FMO DATABASE

FMODB ID: 3Z8ML

Calculation Name: 5C0Z-A-Xray547

Preferred Name:

Target Type:

Ligand Name: heme c | hexacyanoferrate(3-)

Ligand 3-letter code: HEC | FC6

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5C0Z

Chain ID: A

ChEMBL ID:

UniProt ID: P62898

Base Structure: X-ray

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-786830.115169
FMO2-HF: Nuclear repulsion	746504.471326
FMO2-HF: Total energy	-40325.643844
FMO2-MP2: Total energy	-40442.783527

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:GLY)

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

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.
138.032	141.062	11.036	-7.556	-6.51	-0.069

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.908

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	VAL	0	0.061	0.017	3.816	3.661	4.354	-0.002	-0.196	-0.494	0.000
90	A	90	GLU	-1	-0.842	-0.947	4.820	-30.150	-30.023	-0.001	-0.009	-0.117	0.000
92	A	92	ALA	0	0.071	0.024	3.139	-1.038	-0.514	0.017	-0.280	-0.261	-0.001
93	A	93	ASP	-1	-0.869	-0.924	2.081	-97.687	-95.128	8.619	-6.890	-4.288	-0.052
94	A	94	LEU	0	-0.017	-0.003	2.869	3.698	2.435	0.062	1.182	0.019	-0.001
96	A	96	ALA	0	0.008	0.007	1.926	0.474	0.643	2.342	-1.236	-1.275	-0.014
97	A	97	TYR	0	-0.002	-0.003	4.031	6.723	6.944	-0.001	-0.127	-0.094	-0.001
4	A	4	GLU	-1	-0.871	-0.933	6.225	-22.059	-22.059	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.830	0.908	6.047	40.050	40.050	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.029	0.005	5.860	3.256	3.256	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.976	0.998	6.719	24.980	24.980	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.899	0.946	10.210	28.534	28.534	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.005	0.005	7.068	2.004	2.004	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.045	0.014	10.518	1.800	1.800	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.017	-0.015	12.217	1.728	1.728	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.003	0.008	14.338	0.159	0.159	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.878	0.937	12.588	22.433	22.433	0.000	0.000	0.000	0.000
14	A	14	CYS	0	-0.035	-0.011	13.653	-0.124	-0.124	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.026	0.017	16.006	0.942	0.942	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.028	0.021	17.679	1.270	1.270	0.000	0.000	0.000	0.000
17	A	17	CYS	0	-0.003	0.000	20.037	0.855	0.855	0.000	0.000	0.000	0.000
18	A	18	HIS	0	-0.051	-0.030	17.486	0.335	0.335	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.017	-0.021	19.189	-0.126	-0.126	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.033	-0.029	13.970	-0.461	-0.461	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.759	-0.883	17.010	-15.896	-15.896	0.000	0.000	0.000	0.000
22	A	22	LYS	1	1.024	1.012	19.042	13.916	13.916	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.001	0.001	21.166	0.488	0.488	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.018	0.002	22.326	0.454	0.454	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.945	0.976	23.329	12.839	12.839	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.043	0.027	24.021	-1.003	-1.003	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.819	0.904	21.262	14.425	14.425	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.026	0.012	24.126	0.246	0.246	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.009	0.004	21.907	0.170	0.170	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.050	-0.012	20.624	0.210	0.210	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.012	-0.019	20.358	-0.914	-0.914	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.076	-0.050	14.838	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.016	-0.010	16.229	-0.683	-0.683	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.051	0.026	16.958	0.887	0.887	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.066	-0.033	13.831	0.604	0.604	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.005	-0.015	8.818	-0.262	-0.262	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.030	0.019	14.216	0.740	0.740	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.856	0.942	16.971	17.001	17.001	0.000	0.000	0.000	0.000
39	A	39	LYS	1	0.940	0.967	18.717	12.725	12.725	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.017	-0.015	20.104	-0.244	-0.244	0.000	0.000	0.000	0.000
41	A	41	GLY	0	0.050	0.028	21.869	0.550	0.550	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.059	-0.032	22.787	0.883	0.883	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.018	0.017	22.079	-0.037	-0.037	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.049	0.014	23.759	0.483	0.483	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.050	0.024	27.065	-0.093	-0.093	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.035	-0.002	25.619	0.095	0.095	0.000	0.000	0.000	0.000
47	A	47	SER	0	0.030	0.018	27.944	0.178	0.178	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.051	-0.026	21.763	-0.112	-0.112	0.000	0.000	0.000	0.000
49	A	49	THR	0	0.015	0.007	27.336	0.228	0.228	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.819	-0.919	28.226	-10.164	-10.164	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.017	0.005	27.113	-0.166	-0.166	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.029	-0.036	21.523	-0.533	-0.533	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.900	0.944	24.801	10.799	10.799	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.036	0.015	27.281	-0.139	-0.139	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.834	0.942	21.093	14.276	14.276	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.036	0.022	24.245	-0.180	-0.180	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.050	-0.017	17.855	-0.079	-0.079	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.012	-0.005	17.073	0.506	0.506	0.000	0.000	0.000	0.000
59	A	59	TRP	0	-0.001	0.009	14.565	-0.835	-0.835	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.086	0.028	11.994	0.183	0.183	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.867	-0.925	5.722	-47.543	-47.543	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.849	-0.919	9.277	-25.358	-25.358	0.000	0.000	0.000	0.000
63	A	63	THR	0	-0.006	-0.027	11.768	0.121	0.121	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.014	-0.003	10.463	1.046	1.046	0.000	0.000	0.000	0.000
65	A	65	MET	0	-0.039	-0.021	7.955	-1.186	-1.186	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.861	-0.923	10.958	-16.039	-16.039	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.023	-0.032	14.766	1.196	1.196	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.003	-0.015	10.272	0.832	0.832	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.906	-0.929	13.519	-20.208	-20.208	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.022	-0.026	14.739	1.194	1.194	0.000	0.000	0.000	0.000
71	A	71	PRO	0	0.058	0.035	17.114	0.486	0.486	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.978	0.983	19.245	12.548	12.548	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.951	0.989	20.651	15.174	15.174	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.019	0.020	17.930	0.488	0.488	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.012	-0.009	20.574	0.263	0.263	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.039	0.021	23.382	0.101	0.101	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.061	0.029	26.473	0.240	0.240	0.000	0.000	0.000	0.000
78	A	78	THR	0	-0.046	-0.016	22.111	0.274	0.274	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.943	0.977	25.280	11.251	11.251	0.000	0.000	0.000	0.000
80	A	80	MET	0	-0.020	0.013	16.352	0.023	0.023	0.000	0.000	0.000	0.000
81	A	81	ILE	0	0.015	0.008	22.409	-0.238	-0.238	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.001	-0.001	14.650	-0.271	-0.271	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.008	-0.003	19.701	0.100	0.100	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.011	0.016	15.648	0.104	0.104	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.073	-0.037	10.010	0.385	0.385	0.000	0.000	0.000	0.000
86	A	86	LYS	1	1.024	1.002	12.446	15.337	15.337	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.960	0.991	10.460	20.702	20.702	0.000	0.000	0.000	0.000
88	A	88	LYS	1	1.051	1.014	8.607	26.957	26.957	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.026	0.023	5.520	-3.697	-3.697	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.787	0.877	6.585	23.113	23.113	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.001	-0.002	5.584	2.574	2.574	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.015	0.009	7.248	3.767	3.767	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.841	0.935	6.233	44.099	44.099	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.924	0.979	6.951	39.045	39.045	0.000	0.000	0.000	0.000
101	A	101	ALA	0	0.097	0.042	10.066	2.013	2.013	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.109	-0.072	11.897	1.851	1.851	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.102	-0.066	11.603	2.405	2.405	0.000	0.000	0.000	0.000
104	A	104	GLU	-2	-1.787	-1.859	14.007	-37.919	-37.919	0.000	0.000	0.000	0.000

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