FMO DATABASE

FMODB ID: Y12K2

Calculation Name: 1F1C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c

Ligand 3-letter code: HEC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F1C

Chain ID: A

ChEMBL ID:

UniProt ID: P82603

Base Structure: X-ray

Registration Date: 2025-10-05

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	129
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1095277.841244
FMO2-HF: Nuclear repulsion	1045714.330536
FMO2-HF: Total energy	-49563.510708
FMO2-MP2: Total energy	-49709.115836

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-19.738	-13.301	9.095	-3.645	-11.886	-0.026

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.917

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	5	GLU	-1	-0.768	-0.895	3.145	-38.480	-35.889	0.075	-1.200	-1.465	-0.006
5	A	7	LEU	0	-0.017	-0.019	2.402	-1.316	-0.834	3.018	-0.776	-2.724	-0.010
6	A	8	ARG	1	0.714	0.840	2.377	43.941	45.198	2.010	-0.551	-2.717	-0.005
7	A	9	THR	0	0.019	0.013	4.718	3.989	4.058	-0.001	-0.019	-0.049	0.000
21	A	23	LEU	0	0.020	-0.005	2.330	-0.619	-0.072	1.336	-0.331	-1.552	0.003
22	A	24	LYS	1	0.952	0.965	4.650	23.606	23.676	-0.001	-0.004	-0.065	0.000
24	A	26	ILE	0	0.085	0.041	3.268	0.499	0.934	0.038	-0.095	-0.377	0.000
119	A	121	LEU	0	-0.058	-0.026	2.288	-3.455	-2.886	1.950	-0.456	-2.063	-0.006
123	A	125	VAL	0	-0.074	-0.048	2.616	-3.868	-3.451	0.670	-0.213	-0.874	-0.002
4	A	6	GLU	-1	-0.898	-0.920	5.850	-25.977	-25.977	0.000	0.000	0.000	0.000
8	A	10	PHE	0	-0.013	-0.020	4.810	-0.511	-0.511	0.000	0.000	0.000	0.000
9	A	11	PRO	0	0.093	0.044	10.426	0.365	0.365	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.023	-0.014	14.104	-0.164	-0.164	0.000	0.000	0.000	0.000
11	A	13	ASN	0	-0.010	-0.041	15.410	0.419	0.419	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.045	0.021	18.452	-0.434	-0.434	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.046	-0.023	20.876	0.323	0.323	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.013	0.017	18.788	0.246	0.246	0.000	0.000	0.000	0.000
15	A	17	ASP	-1	-0.856	-0.890	18.266	-14.138	-14.138	0.000	0.000	0.000	0.000
16	A	18	THR	0	-0.040	-0.033	13.075	-0.390	-0.390	0.000	0.000	0.000	0.000
17	A	19	ALA	0	0.000	0.008	12.415	0.620	0.620	0.000	0.000	0.000	0.000
18	A	20	VAL	0	0.005	0.003	7.823	-1.503	-1.503	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.025	0.037	7.089	0.537	0.537	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.034	-0.055	6.066	-4.505	-4.505	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.811	-0.860	8.114	-21.996	-21.996	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.893	0.953	6.118	32.679	32.679	0.000	0.000	0.000	0.000
26	A	28	LYS	1	1.001	1.000	8.551	19.469	19.469	0.000	0.000	0.000	0.000
27	A	29	GLY	0	0.070	0.040	10.340	1.355	1.355	0.000	0.000	0.000	0.000
28	A	30	GLN	0	-0.048	-0.020	8.574	0.383	0.383	0.000	0.000	0.000	0.000
29	A	31	GLN	0	-0.079	-0.044	10.733	0.323	0.323	0.000	0.000	0.000	0.000
30	A	32	VAL	0	0.048	0.024	13.829	0.981	0.981	0.000	0.000	0.000	0.000
31	A	33	PHE	0	0.045	0.022	13.174	0.744	0.744	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.028	-0.037	12.988	0.767	0.767	0.000	0.000	0.000	0.000
33	A	35	ALA	0	-0.070	-0.021	16.159	0.768	0.768	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.008	-0.014	18.592	0.738	0.738	0.000	0.000	0.000	0.000
35	A	37	CYS	0	-0.004	0.018	16.969	0.424	0.424	0.000	0.000	0.000	0.000
36	A	38	ALA	0	0.009	-0.001	16.874	0.351	0.351	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.002	0.002	18.675	0.253	0.253	0.000	0.000	0.000	0.000
38	A	40	CYS	0	0.028	0.007	22.178	0.375	0.375	0.000	0.000	0.000	0.000
39	A	41	HIS	1	0.877	0.941	17.817	13.286	13.286	0.000	0.000	0.000	0.000
40	A	42	ALA	0	-0.012	-0.010	17.102	-0.876	-0.876	0.000	0.000	0.000	0.000
41	A	43	LEU	0	-0.030	-0.034	14.948	0.368	0.368	0.000	0.000	0.000	0.000
42	A	44	GLY	0	0.069	0.035	15.442	-0.329	-0.329	0.000	0.000	0.000	0.000
43	A	45	VAL	0	0.041	0.041	16.051	0.473	0.473	0.000	0.000	0.000	0.000
44	A	46	THR	0	-0.013	-0.040	19.877	-0.364	-0.364	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.874	0.927	22.002	12.292	12.292	0.000	0.000	0.000	0.000
46	A	48	THR	0	-0.021	-0.009	25.346	0.139	0.139	0.000	0.000	0.000	0.000
47	A	49	ASN	0	0.011	0.002	26.530	0.265	0.265	0.000	0.000	0.000	0.000
48	A	50	PRO	0	0.025	0.022	24.703	-0.350	-0.350	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.842	-0.909	23.834	-10.608	-10.608	0.000	0.000	0.000	0.000
50	A	52	VAL	0	-0.035	0.004	23.372	-0.334	-0.334	0.000	0.000	0.000	0.000
51	A	53	ASN	0	-0.020	-0.012	19.198	-0.742	-0.742	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.036	-0.025	15.330	-0.144	-0.144	0.000	0.000	0.000	0.000
53	A	55	SER	0	0.080	0.055	14.879	-1.076	-1.076	0.000	0.000	0.000	0.000
54	A	56	PRO	0	-0.034	-0.026	13.306	0.202	0.202	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.853	-0.936	15.391	-14.478	-14.478	0.000	0.000	0.000	0.000
56	A	58	ALA	0	0.019	0.023	18.941	0.582	0.582	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.017	-0.006	14.765	0.398	0.398	0.000	0.000	0.000	0.000
58	A	60	ALA	0	0.004	-0.001	18.547	0.388	0.388	0.000	0.000	0.000	0.000
59	A	61	LEU	0	-0.047	-0.021	20.133	0.471	0.471	0.000	0.000	0.000	0.000
60	A	62	ALA	0	-0.032	0.011	22.119	0.466	0.466	0.000	0.000	0.000	0.000
61	A	63	THR	0	-0.036	0.000	23.921	0.068	0.068	0.000	0.000	0.000	0.000
62	A	64	PRO	0	-0.024	-0.040	24.021	0.173	0.173	0.000	0.000	0.000	0.000
63	A	65	PRO	0	0.031	0.030	21.137	-0.152	-0.152	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.772	0.857	18.798	11.609	11.609	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.813	-0.913	15.682	-14.990	-14.990	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.051	-0.035	14.691	-0.816	-0.816	0.000	0.000	0.000	0.000
67	A	69	ILE	0	-0.008	-0.012	10.803	0.404	0.404	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.010	-0.006	14.778	0.425	0.425	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.045	0.037	18.524	0.534	0.534	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.004	0.012	13.697	0.370	0.370	0.000	0.000	0.000	0.000
71	A	73	VAL	0	-0.033	-0.023	16.355	0.310	0.310	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.881	-0.927	18.698	-10.699	-10.699	0.000	0.000	0.000	0.000
73	A	75	TYR	0	-0.002	0.006	20.077	0.398	0.398	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.027	-0.024	16.778	0.254	0.254	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.782	0.867	21.314	11.832	11.832	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.042	-0.032	24.063	0.555	0.555	0.000	0.000	0.000	0.000
77	A	79	PRO	0	0.002	0.027	24.269	0.004	0.004	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.007	0.012	25.725	0.289	0.289	0.000	0.000	0.000	0.000
79	A	81	THR	0	-0.030	-0.045	26.707	-0.273	-0.273	0.000	0.000	0.000	0.000
80	A	82	TYR	0	-0.032	-0.033	22.877	0.060	0.060	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.816	-0.898	27.133	-9.137	-9.137	0.000	0.000	0.000	0.000
82	A	84	GLY	0	-0.006	-0.004	28.312	0.159	0.159	0.000	0.000	0.000	0.000
83	A	85	PHE	0	-0.089	-0.037	29.142	0.115	0.115	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.003	0.008	32.099	0.251	0.251	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.783	-0.853	30.059	-9.271	-9.271	0.000	0.000	0.000	0.000
86	A	88	ILE	0	0.014	-0.005	26.973	0.233	0.233	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.025	-0.039	28.571	-0.107	-0.107	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.907	-0.954	29.625	-8.237	-8.237	0.000	0.000	0.000	0.000
89	A	91	LEU	0	-0.027	-0.020	30.802	0.061	0.061	0.000	0.000	0.000	0.000
90	A	92	HIS	0	-0.036	-0.017	21.789	-0.447	-0.447	0.000	0.000	0.000	0.000
91	A	93	PRO	0	-0.041	-0.026	22.907	0.067	0.067	0.000	0.000	0.000	0.000
92	A	94	SER	0	0.059	0.027	23.845	-0.222	-0.222	0.000	0.000	0.000	0.000
93	A	95	LEU	0	0.001	-0.007	23.305	0.218	0.218	0.000	0.000	0.000	0.000
94	A	96	LYS	1	0.806	0.901	26.502	9.474	9.474	0.000	0.000	0.000	0.000
95	A	97	SER	0	0.067	0.043	27.851	0.240	0.240	0.000	0.000	0.000	0.000
96	A	98	SER	0	-0.075	-0.047	27.572	0.006	0.006	0.000	0.000	0.000	0.000
97	A	99	ASP	-1	-0.932	-0.965	28.975	-8.721	-8.721	0.000	0.000	0.000	0.000
98	A	100	ILE	0	-0.004	-0.001	30.463	0.113	0.113	0.000	0.000	0.000	0.000
99	A	101	PHE	0	0.010	0.013	26.034	-0.264	-0.264	0.000	0.000	0.000	0.000
100	A	102	PRO	0	0.024	0.001	27.061	-0.329	-0.329	0.000	0.000	0.000	0.000
101	A	103	LYS	1	0.879	0.936	22.410	11.954	11.954	0.000	0.000	0.000	0.000
102	A	104	MET	0	0.021	0.014	21.149	-0.548	-0.548	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.898	0.952	24.506	9.622	9.622	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.049	-0.021	24.132	0.427	0.427	0.000	0.000	0.000	0.000
105	A	107	ILE	0	-0.047	0.003	19.497	-0.424	-0.424	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.011	-0.017	19.166	0.282	0.282	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.755	-0.884	19.520	-12.586	-12.586	0.000	0.000	0.000	0.000
108	A	110	ASP	-1	-0.906	-0.945	16.112	-15.321	-15.321	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.882	-0.926	14.869	-16.345	-16.345	0.000	0.000	0.000	0.000
110	A	112	LEU	0	-0.006	0.006	15.043	-0.737	-0.737	0.000	0.000	0.000	0.000
111	A	113	TYR	0	0.029	0.017	11.874	-0.542	-0.542	0.000	0.000	0.000	0.000
112	A	114	ASN	0	-0.040	-0.031	10.905	-2.112	-2.112	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.030	-0.029	10.213	-1.730	-1.730	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.020	0.029	11.555	-0.688	-0.688	0.000	0.000	0.000	0.000
115	A	117	GLY	0	0.053	0.018	8.615	-0.571	-0.571	0.000	0.000	0.000	0.000
116	A	118	TYR	0	-0.056	-0.029	6.993	-2.830	-2.830	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.017	0.006	7.963	-1.398	-1.398	0.000	0.000	0.000	0.000
118	A	120	LEU	0	0.040	0.026	9.287	-0.427	-0.427	0.000	0.000	0.000	0.000
120	A	122	GLN	0	-0.064	-0.025	6.014	-1.470	-1.470	0.000	0.000	0.000	0.000
121	A	123	PRO	0	0.091	0.043	8.090	-0.874	-0.874	0.000	0.000	0.000	0.000
122	A	124	LYS	1	0.867	0.954	5.144	28.993	28.993	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.856	0.942	5.814	24.070	24.070	0.000	0.000	0.000	0.000
125	A	127	GLY	0	0.051	0.042	9.493	1.412	1.412	0.000	0.000	0.000	0.000
126	A	128	GLU	-1	-0.895	-0.964	11.526	-15.480	-15.480	0.000	0.000	0.000	0.000
127	A	129	GLN	0	-0.119	-0.056	11.775	1.199	1.199	0.000	0.000	0.000	0.000
128	A	130	TRP	0	-0.165	-0.076	11.824	-0.556	-0.556	0.000	0.000	0.000	0.000
129	A	131	GLY	-1	-0.864	-0.920	13.838	-14.443	-14.443	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)