FMO DATABASE

FMODB ID: YNNM2

Calculation Name: 5J0G-A-Xray372

Preferred Name: Superoxide dismutase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

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:

IFIE MAP

IFIE Diagram

Modeling method

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

FMO calculation

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

Total energy (hartree)

FMO2-HF: Electronic energy	-725688.511511
FMO2-HF: Nuclear repulsion	687206.824889
FMO2-HF: Total energy	-38481.686622
FMO2-MP2: Total energy	-38596.717989

3D Structure

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.
-0.472	0.883	-0.009	-0.688	-0.659	0.003

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 : -0.023 / 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	-0.031	-0.020	3.814	-1.489	-0.134	-0.009	-0.688	-0.659	0.003
4	A	4	ARG	1	0.925	0.971	5.472	0.376	0.376	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.007	-0.005	7.813	-0.039	-0.039	0.000	0.000	0.000	0.000
6	A	6	ALA	0	0.055	0.045	11.525	0.063	0.063	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.059	-0.038	14.780	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.057	0.026	17.607	0.016	0.016	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.039	-0.012	21.285	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.002	0.007	23.892	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.016	0.013	26.719	0.006	0.006	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.004	-0.005	29.894	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.034	-0.001	33.568	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.003	-0.031	35.276	0.001	0.001	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.009	0.013	38.141	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.028	0.011	40.873	0.001	0.001	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.039	-0.013	44.030	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.003	0.000	43.340	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.026	-0.005	40.944	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.029	-0.019	35.553	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.862	0.919	35.045	0.031	0.031	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.004	0.004	30.644	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.019	0.010	28.256	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.018	0.018	23.736	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.015	-0.009	23.764	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.044	-0.008	19.006	0.005	0.005	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.950	0.955	18.495	0.025	0.025	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.051	0.019	14.814	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.940	-0.954	10.477	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.024	-0.022	13.530	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.046	-0.029	15.430	0.014	0.014	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.011	0.016	13.831	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	GLN	0	-0.045	-0.029	17.138	0.019	0.019	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.051	0.025	20.334	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.046	-0.001	22.698	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	ILE	0	-0.003	0.006	23.039	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.008	-0.007	26.229	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.036	0.005	25.020	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.854	-0.929	31.043	-0.037	-0.037	0.000	0.000	0.000	0.000
40	A	40	GLN	0	0.025	-0.007	34.712	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.939	0.976	37.021	0.038	0.038	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.898	-0.954	40.467	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.003	0.004	39.206	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.017	-0.028	37.953	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.013	0.040	38.770	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.005	0.017	35.463	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.013	-0.018	31.043	0.004	0.004	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.896	0.967	31.987	0.066	0.066	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.003	-0.011	25.996	0.004	0.004	0.000	0.000	0.000	0.000
50	A	50	TRP	0	-0.053	-0.036	28.739	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.024	0.020	27.314	0.005	0.005	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.006	0.018	24.882	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.023	-0.016	18.549	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.962	0.984	21.176	0.066	0.066	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.030	0.003	18.306	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.009	0.006	14.836	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	57	THR	0	0.008	-0.002	12.269	0.016	0.016	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.846	-0.910	15.221	-0.195	-0.195	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.022	-0.005	16.581	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.005	0.000	16.836	0.011	0.011	0.000	0.000	0.000	0.000
61	A	61	HIS	1	0.812	0.872	12.998	0.309	0.309	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.055	0.042	14.191	0.037	0.037	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.020	0.003	15.593	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.037	0.016	16.142	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.005	0.002	19.286	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	HIS	0	-0.006	-0.003	17.151	-0.026	-0.026	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.004	-0.014	20.011	0.024	0.024	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.012	-0.010	22.535	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.026	0.008	24.900	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.030	0.014	23.514	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.882	-0.938	21.333	-0.209	-0.209	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.011	0.000	21.847	0.015	0.015	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.003	0.008	21.562	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	ASN	0	-0.052	-0.041	17.955	-0.038	-0.038	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.015	0.022	18.880	0.023	0.023	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.004	-0.032	19.217	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.037	-0.001	18.391	0.018	0.018	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.773	-0.903	20.413	-0.140	-0.140	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.886	0.921	21.266	0.134	0.134	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.924	-0.935	22.452	-0.098	-0.098	0.000	0.000	0.000	0.000
81	A	81	GLY	0	-0.057	-0.027	19.651	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.046	-0.037	20.159	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.005	0.006	20.553	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.902	-0.946	22.600	-0.092	-0.092	0.000	0.000	0.000	0.000
85	A	85	VAL	0	-0.041	-0.033	23.289	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	86	SER	0	-0.045	-0.049	26.111	0.013	0.013	0.000	0.000	0.000	0.000
87	A	87	ILE	0	0.005	0.012	24.725	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.930	-0.965	29.324	-0.055	-0.055	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.813	-0.928	28.499	-0.096	-0.096	0.000	0.000	0.000	0.000
90	A	90	SER	0	-0.010	-0.016	31.195	0.007	0.007	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.064	0.006	28.558	0.005	0.005	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.022	0.002	26.874	0.006	0.006	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.061	0.015	30.099	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.041	-0.011	31.312	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.036	-0.028	33.639	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.020	0.009	35.699	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.894	-0.953	34.421	-0.025	-0.025	0.000	0.000	0.000	0.000
98	A	98	HIS	0	-0.033	-0.011	29.991	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.028	0.004	30.833	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.006	-0.016	26.878	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.008	0.002	27.524	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.026	-0.006	27.925	0.004	0.004	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.867	0.951	24.045	0.061	0.061	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.006	-0.008	18.613	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.001	0.014	20.546	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	106	VAL	0	-0.024	-0.024	15.157	0.010	0.010	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.031	0.008	15.201	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	108	HIS	0	-0.018	-0.007	10.603	-0.108	-0.108	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.761	-0.883	9.601	-0.239	-0.239	0.000	0.000	0.000	0.000
110	A	110	LYS	1	0.893	0.944	5.751	1.342	1.342	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.000	-0.007	9.183	0.019	0.019	0.000	0.000	0.000	0.000
112	A	112	GLY	0	-0.029	-0.018	11.860	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.045	-0.004	12.472	-0.081	-0.081	0.000	0.000	0.000	0.000

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