FMO DATABASE

FMODB ID: VYV71

Calculation Name: 2H8F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | acetyl group

Ligand 3-letter code: HEM | ACE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2H8F

Chain ID: A

ChEMBL ID:

UniProt ID: P80043

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1272345.144171
FMO2-HF: Nuclear repulsion	1217715.958957
FMO2-HF: Total energy	-54629.185214
FMO2-MP2: Total energy	-54788.9236

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: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.
71.128	73.001	0.009	-0.757	-1.125	-0.003

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 : 0.871 / 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 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	3	SER	0	0.018	-0.016	3.541	2.020	3.744	0.010	-0.731	-1.003	-0.003
128	A	128	LYS	1	0.884	0.931	4.236	48.729	48.878	-0.001	-0.026	-0.122	0.000
4	A	4	ASP	-1	-0.804	-0.926	5.801	-29.159	-29.159	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.985	0.994	8.867	25.847	25.847	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.761	-0.831	6.516	-43.056	-43.056	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.856	0.928	5.730	37.877	37.877	0.000	0.000	0.000	0.000
8	A	8	ALA	0	-0.007	0.003	9.840	2.259	2.259	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.005	-0.002	12.453	1.668	1.668	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.024	0.011	10.473	1.678	1.678	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.900	0.943	11.412	24.687	24.687	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.003	0.001	15.434	1.374	1.374	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.017	-0.005	16.311	1.199	1.199	0.000	0.000	0.000	0.000
14	A	14	TRP	0	0.061	0.022	16.669	0.916	0.916	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.010	0.003	18.646	1.039	1.039	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.885	0.948	20.590	15.794	15.794	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.033	0.009	18.762	0.590	0.590	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.033	0.022	21.627	0.302	0.302	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.887	0.947	22.155	12.336	12.336	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.002	0.001	24.882	0.518	0.518	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.012	0.012	22.530	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.795	-0.899	23.677	-11.331	-11.331	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.021	-0.010	26.679	0.148	0.148	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.046	0.015	21.051	0.048	0.048	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.022	0.003	23.063	-0.216	-0.216	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.023	-0.003	23.967	0.233	0.233	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.794	-0.859	26.471	-11.188	-11.188	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.018	0.015	22.012	0.055	0.055	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.007	-0.007	23.811	0.005	0.005	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.014	-0.025	25.744	0.430	0.430	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.845	0.902	25.315	11.819	11.819	0.000	0.000	0.000	0.000
32	A	32	MET	0	0.012	0.013	23.383	-0.093	-0.093	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.041	-0.021	25.543	0.171	0.171	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.041	-0.024	28.991	0.431	0.431	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.013	-0.007	26.104	0.233	0.233	0.000	0.000	0.000	0.000
36	A	36	TYR	0	-0.029	-0.017	21.988	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.009	0.021	26.910	-0.139	-0.139	0.000	0.000	0.000	0.000
38	A	38	GLN	0	0.097	0.032	24.915	0.567	0.567	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.021	-0.022	24.250	0.088	0.088	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.915	0.960	26.985	9.531	9.531	0.000	0.000	0.000	0.000
41	A	41	THR	0	0.001	0.006	28.886	0.158	0.158	0.000	0.000	0.000	0.000
42	A	42	TYR	0	0.016	0.021	24.664	0.200	0.200	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.051	-0.037	25.327	-0.120	-0.120	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.012	0.008	30.958	0.335	0.335	0.000	0.000	0.000	0.000
45	A	45	HIS	0	0.004	0.015	30.223	0.422	0.422	0.000	0.000	0.000	0.000
46	A	46	TRP	0	-0.076	-0.046	28.757	-0.012	-0.012	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.062	0.037	35.843	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.781	-0.872	36.195	-8.793	-8.793	0.000	0.000	0.000	0.000
49	A	49	VAL	0	-0.007	0.019	31.723	-0.297	-0.297	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.006	-0.009	34.178	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.043	-0.005	32.178	-0.161	-0.161	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.017	0.010	32.058	0.280	0.280	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.031	-0.017	33.613	0.163	0.163	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.021	-0.003	33.737	-0.264	-0.264	0.000	0.000	0.000	0.000
55	A	55	HIS	1	0.869	0.903	32.198	8.861	8.861	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.002	0.022	28.811	-0.414	-0.414	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.948	0.972	28.878	8.586	8.586	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.029	-0.010	29.602	-0.253	-0.253	0.000	0.000	0.000	0.000
59	A	59	HIS	0	0.006	-0.009	24.262	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.051	0.020	24.868	-0.532	-0.532	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.862	0.916	24.041	9.845	9.845	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.927	0.978	24.072	11.050	11.050	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.009	0.014	19.686	-0.569	-0.569	0.000	0.000	0.000	0.000
64	A	64	MET	0	0.005	0.015	18.440	-0.998	-0.998	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.015	0.017	19.942	-0.391	-0.391	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.022	0.010	18.469	-0.357	-0.357	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.002	-0.002	14.480	-1.197	-1.197	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.003	-0.007	15.638	-0.922	-0.922	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.009	0.008	16.255	-0.412	-0.412	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.059	0.035	11.964	-0.677	-0.677	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.012	-0.018	12.176	-1.664	-1.664	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.101	-0.063	13.707	-0.279	-0.279	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.926	0.968	12.759	18.136	18.136	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.010	0.004	8.341	-1.791	-1.791	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.843	-0.913	7.384	-31.299	-31.299	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.831	-0.891	7.290	-28.953	-28.953	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.003	-0.001	6.473	2.280	2.280	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.877	0.936	9.281	25.294	25.294	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.037	-0.054	10.748	2.253	2.253	0.000	0.000	0.000	0.000
80	A	80	GLY	0	-0.054	-0.031	12.601	1.454	1.454	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.012	-0.011	11.369	1.267	1.267	0.000	0.000	0.000	0.000
82	A	82	MET	0	0.039	0.034	14.644	0.709	0.709	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.896	-0.953	16.453	-13.149	-13.149	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.034	-0.022	17.001	0.675	0.675	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.012	-0.008	15.401	0.473	0.473	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.765	-0.850	17.441	-13.397	-13.397	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.021	-0.009	20.817	0.781	0.781	0.000	0.000	0.000	0.000
88	A	88	HIS	0	-0.078	-0.069	19.305	0.890	0.890	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.030	0.033	19.682	0.417	0.417	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.004	-0.008	21.550	0.627	0.627	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.909	0.956	24.967	10.851	10.851	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.053	-0.031	23.357	0.439	0.439	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.891	0.960	24.404	11.997	11.997	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.000	0.016	20.938	0.104	0.104	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.801	-0.880	20.418	-15.794	-15.794	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.076	0.032	15.682	-0.073	-0.073	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.075	-0.035	16.702	-1.028	-1.028	0.000	0.000	0.000	0.000
98	A	98	ASN	0	-0.006	-0.045	18.361	0.327	0.327	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.027	0.018	14.752	0.230	0.230	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.942	0.985	14.001	17.873	17.873	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.011	0.012	15.887	0.064	0.064	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.045	0.015	18.600	0.360	0.360	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.003	-0.012	12.531	1.053	1.053	0.000	0.000	0.000	0.000
104	A	104	HIS	0	0.054	0.042	16.268	0.271	0.271	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.049	-0.016	18.099	0.689	0.689	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.006	-0.008	17.256	0.547	0.547	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.017	-0.005	13.887	0.433	0.433	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.020	-0.005	18.285	0.572	0.572	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.017	0.006	21.809	0.478	0.478	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.016	0.002	18.153	0.464	0.464	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.023	-0.002	21.126	0.447	0.447	0.000	0.000	0.000	0.000
112	A	112	THR	0	-0.074	-0.049	22.632	0.589	0.589	0.000	0.000	0.000	0.000
113	A	113	MET	0	-0.050	-0.021	25.104	0.338	0.338	0.000	0.000	0.000	0.000
114	A	114	PHE	0	0.006	-0.005	23.009	0.293	0.293	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.045	0.029	23.470	-0.601	-0.601	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.874	0.938	24.485	11.566	11.566	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.894	-0.959	22.109	-12.537	-12.537	0.000	0.000	0.000	0.000
118	A	118	PHE	0	-0.036	-0.012	16.245	-1.023	-1.023	0.000	0.000	0.000	0.000
119	A	119	THR	0	0.016	-0.001	18.762	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	120	PRO	0	0.051	0.010	17.485	-0.928	-0.928	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.875	-0.929	14.627	-18.273	-18.273	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.028	-0.013	13.599	-1.834	-1.834	0.000	0.000	0.000	0.000
123	A	123	HIS	0	0.000	0.008	13.942	-1.984	-1.984	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.040	0.022	9.673	-1.579	-1.579	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.037	-0.041	8.918	-2.393	-2.393	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.018	-0.006	9.298	-2.633	-2.633	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.896	-0.944	10.478	-27.070	-27.070	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.021	-0.013	6.463	-4.086	-4.086	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.013	0.008	8.104	0.154	0.154	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.002	-0.001	7.273	2.166	2.166	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.028	-0.010	6.030	-0.810	-0.810	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.017	-0.013	6.602	2.026	2.026	0.000	0.000	0.000	0.000
134	A	134	ALA	0	-0.013	-0.007	10.179	1.614	1.614	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.020	-0.009	6.160	1.123	1.123	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.001	0.001	8.943	1.475	1.475	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.013	-0.014	10.434	1.974	1.974	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.019	0.002	12.726	1.724	1.724	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.853	-0.909	12.239	-22.469	-22.469	0.000	0.000	0.000	0.000
140	A	140	ARG	1	0.801	0.854	14.140	15.611	15.611	0.000	0.000	0.000	0.000
141	A	141	TYR	0	-0.089	-0.068	17.331	0.844	0.844	0.000	0.000	0.000	0.000
142	A	142	ARG	0	0.029	0.041	15.520	2.029	2.029	0.000	0.000	0.000	0.000

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