FMO DATABASE

FMODB ID: VV431

Calculation Name: 2KMY-A-Other547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KMY

Chain ID: A

ChEMBL ID:

UniProt ID: B8J2Z0

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-730849.498951
FMO2-HF: Nuclear repulsion	688551.279623
FMO2-HF: Total energy	-42298.219328
FMO2-MP2: Total energy	-42415.37094

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:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-51.244	-43.67	6.503	-6.75	-7.329	-0.073

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.924

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	ALA	0	0.031	0.016	3.477	-1.842	-0.626	0.016	-0.615	-0.617	0.000
30	A	30	CYS	0	0.005	-0.013	5.021	-0.486	-0.418	-0.001	-0.016	-0.051	0.000
41	A	41	GLU	-1	-0.862	-0.944	2.307	-107.314	-103.096	3.920	-4.185	-3.954	-0.053
43	A	43	TYR	0	0.039	0.008	2.538	-9.632	-7.560	2.568	-1.934	-2.707	-0.020
4	A	4	VAL	0	-0.005	-0.003	6.223	0.519	0.519	0.000	0.000	0.000	0.000
5	A	5	PRO	0	-0.022	-0.017	7.250	2.098	2.098	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.872	-0.923	10.484	-19.635	-19.635	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.964	0.968	13.742	15.600	15.600	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.066	-0.038	14.999	-0.776	-0.776	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.001	0.015	12.859	0.264	0.264	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.856	-0.947	16.129	-12.971	-12.971	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.021	-0.011	16.869	-0.443	-0.443	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.855	0.934	19.335	13.999	13.999	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.037	0.019	21.969	-0.383	-0.383	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.026	-0.015	24.556	0.102	0.102	0.000	0.000	0.000	0.000
15	A	15	GLN	0	0.032	0.002	28.050	0.135	0.135	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.942	0.980	27.315	10.134	10.134	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.012	-0.009	22.522	-0.444	-0.444	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.012	0.032	21.222	0.383	0.383	0.000	0.000	0.000	0.000
19	A	19	MET	0	0.011	0.013	19.897	-0.707	-0.707	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.026	0.004	12.204	0.523	0.523	0.000	0.000	0.000	0.000
21	A	21	PRO	0	-0.009	-0.001	15.710	-0.852	-0.852	0.000	0.000	0.000	0.000
22	A	22	HIS	0	0.101	0.027	9.444	-1.383	-1.383	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.053	0.037	12.610	-0.358	-0.358	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.043	-0.033	14.468	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	HIS	0	-0.070	-0.043	12.633	1.224	1.224	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.924	-0.954	10.499	-20.994	-20.994	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.958	0.980	10.542	15.407	15.407	0.000	0.000	0.000	0.000
28	A	28	VAL	0	-0.067	-0.019	12.010	0.604	0.604	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.863	-0.923	8.878	-27.272	-27.272	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.040	0.022	7.058	1.262	1.262	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.051	-0.021	8.615	2.491	2.491	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.056	-0.034	10.594	2.068	2.068	0.000	0.000	0.000	0.000
34	A	34	HIS	0	-0.022	-0.002	7.197	0.736	0.736	0.000	0.000	0.000	0.000
35	A	35	HIS	1	0.830	0.922	8.379	19.246	19.246	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.025	0.006	7.875	-0.751	-0.751	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.016	0.000	10.537	2.268	2.268	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.879	-0.942	12.616	-19.489	-19.489	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.003	0.014	13.567	0.346	0.346	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.901	0.944	8.225	31.013	31.013	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.021	-0.024	6.628	2.059	2.059	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.002	0.020	6.730	1.642	1.642	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.975	0.987	10.432	18.471	18.471	0.000	0.000	0.000	0.000
46	A	46	CYS	0	0.051	0.027	13.207	0.158	0.158	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.054	0.029	15.094	0.455	0.455	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.048	-0.041	14.414	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	SER	0	0.003	-0.017	16.999	0.296	0.296	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.007	0.009	18.951	-0.553	-0.553	0.000	0.000	0.000	0.000
51	A	51	CYS	0	-0.038	-0.016	16.014	-0.343	-0.343	0.000	0.000	0.000	0.000
52	A	52	HIS	0	-0.049	-0.028	16.277	-0.152	-0.152	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.860	-0.940	19.737	-13.478	-13.478	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.781	-0.873	21.795	-10.663	-10.663	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.033	-0.028	22.021	-0.232	-0.232	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.055	-0.028	25.460	0.311	0.311	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.015	0.001	28.557	0.344	0.344	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.924	0.947	27.804	9.064	9.064	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.949	0.963	27.718	9.207	9.207	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.103	0.059	26.714	0.256	0.256	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.919	-0.964	21.538	-12.898	-12.898	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.987	0.993	21.179	11.921	11.921	0.000	0.000	0.000	0.000
63	A	63	SER	0	-0.016	0.006	22.753	0.056	0.056	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.023	0.001	18.742	-0.322	-0.322	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.028	-0.013	21.823	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.025	0.009	23.859	0.350	0.350	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.029	-0.009	18.493	0.031	0.031	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.015	-0.001	19.280	-0.636	-0.636	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.018	-0.031	21.633	0.187	0.187	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.005	0.030	24.001	0.558	0.558	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.919	0.956	24.146	10.076	10.076	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.004	0.002	26.387	0.213	0.213	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.930	-0.954	25.507	-10.929	-10.929	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.017	-0.017	21.338	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.914	0.949	19.453	13.197	13.197	0.000	0.000	0.000	0.000
76	A	76	HIS	0	0.043	0.023	15.258	-0.530	-0.530	0.000	0.000	0.000	0.000
77	A	77	THR	0	-0.004	0.005	16.219	1.244	1.244	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.039	0.009	16.892	-0.767	-0.767	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.015	-0.015	18.214	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.039	0.022	19.728	0.255	0.255	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.002	0.015	21.743	0.526	0.526	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.021	-0.012	17.665	0.455	0.455	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.017	0.002	18.807	0.783	0.783	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.006	0.017	22.856	0.474	0.474	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.925	0.947	22.180	13.220	13.220	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.007	0.019	20.981	0.120	0.120	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.034	-0.028	24.362	0.281	0.281	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.042	-0.011	27.584	0.382	0.382	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.898	-0.945	27.601	-10.275	-10.275	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.885	0.952	26.535	10.950	10.950	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.077	0.033	29.884	-0.203	-0.203	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.887	-0.947	32.373	-8.646	-8.646	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.019	-0.009	26.281	-0.080	-0.080	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.974	1.002	28.241	8.553	8.553	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.933	0.961	29.633	9.056	9.056	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.844	-0.923	26.385	-10.503	-10.503	0.000	0.000	0.000	0.000
97	A	97	LEU	0	0.004	-0.009	21.801	-0.361	-0.361	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.006	-0.026	25.323	0.056	0.056	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.028	0.010	27.347	0.120	0.120	0.000	0.000	0.000	0.000
100	A	100	CYS	0	-0.030	-0.015	28.941	-0.200	-0.200	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.031	0.013	30.910	-0.059	-0.059	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.842	0.915	31.904	9.129	9.129	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.001	0.003	27.579	-0.048	-0.048	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.842	0.902	23.293	11.309	11.309	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.068	-0.021	22.596	-0.610	-0.610	0.000	0.000	0.000	0.000
106	A	106	HIS	0	0.004	0.005	24.560	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	107	PRO	-1	-0.823	-0.889	27.621	-9.123	-9.123	0.000	0.000	0.000	0.000

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