FMO DATABASE

FMODB ID: K22K3

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	OptHSide
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	-715018.375257
FMO2-HF: Nuclear repulsion	677234.700062
FMO2-HF: Total energy	-37783.675195
FMO2-MP2: Total energy	-37896.758199

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.
-17.232	-7.236	6.566	-7.261	-9.302	-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 : -0.014 / 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	0.886	0.914	3.093	-0.736	2.266	0.005	-1.640	-1.366	0.006
4	A	4	ALA	0	0.018	0.023	3.193	-0.703	0.315	0.080	-0.486	-0.612	-0.004
5	A	5	VAL	0	0.015	0.005	5.250	-0.025	-0.031	-0.001	-0.001	0.008	0.000
6	A	6	ALA	0	-0.003	0.019	8.924	0.106	0.106	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.002	-0.006	11.786	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.040	-0.008	15.018	0.023	0.023	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.850	0.902	17.789	0.049	0.049	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.067	0.021	20.966	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.883	-0.898	24.100	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.017	-0.011	27.888	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.025	-0.020	28.226	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.016	0.008	23.340	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.032	-0.022	21.567	0.008	0.008	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.051	0.026	19.268	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	17	ILE	0	-0.040	0.002	14.051	0.020	0.020	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.005	0.003	12.278	-0.012	-0.012	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.011	-0.004	10.081	0.035	0.035	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.051	0.016	6.866	0.021	0.021	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.853	-0.908	6.885	-1.042	-1.042	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.050	0.019	5.457	-0.933	-0.933	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.832	0.914	6.644	0.233	0.233	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.822	-0.912	7.920	-0.808	-0.808	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.008	0.001	5.756	-0.127	-0.127	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.021	-0.014	6.793	-0.028	-0.028	0.000	0.000	0.000	0.000
27	A	27	GLY	0	-0.008	0.014	9.251	0.194	0.194	0.000	0.000	0.000	0.000
28	A	28	PRO	0	0.024	0.023	10.287	-0.193	-0.193	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.004	-0.012	7.988	-0.256	-0.256	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.867	0.945	10.440	0.836	0.836	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.016	-0.001	10.801	-0.122	-0.122	0.000	0.000	0.000	0.000
32	A	32	TRP	0	-0.069	-0.061	12.322	0.155	0.155	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.031	0.025	14.203	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.042	-0.009	16.672	0.026	0.026	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.000	-0.007	18.814	0.006	0.006	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.927	0.975	21.444	0.156	0.156	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.047	0.020	24.806	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.045	-0.015	23.506	0.007	0.007	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.032	0.012	27.881	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.757	-0.851	29.798	-0.105	-0.105	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.024	-0.006	30.455	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.019	-0.007	27.297	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	43	HIS	1	0.807	0.894	24.463	0.147	0.147	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.070	0.044	23.437	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	45	PHE	0	-0.008	-0.016	15.410	0.012	0.012	0.000	0.000	0.000	0.000
46	A	46	HIS	0	0.026	0.017	16.617	-0.029	-0.029	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.005	-0.005	11.442	0.027	0.027	0.000	0.000	0.000	0.000
48	A	48	HIS	0	0.023	0.015	14.531	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.002	0.012	15.300	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.013	-0.002	17.344	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.020	-0.004	15.466	-0.026	-0.026	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.055	0.027	14.098	-0.081	-0.081	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.899	-0.937	14.933	-0.274	-0.274	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.004	0.000	13.181	-0.052	-0.052	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.008	0.017	17.630	0.011	0.011	0.000	0.000	0.000	0.000
56	A	56	ASN	0	-0.063	-0.053	21.424	0.028	0.028	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.024	0.026	19.995	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.002	-0.032	23.004	0.018	0.018	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.026	0.002	26.178	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.765	-0.891	27.644	-0.121	-0.121	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.786	0.850	30.572	0.096	0.096	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.923	-0.937	30.926	-0.083	-0.083	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.049	-0.024	29.579	0.003	0.003	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.048	-0.044	24.762	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.013	0.015	23.149	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.896	-0.949	21.673	-0.211	-0.211	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.038	-0.031	16.835	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.012	-0.020	17.529	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.027	0.018	16.061	0.031	0.031	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.960	-0.974	14.349	-0.782	-0.782	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.785	-0.910	13.490	-0.618	-0.618	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.047	-0.029	12.922	-0.139	-0.139	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.048	0.002	13.799	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	ILE	0	-0.033	-0.004	9.774	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.073	0.025	6.847	-0.403	-0.403	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.040	-0.013	2.471	-0.272	0.550	0.427	-0.351	-0.899	-0.001
77	A	77	SER	0	-0.034	-0.021	2.147	-7.951	-5.581	3.398	-2.960	-2.807	-0.036
78	A	78	GLY	0	0.029	0.004	3.851	0.297	0.421	0.004	-0.051	-0.078	0.000
79	A	79	ASP	-1	-0.858	-0.927	7.406	-0.144	-0.144	0.000	0.000	0.000	0.000
80	A	80	HIS	0	-0.087	-0.052	10.225	0.118	0.118	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.026	0.008	4.138	-0.354	-0.301	-0.001	-0.006	-0.046	0.000
82	A	82	ILE	0	0.003	-0.014	6.808	0.400	0.400	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.014	-0.005	2.429	-0.311	0.086	1.074	-0.366	-1.106	0.000
84	A	84	GLY	0	-0.016	-0.004	5.827	0.241	0.241	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.816	0.905	9.174	0.350	0.350	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.005	-0.012	11.196	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	LEU	0	0.001	0.021	12.562	-0.037	-0.037	0.000	0.000	0.000	0.000
88	A	88	VAL	0	-0.004	-0.018	14.388	0.056	0.056	0.000	0.000	0.000	0.000
89	A	89	VAL	0	0.024	0.011	18.162	-0.031	-0.031	0.000	0.000	0.000	0.000
90	A	90	HIS	0	-0.019	0.000	20.934	0.019	0.019	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.696	-0.854	24.543	-0.074	-0.074	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.822	0.915	26.889	0.095	0.095	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.037	0.029	28.531	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.027	-0.028	29.423	0.010	0.010	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.003	0.002	28.873	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.005	-0.002	29.182	0.010	0.010	0.000	0.000	0.000	0.000
97	A	97	ALA	0	0.007	-0.004	27.903	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.006	-0.002	27.555	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.013	-0.005	27.096	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.779	0.872	27.093	0.059	0.059	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.004	0.006	21.625	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.053	0.037	21.604	0.014	0.014	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.057	-0.039	17.807	-0.015	-0.015	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.061	0.034	15.341	0.023	0.023	0.000	0.000	0.000	0.000
105	A	105	VAL	0	-0.051	-0.019	10.744	-0.047	-0.047	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.013	0.000	6.508	0.010	0.010	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.033	0.020	7.592	0.124	0.124	0.000	0.000	0.000	0.000
108	A	108	ILE	0	-0.005	-0.013	2.469	-1.067	-0.423	0.885	-0.389	-1.139	0.001
109	A	109	ALA	0	-0.021	-0.004	3.966	-0.060	-0.006	-0.001	-0.017	-0.037	0.000
110	A	110	GLN	0	0.028	0.014	2.774	-2.781	-1.263	0.696	-0.994	-1.220	-0.009

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