FMO DATABASE

FMODB ID: Z73RN

Calculation Name: 2BH4-X-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BH4

Chain ID: X

ChEMBL ID:

UniProt ID: Q00499

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	121
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-940513.794238
FMO2-HF: Nuclear repulsion	894737.630948
FMO2-HF: Total energy	-45776.16329
FMO2-MP2: Total energy	-45909.197651

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:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
10.19	11.724	-0.019	-0.519	-0.994	0.002

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.040

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	4	ASP	-1	-0.789	-0.898	3.809	0.545	1.997	-0.018	-0.506	-0.927	0.002
108	A	109	ALA	0	0.065	0.027	4.287	0.544	0.626	-0.001	-0.013	-0.067	0.000
4	A	5	ALA	0	0.078	0.029	5.943	0.446	0.446	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.036	0.025	8.909	0.301	0.301	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.782	0.873	6.786	5.567	5.567	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.011	-0.003	10.050	0.208	0.208	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.900	-0.946	11.564	-0.439	-0.439	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.896	0.950	13.665	1.792	1.792	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.820	-0.906	12.904	-2.391	-2.391	0.000	0.000	0.000	0.000
11	A	12	PHE	0	0.076	0.032	15.499	0.162	0.162	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.040	-0.025	17.099	0.341	0.341	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.811	0.891	17.039	2.205	2.205	0.000	0.000	0.000	0.000
14	A	15	CYS	0	-0.022	0.007	16.781	0.006	0.006	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.924	0.966	20.309	0.902	0.902	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.014	0.013	22.707	0.102	0.102	0.000	0.000	0.000	0.000
17	A	18	CYS	0	-0.062	-0.032	24.102	0.072	0.072	0.000	0.000	0.000	0.000
18	A	19	HIS	0	-0.043	-0.025	21.624	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	20	MET	0	0.017	0.010	23.187	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.001	0.005	17.949	-0.035	-0.035	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.041	-0.036	21.147	0.048	0.048	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.080	0.047	23.068	0.006	0.006	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.000	-0.018	23.558	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.849	-0.891	26.787	0.184	0.184	0.000	0.000	0.000	0.000
25	A	26	GLY	0	-0.014	-0.001	28.081	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.058	-0.045	24.936	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.918	-0.959	24.907	-0.248	-0.248	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.020	-0.006	18.357	0.031	0.031	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.046	-0.033	18.721	-0.080	-0.080	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.976	0.998	21.911	0.316	0.316	0.000	0.000	0.000	0.000
31	A	32	GLY	0	0.005	-0.015	24.831	-0.072	-0.072	0.000	0.000	0.000	0.000
32	A	33	GLY	0	-0.048	-0.002	25.823	0.070	0.070	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.970	0.970	26.885	0.265	0.265	0.000	0.000	0.000	0.000
34	A	35	THR	0	-0.002	0.006	27.820	0.036	0.036	0.000	0.000	0.000	0.000
35	A	36	GLY	0	-0.010	-0.003	24.781	-0.019	-0.019	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.030	-0.001	23.234	0.026	0.026	0.000	0.000	0.000	0.000
37	A	38	ASN	0	0.035	-0.001	22.677	-0.136	-0.136	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.028	-0.014	17.948	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	TYR	0	0.066	0.035	17.894	-0.041	-0.041	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.000	-0.006	18.111	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	42	VAL	0	-0.070	-0.033	15.574	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	43	VAL	0	0.004	-0.010	11.853	-0.140	-0.140	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.070	0.042	15.034	0.176	0.176	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.841	0.934	17.323	0.277	0.277	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.854	0.924	20.102	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.007	0.013	19.417	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.048	-0.041	22.831	0.054	0.054	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.018	-0.022	24.054	0.046	0.046	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.044	-0.016	24.322	0.039	0.039	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.857	-0.933	27.088	-0.054	-0.054	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.010	0.008	30.673	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	53	PHE	0	-0.035	-0.021	27.855	-0.018	-0.018	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.859	0.928	30.822	0.245	0.245	0.000	0.000	0.000	0.000
54	A	55	TYR	0	0.032	0.025	24.406	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.021	0.011	29.015	0.027	0.027	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.794	-0.904	29.561	-0.392	-0.392	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.012	0.014	28.373	0.014	0.014	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.015	-0.011	22.273	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.008	-0.007	26.247	0.025	0.025	0.000	0.000	0.000	0.000
60	A	61	GLU	-1	-0.802	-0.883	29.076	-0.375	-0.375	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.033	-0.011	22.711	0.021	0.021	0.000	0.000	0.000	0.000
62	A	63	ALA	0	0.012	0.006	25.899	0.035	0.035	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.972	-0.982	26.742	-0.171	-0.171	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.787	0.854	29.006	0.401	0.401	0.000	0.000	0.000	0.000
65	A	66	ASN	0	-0.037	-0.008	24.738	0.024	0.024	0.000	0.000	0.000	0.000
66	A	67	PRO	0	-0.001	0.007	25.922	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	ASP	-1	-0.892	-0.944	24.615	0.011	0.011	0.000	0.000	0.000	0.000
68	A	69	MET	0	-0.005	0.013	20.585	0.002	0.002	0.000	0.000	0.000	0.000
69	A	70	VAL	0	0.002	-0.005	17.795	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	71	TRP	0	-0.034	-0.027	15.899	-0.169	-0.169	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.022	0.004	13.334	0.063	0.063	0.000	0.000	0.000	0.000
72	A	73	GLU	-1	-0.872	-0.962	7.684	0.115	0.115	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.001	0.004	9.876	-0.890	-0.890	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.729	-0.846	10.743	-1.315	-1.315	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.027	-0.009	11.915	-0.086	-0.086	0.000	0.000	0.000	0.000
76	A	77	ILE	0	0.000	-0.006	6.500	-0.390	-0.390	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.893	-0.931	10.883	-1.881	-1.881	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.003	-0.005	13.905	0.130	0.130	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.059	-0.034	13.013	0.160	0.160	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.050	-0.034	12.614	-0.147	-0.147	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.884	-0.975	14.969	-1.293	-1.293	0.000	0.000	0.000	0.000
82	A	83	PRO	0	-0.014	0.003	18.534	0.112	0.112	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.807	0.909	20.541	0.836	0.836	0.000	0.000	0.000	0.000
84	A	85	PRO	0	0.007	0.006	20.059	0.104	0.104	0.000	0.000	0.000	0.000
85	A	86	TRP	0	0.036	0.012	16.907	0.128	0.128	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.008	-0.012	20.356	0.109	0.109	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.054	-0.005	23.654	0.082	0.082	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.892	-0.927	19.715	-1.052	-1.052	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.833	0.914	17.232	1.166	1.166	0.000	0.000	0.000	0.000
90	A	91	THR	0	-0.059	-0.032	23.581	0.082	0.082	0.000	0.000	0.000	0.000
91	A	92	GLY	0	0.047	0.036	26.823	0.065	0.065	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.825	-0.910	28.552	-0.458	-0.458	0.000	0.000	0.000	0.000
93	A	94	SER	0	-0.015	-0.012	29.232	-0.045	-0.045	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.049	-0.042	30.383	-0.045	-0.045	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.034	0.041	27.968	0.008	0.008	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.859	0.915	29.136	0.344	0.344	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.056	0.020	25.486	0.014	0.014	0.000	0.000	0.000	0.000
98	A	99	LYS	1	0.903	0.935	28.492	0.621	0.621	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.923	0.996	20.097	1.176	1.176	0.000	0.000	0.000	0.000
100	A	101	THR	0	0.053	0.010	23.709	-0.039	-0.039	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.021	-0.009	18.549	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.920	0.967	18.621	1.340	1.340	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.027	0.002	12.896	0.136	0.136	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.031	0.004	14.726	-0.277	-0.277	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.931	0.967	12.358	2.649	2.649	0.000	0.000	0.000	0.000
106	A	107	ASN	0	-0.036	-0.040	9.423	1.021	1.021	0.000	0.000	0.000	0.000
107	A	108	GLN	0	0.064	0.032	9.647	-0.783	-0.783	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.826	-0.896	6.437	-9.623	-9.623	0.000	0.000	0.000	0.000
110	A	111	VAL	0	-0.002	-0.012	7.834	1.343	1.343	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.011	0.009	8.467	0.761	0.761	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.057	0.039	5.592	0.960	0.960	0.000	0.000	0.000	0.000
113	A	114	PHE	0	-0.063	-0.038	7.670	1.241	1.241	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.026	-0.018	11.095	0.488	0.488	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.057	0.046	9.089	0.287	0.287	0.000	0.000	0.000	0.000
116	A	117	GLN	0	-0.029	-0.013	10.561	0.098	0.098	0.000	0.000	0.000	0.000
117	A	118	HIS	1	0.822	0.917	12.151	0.146	0.146	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.009	-0.018	14.294	-0.248	-0.248	0.000	0.000	0.000	0.000
119	A	120	PRO	0	-0.023	-0.001	15.179	0.148	0.148	0.000	0.000	0.000	0.000
120	A	121	ASP	-1	-0.947	-0.966	16.329	1.029	1.029	0.000	0.000	0.000	0.000
121	A	122	ALA	-1	-0.964	-0.964	14.918	1.315	1.315	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)