FMO DATABASE

FMODB ID: MVR6Z

Calculation Name: 4WZ0-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4WZ0

Chain ID: A

ChEMBL ID:

UniProt ID: Q5X159

Base Structure: X-ray

Registration Date: 2023-06-22

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	109
LigandCharge	CSD=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-828473.291807
FMO2-HF: Nuclear repulsion	785046.241315
FMO2-HF: Total energy	-43427.050491
FMO2-MP2: Total energy	-43555.609543

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:9:ILE)

Summations of interaction energy for fragment #1(A:9:ILE)

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.
-8.586	-3.262	5.808	-3.524	-7.607	0.007

Interaction energy analysis for fragmet #1(A:9:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.005

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	11	HIS	0	0.008	-0.017	2.941	-3.203	1.672	2.016	-2.239	-4.652	-0.013
4	A	12	LYS	1	0.812	0.910	3.582	2.426	2.579	0.014	0.032	-0.199	0.000
5	A	13	SER	0	-0.006	-0.046	6.635	0.562	0.562	0.000	0.000	0.000	0.000
6	A	14	LYS	1	0.851	0.948	1.922	-6.640	-6.344	3.778	-1.317	-2.756	0.020
7	A	15	TYR	0	0.078	0.014	6.511	0.175	0.175	0.000	0.000	0.000	0.000
8	A	16	LEU	0	-0.012	-0.005	8.696	0.133	0.133	0.000	0.000	0.000	0.000
9	A	17	ARG	1	0.818	0.891	7.783	-0.484	-0.484	0.000	0.000	0.000	0.000
10	A	18	GLU	-1	-0.807	-0.896	8.148	0.540	0.540	0.000	0.000	0.000	0.000
11	A	19	ALA	0	0.051	0.023	11.994	0.027	0.027	0.000	0.000	0.000	0.000
12	A	20	ALA	0	-0.008	-0.005	14.162	0.021	0.021	0.000	0.000	0.000	0.000
13	A	21	LEU	0	-0.011	0.006	15.090	0.021	0.021	0.000	0.000	0.000	0.000
14	A	22	GLU	-1	-0.781	-0.872	16.052	-0.064	-0.064	0.000	0.000	0.000	0.000
15	A	23	ALA	0	-0.013	-0.009	17.901	0.004	0.004	0.000	0.000	0.000	0.000
16	A	24	ASN	0	-0.086	-0.052	19.524	0.006	0.006	0.000	0.000	0.000	0.000
17	A	25	LEU	0	-0.034	-0.012	19.076	0.013	0.013	0.000	0.000	0.000	0.000
18	A	26	SER	0	-0.059	-0.021	21.359	0.004	0.004	0.000	0.000	0.000	0.000
19	A	27	HIS	0	0.000	0.002	23.818	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	28	PRO	0	0.027	-0.003	26.871	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	29	GLU	-1	-0.741	-0.861	28.008	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	30	THR	0	-0.058	-0.013	24.383	0.003	0.003	0.000	0.000	0.000	0.000
23	A	31	THR	0	-0.003	-0.018	23.124	-0.012	-0.012	0.000	0.000	0.000	0.000
24	A	32	PRO	0	-0.021	0.001	19.411	0.004	0.004	0.000	0.000	0.000	0.000
25	A	33	THR	0	0.056	0.011	17.329	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	34	MET	0	-0.051	-0.006	10.615	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	35	LEU	0	-0.027	-0.005	15.380	-0.076	-0.076	0.000	0.000	0.000	0.000
28	A	36	THR	0	-0.062	-0.044	18.042	0.000	0.000	0.000	0.000	0.000	0.000
29	A	37	CSD	-1	-0.794	-0.884	17.709	-0.335	-0.335	0.000	0.000	0.000	0.000
30	A	38	PRO	0	-0.012	-0.006	15.507	0.031	0.031	0.000	0.000	0.000	0.000
31	A	39	ILE	0	-0.071	-0.032	18.675	0.026	0.026	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.868	-0.914	21.767	-0.191	-0.191	0.000	0.000	0.000	0.000
33	A	41	SER	0	-0.072	-0.026	22.596	0.019	0.019	0.000	0.000	0.000	0.000
34	A	42	GLY	0	0.032	0.019	23.284	0.018	0.018	0.000	0.000	0.000	0.000
35	A	43	PHE	0	-0.015	-0.017	21.765	-0.023	-0.023	0.000	0.000	0.000	0.000
36	A	44	LEU	0	-0.043	-0.012	16.122	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	45	LYS	1	0.920	0.950	20.390	0.217	0.217	0.000	0.000	0.000	0.000
38	A	46	ASP	-1	-0.826	-0.904	20.638	-0.413	-0.413	0.000	0.000	0.000	0.000
39	A	47	PRO	0	0.002	0.022	15.188	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	48	VAL	0	-0.016	-0.012	14.437	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	49	ILE	0	-0.013	-0.009	7.172	0.050	0.050	0.000	0.000	0.000	0.000
42	A	50	THR	0	0.013	0.018	10.094	-0.146	-0.146	0.000	0.000	0.000	0.000
43	A	51	PRO	0	0.006	-0.015	6.900	-0.386	-0.386	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.812	-0.866	5.400	-0.991	-0.991	0.000	0.000	0.000	0.000
45	A	53	GLY	0	0.004	0.007	6.119	0.200	0.200	0.000	0.000	0.000	0.000
46	A	54	PHE	0	-0.032	-0.007	6.825	0.257	0.257	0.000	0.000	0.000	0.000
47	A	55	VAL	0	-0.005	-0.010	10.438	-0.184	-0.184	0.000	0.000	0.000	0.000
48	A	56	TYR	0	-0.002	-0.032	12.845	0.125	0.125	0.000	0.000	0.000	0.000
49	A	57	ASN	0	0.048	-0.003	16.580	-0.064	-0.064	0.000	0.000	0.000	0.000
50	A	58	LYS	1	0.849	0.911	19.189	0.420	0.420	0.000	0.000	0.000	0.000
51	A	59	SER	0	-0.004	-0.014	20.009	0.003	0.003	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.013	-0.023	21.476	0.010	0.010	0.000	0.000	0.000	0.000
53	A	61	ILE	0	0.022	0.010	16.535	0.019	0.019	0.000	0.000	0.000	0.000
54	A	62	LEU	0	-0.034	-0.016	19.975	0.004	0.004	0.000	0.000	0.000	0.000
55	A	63	LYS	1	1.031	1.022	22.111	0.195	0.195	0.000	0.000	0.000	0.000
56	A	64	TRP	0	-0.024	0.000	19.962	0.045	0.045	0.000	0.000	0.000	0.000
57	A	65	LEU	0	-0.041	-0.032	17.767	0.017	0.017	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.990	-0.991	22.065	-0.216	-0.216	0.000	0.000	0.000	0.000
59	A	67	THR	0	-0.070	-0.027	25.137	0.024	0.024	0.000	0.000	0.000	0.000
60	A	68	LYS	1	0.862	0.943	22.480	0.195	0.195	0.000	0.000	0.000	0.000
61	A	69	LYS	1	0.953	0.992	20.605	0.240	0.240	0.000	0.000	0.000	0.000
62	A	70	GLU	-1	-0.807	-0.907	17.322	-0.172	-0.172	0.000	0.000	0.000	0.000
63	A	71	ASP	-1	-0.730	-0.852	13.703	-0.456	-0.456	0.000	0.000	0.000	0.000
64	A	72	PRO	0	-0.022	-0.013	15.795	0.054	0.054	0.000	0.000	0.000	0.000
65	A	73	GLN	0	-0.019	-0.021	14.006	0.097	0.097	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.066	-0.066	11.663	0.064	0.064	0.000	0.000	0.000	0.000
67	A	75	ARG	1	0.808	0.899	13.997	0.171	0.171	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.860	0.928	9.480	0.096	0.096	0.000	0.000	0.000	0.000
69	A	77	PRO	0	-0.023	-0.023	14.651	-0.042	-0.042	0.000	0.000	0.000	0.000
70	A	78	LEU	0	0.005	0.017	12.815	-0.087	-0.087	0.000	0.000	0.000	0.000
71	A	79	THR	0	-0.070	-0.072	15.737	0.089	0.089	0.000	0.000	0.000	0.000
72	A	80	ALA	0	0.092	0.026	16.365	-0.069	-0.069	0.000	0.000	0.000	0.000
73	A	81	LYS	1	0.821	0.899	14.318	0.614	0.614	0.000	0.000	0.000	0.000
74	A	82	ASP	-1	-0.813	-0.865	12.064	-0.837	-0.837	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.007	0.012	12.100	-0.161	-0.161	0.000	0.000	0.000	0.000
76	A	84	GLN	0	0.038	0.022	9.755	0.024	0.024	0.000	0.000	0.000	0.000
77	A	85	PRO	0	0.013	0.003	13.213	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	86	PHE	0	0.008	0.003	10.116	-0.181	-0.181	0.000	0.000	0.000	0.000
79	A	87	PRO	0	0.040	0.022	13.924	0.074	0.074	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.768	-0.888	13.022	-0.908	-0.908	0.000	0.000	0.000	0.000
81	A	89	LEU	0	0.019	0.017	13.170	0.070	0.070	0.000	0.000	0.000	0.000
82	A	90	LEU	0	-0.003	-0.004	15.204	0.068	0.068	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.039	-0.001	17.517	0.052	0.052	0.000	0.000	0.000	0.000
84	A	92	ILE	0	-0.005	-0.001	14.548	0.039	0.039	0.000	0.000	0.000	0.000
85	A	93	VAL	0	-0.001	0.003	18.174	0.036	0.036	0.000	0.000	0.000	0.000
86	A	94	ASN	0	-0.045	-0.026	20.574	0.041	0.041	0.000	0.000	0.000	0.000
87	A	95	ARG	1	0.837	0.881	22.540	0.205	0.205	0.000	0.000	0.000	0.000
88	A	96	PHE	0	0.021	0.035	22.001	0.018	0.018	0.000	0.000	0.000	0.000
89	A	97	VAL	0	0.053	0.027	24.036	0.017	0.017	0.000	0.000	0.000	0.000
90	A	98	GLU	-1	-0.797	-0.852	26.446	-0.146	-0.146	0.000	0.000	0.000	0.000
91	A	99	THR	0	-0.038	-0.037	26.593	0.016	0.016	0.000	0.000	0.000	0.000
92	A	100	GLN	0	-0.052	-0.014	26.957	0.002	0.002	0.000	0.000	0.000	0.000
93	A	101	THR	0	0.020	-0.001	29.438	0.009	0.009	0.000	0.000	0.000	0.000
94	A	102	ASN	0	-0.045	-0.032	31.949	0.009	0.009	0.000	0.000	0.000	0.000
95	A	103	TYR	0	0.000	0.010	31.729	0.009	0.009	0.000	0.000	0.000	0.000
96	A	104	GLU	-1	-0.861	-0.934	31.934	-0.062	-0.062	0.000	0.000	0.000	0.000
97	A	105	LYS	1	0.927	0.972	35.352	0.065	0.065	0.000	0.000	0.000	0.000
98	A	106	LEU	0	-0.062	-0.035	36.347	0.004	0.004	0.000	0.000	0.000	0.000
99	A	107	LYS	1	0.855	0.901	35.461	0.034	0.034	0.000	0.000	0.000	0.000
100	A	108	ASN	0	-0.019	-0.024	38.265	0.006	0.006	0.000	0.000	0.000	0.000
101	A	109	ARG	1	0.938	0.984	40.768	0.040	0.040	0.000	0.000	0.000	0.000
102	A	110	LEU	0	-0.011	-0.004	39.874	0.002	0.002	0.000	0.000	0.000	0.000
103	A	111	VAL	0	0.018	0.007	41.463	0.003	0.003	0.000	0.000	0.000	0.000
104	A	112	GLN	0	0.006	0.004	44.260	0.004	0.004	0.000	0.000	0.000	0.000
105	A	113	ASN	0	0.003	-0.009	46.709	0.000	0.000	0.000	0.000	0.000	0.000
106	A	114	ALA	0	0.001	-0.002	46.724	0.002	0.002	0.000	0.000	0.000	0.000
107	A	115	ARG	1	0.866	0.933	45.019	0.025	0.025	0.000	0.000	0.000	0.000
108	A	116	VAL	0	-0.034	-0.009	50.452	0.000	0.000	0.000	0.000	0.000	0.000
109	A	117	ALA	0	-0.030	0.008	51.652	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:9:ILE)