	13.213	-40.860	-40.860	0.000	0.000	0.000	0.000
33	A	38	LEU	0	-0.053	-0.022	9.268	0.292	0.292	0.000	0.000	0.000	0.000
34	A	39	GLY	0	-0.008	0.005	13.420	1.166	1.166	0.000	0.000	0.000	0.000
35	A	40	GLY	0	0.002	0.012	16.291	1.876	1.876	0.000	0.000	0.000	0.000
36	A	41	HIS	0	0.039	0.005	17.761	1.354	1.354	0.000	0.000	0.000	0.000
37	A	42	SER	0	0.056	0.003	21.452	-0.789	-0.789	0.000	0.000	0.000	0.000
38	A	43	LEU	0	-0.027	0.000	23.527	0.036	0.036	0.000	0.000	0.000	0.000
39	A	44	GLN	0	-0.028	-0.003	18.693	0.431	0.431	0.000	0.000	0.000	0.000
40	A	45	ALA	0	0.050	0.026	18.558	-0.706	-0.706	0.000	0.000	0.000	0.000
41	A	46	THR	0	-0.013	-0.016	19.595	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	47	LYS	1	0.926	0.972	21.294	26.147	26.147	0.000	0.000	0.000	0.000
43	A	48	LEU	0	0.028	0.030	13.596	0.319	0.319	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.036	0.015	17.213	-0.446	-0.446	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.051	-0.040	18.454	0.759	0.759	0.000	0.000	0.000	0.000
46	A	51	ARG	1	0.711	0.832	17.894	34.120	34.120	0.000	0.000	0.000	0.000
47	A	52	ILE	0	0.016	0.013	13.296	-0.099	-0.099	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.801	0.888	16.628	26.747	26.747	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.062	-0.031	19.849	0.763	0.763	0.000	0.000	0.000	0.000
50	A	55	GLU	-1	-0.762	-0.866	17.066	-33.470	-33.470	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.026	-0.018	12.280	-1.250	-1.250	0.000	0.000	0.000	0.000
52	A	57	ASP	-1	-0.916	-0.937	17.606	-25.060	-25.060	0.000	0.000	0.000	0.000
53	A	58	ALA	0	-0.009	0.008	17.058	0.599	0.599	0.000	0.000	0.000	0.000
54	A	59	GLU	-1	-0.933	-0.975	19.101	-23.604	-23.604	0.000	0.000	0.000	0.000
55	A	60	LEU	0	0.023	0.008	15.121	0.254	0.254	0.000	0.000	0.000	0.000
56	A	61	PRO	0	0.038	0.035	18.498	0.906	0.906	0.000	0.000	0.000	0.000
57	A	62	LEU	0	-0.012	-0.017	18.755	-1.126	-1.126	0.000	0.000	0.000	0.000
58	A	63	ARG	1	0.927	0.965	19.387	24.170	24.170	0.000	0.000	0.000	0.000
59	A	64	ASP	-1	-0.774	-0.893	15.691	-30.885	-30.885	0.000	0.000	0.000	0.000
60	A	65	PHE	0	-0.001	-0.010	14.213	-1.840	-1.840	0.000	0.000	0.000	0.000
61	A	66	PHE	0	-0.055	-0.032	14.829	-1.451	-1.451	0.000	0.000	0.000	0.000
62	A	67	GLU	-1	-0.970	-0.986	15.903	-30.116	-30.116	0.000	0.000	0.000	0.000
63	A	68	HIS	0	-0.018	0.000	10.618	-3.828	-3.828	0.000	0.000	0.000	0.000
64	A	69	PRO	0	0.003	0.026	11.140	-2.566	-2.566	0.000	0.000	0.000	0.000
65	A	70	ASN	0	-0.001	-0.008	6.544	-6.842	-6.842	0.000	0.000	0.000	0.000
66	A	71	VAL	0	0.004	0.019	5.276	1.772	1.772	0.000	0.000	0.000	0.000
69	A	74	LEU	0	-0.002	-0.016	7.568	4.779	4.779	0.000	0.000	0.000	0.000
70	A	75	ALA	0	-0.018	-0.021	5.908	3.427	3.427	0.000	0.000	0.000	0.000
71	A	76	VAL	0	-0.022	-0.012	6.566	3.609	3.609	0.000	0.000	0.000	0.000
72	A	77	LEU	0	-0.051	-0.020	9.133	3.525	3.525	0.000	0.000	0.000	0.000
73	A	78	ILE	0	-0.096	-0.034	11.359	2.654	2.654	0.000	0.000	0.000	0.000
74	A	79	GLY	-1	-0.961	-0.963	11.571	-37.873	-37.873	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ARG)