FMO DATABASE

FMODB ID: QNNKY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-714497.068319
FMO2-HF: Nuclear repulsion	676713.88668
FMO2-HF: Total energy	-37783.181638
FMO2-MP2: Total energy	-37896.264515

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.
-17.53	-7.645	6.017	-6.964	-8.936	-0.043

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 : -0.010 / q_NPA : -0.004

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	0.860	0.914	3.002	-0.607	2.339	0.015	-1.615	-1.345	0.005
4	A	4	ALA	0	0.020	0.022	3.153	-0.806	0.236	0.093	-0.501	-0.634	-0.004
5	A	5	VAL	0	0.016	0.007	5.250	-0.003	-0.008	-0.001	-0.001	0.007	0.000
6	A	6	ALA	0	0.001	0.018	8.928	0.102	0.102	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.012	-0.010	11.812	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.039	-0.009	15.036	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.927	0.956	17.814	0.053	0.053	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.078	0.025	20.996	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.992	-0.987	24.063	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.031	-0.022	27.851	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.034	-0.019	28.247	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.018	0.008	23.251	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.025	-0.020	21.582	0.006	0.006	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.039	0.018	19.281	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.042	0.002	13.978	0.018	0.018	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.004	0.006	12.177	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.017	-0.008	10.068	0.019	0.019	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.054	0.018	6.757	0.028	0.028	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.862	-0.926	6.864	-1.079	-1.079	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.059	0.021	5.569	-0.950	-0.950	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.925	0.980	6.644	0.197	0.197	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.911	-0.974	7.830	-0.789	-0.789	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.009	-0.008	5.683	-0.156	-0.156	0.000	0.000	0.000	0.000
26	A	26	ASN	0	0.001	-0.003	6.728	-0.075	-0.075	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.017	0.013	9.160	0.190	0.190	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.024	0.029	10.372	-0.204	-0.204	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.008	-0.010	7.987	-0.259	-0.259	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.878	0.958	10.430	0.862	0.862	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.022	0.001	10.757	-0.137	-0.137	0.000	0.000	0.000	0.000
32	A	32	TRP	0	-0.075	-0.062	11.966	0.166	0.166	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.020	0.017	14.193	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.028	-0.002	16.661	0.027	0.027	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.007	-0.005	18.832	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.961	0.985	21.454	0.149	0.149	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.040	0.016	24.813	0.003	0.003	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.039	-0.014	23.531	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.022	0.008	27.836	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.810	-0.900	29.759	-0.115	-0.115	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.029	-0.006	30.439	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.019	-0.008	27.364	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	43	HIS	1	0.803	0.886	24.447	0.161	0.161	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.066	0.045	23.422	-0.019	-0.019	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.006	-0.012	15.409	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	HIS	0	0.049	0.022	16.595	-0.028	-0.028	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.002	-0.001	11.400	0.026	0.026	0.000	0.000	0.000	0.000
48	A	48	HIS	0	0.010	0.006	14.543	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.000	-0.001	15.333	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.014	0.000	17.393	-0.015	-0.015	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.014	0.001	15.516	-0.031	-0.031	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.057	0.028	14.109	-0.084	-0.084	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.887	-0.930	14.961	-0.295	-0.295	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.001	0.002	13.421	-0.056	-0.056	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.001	0.009	17.629	0.012	0.012	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.056	-0.044	21.421	0.022	0.022	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.021	0.019	20.011	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.009	-0.031	22.974	0.025	0.025	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.030	-0.003	26.135	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.773	-0.896	27.600	-0.131	-0.131	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.854	0.910	30.523	0.104	0.104	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.924	-0.937	30.724	-0.094	-0.094	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.057	-0.032	29.589	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.045	-0.037	24.666	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.016	0.018	23.061	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.903	-0.947	21.702	-0.230	-0.230	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.046	-0.036	16.835	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.045	-0.040	17.495	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.038	0.035	15.537	0.036	0.036	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.943	-0.975	14.516	-0.813	-0.813	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.825	-0.913	13.361	-0.642	-0.642	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.033	-0.037	12.930	-0.126	-0.126	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.039	0.007	13.871	0.014	0.014	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.037	-0.011	9.859	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.079	0.028	6.910	-0.405	-0.405	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.046	-0.019	2.502	-0.271	0.560	0.391	-0.349	-0.873	-0.001
77	A	77	SER	0	-0.031	-0.018	2.147	-8.015	-5.816	3.302	-2.813	-2.688	-0.034
78	A	78	GLY	0	0.017	-0.002	3.887	0.334	0.450	0.004	-0.048	-0.071	0.000
79	A	79	ASP	-1	-0.873	-0.945	7.422	-0.186	-0.186	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.070	-0.032	10.208	0.120	0.120	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.017	0.013	4.191	-0.309	-0.261	-0.001	-0.004	-0.043	0.000
82	A	82	ILE	0	0.001	-0.019	6.760	0.426	0.426	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.012	-0.003	2.524	-0.364	0.166	0.709	-0.285	-0.955	0.000
84	A	84	GLY	0	-0.020	-0.005	5.854	0.259	0.259	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.818	0.908	9.193	0.436	0.436	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.004	-0.005	11.199	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	LEU	0	-0.009	0.011	12.582	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.002	-0.015	14.376	0.058	0.058	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.023	0.012	18.149	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.033	-0.007	20.913	0.022	0.022	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.739	-0.890	24.527	-0.091	-0.091	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.869	0.938	26.863	0.095	0.095	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.017	0.017	28.513	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.043	-0.036	29.400	0.010	0.010	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.001	0.001	28.870	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.006	0.000	29.168	0.011	0.011	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.004	-0.005	27.911	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.003	-0.005	27.574	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.022	-0.011	27.098	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.890	0.965	27.087	0.068	0.068	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.007	0.006	21.549	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.067	0.041	21.297	0.015	0.015	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.064	-0.041	17.779	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.056	0.031	15.306	0.026	0.026	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.046	-0.016	10.721	-0.050	-0.050	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.009	0.001	6.457	0.013	0.013	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.032	0.018	7.570	0.113	0.113	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.002	-0.009	2.594	-1.042	-0.375	0.627	-0.315	-0.979	0.001
109	A	109	ALA	0	-0.021	-0.005	3.929	-0.035	0.026	-0.001	-0.018	-0.042	0.000
110	A	110	GLN	0	0.036	0.014	2.684	-2.952	-1.502	0.879	-1.015	-1.313	-0.010

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