FMO DATABASE

FMODB ID: RL468

Calculation Name: 2ZBO-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | sulfate ion

Ligand 3-letter code: HEM | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2ZBO

Chain ID: A

ChEMBL ID:

UniProt ID: Q76FN8

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	86
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-543678.583127
FMO2-HF: Nuclear repulsion	510479.470789
FMO2-HF: Total energy	-33199.112337
FMO2-MP2: Total energy	-33292.6087

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.
-194.718	-185.337	11.259	-10.389	-10.25	-0.102

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 : 0.812 / q_NPA : 0.901

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

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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	ILE	0	0.001	-0.021	3.160	3.863	5.362	0.092	-0.525	-1.065	0.000
4	A	28	ASN	0	-0.034	-0.011	4.915	4.951	5.066	-0.001	-0.004	-0.110	0.000
71	A	95	GLU	-1	-0.877	-0.948	2.409	-77.785	-72.446	0.979	-3.494	-2.824	-0.037
72	A	96	ASP	-1	-0.784	-0.889	2.174	-89.645	-87.529	7.577	-5.428	-4.266	-0.055
73	A	97	VAL	0	-0.038	-0.023	3.241	3.761	3.414	-0.002	0.450	-0.101	-0.001
75	A	99	SER	0	-0.018	-0.022	2.449	-0.157	0.470	2.615	-1.371	-1.871	-0.009
76	A	100	PHE	0	-0.041	-0.012	4.532	3.494	3.526	-0.001	-0.017	-0.013	0.000
5	A	29	HIS	0	-0.013	-0.011	6.194	4.694	4.694	0.000	0.000	0.000	0.000
6	A	30	GLY	0	0.044	0.015	5.297	2.998	2.998	0.000	0.000	0.000	0.000
7	A	31	GLU	-1	-0.924	-0.960	6.116	-20.499	-20.499	0.000	0.000	0.000	0.000
8	A	32	ASN	0	-0.001	0.004	9.330	4.100	4.100	0.000	0.000	0.000	0.000
9	A	33	VAL	0	0.006	0.007	8.589	2.457	2.457	0.000	0.000	0.000	0.000
10	A	34	PHE	0	0.033	-0.006	9.896	2.164	2.164	0.000	0.000	0.000	0.000
11	A	35	THR	0	-0.043	-0.032	11.514	2.181	2.181	0.000	0.000	0.000	0.000
12	A	36	ALA	0	-0.023	0.006	13.923	1.337	1.337	0.000	0.000	0.000	0.000
13	A	37	ASN	0	-0.076	-0.040	13.133	1.730	1.730	0.000	0.000	0.000	0.000
14	A	38	CYS	0	-0.015	-0.003	11.996	0.552	0.552	0.000	0.000	0.000	0.000
15	A	39	SER	0	-0.014	-0.009	15.341	1.151	1.151	0.000	0.000	0.000	0.000
16	A	40	ALA	0	0.004	-0.008	17.206	0.582	0.582	0.000	0.000	0.000	0.000
17	A	41	CYS	0	-0.056	-0.028	18.935	0.845	0.845	0.000	0.000	0.000	0.000
18	A	42	HIS	0	0.005	-0.002	16.035	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	43	ALA	0	0.044	0.024	17.069	-0.690	-0.690	0.000	0.000	0.000	0.000
20	A	44	GLY	0	-0.011	-0.013	18.143	0.535	0.535	0.000	0.000	0.000	0.000
21	A	45	GLY	0	0.047	0.036	16.346	0.137	0.137	0.000	0.000	0.000	0.000
22	A	46	ASN	0	-0.029	-0.011	17.234	0.355	0.355	0.000	0.000	0.000	0.000
23	A	47	ASN	0	-0.002	-0.030	19.284	-0.262	-0.262	0.000	0.000	0.000	0.000
24	A	48	VAL	0	-0.013	0.004	21.602	0.557	0.557	0.000	0.000	0.000	0.000
25	A	49	ILE	0	-0.012	-0.002	23.712	0.503	0.503	0.000	0.000	0.000	0.000
26	A	50	MET	0	-0.039	-0.028	23.759	0.544	0.544	0.000	0.000	0.000	0.000
27	A	51	PRO	0	0.035	0.017	23.905	-0.449	-0.449	0.000	0.000	0.000	0.000
28	A	52	GLU	-1	-0.920	-0.957	24.088	-10.886	-10.886	0.000	0.000	0.000	0.000
29	A	53	LYS	1	0.790	0.901	20.988	12.270	12.270	0.000	0.000	0.000	0.000
30	A	54	THR	0	0.028	0.021	19.728	-0.683	-0.683	0.000	0.000	0.000	0.000
31	A	55	LEU	0	0.002	0.003	13.273	-0.369	-0.369	0.000	0.000	0.000	0.000
32	A	56	GLN	0	0.075	0.045	15.229	-1.643	-1.643	0.000	0.000	0.000	0.000
33	A	57	LYS	1	0.906	0.920	14.957	18.779	18.779	0.000	0.000	0.000	0.000
34	A	58	ASP	-1	-0.852	-0.901	17.255	-13.646	-13.646	0.000	0.000	0.000	0.000
35	A	59	ALA	0	0.028	0.032	20.062	0.247	0.247	0.000	0.000	0.000	0.000
36	A	60	LEU	0	0.015	0.008	13.665	0.121	0.121	0.000	0.000	0.000	0.000
37	A	61	SER	0	-0.045	-0.047	17.558	-0.288	-0.288	0.000	0.000	0.000	0.000
38	A	62	THR	0	-0.070	-0.043	19.045	0.446	0.446	0.000	0.000	0.000	0.000
39	A	63	ASN	0	-0.078	-0.051	19.753	0.873	0.873	0.000	0.000	0.000	0.000
40	A	64	GLN	0	-0.044	-0.019	18.562	-0.345	-0.345	0.000	0.000	0.000	0.000
41	A	65	MET	0	-0.012	0.005	14.218	-0.525	-0.525	0.000	0.000	0.000	0.000
42	A	66	ASN	0	-0.012	0.010	13.469	-1.853	-1.853	0.000	0.000	0.000	0.000
43	A	67	SER	0	-0.002	-0.018	11.137	-0.315	-0.315	0.000	0.000	0.000	0.000
44	A	68	VAL	0	0.101	0.052	5.238	2.122	2.122	0.000	0.000	0.000	0.000
45	A	69	GLY	0	0.013	0.032	8.193	0.364	0.364	0.000	0.000	0.000	0.000
46	A	70	ALA	0	0.009	0.007	10.896	0.994	0.994	0.000	0.000	0.000	0.000
47	A	71	ILE	0	0.018	0.009	9.508	1.022	1.022	0.000	0.000	0.000	0.000
48	A	72	THR	0	0.029	-0.003	7.154	1.572	1.572	0.000	0.000	0.000	0.000
49	A	73	TYR	0	0.008	0.029	9.925	1.731	1.731	0.000	0.000	0.000	0.000
50	A	74	GLN	0	0.009	-0.025	13.615	1.546	1.546	0.000	0.000	0.000	0.000
51	A	75	VAL	0	0.004	0.008	10.945	1.240	1.240	0.000	0.000	0.000	0.000
52	A	76	THR	0	0.015	-0.010	12.401	0.702	0.702	0.000	0.000	0.000	0.000
53	A	77	ASN	0	-0.043	-0.045	14.540	1.468	1.468	0.000	0.000	0.000	0.000
54	A	78	GLY	0	0.014	0.031	17.182	0.933	0.933	0.000	0.000	0.000	0.000
55	A	79	LYS	1	0.907	0.938	18.978	13.603	13.603	0.000	0.000	0.000	0.000
56	A	80	ASN	0	-0.053	-0.032	21.099	0.037	0.037	0.000	0.000	0.000	0.000
57	A	81	ALA	0	0.039	0.026	24.595	0.175	0.175	0.000	0.000	0.000	0.000
58	A	82	MET	0	-0.027	0.018	14.854	0.132	0.132	0.000	0.000	0.000	0.000
59	A	83	PRO	0	0.010	0.000	19.571	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	84	ALA	0	0.038	0.019	18.157	-0.679	-0.679	0.000	0.000	0.000	0.000
61	A	85	PHE	0	-0.032	-0.022	14.305	0.652	0.652	0.000	0.000	0.000	0.000
62	A	86	GLY	0	0.049	0.027	14.840	-0.548	-0.548	0.000	0.000	0.000	0.000
63	A	87	GLY	0	-0.041	-0.008	15.876	0.008	0.008	0.000	0.000	0.000	0.000
64	A	88	ARG	1	0.776	0.884	16.556	16.751	16.751	0.000	0.000	0.000	0.000
65	A	89	LEU	0	-0.026	-0.002	11.155	0.055	0.055	0.000	0.000	0.000	0.000
66	A	90	SER	0	-0.011	-0.021	10.102	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	91	ASP	-1	-0.883	-0.964	9.681	-25.516	-25.516	0.000	0.000	0.000	0.000
68	A	92	ASP	-1	-0.905	-0.944	5.660	-42.292	-42.292	0.000	0.000	0.000	0.000
69	A	93	ASP	-1	-0.793	-0.868	5.362	-32.367	-32.367	0.000	0.000	0.000	0.000
70	A	94	ILE	0	-0.034	-0.015	7.237	-0.280	-0.280	0.000	0.000	0.000	0.000
74	A	98	ALA	0	-0.023	-0.013	5.877	2.701	2.701	0.000	0.000	0.000	0.000
77	A	101	VAL	0	0.002	0.003	6.403	3.259	3.259	0.000	0.000	0.000	0.000
78	A	102	LEU	0	-0.007	-0.005	7.663	2.349	2.349	0.000	0.000	0.000	0.000
79	A	103	SER	0	-0.033	-0.012	6.785	3.237	3.237	0.000	0.000	0.000	0.000
80	A	104	GLN	0	0.033	0.008	8.776	1.269	1.269	0.000	0.000	0.000	0.000
81	A	105	SER	0	-0.018	-0.021	11.762	2.036	2.036	0.000	0.000	0.000	0.000
82	A	106	GLU	-1	-0.878	-0.919	11.460	-18.870	-18.870	0.000	0.000	0.000	0.000
83	A	107	LYS	1	0.880	0.959	11.692	23.665	23.665	0.000	0.000	0.000	0.000
84	A	108	SER	0	-0.042	-0.018	15.473	1.274	1.274	0.000	0.000	0.000	0.000
85	A	109	TRP	0	-0.082	-0.044	11.982	0.563	0.563	0.000	0.000	0.000	0.000
86	A	110	ASN	-1	-0.971	-0.960	16.606	-15.738	-15.738	0.000	0.000	0.000	0.000

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