FMO DATABASE

FMODB ID: ZLKQN

Calculation Name: 5MCS-A-Other547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5MCS

Chain ID: A

ChEMBL ID:

UniProt ID: Q74AE4

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-445367.151707
FMO2-HF: Nuclear repulsion	415733.386766
FMO2-HF: Total energy	-29633.764941
FMO2-MP2: Total energy	-29718.376963

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:25:ALA)

Summations of interaction energy for fragment #1(A:25: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.
-6.369	-1.47	0.352	-2.06	-3.191	-0.016

Interaction energy analysis for fragmet #1(A:25:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.902 / q_NPA : 0.942

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	27	GLY	0	0.087	0.045	3.860	-0.426	0.591	-0.007	-0.411	-0.599	0.001
4	A	28	GLY	0	0.020	-0.005	2.902	5.530	6.297	0.137	-0.361	-0.544	-0.002
5	A	29	GLU	-1	-0.996	-0.992	2.763	-66.436	-63.951	0.205	-1.105	-1.585	-0.013
6	A	30	LEU	0	0.027	0.020	3.944	9.253	9.500	0.003	-0.073	-0.176	-0.001
74	A	98	TYR	0	-0.033	0.001	3.342	-4.204	-3.821	0.014	-0.110	-0.287	-0.001
7	A	31	PHE	0	0.058	0.012	6.228	5.109	5.109	0.000	0.000	0.000	0.000
8	A	32	ALA	0	-0.033	-0.024	5.424	5.278	5.278	0.000	0.000	0.000	0.000
9	A	33	THR	0	-0.019	-0.004	7.115	3.070	3.070	0.000	0.000	0.000	0.000
10	A	34	HIS	0	0.007	0.000	10.117	3.338	3.338	0.000	0.000	0.000	0.000
11	A	35	CYS	0	-0.061	-0.017	10.298	1.589	1.589	0.000	0.000	0.000	0.000
12	A	36	ALA	0	0.042	0.023	9.469	1.783	1.783	0.000	0.000	0.000	0.000
13	A	37	GLY	0	0.021	0.014	11.463	1.414	1.414	0.000	0.000	0.000	0.000
14	A	38	CYS	0	-0.047	-0.036	14.531	1.822	1.822	0.000	0.000	0.000	0.000
15	A	39	HIS	1	0.801	0.908	13.060	20.473	20.473	0.000	0.000	0.000	0.000
16	A	40	PRO	0	0.067	0.043	12.425	-2.179	-2.179	0.000	0.000	0.000	0.000
17	A	41	GLN	0	0.019	-0.013	11.834	1.522	1.522	0.000	0.000	0.000	0.000
18	A	42	GLY	0	0.019	0.026	11.997	0.860	0.860	0.000	0.000	0.000	0.000
19	A	43	GLY	0	0.011	0.013	13.073	1.313	1.313	0.000	0.000	0.000	0.000
20	A	44	ASN	0	-0.064	-0.058	16.279	-0.989	-0.989	0.000	0.000	0.000	0.000
21	A	45	THR	0	0.036	0.018	17.886	0.266	0.266	0.000	0.000	0.000	0.000
22	A	46	VAL	0	0.032	0.033	20.434	0.659	0.659	0.000	0.000	0.000	0.000
23	A	47	HIS	0	-0.035	-0.039	22.348	0.806	0.806	0.000	0.000	0.000	0.000
24	A	48	PRO	0	0.031	0.018	22.442	-0.621	-0.621	0.000	0.000	0.000	0.000
25	A	49	GLU	-1	-0.876	-0.927	23.730	-11.297	-11.297	0.000	0.000	0.000	0.000
26	A	50	LYS	1	0.839	0.906	22.132	12.043	12.043	0.000	0.000	0.000	0.000
27	A	51	THR	0	0.078	0.057	18.098	-0.628	-0.628	0.000	0.000	0.000	0.000
28	A	52	LEU	0	0.003	0.006	12.368	0.328	0.328	0.000	0.000	0.000	0.000
29	A	53	ALA	0	0.041	0.036	15.880	-0.478	-0.478	0.000	0.000	0.000	0.000
30	A	54	ARG	1	0.894	0.931	18.073	13.940	13.940	0.000	0.000	0.000	0.000
31	A	55	ALA	0	0.040	0.021	19.454	0.446	0.446	0.000	0.000	0.000	0.000
32	A	56	ARG	1	0.902	0.954	21.465	12.396	12.396	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.868	0.921	14.503	18.727	18.727	0.000	0.000	0.000	0.000
34	A	58	GLU	-1	-0.854	-0.912	20.953	-12.191	-12.191	0.000	0.000	0.000	0.000
35	A	59	ALA	0	-0.021	-0.004	23.694	0.297	0.297	0.000	0.000	0.000	0.000
36	A	60	ASN	0	-0.037	-0.024	23.725	0.334	0.334	0.000	0.000	0.000	0.000
37	A	61	GLY	0	0.044	0.039	23.862	0.110	0.110	0.000	0.000	0.000	0.000
38	A	62	ILE	0	-0.047	-0.022	17.943	-0.093	-0.093	0.000	0.000	0.000	0.000
39	A	63	ARG	1	0.876	0.936	17.793	12.806	12.806	0.000	0.000	0.000	0.000
40	A	64	THR	0	0.005	-0.028	17.371	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	65	VAL	0	0.018	0.018	13.027	0.014	0.014	0.000	0.000	0.000	0.000
42	A	66	ARG	1	0.993	0.988	15.155	14.055	14.055	0.000	0.000	0.000	0.000
43	A	67	ASP	-1	-0.792	-0.867	18.270	-14.674	-14.674	0.000	0.000	0.000	0.000
44	A	68	VAL	0	-0.060	-0.030	12.786	0.268	0.268	0.000	0.000	0.000	0.000
45	A	69	ALA	0	0.010	0.003	14.403	-1.413	-1.413	0.000	0.000	0.000	0.000
46	A	70	ALA	0	-0.030	-0.018	16.785	0.503	0.503	0.000	0.000	0.000	0.000
47	A	71	TYR	0	0.024	-0.002	19.984	0.446	0.446	0.000	0.000	0.000	0.000
48	A	72	ILE	0	-0.002	0.003	14.786	0.389	0.389	0.000	0.000	0.000	0.000
49	A	73	ARG	1	0.981	1.006	18.705	13.152	13.152	0.000	0.000	0.000	0.000
50	A	74	ASN	0	-0.096	-0.062	21.039	0.718	0.718	0.000	0.000	0.000	0.000
51	A	75	PRO	0	0.012	0.040	20.905	0.320	0.320	0.000	0.000	0.000	0.000
52	A	76	GLY	0	0.022	0.012	23.685	0.482	0.482	0.000	0.000	0.000	0.000
53	A	77	PRO	0	0.012	-0.006	24.954	-0.410	-0.410	0.000	0.000	0.000	0.000
54	A	78	GLY	0	0.005	0.001	24.866	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	79	MET	0	-0.063	-0.030	18.396	-0.909	-0.909	0.000	0.000	0.000	0.000
56	A	80	PRO	0	0.017	0.006	19.115	0.506	0.506	0.000	0.000	0.000	0.000
57	A	81	ALA	0	0.008	0.013	20.559	-0.141	-0.141	0.000	0.000	0.000	0.000
58	A	82	PHE	0	-0.025	-0.018	15.211	-0.315	-0.315	0.000	0.000	0.000	0.000
59	A	83	GLY	0	0.033	0.011	18.621	0.177	0.177	0.000	0.000	0.000	0.000
60	A	84	GLU	-1	-0.946	-0.992	19.188	-14.143	-14.143	0.000	0.000	0.000	0.000
61	A	85	ALA	0	-0.024	-0.005	20.277	-0.157	-0.157	0.000	0.000	0.000	0.000
62	A	86	MET	0	-0.043	-0.013	15.958	-0.188	-0.188	0.000	0.000	0.000	0.000
63	A	87	ILE	0	0.006	-0.001	11.990	-1.430	-1.430	0.000	0.000	0.000	0.000
64	A	88	PRO	0	0.032	0.040	15.347	0.943	0.943	0.000	0.000	0.000	0.000
65	A	89	PRO	0	0.043	-0.005	16.435	-1.157	-1.157	0.000	0.000	0.000	0.000
66	A	90	ALA	0	-0.007	-0.003	16.790	-0.375	-0.375	0.000	0.000	0.000	0.000
67	A	91	ASP	-1	-0.875	-0.943	12.473	-24.967	-24.967	0.000	0.000	0.000	0.000
68	A	92	ALA	0	-0.027	-0.009	12.083	-2.171	-2.171	0.000	0.000	0.000	0.000
69	A	93	LEU	0	-0.019	-0.018	13.264	-0.727	-0.727	0.000	0.000	0.000	0.000
70	A	94	LYS	1	0.964	1.005	7.225	35.695	35.695	0.000	0.000	0.000	0.000
71	A	95	ILE	0	-0.038	-0.026	8.670	-4.736	-4.736	0.000	0.000	0.000	0.000
72	A	96	GLY	0	0.024	-0.001	9.361	-1.067	-1.067	0.000	0.000	0.000	0.000
73	A	97	GLU	-1	-0.911	-0.962	8.306	-28.518	-28.518	0.000	0.000	0.000	0.000
75	A	99	VAL	0	-0.061	-0.032	6.830	0.802	0.802	0.000	0.000	0.000	0.000
76	A	100	VAL	0	-0.003	-0.008	9.672	2.285	2.285	0.000	0.000	0.000	0.000
77	A	101	ALA	0	-0.012	0.000	6.628	0.915	0.915	0.000	0.000	0.000	0.000
78	A	102	SER	0	-0.015	-0.012	8.546	-1.002	-1.002	0.000	0.000	0.000	0.000
79	A	103	PHE	0	-0.064	-0.038	10.545	1.466	1.466	0.000	0.000	0.000	0.000
80	A	104	PRO	-1	-0.852	-0.909	13.492	-16.925	-16.925	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:ALA)