FMO DATABASE

FMODB ID: 7YZLK

Calculation Name: 1J30-A-Xray547

Preferred Name:

Target Type:

Ligand Name: fe (iii) ion | oxygen molecule

Ligand 3-letter code: FE | OXY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J30

Chain ID: A

ChEMBL ID:

UniProt ID: F9VPE5

Base Structure: X-ray

Registration Date: 2025-10-03

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	141
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1127089.647314
FMO2-HF: Nuclear repulsion	1072259.45026
FMO2-HF: Total energy	-54830.197053
FMO2-MP2: Total energy	-54991.50496

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:ASP)

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

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.
-33.738	-30.428	11.092	-7.08	-7.322	0.076

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.016

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	LYS	1	1.011	1.019	1.837	-40.439	-38.011	11.067	-6.845	-6.650	0.072
4	A	6	GLY	0	-0.006	0.001	3.697	-5.586	-5.084	0.026	-0.202	-0.327	0.004
66	A	68	GLY	0	-0.036	-0.014	4.139	7.639	7.870	0.000	-0.029	-0.202	0.000
67	A	69	LEU	0	-0.098	-0.037	4.795	2.848	2.997	-0.001	-0.004	-0.143	0.000
5	A	7	THR	0	-0.045	-0.035	5.012	-3.474	-3.474	0.000	0.000	0.000	0.000
6	A	8	LYS	1	0.948	0.958	7.751	0.463	0.463	0.000	0.000	0.000	0.000
7	A	9	THR	0	0.010	-0.006	8.299	0.683	0.683	0.000	0.000	0.000	0.000
8	A	10	ALA	0	0.043	0.033	6.668	0.051	0.051	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.823	-0.902	8.758	2.210	2.210	0.000	0.000	0.000	0.000
10	A	12	ASN	0	-0.021	-0.016	12.132	0.126	0.126	0.000	0.000	0.000	0.000
11	A	13	LEU	0	0.010	0.020	9.437	-0.146	-0.146	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.906	0.956	12.668	-2.467	-2.467	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.005	-0.010	14.212	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.019	0.010	16.415	-0.127	-0.127	0.000	0.000	0.000	0.000
15	A	17	PHE	0	0.037	0.006	16.459	-0.038	-0.038	0.000	0.000	0.000	0.000
16	A	18	ILE	0	0.000	0.019	18.103	-0.061	-0.061	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.020	0.009	20.459	-0.063	-0.063	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.823	-0.934	20.635	-0.161	-0.161	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.030	-0.018	21.283	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	22	MET	0	-0.028	-0.025	23.938	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	23	ALA	0	-0.051	-0.011	25.866	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.066	0.030	26.758	0.034	0.034	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.876	0.927	27.406	-0.414	-0.414	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.932	0.974	29.406	-0.161	-0.161	0.000	0.000	0.000	0.000
25	A	27	TYR	0	-0.001	0.001	29.443	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.024	0.011	31.291	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	29	TYR	0	-0.049	-0.018	34.287	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	30	PHE	0	0.004	-0.019	34.554	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.001	0.008	37.179	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	32	LYS	1	0.965	0.986	38.617	-0.228	-0.228	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.861	0.940	40.935	-0.112	-0.112	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.006	0.005	41.638	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.814	-0.873	42.270	0.067	0.067	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.968	-0.977	44.947	0.120	0.120	0.000	0.000	0.000	0.000
35	A	37	GLU	-1	-0.879	-0.946	46.699	0.056	0.056	0.000	0.000	0.000	0.000
36	A	38	GLY	0	-0.006	0.016	47.967	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	39	TYR	0	-0.028	-0.015	45.145	-0.020	-0.020	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.032	0.001	44.205	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.939	-0.963	42.853	-0.107	-0.107	0.000	0.000	0.000	0.000
40	A	42	ILE	0	0.026	0.010	40.602	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	43	ALA	0	0.026	0.007	39.403	0.001	0.001	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.021	-0.011	38.520	0.013	0.013	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.004	0.001	35.774	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	46	LEU	0	-0.018	-0.011	35.031	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	47	ARG	1	0.790	0.847	33.635	-0.060	-0.060	0.000	0.000	0.000	0.000
46	A	48	SER	0	-0.007	0.003	32.759	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.012	0.000	30.129	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.003	0.002	29.117	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.890	-0.922	28.172	0.075	0.075	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.013	-0.001	26.674	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.856	-0.953	24.594	-0.194	-0.194	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.037	-0.024	23.335	0.077	0.077	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.001	0.003	22.437	0.040	0.040	0.000	0.000	0.000	0.000
54	A	56	HIS	1	0.782	0.906	20.160	0.224	0.224	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.018	0.008	18.672	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	58	PHE	0	0.024	-0.002	18.026	0.166	0.166	0.000	0.000	0.000	0.000
57	A	59	GLY	0	0.076	0.050	16.470	0.059	0.059	0.000	0.000	0.000	0.000
58	A	60	HIS	0	-0.066	-0.040	14.247	-0.203	-0.203	0.000	0.000	0.000	0.000
59	A	61	LEU	0	0.012	0.005	13.096	0.309	0.309	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.826	-0.887	13.092	0.607	0.607	0.000	0.000	0.000	0.000
61	A	63	PHE	0	-0.068	-0.046	9.639	-0.164	-0.164	0.000	0.000	0.000	0.000
62	A	64	ILE	0	-0.018	-0.010	8.425	0.244	0.244	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.843	0.912	8.386	0.678	0.678	0.000	0.000	0.000	0.000
64	A	66	GLN	0	-0.050	-0.033	9.036	0.610	0.610	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.029	-0.003	4.976	-1.795	-1.795	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.071	-0.054	7.117	-1.062	-1.062	0.000	0.000	0.000	0.000
69	A	71	ASP	-1	-0.803	-0.885	10.632	1.765	1.765	0.000	0.000	0.000	0.000
70	A	72	PRO	0	-0.048	-0.040	13.682	0.082	0.082	0.000	0.000	0.000	0.000
71	A	73	ALA	0	-0.024	0.003	15.318	-0.120	-0.120	0.000	0.000	0.000	0.000
72	A	74	THR	0	-0.040	-0.040	16.892	0.040	0.040	0.000	0.000	0.000	0.000
73	A	75	ASP	-1	-0.886	-0.917	12.169	5.428	5.428	0.000	0.000	0.000	0.000
74	A	76	LYS	1	0.910	0.971	14.198	-2.778	-2.778	0.000	0.000	0.000	0.000
75	A	77	PRO	0	0.021	0.009	11.494	0.228	0.228	0.000	0.000	0.000	0.000
76	A	78	ILE	0	0.042	0.008	12.261	-0.565	-0.565	0.000	0.000	0.000	0.000
77	A	79	GLY	0	0.011	0.013	13.137	-0.302	-0.302	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.010	-0.013	13.676	-0.427	-0.427	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.077	0.027	17.429	0.090	0.090	0.000	0.000	0.000	0.000
80	A	82	GLU	-1	-0.832	-0.907	20.521	1.486	1.486	0.000	0.000	0.000	0.000
81	A	83	GLN	0	0.027	0.018	13.907	0.099	0.099	0.000	0.000	0.000	0.000
82	A	84	MET	0	-0.006	0.001	16.835	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	85	ILE	0	-0.004	0.009	19.052	-0.070	-0.070	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.840	-0.930	19.181	2.151	2.151	0.000	0.000	0.000	0.000
85	A	87	SER	0	-0.061	-0.036	17.414	0.038	0.038	0.000	0.000	0.000	0.000
86	A	88	ALA	0	0.027	0.016	19.348	-0.077	-0.077	0.000	0.000	0.000	0.000
87	A	89	ILE	0	-0.024	-0.016	22.812	-0.095	-0.095	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.029	-0.002	20.444	-0.068	-0.068	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.038	0.016	22.093	-0.046	-0.046	0.000	0.000	0.000	0.000
90	A	92	GLU	0	0.013	-0.040	23.101	-0.106	-0.106	0.000	0.000	0.000	0.000
91	A	93	THR	0	-0.031	-0.039	26.075	-0.120	-0.120	0.000	0.000	0.000	0.000
92	A	94	TYR	0	-0.014	0.024	24.654	-0.068	-0.068	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.876	-0.954	25.661	0.986	0.986	0.000	0.000	0.000	0.000
94	A	96	TRP	0	0.000	-0.003	28.545	-0.097	-0.097	0.000	0.000	0.000	0.000
95	A	97	THR	0	-0.103	-0.069	29.385	-0.040	-0.040	0.000	0.000	0.000	0.000
96	A	98	GLN	0	-0.040	-0.021	27.296	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	99	MET	0	-0.027	0.014	27.649	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.008	0.007	29.862	-0.079	-0.079	0.000	0.000	0.000	0.000
99	A	101	PRO	0	0.032	0.009	33.021	-0.055	-0.055	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.010	0.014	33.592	-0.040	-0.040	0.000	0.000	0.000	0.000
101	A	103	PHE	0	-0.024	-0.026	29.204	-0.032	-0.032	0.000	0.000	0.000	0.000
102	A	104	ALA	0	0.004	0.006	35.079	-0.045	-0.045	0.000	0.000	0.000	0.000
103	A	105	LYS	1	0.793	0.883	37.938	-0.609	-0.609	0.000	0.000	0.000	0.000
104	A	106	VAL	0	0.032	0.017	35.892	-0.028	-0.028	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.038	0.023	38.826	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	108	ARG	1	0.828	0.913	40.560	-0.479	-0.479	0.000	0.000	0.000	0.000
107	A	109	GLU	-1	-0.873	-0.920	40.702	0.506	0.506	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.960	-0.983	39.735	0.434	0.434	0.000	0.000	0.000	0.000
109	A	111	GLY	0	-0.028	0.001	43.646	-0.021	-0.021	0.000	0.000	0.000	0.000
110	A	112	PHE	0	-0.023	-0.012	41.614	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	113	PRO	0	0.014	-0.002	43.397	0.023	0.023	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.889	-0.950	44.417	0.306	0.306	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.008	-0.006	38.959	0.015	0.015	0.000	0.000	0.000	0.000
114	A	116	ALA	0	0.026	0.017	39.590	0.032	0.032	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.941	-0.972	40.280	0.395	0.395	0.000	0.000	0.000	0.000
116	A	118	TRP	0	-0.015	0.011	35.688	0.003	0.003	0.000	0.000	0.000	0.000
117	A	119	PHE	0	0.041	0.009	34.351	0.028	0.028	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.859	-0.946	36.580	0.579	0.579	0.000	0.000	0.000	0.000
119	A	121	THR	0	-0.105	-0.064	38.851	0.007	0.007	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.002	0.006	33.116	0.007	0.007	0.000	0.000	0.000	0.000
121	A	123	ALA	0	0.026	0.019	33.937	0.040	0.040	0.000	0.000	0.000	0.000
122	A	124	ARG	1	0.904	0.950	34.796	-0.469	-0.469	0.000	0.000	0.000	0.000
123	A	125	ALA	0	-0.001	0.019	34.702	0.006	0.006	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.756	-0.839	30.058	0.805	0.805	0.000	0.000	0.000	0.000
125	A	127	LYS	1	0.892	0.959	31.018	-0.646	-0.646	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.014	-0.014	33.075	0.011	0.011	0.000	0.000	0.000	0.000
127	A	129	HIS	0	-0.103	-0.068	29.760	-0.050	-0.050	0.000	0.000	0.000	0.000
128	A	130	ALA	0	0.019	0.015	28.639	0.039	0.039	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.894	-0.954	29.675	0.751	0.751	0.000	0.000	0.000	0.000
130	A	132	LYS	1	0.886	0.942	31.841	-0.595	-0.595	0.000	0.000	0.000	0.000
131	A	133	PHE	0	0.038	0.010	26.311	0.000	0.000	0.000	0.000	0.000	0.000
132	A	134	GLN	0	0.030	0.008	27.776	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	135	ASN	0	-0.051	-0.025	29.132	0.008	0.008	0.000	0.000	0.000	0.000
134	A	136	VAL	0	0.024	0.020	26.942	-0.021	-0.021	0.000	0.000	0.000	0.000
135	A	137	LEU	0	-0.001	0.002	23.194	0.002	0.002	0.000	0.000	0.000	0.000
136	A	138	LYS	1	0.873	0.931	27.039	-0.797	-0.797	0.000	0.000	0.000	0.000
137	A	139	GLN	0	-0.007	0.007	30.290	-0.019	-0.019	0.000	0.000	0.000	0.000
138	A	140	LEU	0	-0.041	-0.028	24.214	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.778	0.868	21.729	-1.682	-1.682	0.000	0.000	0.000	0.000
140	A	142	GLY	0	-0.065	-0.012	27.455	0.000	0.000	0.000	0.000	0.000	0.000
141	A	143	GLY	-1	-0.970	-0.973	30.766	0.589	0.589	0.000	0.000	0.000	0.000

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