FMO DATABASE

FMODB ID: 97662

Calculation Name: 1A4F-B-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: 1A4F

Chain ID: B

ChEMBL ID:

UniProt ID: P01990

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1353031.635968
FMO2-HF: Nuclear repulsion	1296507.271316
FMO2-HF: Total energy	-56524.364652
FMO2-MP2: Total energy	-56691.110391

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:VAL)

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

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.
59.342	65.787	3.607	-2.936	-7.116	-0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.914

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	TRP	0	-0.033	-0.035	2.885	-9.585	-4.520	1.013	-2.294	-3.785	-0.021
4	A	4	SER	0	-0.018	-0.044	4.509	2.420	2.484	-0.001	-0.012	-0.051	0.000
79	A	79	ASP	-1	-0.825	-0.908	4.920	-50.372	-50.305	-0.001	-0.006	-0.060	0.000
81	A	81	ILE	0	0.037	0.029	4.605	3.299	3.389	-0.001	-0.002	-0.086	0.000
132	A	132	LYS	1	0.739	0.877	2.460	46.509	47.354	0.733	-0.258	-1.320	-0.001
135	A	135	ARG	1	0.974	0.994	4.068	35.133	35.252	-0.001	-0.019	-0.099	0.000
136	A	136	VAL	0	-0.041	-0.031	2.431	-2.157	-1.994	1.866	-0.344	-1.685	-0.003
137	A	137	VAL	0	-0.003	0.008	5.380	0.228	0.260	-0.001	-0.001	-0.030	0.000
5	A	5	ALA	0	0.037	0.013	8.224	-0.622	-0.622	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.767	-0.865	11.080	-22.063	-22.063	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.785	-0.877	6.125	-39.150	-39.150	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.879	0.930	6.859	36.558	36.558	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.029	0.011	9.500	1.409	1.409	0.000	0.000	0.000	0.000
10	A	10	LEU	0	0.011	0.002	11.651	0.978	0.978	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.016	-0.001	7.177	0.777	0.777	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.043	-0.047	11.581	1.221	1.221	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.006	-0.005	14.112	1.025	1.025	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.009	0.005	15.179	0.837	0.837	0.000	0.000	0.000	0.000
15	A	15	TRP	0	0.037	0.003	14.428	0.513	0.513	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.020	0.000	16.490	0.598	0.598	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.830	0.897	19.592	13.917	13.917	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.017	-0.002	17.410	0.455	0.455	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.009	0.015	20.702	-0.122	-0.122	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.066	0.011	19.696	0.070	0.070	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.026	-0.015	21.800	-0.058	-0.058	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.865	-0.929	25.154	-10.462	-10.462	0.000	0.000	0.000	0.000
23	A	23	CYS	0	-0.046	-0.030	21.082	0.108	0.108	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.063	0.030	21.064	-0.323	-0.323	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.054	-0.017	22.001	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.785	-0.855	24.305	-11.315	-11.315	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.015	0.006	20.006	0.119	0.119	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.005	-0.003	22.133	-0.057	-0.057	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.014	-0.004	23.658	0.230	0.230	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.865	0.909	23.665	11.662	11.662	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.007	0.007	20.556	0.107	0.107	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.019	-0.003	23.715	0.259	0.259	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.036	-0.010	27.194	0.446	0.446	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.034	-0.012	24.526	0.278	0.278	0.000	0.000	0.000	0.000
35	A	35	TYR	0	0.025	0.016	20.931	0.132	0.132	0.000	0.000	0.000	0.000
36	A	36	PRO	0	0.045	0.037	25.649	-0.193	-0.193	0.000	0.000	0.000	0.000
37	A	37	TRP	0	0.020	-0.002	22.953	0.441	0.441	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.028	-0.031	23.036	0.077	0.077	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.005	-0.022	26.031	0.107	0.107	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.945	0.983	28.805	9.821	9.821	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.027	-0.019	24.267	0.158	0.158	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.005	-0.003	23.220	-0.154	-0.154	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.038	0.029	29.196	0.304	0.304	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.011	-0.006	30.837	0.260	0.260	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.014	-0.026	27.253	0.040	0.040	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.035	0.028	33.265	0.169	0.169	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.010	0.018	36.375	-0.069	-0.069	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.022	0.004	30.849	-0.174	-0.174	0.000	0.000	0.000	0.000
49	A	49	SER	0	-0.011	-0.017	34.616	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.046	0.022	36.311	0.072	0.072	0.000	0.000	0.000	0.000
51	A	51	PRO	0	0.077	0.032	33.020	-0.140	-0.140	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.040	0.013	33.594	-0.183	-0.183	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.016	0.002	35.893	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.017	-0.004	29.846	-0.114	-0.114	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.017	-0.016	29.872	-0.244	-0.244	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.006	0.009	32.151	-0.110	-0.110	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.027	-0.016	32.363	-0.076	-0.076	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.039	0.002	31.974	-0.346	-0.346	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.018	0.013	30.959	-0.183	-0.183	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.032	0.028	27.470	-0.447	-0.447	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.916	0.948	27.040	9.456	9.456	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.029	-0.012	27.171	-0.351	-0.351	0.000	0.000	0.000	0.000
63	A	63	HIS	0	0.011	-0.003	22.650	-0.152	-0.152	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.075	0.027	22.836	-0.616	-0.616	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.934	0.981	21.860	10.489	10.489	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.942	0.987	21.881	11.822	11.822	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.012	0.013	17.837	-0.745	-0.745	0.000	0.000	0.000	0.000
68	A	68	LEU	0	0.018	0.003	16.440	-1.022	-1.022	0.000	0.000	0.000	0.000
69	A	69	THR	0	-0.058	-0.042	17.206	-0.469	-0.469	0.000	0.000	0.000	0.000
70	A	70	SER	0	0.005	0.016	15.751	-0.724	-0.724	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.029	-0.004	10.999	-1.493	-1.493	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.032	0.013	12.742	-1.329	-1.329	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.892	-0.946	14.080	-18.399	-18.399	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.020	-0.016	8.984	-1.406	-1.406	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.009	-0.006	9.388	-2.228	-2.228	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.847	0.925	11.350	20.436	20.436	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.017	0.000	10.502	0.272	0.272	0.000	0.000	0.000	0.000
78	A	78	LEU	0	0.032	0.015	5.972	-2.509	-2.509	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.009	-0.007	6.206	-2.047	-2.047	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.927	0.960	7.419	28.697	28.697	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.013	-0.025	9.056	2.912	2.912	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.008	0.004	10.851	2.033	2.033	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.038	0.013	10.105	1.328	1.328	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.028	-0.002	13.178	0.868	0.868	0.000	0.000	0.000	0.000
87	A	87	GLN	0	0.050	0.025	14.615	0.428	0.428	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.016	-0.003	15.498	0.828	0.828	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.018	-0.007	14.154	0.610	0.610	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.777	-0.872	16.111	-15.048	-15.048	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.092	-0.034	19.661	0.898	0.898	0.000	0.000	0.000	0.000
92	A	92	HIS	0	-0.014	-0.038	17.641	1.073	1.073	0.000	0.000	0.000	0.000
93	A	93	CYS	0	-0.024	0.009	17.003	0.230	0.230	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.856	-0.936	19.754	-13.786	-13.786	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.852	0.919	22.973	13.240	13.240	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.047	-0.024	22.212	0.419	0.419	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.869	0.953	22.345	12.774	12.774	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.004	0.008	19.140	0.303	0.303	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.832	-0.897	19.206	-15.658	-15.658	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.057	0.010	13.983	-0.098	-0.098	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.794	-0.866	15.106	-17.299	-17.299	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.046	-0.040	16.889	0.525	0.525	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.009	-0.004	13.402	0.117	0.117	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.811	0.889	12.814	16.198	16.198	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.024	0.000	14.020	0.092	0.092	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.015	-0.008	17.040	0.499	0.499	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.018	-0.005	13.572	0.052	0.052	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.807	-0.914	14.282	-18.022	-18.022	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.033	-0.005	16.012	0.620	0.620	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.008	0.002	14.082	0.572	0.572	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.038	-0.015	12.154	0.210	0.210	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.003	0.009	16.272	0.584	0.584	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.053	-0.021	19.889	0.582	0.582	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.018	-0.014	15.090	0.523	0.523	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.028	0.012	19.050	0.407	0.407	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.036	-0.024	20.520	0.511	0.511	0.000	0.000	0.000	0.000
117	A	117	HIS	1	0.797	0.879	22.057	12.321	12.321	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.011	0.011	19.374	0.169	0.169	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.027	0.017	22.656	0.207	0.207	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.936	0.956	22.334	9.849	9.849	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.824	-0.871	20.000	-13.375	-13.375	0.000	0.000	0.000	0.000
122	A	122	PHE	0	-0.025	-0.014	14.728	-0.887	-0.887	0.000	0.000	0.000	0.000
123	A	123	THR	0	0.032	0.013	17.516	-0.098	-0.098	0.000	0.000	0.000	0.000
124	A	124	PRO	0	0.053	0.014	16.612	-0.747	-0.747	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.863	-0.925	13.789	-18.363	-18.363	0.000	0.000	0.000	0.000
126	A	126	CYS	0	-0.052	-0.011	12.362	-1.982	-1.982	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.003	-0.002	12.414	-0.773	-0.773	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.007	0.004	10.848	-1.209	-1.209	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.008	0.002	7.851	-2.723	-2.723	0.000	0.000	0.000	0.000
130	A	130	TRP	0	0.013	-0.008	7.578	-3.090	-3.090	0.000	0.000	0.000	0.000
131	A	131	GLN	0	0.015	0.003	9.499	0.228	0.228	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.005	0.005	5.483	-3.493	-3.493	0.000	0.000	0.000	0.000
134	A	134	VAL	0	0.012	0.013	6.516	-0.697	-0.697	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.016	0.011	8.871	1.478	1.478	0.000	0.000	0.000	0.000
139	A	139	HIS	0	-0.022	-0.012	6.089	-1.751	-1.751	0.000	0.000	0.000	0.000
140	A	140	ALA	0	-0.028	-0.021	7.677	1.152	1.152	0.000	0.000	0.000	0.000
141	A	141	LEU	0	-0.013	-0.008	9.103	1.902	1.902	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.025	0.026	11.404	1.637	1.637	0.000	0.000	0.000	0.000
143	A	143	ARG	1	0.945	0.974	8.385	29.548	29.548	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.835	0.905	12.457	18.093	18.093	0.000	0.000	0.000	0.000
145	A	145	TYR	0	-0.052	-0.034	15.500	1.338	1.338	0.000	0.000	0.000	0.000
146	A	146	HIS	-1	-0.991	-0.986	12.903	-18.567	-18.567	0.000	0.000	0.000	0.000

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