FMO DATABASE

FMODB ID: 3ZK7L

Calculation Name: 3S1I-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | oxygen molecule

Ligand 3-letter code: HEM | OXY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3S1I

Chain ID: A

ChEMBL ID:

UniProt ID: B3DUZ7

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1169906.166304
FMO2-HF: Nuclear repulsion	1118478.059539
FMO2-HF: Total energy	-51428.106765
FMO2-MP2: Total energy	-51579.805622

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:ILE)

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

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.
-56.519	-49.04	22.518	-11.85	-18.15	-0.105

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.808 / q_NPA : 0.888

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	GLN	0	0.062	0.008	3.565	-4.325	-2.124	0.041	-0.943	-1.299	0.001
5	A	6	GLU	-1	-0.765	-0.863	2.009	-105.509	-105.047	14.601	-8.191	-6.872	-0.087
6	A	7	LYS	1	0.845	0.933	2.399	45.341	45.783	2.564	-0.655	-2.351	-0.003
7	A	8	GLU	-1	-0.843	-0.914	4.020	-23.268	-23.160	0.004	-0.024	-0.088	0.000
9	A	10	ILE	0	-0.015	0.029	4.199	2.262	2.432	-0.001	-0.014	-0.156	0.000
64	A	65	ILE	0	0.005	0.008	3.072	-3.175	-2.594	0.092	-0.115	-0.559	0.000
65	A	66	ASP	-1	-0.807	-0.916	3.676	-37.468	-37.069	0.008	-0.132	-0.275	-0.001
67	A	68	LEU	0	0.044	0.024	2.927	1.234	1.955	0.128	-0.169	-0.681	-0.002
117	A	118	ALA	0	-0.005	0.000	4.181	-4.149	-3.987	0.000	-0.022	-0.140	0.000
118	A	119	TRP	0	0.022	-0.018	3.710	-5.028	-4.553	0.011	-0.148	-0.338	-0.001
120	A	121	LYS	1	0.837	0.903	2.551	58.379	59.046	1.433	-0.537	-1.562	0.000
121	A	122	VAL	0	-0.007	-0.002	2.565	-3.374	-2.295	1.480	-0.494	-2.064	-0.006
122	A	123	TYR	0	-0.048	-0.024	3.608	2.685	2.744	0.016	0.015	-0.091	0.000
124	A	125	ILE	0	0.011	0.002	2.447	-0.174	-0.221	2.141	-0.421	-1.674	-0.006
4	A	5	LYS	1	0.950	0.976	5.602	33.911	33.911	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.011	0.013	6.803	2.413	2.413	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.778	0.866	7.358	30.624	30.624	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.957	-0.978	9.744	-18.393	-18.393	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.005	-0.024	9.663	1.544	1.544	0.000	0.000	0.000	0.000
13	A	14	TRP	0	0.064	0.026	11.221	1.275	1.275	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.888	0.947	12.922	18.830	18.830	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.892	0.946	15.465	16.679	16.679	0.000	0.000	0.000	0.000
16	A	17	ILE	0	0.033	0.023	12.086	0.703	0.703	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.899	-0.928	16.171	-13.358	-13.358	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.002	-0.015	17.680	0.546	0.546	0.000	0.000	0.000	0.000
19	A	20	ASN	0	-0.007	0.003	19.874	1.048	1.048	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.869	0.922	18.535	13.768	13.768	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.034	-0.020	19.814	-0.340	-0.340	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.823	-0.919	23.124	-11.612	-11.612	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.020	0.019	16.799	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.024	0.010	19.199	-0.247	-0.247	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.083	-0.051	20.101	0.230	0.230	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.008	0.013	21.266	0.280	0.280	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.024	0.015	17.169	0.021	0.021	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.009	-0.016	19.660	0.006	0.006	0.000	0.000	0.000	0.000
29	A	30	ALA	0	-0.028	-0.005	22.745	0.307	0.307	0.000	0.000	0.000	0.000
30	A	31	ASN	0	-0.031	-0.034	21.003	0.762	0.762	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.010	-0.008	19.493	0.138	0.138	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.041	-0.038	22.389	0.208	0.208	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.941	0.981	25.896	10.745	10.745	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.972	-0.979	22.291	-11.482	-11.482	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.901	-0.958	21.773	-12.041	-12.041	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.006	0.007	24.862	0.078	0.078	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.039	-0.019	26.479	0.154	0.154	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.034	0.013	22.427	0.104	0.104	0.000	0.000	0.000	0.000
39	A	40	SER	0	-0.038	-0.027	25.600	0.053	0.053	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.012	-0.014	27.570	0.067	0.067	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.021	0.007	24.053	0.196	0.196	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.061	-0.033	21.517	-0.127	-0.127	0.000	0.000	0.000	0.000
43	A	44	GLN	0	0.008	0.006	27.367	0.327	0.327	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.028	-0.011	27.856	0.421	0.421	0.000	0.000	0.000	0.000
45	A	46	PRO	0	0.029	0.014	28.698	-0.194	-0.194	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.111	0.064	25.029	-0.279	-0.279	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.033	0.021	25.437	-0.430	-0.430	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.114	-0.077	26.255	-0.213	-0.213	0.000	0.000	0.000	0.000
49	A	50	GLN	0	0.023	0.006	20.710	0.004	0.004	0.000	0.000	0.000	0.000
50	A	51	SER	0	0.033	0.021	21.272	-0.809	-0.809	0.000	0.000	0.000	0.000
51	A	52	ARG	1	0.955	0.974	20.331	10.274	10.274	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.960	0.983	20.374	10.936	10.936	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.023	0.030	14.817	-0.542	-0.542	0.000	0.000	0.000	0.000
54	A	55	MET	0	0.023	0.015	15.791	-1.173	-1.173	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.032	-0.009	16.216	-0.245	-0.245	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.002	-0.005	12.920	-0.534	-0.534	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.004	0.001	10.872	-1.385	-1.385	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.043	0.015	11.368	-1.348	-1.348	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.034	-0.012	12.193	-0.467	-0.467	0.000	0.000	0.000	0.000
60	A	61	LEU	0	-0.002	-0.004	7.382	-0.990	-0.990	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.022	-0.011	7.268	-2.676	-2.676	0.000	0.000	0.000	0.000
62	A	63	GLN	0	-0.059	-0.028	8.806	-0.616	-0.616	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.013	0.003	8.691	0.382	0.382	0.000	0.000	0.000	0.000
66	A	67	ASN	0	-0.051	-0.032	6.080	-1.949	-1.949	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.895	-0.943	6.689	-27.274	-27.274	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.031	-0.010	9.563	2.184	2.184	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.056	-0.030	8.541	1.624	1.624	0.000	0.000	0.000	0.000
71	A	72	ILE	0	0.024	0.023	10.087	0.753	0.753	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.041	0.016	12.363	0.686	0.686	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.016	0.008	14.035	0.737	0.737	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.009	-0.002	9.256	0.614	0.614	0.000	0.000	0.000	0.000
75	A	76	GLN	0	0.069	0.039	13.709	1.071	1.071	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.925	-0.960	16.243	-13.251	-13.251	0.000	0.000	0.000	0.000
77	A	78	LEU	0	-0.093	-0.053	14.825	0.921	0.921	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.074	0.045	16.694	0.553	0.553	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.882	0.941	17.684	13.101	13.101	0.000	0.000	0.000	0.000
80	A	81	ARG	1	0.926	0.963	19.412	14.170	14.170	0.000	0.000	0.000	0.000
81	A	82	HIS	0	-0.004	-0.014	18.534	0.367	0.367	0.000	0.000	0.000	0.000
82	A	83	LYS	1	1.000	1.008	21.264	12.487	12.487	0.000	0.000	0.000	0.000
83	A	84	GLN	0	-0.079	-0.049	23.354	0.257	0.257	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.050	-0.019	21.985	0.288	0.288	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.037	0.022	25.621	0.113	0.113	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.042	-0.014	19.214	0.026	0.026	0.000	0.000	0.000	0.000
87	A	88	VAL	0	-0.013	-0.016	21.826	0.040	0.040	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.836	-0.928	18.077	-15.162	-15.162	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.039	-0.026	17.436	-0.789	-0.789	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.069	0.029	19.228	-0.307	-0.307	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.040	0.031	13.742	-0.378	-0.378	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.005	0.000	13.634	-0.831	-0.831	0.000	0.000	0.000	0.000
93	A	94	LEU	0	0.019	0.030	14.715	-0.452	-0.452	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.006	0.004	14.421	0.164	0.164	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.033	0.004	12.059	-0.188	-0.188	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.835	-0.901	12.716	-16.638	-16.638	0.000	0.000	0.000	0.000
97	A	98	CYS	0	0.021	0.026	14.671	0.464	0.464	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.027	0.002	11.760	0.447	0.447	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.033	-0.026	9.223	0.168	0.168	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.859	0.915	13.263	15.471	15.471	0.000	0.000	0.000	0.000
101	A	102	SER	0	0.063	0.014	16.915	0.813	0.813	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.064	-0.023	12.476	0.480	0.480	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.052	-0.036	14.872	0.423	0.423	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.899	-0.937	17.345	-11.780	-11.780	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.046	-0.029	20.048	0.530	0.530	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.020	-0.006	15.865	0.225	0.225	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.042	0.034	19.767	0.353	0.353	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.028	-0.029	18.807	-0.739	-0.739	0.000	0.000	0.000	0.000
109	A	110	GLY	0	-0.034	0.000	18.943	-0.262	-0.262	0.000	0.000	0.000	0.000
110	A	111	PHE	0	-0.024	-0.023	10.668	-0.858	-0.858	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.016	-0.002	13.241	0.085	0.085	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.783	-0.889	12.793	-21.578	-21.578	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.858	-0.921	10.135	-22.895	-22.895	0.000	0.000	0.000	0.000
114	A	115	ALA	0	0.017	0.007	8.424	-3.486	-3.486	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.886	0.938	8.261	18.931	18.931	0.000	0.000	0.000	0.000
116	A	117	ALA	0	0.008	0.014	7.772	-1.286	-1.286	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.043	-0.026	6.208	1.330	1.330	0.000	0.000	0.000	0.000
123	A	124	GLY	0	0.014	0.005	6.234	2.037	2.037	0.000	0.000	0.000	0.000
125	A	126	ALA	0	-0.002	-0.003	6.539	2.876	2.876	0.000	0.000	0.000	0.000
126	A	127	ALA	0	0.004	-0.006	8.774	2.089	2.089	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.001	0.013	8.209	-0.766	-0.766	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.003	0.007	9.232	1.559	1.559	0.000	0.000	0.000	0.000
129	A	130	MET	0	-0.128	-0.052	11.783	1.361	1.361	0.000	0.000	0.000	0.000
130	A	131	THR	0	-0.083	-0.067	14.247	1.106	1.106	0.000	0.000	0.000	0.000
131	A	132	ALA	-1	-0.966	-0.957	14.775	-17.460	-17.460	0.000	0.000	0.000	0.000

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