FMO DATABASE

FMODB ID: KKQZ3

Calculation Name: 1F1F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F1F

Chain ID: A

ChEMBL ID:

UniProt ID: P00118

Base Structure: X-ray

Registration Date: 2025-09-02

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	88
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-544505.042352
FMO2-HF: Nuclear repulsion	511830.716731
FMO2-HF: Total energy	-32674.325621
FMO2-MP2: Total energy	-32767.920122

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:ASP)

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

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.
-17.246	-13.761	14.682	-9.892	-8.276	-0.092

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.038

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	ALA	0	0.027	0.016	3.872	0.010	1.581	-0.002	-0.711	-0.858	0.000
4	A	5	ALA	0	0.013	0.018	2.582	3.509	4.459	0.159	-0.419	-0.690	0.000
5	A	6	GLY	0	0.056	0.023	4.095	4.619	5.080	-0.001	-0.224	-0.237	0.001
71	A	72	LEU	0	0.039	0.036	4.725	0.740	0.911	-0.001	-0.004	-0.166	0.000
75	A	76	ASP	-1	-0.851	-0.917	1.903	-44.259	-44.348	14.523	-8.464	-5.970	-0.093
76	A	77	VAL	0	-0.057	-0.044	3.619	0.493	0.490	0.000	0.013	-0.009	0.000
78	A	79	ALA	0	0.057	0.026	3.920	-0.409	0.015	0.004	-0.083	-0.346	0.000
6	A	7	ALA	0	0.028	0.012	5.651	2.783	2.783	0.000	0.000	0.000	0.000
7	A	8	SER	0	-0.030	-0.004	7.820	1.888	1.888	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.022	-0.006	7.192	1.306	1.306	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.048	0.004	9.540	1.189	1.189	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.055	-0.045	11.490	0.698	0.698	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.004	0.011	12.761	0.408	0.408	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.063	-0.032	12.463	0.651	0.651	0.000	0.000	0.000	0.000
13	A	14	CYS	0	-0.030	-0.003	13.240	0.245	0.245	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.019	0.008	15.568	0.280	0.280	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.004	-0.001	17.156	0.164	0.164	0.000	0.000	0.000	0.000
16	A	17	CYS	0	-0.021	-0.003	19.399	0.147	0.147	0.000	0.000	0.000	0.000
17	A	18	HIS	1	0.834	0.902	16.657	0.775	0.775	0.000	0.000	0.000	0.000
18	A	19	MET	0	0.064	0.037	17.436	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.014	0.002	18.399	0.129	0.129	0.000	0.000	0.000	0.000
20	A	21	GLY	0	0.094	0.058	16.672	0.115	0.115	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.936	0.968	17.577	0.577	0.577	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.041	-0.037	19.903	-0.087	-0.087	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.000	0.004	22.385	0.053	0.053	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.007	0.017	23.706	0.030	0.030	0.000	0.000	0.000	0.000
25	A	26	VAL	0	-0.026	-0.024	25.044	0.052	0.052	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.036	0.015	25.092	0.015	0.015	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.025	-0.011	25.859	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.893	0.962	22.375	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.026	-0.024	20.813	-0.063	-0.063	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.004	-0.004	14.220	0.055	0.055	0.000	0.000	0.000	0.000
31	A	32	SER	0	0.033	0.017	16.323	0.071	0.071	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.901	0.952	16.791	-0.569	-0.569	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.014	0.005	18.141	0.089	0.089	0.000	0.000	0.000	0.000
34	A	35	ASP	-1	-0.788	-0.881	21.292	0.109	0.109	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.019	-0.006	14.840	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.039	0.025	18.932	0.063	0.063	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.813	0.921	20.658	-0.218	-0.218	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.079	-0.045	22.242	-0.043	-0.043	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.058	-0.015	15.938	-0.076	-0.076	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.922	0.948	19.843	-0.469	-0.469	0.000	0.000	0.000	0.000
41	A	42	GLY	0	0.141	0.080	18.762	0.047	0.047	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.055	-0.032	13.830	0.207	0.207	0.000	0.000	0.000	0.000
43	A	44	ASP	-1	-0.955	-0.986	16.112	1.218	1.218	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.929	-0.943	17.741	1.322	1.322	0.000	0.000	0.000	0.000
45	A	46	ASP	-1	-0.867	-0.954	11.276	4.238	4.238	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.029	0.013	11.976	-0.117	-0.117	0.000	0.000	0.000	0.000
47	A	48	VAL	0	-0.019	-0.009	6.374	-0.459	-0.459	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.074	0.034	9.685	-0.643	-0.643	0.000	0.000	0.000	0.000
49	A	50	ALA	0	-0.002	0.010	11.806	-0.522	-0.522	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.034	-0.022	11.352	-0.462	-0.462	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.062	0.027	9.853	-0.568	-0.568	0.000	0.000	0.000	0.000
52	A	53	TYR	0	0.009	0.019	11.809	-0.473	-0.473	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.020	-0.019	15.459	-0.340	-0.340	0.000	0.000	0.000	0.000
54	A	55	VAL	0	0.005	0.001	11.429	-0.211	-0.211	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.005	-0.015	13.947	-0.231	-0.231	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.052	-0.038	15.682	-0.193	-0.193	0.000	0.000	0.000	0.000
57	A	58	GLY	0	0.004	0.025	18.435	-0.081	-0.081	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.872	0.911	20.042	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	60	ASN	0	-0.045	-0.025	23.574	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.057	0.035	25.379	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	62	MET	0	-0.042	0.012	15.984	-0.120	-0.120	0.000	0.000	0.000	0.000
62	A	63	PRO	0	0.017	0.004	19.362	0.083	0.083	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.046	0.032	18.375	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.046	-0.045	14.586	-0.151	-0.151	0.000	0.000	0.000	0.000
65	A	66	ASN	0	0.006	0.006	15.801	-0.088	-0.088	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.008	0.007	17.026	0.021	0.021	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.854	0.923	16.277	1.226	1.226	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.029	-0.006	10.899	-0.280	-0.280	0.000	0.000	0.000	0.000
69	A	70	SER	0	0.025	0.001	9.879	0.301	0.301	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.062	-0.003	10.125	-0.412	-0.412	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.060	0.043	5.713	-0.563	-0.563	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.036	-0.014	7.129	-0.501	-0.501	0.000	0.000	0.000	0.000
74	A	75	GLU	-1	-0.845	-0.928	5.250	5.762	5.762	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.013	0.005	6.927	0.370	0.370	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.040	-0.023	5.562	-0.622	-0.622	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.026	-0.017	6.973	0.317	0.317	0.000	0.000	0.000	0.000
81	A	82	VAL	0	0.013	0.015	8.963	-0.083	-0.083	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.795	-0.892	7.092	-0.339	-0.339	0.000	0.000	0.000	0.000
83	A	84	GLN	0	-0.012	0.007	9.159	-0.220	-0.220	0.000	0.000	0.000	0.000
84	A	85	ALA	0	-0.017	0.004	11.952	0.021	0.021	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.914	-0.976	12.312	1.054	1.054	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.778	0.856	9.814	0.292	0.292	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.057	-0.017	14.898	-0.047	-0.047	0.000	0.000	0.000	0.000
88	A	89	TRP	-1	-0.973	-0.976	12.616	-0.913	-0.913	0.000	0.000	0.000	0.000

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