FMO DATABASE

FMODB ID: 1663Z

Calculation Name: 5J0G-A-Xray372

Preferred Name: Superoxide dismutase

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5J0G

Chain ID: A

ChEMBL ID: CHEMBL2354

UniProt ID: P00441

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	113
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-727771.228056
FMO2-HF: Nuclear repulsion	689288.9713
FMO2-HF: Total energy	-38482.256756
FMO2-MP2: Total energy	-38597.376377

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:ALA)

Summations of interaction energy for fragment #1(A:1: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.
-0.797	0.403	-0.012	-0.606	-0.581	0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.024

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	SER	0	-0.018	-0.011	3.859	-1.428	-0.228	-0.012	-0.606	-0.581	0.002
4	A	4	ARG	1	0.846	0.905	5.795	0.191	0.191	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.009	0.000	8.090	-0.099	-0.099	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.031	0.027	11.843	0.072	0.072	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.057	-0.034	15.181	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.059	0.025	17.619	0.011	0.011	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.041	-0.014	21.175	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.009	0.012	24.041	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.018	0.020	26.867	0.005	0.005	0.000	0.000	0.000	0.000
12	A	12	ILE	0	-0.006	-0.016	29.982	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.030	-0.001	33.643	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.023	-0.036	35.548	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.025	0.021	38.249	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.046	0.016	40.875	0.000	0.000	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.022	-0.004	44.413	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.007	0.009	43.155	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.032	-0.009	41.256	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.042	-0.026	35.905	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.862	0.923	35.485	0.010	0.010	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.012	0.005	30.960	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.000	-0.002	28.453	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.015	0.021	23.866	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.012	-0.004	24.109	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.033	-0.009	19.633	0.007	0.007	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.807	0.888	17.313	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.064	0.038	14.777	0.004	0.004	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.836	-0.887	10.502	0.199	0.199	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.009	-0.009	13.599	-0.031	-0.031	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.028	-0.011	15.876	0.012	0.012	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.018	0.010	14.356	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.015	0.008	17.659	0.025	0.025	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.049	0.015	20.638	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.041	-0.001	23.168	0.013	0.013	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.009	0.006	23.633	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.010	0.007	26.793	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.032	0.002	25.369	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.829	-0.901	31.475	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.027	0.014	35.199	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.809	0.885	37.276	0.023	0.023	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.748	-0.865	40.734	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.009	0.011	39.497	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.048	-0.032	37.919	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.008	0.023	38.972	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.017	0.014	35.888	0.000	0.000	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.025	-0.015	31.469	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.830	0.919	32.238	0.045	0.045	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.020	0.001	26.653	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	TRP	0	-0.061	-0.055	29.483	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.029	0.018	27.918	0.007	0.007	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.009	0.015	25.269	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.003	-0.008	19.064	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.928	0.960	21.213	0.031	0.031	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.042	0.014	18.969	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.020	0.001	15.015	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.008	0.002	12.227	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.770	-0.856	15.258	-0.167	-0.167	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.027	-0.014	16.277	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.004	-0.002	17.037	0.012	0.012	0.000	0.000	0.000	0.000
61	A	61	HIS	1	0.822	0.912	13.361	0.256	0.256	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.050	0.042	14.592	0.035	0.035	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.024	-0.008	16.108	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.003	-0.007	16.516	-0.019	-0.019	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.006	0.009	19.819	0.007	0.007	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.030	0.017	18.081	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.012	0.008	20.376	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.001	-0.011	22.611	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.026	0.011	25.154	0.004	0.004	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.059	0.037	23.763	0.003	0.003	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.863	-0.933	20.959	-0.158	-0.158	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.008	-0.002	22.111	0.011	0.011	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.016	0.020	21.201	0.000	0.000	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.075	-0.065	17.353	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.023	0.032	19.263	0.020	0.020	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.009	-0.033	19.223	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.023	0.004	18.239	0.017	0.017	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.773	-0.905	20.296	-0.119	-0.119	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.772	0.854	21.038	0.130	0.130	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.918	-0.941	22.424	-0.076	-0.076	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.042	-0.015	19.823	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.059	-0.045	20.410	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.004	-0.001	20.534	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.890	-0.947	22.636	-0.064	-0.064	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.041	-0.028	23.650	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.019	-0.016	26.496	0.011	0.011	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.014	0.014	24.885	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.935	-0.973	29.540	-0.035	-0.035	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.765	-0.872	29.641	-0.065	-0.065	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.071	-0.057	31.798	0.006	0.006	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.029	0.014	28.719	0.004	0.004	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.012	-0.001	27.091	0.006	0.006	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.036	-0.005	30.127	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.028	-0.008	31.413	0.002	0.002	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.044	-0.034	33.683	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.042	0.026	35.849	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.880	-0.949	34.179	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.040	-0.016	30.149	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.033	-0.001	30.146	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.022	0.001	26.907	0.004	0.004	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.002	-0.007	27.437	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.028	-0.009	28.082	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.780	0.892	23.936	0.019	0.019	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.016	-0.018	18.383	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.017	0.025	20.779	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.039	-0.034	15.486	0.017	0.017	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.020	0.007	16.026	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	108	HIS	0	-0.033	-0.012	11.203	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.793	-0.906	10.324	-0.124	-0.124	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.819	0.896	6.386	0.909	0.909	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.050	0.035	9.570	0.041	0.041	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.030	-0.006	11.372	-0.084	-0.084	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.040	0.006	11.569	-0.115	-0.115	0.000	0.000	0.000	0.000

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