FMO DATABASE

FMODB ID: G8M11

Calculation Name: 2KSC-A-Other547

Preferred Name:

Target Type:

Ligand Name: heme b/c

Ligand 3-letter code: HEB

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KSC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RT58

Base Structure: SolutionNMR

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	123
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-983658.246305
FMO2-HF: Nuclear repulsion	935635.985583
FMO2-HF: Total energy	-48022.260722
FMO2-MP2: Total energy	-48162.733898

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:ALA)

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

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.
-171.964	-174.57	24.203	-13.091	-8.506	-0.135

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.805 / q_NPA : 0.878

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	LEU	0	0.073	0.037	3.893	-1.920	-0.818	-0.012	-0.551	-0.540	0.002
5	A	6	GLU	-1	-0.874	-0.910	1.781	-137.979	-142.014	24.213	-12.475	-7.702	-0.137
6	A	7	LYS	1	0.915	0.967	3.666	56.539	56.866	0.002	-0.065	-0.264	0.000
4	A	5	TYR	0	0.021	-0.006	6.947	1.519	1.519	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.016	0.009	6.890	3.675	3.675	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.013	0.020	8.891	2.344	2.344	0.000	0.000	0.000	0.000
9	A	10	GLY	0	-0.002	-0.015	10.316	1.888	1.888	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.031	-0.016	12.803	-0.548	-0.548	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.067	0.029	14.084	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.010	0.011	14.001	0.854	0.854	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.020	-0.016	12.510	-0.041	-0.041	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.907	-0.948	15.287	-16.740	-16.740	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.023	0.002	18.876	0.656	0.656	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.019	0.006	16.383	0.666	0.666	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.004	-0.014	16.680	0.473	0.473	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.975	-0.979	19.311	-12.138	-12.138	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.948	0.978	21.207	14.198	14.198	0.000	0.000	0.000	0.000
20	A	21	PHE	0	0.019	0.015	20.519	0.481	0.481	0.000	0.000	0.000	0.000
21	A	22	TYR	0	0.004	-0.011	22.549	0.551	0.551	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.012	0.003	24.535	0.517	0.517	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.837	0.913	25.130	12.453	12.453	0.000	0.000	0.000	0.000
24	A	25	VAL	0	-0.020	-0.016	23.740	0.358	0.358	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.043	-0.012	26.978	0.345	0.345	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.004	0.008	30.002	0.386	0.386	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.765	-0.849	29.563	-9.714	-9.714	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.900	-0.957	31.454	-8.633	-8.633	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.787	0.860	31.170	9.745	9.745	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.031	0.007	27.667	0.085	0.085	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.061	-0.040	30.213	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.921	0.958	31.628	8.414	8.414	0.000	0.000	0.000	0.000
33	A	34	PHE	0	-0.015	-0.001	29.545	0.153	0.153	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.018	-0.015	24.483	-0.154	-0.154	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.007	0.020	30.283	0.032	0.032	0.000	0.000	0.000	0.000
36	A	37	ASN	0	-0.007	-0.005	32.195	0.294	0.294	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.078	-0.028	26.840	-0.205	-0.205	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.792	-0.890	28.325	-11.081	-11.081	0.000	0.000	0.000	0.000
39	A	40	MET	0	0.066	0.001	28.336	-0.372	-0.372	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.074	-0.022	26.389	-0.383	-0.383	0.000	0.000	0.000	0.000
41	A	42	LYS	1	0.921	0.944	23.951	11.097	11.097	0.000	0.000	0.000	0.000
42	A	43	GLN	0	-0.005	0.017	23.453	-0.361	-0.361	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.980	0.991	22.371	11.911	11.911	0.000	0.000	0.000	0.000
44	A	45	GLN	0	-0.047	-0.008	18.287	-0.095	-0.095	0.000	0.000	0.000	0.000
45	A	46	HIS	0	0.055	0.034	18.511	-1.018	-1.018	0.000	0.000	0.000	0.000
46	A	47	GLN	0	0.031	0.007	18.674	-0.361	-0.361	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.968	0.995	13.269	21.689	21.689	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.927	-0.958	14.028	-21.391	-21.391	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.013	-0.005	13.813	-1.271	-1.271	0.000	0.000	0.000	0.000
50	A	51	MET	0	0.015	0.002	14.467	-0.399	-0.399	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.065	-0.051	9.309	-1.999	-1.999	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.028	-0.012	9.923	-2.373	-2.373	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.028	0.015	11.211	-0.498	-0.498	0.000	0.000	0.000	0.000
54	A	55	PHE	0	-0.041	-0.015	8.464	0.041	0.041	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.014	0.011	7.737	-3.006	-3.006	0.000	0.000	0.000	0.000
56	A	57	GLY	0	-0.022	0.009	6.413	-3.231	-3.231	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.028	-0.035	7.126	2.440	2.440	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.970	-0.979	5.622	-40.576	-40.576	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.899	0.925	7.645	24.219	24.219	0.000	0.000	0.000	0.000
60	A	61	PHE	0	0.074	0.048	10.880	1.261	1.261	0.000	0.000	0.000	0.000
61	A	62	PRO	0	-0.024	0.001	13.986	0.506	0.506	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.056	0.020	16.563	0.951	0.951	0.000	0.000	0.000	0.000
63	A	64	ARG	1	0.943	0.957	19.224	13.043	13.043	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.031	0.018	20.288	0.331	0.331	0.000	0.000	0.000	0.000
65	A	66	MET	0	0.001	0.000	17.774	0.075	0.075	0.000	0.000	0.000	0.000
66	A	67	ARG	1	0.790	0.911	21.131	12.049	12.049	0.000	0.000	0.000	0.000
67	A	68	ALA	0	0.055	0.022	24.317	0.245	0.245	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.004	0.002	23.440	0.294	0.294	0.000	0.000	0.000	0.000
69	A	70	HIS	0	-0.021	-0.029	20.838	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.057	-0.024	26.206	0.078	0.078	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.896	-0.946	29.218	-9.900	-9.900	0.000	0.000	0.000	0.000
72	A	73	LEU	0	-0.079	-0.035	26.494	0.245	0.245	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.012	-0.004	29.767	0.301	0.301	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.909	-0.945	32.391	-8.474	-8.474	0.000	0.000	0.000	0.000
75	A	76	ASN	0	-0.105	-0.045	33.907	0.501	0.501	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.031	-0.020	33.174	0.234	0.234	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.021	0.012	33.899	-0.147	-0.147	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.032	-0.021	27.195	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.027	-0.035	31.025	0.204	0.204	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.769	-0.888	28.526	-10.423	-10.423	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.016	0.010	28.443	-0.303	-0.303	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.006	0.020	29.228	-0.192	-0.192	0.000	0.000	0.000	0.000
83	A	84	PHE	0	-0.026	-0.005	20.215	-0.279	-0.279	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.924	-0.968	24.667	-11.367	-11.367	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.033	0.027	26.114	-0.235	-0.235	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.046	-0.023	22.452	-0.196	-0.196	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.008	0.005	21.609	-0.606	-0.606	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.911	-0.956	22.430	-10.969	-10.969	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.019	-0.017	24.641	-0.026	-0.026	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.013	0.004	16.675	-0.238	-0.238	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.033	0.017	20.888	-0.432	-0.432	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.006	-0.004	22.152	-0.073	-0.073	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.049	-0.048	20.589	0.211	0.211	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.018	-0.013	16.621	-0.392	-0.392	0.000	0.000	0.000	0.000
95	A	96	GLN	0	0.024	0.011	20.074	0.254	0.254	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.914	-0.938	23.385	-12.114	-12.114	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.106	-0.049	17.680	0.073	0.073	0.000	0.000	0.000	0.000
98	A	99	ASN	0	-0.060	-0.024	20.710	-0.096	-0.096	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.011	0.009	17.050	-0.286	-0.286	0.000	0.000	0.000	0.000
100	A	101	SER	0	-0.017	-0.007	19.821	0.832	0.832	0.000	0.000	0.000	0.000
101	A	102	GLN	0	0.050	0.011	20.097	-0.841	-0.841	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.842	-0.920	19.963	-14.063	-14.063	0.000	0.000	0.000	0.000
103	A	104	LEU	0	-0.024	-0.013	15.125	-0.464	-0.464	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.038	-0.015	16.214	-1.015	-1.015	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.864	-0.938	18.611	-13.640	-13.640	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.944	-0.965	14.420	-19.797	-19.797	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.029	-0.016	13.696	-0.544	-0.544	0.000	0.000	0.000	0.000
108	A	109	VAL	0	-0.002	-0.008	15.498	0.036	0.036	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.055	-0.034	16.542	0.575	0.575	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.052	-0.009	10.817	0.073	0.073	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.020	-0.012	14.642	0.249	0.249	0.000	0.000	0.000	0.000
112	A	113	GLY	0	-0.002	0.012	16.986	0.691	0.691	0.000	0.000	0.000	0.000
113	A	114	SER	0	-0.060	-0.041	16.002	0.416	0.416	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.007	-0.010	18.609	0.318	0.318	0.000	0.000	0.000	0.000
115	A	116	GLN	0	-0.045	-0.016	17.490	0.756	0.756	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.083	0.042	17.826	0.403	0.403	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.902	0.939	19.896	11.309	11.309	0.000	0.000	0.000	0.000
118	A	119	ASN	0	-0.012	-0.024	23.290	0.567	0.567	0.000	0.000	0.000	0.000
119	A	120	ASP	-1	-0.860	-0.924	20.412	-13.232	-13.232	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.028	-0.011	22.446	0.274	0.274	0.000	0.000	0.000	0.000
121	A	122	LEU	0	-0.060	-0.035	24.927	0.395	0.395	0.000	0.000	0.000	0.000
122	A	123	ASN	0	-0.041	-0.015	26.848	0.211	0.211	0.000	0.000	0.000	0.000
123	A	124	ARG	0	0.083	0.065	27.586	-0.946	-0.946	0.000	0.000	0.000	0.000

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