FMO DATABASE

FMODB ID: 4LLQN

Calculation Name: 4BCZ-A-Xray372

Preferred Name: Superoxide dismutase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4BCZ

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	OptAll
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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-714244.037162
FMO2-HF: Nuclear repulsion	676460.212855
FMO2-HF: Total energy	-37783.824307
FMO2-MP2: Total energy	-37896.921929

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.
-16.312	-8.957	11.517	-8.411	-10.457	-0.049

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 : -0.017 / q_NPA : -0.009

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	LYS	1	0.884	0.917	2.885	-0.504	2.265	0.047	-1.555	-1.260	0.004
4	A	4	ALA	0	0.013	0.013	3.062	-0.782	0.447	0.153	-0.612	-0.770	-0.006
5	A	5	VAL	0	0.004	0.000	5.151	-0.106	-0.112	-0.001	-0.002	0.009	0.000
6	A	6	ALA	0	0.014	0.023	8.893	0.114	0.114	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.015	-0.004	11.692	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.033	-0.013	15.011	0.018	0.018	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.785	0.864	17.696	0.018	0.018	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.083	0.040	21.217	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.844	-0.885	24.179	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.014	-0.019	27.772	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.012	-0.003	28.244	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.002	0.019	23.516	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.013	-0.007	21.671	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.067	0.031	19.381	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.040	-0.003	13.866	0.028	0.028	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.014	0.007	12.175	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	19	ASN	0	0.005	0.004	10.038	0.057	0.057	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.042	0.008	6.766	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.848	-0.910	6.727	-0.938	-0.938	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.040	0.021	5.288	-1.070	-1.070	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.822	0.907	6.656	0.327	0.327	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.778	-0.888	8.361	-0.726	-0.726	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.012	-0.008	5.782	-0.084	-0.084	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.034	-0.014	6.700	0.126	0.126	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.005	0.013	9.573	0.226	0.226	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.024	0.015	10.283	-0.218	-0.218	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.022	-0.016	7.655	-0.300	-0.300	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.843	0.924	10.116	0.794	0.794	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.026	0.003	10.397	-0.129	-0.129	0.000	0.000	0.000	0.000
32	A	32	TRP	0	-0.057	-0.051	12.117	0.137	0.137	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.028	0.021	13.984	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.060	-0.018	16.527	0.020	0.020	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.020	0.003	18.435	0.009	0.009	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.874	0.950	21.282	0.129	0.129	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.045	0.025	24.843	0.008	0.008	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.044	-0.015	23.502	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.030	0.012	27.814	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.767	-0.858	29.731	-0.090	-0.090	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.023	-0.009	30.525	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.023	-0.011	26.910	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	HIS	1	0.816	0.909	24.366	0.124	0.124	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.068	0.047	23.374	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.020	-0.025	15.319	0.015	0.015	0.000	0.000	0.000	0.000
46	A	46	HIS	0	0.009	0.006	16.522	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.027	0.009	11.170	0.028	0.028	0.000	0.000	0.000	0.000
48	A	48	HIS	0	0.044	0.023	14.387	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.002	0.009	14.990	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.018	0.002	16.796	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.019	0.002	14.952	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.054	0.024	13.607	-0.088	-0.088	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.887	-0.940	14.656	-0.253	-0.253	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.008	0.001	13.073	-0.059	-0.059	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.011	0.015	17.570	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.077	-0.066	21.395	0.040	0.040	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.023	0.033	19.703	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.011	-0.033	22.757	0.015	0.015	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.012	0.008	26.067	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.791	-0.904	27.634	-0.102	-0.102	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.793	0.848	30.604	0.082	0.082	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.924	-0.936	31.137	-0.067	-0.067	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.019	-0.004	29.641	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.072	-0.053	25.055	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.030	0.018	23.217	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.848	-0.936	21.480	-0.172	-0.172	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.023	-0.020	16.789	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.023	-0.018	17.298	-0.040	-0.040	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.023	0.019	15.962	0.029	0.029	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.934	-0.969	13.928	-0.750	-0.750	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.767	-0.872	13.523	-0.581	-0.581	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.073	-0.060	13.023	-0.115	-0.115	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.029	0.013	13.923	0.027	0.027	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.027	-0.011	9.676	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.050	0.008	6.666	-0.328	-0.328	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.027	-0.006	2.401	-0.560	0.510	0.563	-0.538	-1.094	-0.002
77	A	77	SER	0	-0.036	-0.018	1.955	-7.781	-7.843	7.390	-3.902	-3.425	-0.038
78	A	78	GLY	0	0.043	0.022	3.775	0.346	0.507	0.009	-0.074	-0.097	0.000
79	A	79	ASP	-1	-0.864	-0.928	7.122	-0.100	-0.100	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.069	-0.051	9.976	0.103	0.103	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.049	-0.002	3.974	-0.251	-0.190	-0.001	-0.011	-0.048	0.000
82	A	82	ILE	0	0.021	-0.004	6.734	0.379	0.379	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.008	-0.004	2.319	-0.357	0.033	1.215	-0.417	-1.188	0.000
84	A	84	GLY	0	-0.029	-0.012	5.836	0.205	0.205	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.797	0.903	9.132	0.292	0.292	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.016	-0.019	11.082	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.007	0.019	12.324	-0.042	-0.042	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.023	-0.028	14.103	0.058	0.058	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.030	0.012	17.918	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.023	0.002	20.780	0.018	0.018	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.744	-0.867	24.439	-0.049	-0.049	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.781	0.894	26.756	0.084	0.084	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.046	0.036	28.242	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.006	-0.002	29.593	0.007	0.007	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.011	0.000	28.725	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.012	0.004	28.991	0.010	0.010	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.014	-0.001	27.630	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.013	-0.009	27.538	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.014	0.000	26.977	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.766	0.858	27.090	0.041	0.041	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.012	0.004	21.582	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.039	0.028	21.399	0.015	0.015	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.064	-0.036	17.911	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.070	0.028	15.325	0.018	0.018	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.047	-0.016	10.457	-0.044	-0.044	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.001	0.007	6.230	0.020	0.020	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.025	0.024	7.456	0.144	0.144	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.003	-0.018	2.452	-1.004	-0.545	1.454	-0.495	-1.418	0.001
109	A	109	ALA	0	-0.014	0.000	3.930	-0.172	-0.108	-0.001	-0.019	-0.044	0.000
110	A	110	GLN	0	0.011	0.003	2.716	-2.255	-1.035	0.689	-0.786	-1.122	-0.008

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