FMO DATABASE

FMODB ID: LZ4L9

Calculation Name: 4IZE-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine

ligand 3-letter code: CME

PDB ID: 4IZE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZH8

Base Structure: X-ray

Registration Date: 2023-09-19

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1502515.806853
FMO2-HF: Nuclear repulsion	1441624.556443
FMO2-HF: Total energy	-60891.250411
FMO2-MP2: Total energy	-61065.64394

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:18:SER)

Summations of interaction energy for fragment #1(A:18:SER)

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.
1.112	3.15	-0.004	-0.943	-1.09	0.004

Interaction energy analysis for fragmet #1(A:18:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.030

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	20	CME	0	0.010	0.013	3.877	-0.731	1.040	-0.009	-0.849	-0.913	0.004
4	A	21	LYS	1	0.925	0.954	5.711	1.435	1.435	0.000	0.000	0.000	0.000
5	A	22	PRO	0	0.031	0.017	8.030	0.057	0.057	0.000	0.000	0.000	0.000
6	A	23	ILE	0	-0.015	0.005	8.981	-0.194	-0.194	0.000	0.000	0.000	0.000
7	A	24	THR	0	0.005	-0.017	11.535	0.055	0.055	0.000	0.000	0.000	0.000
8	A	25	GLY	0	0.014	0.003	15.361	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	26	THR	0	-0.036	-0.005	18.585	0.000	0.000	0.000	0.000	0.000	0.000
10	A	27	ILE	0	0.014	0.016	19.143	0.015	0.015	0.000	0.000	0.000	0.000
11	A	28	ASN	0	-0.010	0.000	22.736	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.717	-0.817	25.556	0.065	0.065	0.000	0.000	0.000	0.000
13	A	30	LEU	0	0.030	0.001	27.494	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	31	ASN	0	-0.083	-0.022	30.017	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	32	GLN	0	-0.034	-0.027	28.175	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	33	GLN	0	-0.050	-0.037	31.115	-0.012	-0.012	0.000	0.000	0.000	0.000
17	A	34	VAL	0	-0.034	-0.028	26.311	0.009	0.009	0.000	0.000	0.000	0.000
18	A	35	TRP	0	0.024	-0.001	21.690	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	36	THR	0	-0.003	-0.006	26.705	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	37	LEU	0	0.019	0.005	26.713	0.005	0.005	0.000	0.000	0.000	0.000
21	A	38	GLN	0	-0.002	0.002	29.320	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	39	GLY	0	0.027	0.009	32.918	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	GLN	0	-0.040	-0.033	29.591	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	41	ASN	0	-0.007	0.015	29.747	0.006	0.006	0.000	0.000	0.000	0.000
25	A	42	LEU	0	0.050	0.027	23.832	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	43	VAL	0	-0.008	-0.001	28.496	0.005	0.005	0.000	0.000	0.000	0.000
27	A	44	ALA	0	0.013	0.027	30.396	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	45	VAL	0	0.026	0.010	31.398	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	46	PRO	0	-0.004	0.001	32.203	0.002	0.002	0.000	0.000	0.000	0.000
30	A	47	ARG	1	0.895	0.932	25.169	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	48	SER	0	-0.051	-0.025	32.629	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	49	ASP	-1	-0.813	-0.875	35.503	0.003	0.003	0.000	0.000	0.000	0.000
33	A	50	SER	0	-0.050	-0.024	34.110	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	51	VAL	0	-0.004	0.013	32.024	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	52	THR	0	-0.020	-0.013	27.956	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	53	PRO	0	-0.018	-0.012	25.415	0.004	0.004	0.000	0.000	0.000	0.000
37	A	54	VAL	0	-0.009	0.004	23.493	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	55	THR	0	-0.023	-0.009	19.396	0.001	0.001	0.000	0.000	0.000	0.000
39	A	56	VAL	0	0.008	0.001	17.967	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	57	ALA	0	-0.015	-0.019	14.871	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	58	VAL	0	0.020	0.006	11.615	0.027	0.027	0.000	0.000	0.000	0.000
42	A	59	ILE	0	-0.019	-0.021	6.695	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	60	THR	0	0.014	0.005	6.778	-0.211	-0.211	0.000	0.000	0.000	0.000
44	A	61	CYS	0	-0.048	-0.010	7.278	0.146	0.146	0.000	0.000	0.000	0.000
45	A	62	LYS	1	0.855	0.923	4.933	0.822	0.822	0.000	0.000	0.000	0.000
46	A	63	TYR	0	-0.032	-0.029	6.716	-0.130	-0.130	0.000	0.000	0.000	0.000
47	A	64	PRO	0	-0.007	-0.001	8.670	-0.025	-0.025	0.000	0.000	0.000	0.000
48	A	65	GLU	-1	-0.839	-0.930	10.897	0.254	0.254	0.000	0.000	0.000	0.000
49	A	66	ALA	0	-0.031	-0.003	13.546	-0.037	-0.037	0.000	0.000	0.000	0.000
50	A	67	LEU	0	-0.050	-0.024	13.525	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.826	-0.906	16.860	0.181	0.181	0.000	0.000	0.000	0.000
52	A	69	GLN	0	-0.051	-0.042	15.275	0.062	0.062	0.000	0.000	0.000	0.000
53	A	70	GLY	0	-0.022	-0.012	18.247	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	71	ARG	1	0.755	0.845	19.570	-0.186	-0.186	0.000	0.000	0.000	0.000
55	A	72	GLY	0	0.000	-0.004	17.570	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	73	ASP	-1	-0.891	-0.945	12.143	0.730	0.730	0.000	0.000	0.000	0.000
57	A	74	PRO	0	0.005	0.015	11.537	-0.059	-0.059	0.000	0.000	0.000	0.000
58	A	75	ILE	0	-0.033	-0.019	11.178	0.125	0.125	0.000	0.000	0.000	0.000
59	A	76	TYR	0	0.068	0.032	10.664	-0.081	-0.081	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.022	-0.016	13.497	0.029	0.029	0.000	0.000	0.000	0.000
61	A	78	GLY	0	0.036	0.012	16.272	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.046	-0.008	18.425	0.010	0.010	0.000	0.000	0.000	0.000
63	A	80	GLN	0	-0.023	-0.034	16.562	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	81	ASN	0	-0.064	-0.011	20.888	0.000	0.000	0.000	0.000	0.000	0.000
65	A	82	PRO	0	0.054	0.025	24.224	0.006	0.006	0.000	0.000	0.000	0.000
66	A	83	GLU	-1	-0.824	-0.918	16.957	-0.134	-0.134	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.038	-0.009	20.800	0.001	0.001	0.000	0.000	0.000	0.000
68	A	85	CYS	0	-0.042	-0.007	17.589	0.013	0.013	0.000	0.000	0.000	0.000
69	A	86	LEU	0	-0.010	-0.015	19.532	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	87	TYR	0	-0.024	-0.017	20.143	0.011	0.011	0.000	0.000	0.000	0.000
71	A	88	CYS	0	-0.007	0.044	22.128	0.004	0.004	0.000	0.000	0.000	0.000
72	A	89	GLU	-1	-0.821	-0.899	24.874	0.007	0.007	0.000	0.000	0.000	0.000
73	A	90	LYS	1	0.808	0.900	28.011	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	91	VAL	0	0.036	0.017	30.749	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	92	GLY	0	0.023	0.024	33.538	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	93	GLU	-1	-0.853	-0.938	34.490	0.041	0.041	0.000	0.000	0.000	0.000
77	A	94	GLN	0	-0.026	-0.011	33.515	0.005	0.005	0.000	0.000	0.000	0.000
78	A	95	PRO	0	-0.023	0.011	28.013	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	96	THR	0	-0.003	-0.005	29.746	0.000	0.000	0.000	0.000	0.000	0.000
80	A	97	LEU	0	-0.012	-0.007	23.621	0.003	0.003	0.000	0.000	0.000	0.000
81	A	98	GLN	0	-0.029	-0.019	25.788	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.019	0.008	23.323	0.008	0.008	0.000	0.000	0.000	0.000
83	A	100	LYS	1	0.827	0.895	23.098	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	101	GLU	-1	-0.923	-0.961	22.872	-0.072	-0.072	0.000	0.000	0.000	0.000
85	A	102	GLN	0	-0.025	-0.017	17.447	0.001	0.001	0.000	0.000	0.000	0.000
86	A	103	LYS	1	0.891	0.934	16.718	0.173	0.173	0.000	0.000	0.000	0.000
87	A	104	ILE	0	0.067	0.016	12.823	0.004	0.004	0.000	0.000	0.000	0.000
88	A	105	MET	0	-0.017	-0.010	8.146	0.085	0.085	0.000	0.000	0.000	0.000
89	A	106	ASP	-1	-0.897	-0.909	11.751	-0.191	-0.191	0.000	0.000	0.000	0.000
90	A	107	LEU	0	0.031	0.014	13.464	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	108	TYR	0	-0.030	-0.021	3.816	-0.382	-0.115	0.005	-0.094	-0.177	0.000
92	A	109	GLY	0	-0.003	-0.003	9.103	-0.091	-0.091	0.000	0.000	0.000	0.000
93	A	110	GLN	0	-0.034	-0.020	10.914	-0.061	-0.061	0.000	0.000	0.000	0.000
94	A	111	PRO	0	-0.006	0.021	11.402	-0.024	-0.024	0.000	0.000	0.000	0.000
95	A	112	GLU	-1	-0.906	-0.946	12.951	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	113	PRO	0	-0.010	-0.010	13.036	0.003	0.003	0.000	0.000	0.000	0.000
97	A	114	VAL	0	0.028	0.012	14.040	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	115	LYS	1	0.899	0.940	16.754	-0.141	-0.141	0.000	0.000	0.000	0.000
99	A	116	PRO	0	0.006	0.004	18.620	0.013	0.013	0.000	0.000	0.000	0.000
100	A	117	PHE	0	0.013	-0.009	17.172	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	118	LEU	0	-0.036	-0.007	12.799	0.026	0.026	0.000	0.000	0.000	0.000
102	A	119	PHE	0	0.015	-0.014	16.115	-0.033	-0.033	0.000	0.000	0.000	0.000
103	A	120	TYR	0	0.030	0.008	16.116	0.063	0.063	0.000	0.000	0.000	0.000
104	A	121	ARG	1	0.802	0.858	13.182	-0.410	-0.410	0.000	0.000	0.000	0.000
105	A	122	ALA	0	0.043	0.029	17.066	0.046	0.046	0.000	0.000	0.000	0.000
106	A	123	LYS	1	0.830	0.914	12.337	-0.582	-0.582	0.000	0.000	0.000	0.000
107	A	124	THR	0	0.005	-0.013	19.323	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	125	GLY	0	0.008	0.017	22.651	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	126	ARG	1	0.835	0.894	21.677	-0.071	-0.071	0.000	0.000	0.000	0.000
110	A	127	THR	0	-0.038	-0.009	22.285	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	128	SER	0	-0.016	-0.026	18.747	0.044	0.044	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.024	0.039	21.041	-0.016	-0.016	0.000	0.000	0.000	0.000
113	A	130	LEU	0	0.009	-0.015	18.301	0.028	0.028	0.000	0.000	0.000	0.000
114	A	131	GLU	-1	-0.750	-0.851	20.924	0.153	0.153	0.000	0.000	0.000	0.000
115	A	132	SER	0	-0.019	-0.047	20.545	0.020	0.020	0.000	0.000	0.000	0.000
116	A	133	VAL	0	-0.009	-0.005	16.731	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	134	ALA	0	-0.038	-0.008	20.124	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	135	PHE	0	-0.065	-0.040	22.747	-0.014	-0.014	0.000	0.000	0.000	0.000
119	A	136	PRO	0	0.061	0.023	24.016	0.002	0.002	0.000	0.000	0.000	0.000
120	A	137	ASP	-1	-0.846	-0.906	25.571	0.121	0.121	0.000	0.000	0.000	0.000
121	A	138	TRP	0	-0.022	0.003	26.567	-0.015	-0.015	0.000	0.000	0.000	0.000
122	A	139	PHE	0	-0.021	-0.024	24.398	0.012	0.012	0.000	0.000	0.000	0.000
123	A	140	ILE	0	-0.015	-0.005	21.563	-0.014	-0.014	0.000	0.000	0.000	0.000
124	A	141	ALA	0	-0.002	-0.008	25.502	0.007	0.007	0.000	0.000	0.000	0.000
125	A	142	SER	0	0.012	0.001	28.486	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	143	SER	0	0.037	-0.003	30.739	0.002	0.002	0.000	0.000	0.000	0.000
127	A	144	LYS	1	0.918	0.972	34.457	-0.034	-0.034	0.000	0.000	0.000	0.000
128	A	145	ARG	1	0.864	0.879	35.782	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	146	ASP	-1	-0.828	-0.898	35.664	0.009	0.009	0.000	0.000	0.000	0.000
130	A	147	GLN	0	-0.082	-0.026	35.045	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	148	PRO	0	0.020	-0.007	32.177	0.001	0.001	0.000	0.000	0.000	0.000
132	A	149	ILE	0	-0.046	-0.013	25.886	0.005	0.005	0.000	0.000	0.000	0.000
133	A	150	ILE	0	-0.039	-0.013	29.273	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	151	LEU	0	0.014	0.002	24.715	0.010	0.010	0.000	0.000	0.000	0.000
135	A	152	THR	0	-0.018	-0.019	28.510	-0.008	-0.008	0.000	0.000	0.000	0.000
136	A	153	SER	0	0.083	0.046	29.559	0.008	0.008	0.000	0.000	0.000	0.000
137	A	154	GLU	-1	-0.868	-0.909	31.550	0.056	0.056	0.000	0.000	0.000	0.000
138	A	155	LEU	0	0.016	0.001	28.390	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	156	GLY	0	-0.009	-0.006	32.438	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	157	LYS	1	0.817	0.907	34.631	-0.058	-0.058	0.000	0.000	0.000	0.000
141	A	158	SER	0	-0.069	-0.048	36.528	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	159	TYR	0	-0.001	-0.004	32.196	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	160	ASN	0	-0.037	-0.013	30.360	0.005	0.005	0.000	0.000	0.000	0.000
144	A	161	THR	0	0.043	0.015	27.163	-0.002	-0.002	0.000	0.000	0.000	0.000
145	A	162	ALA	0	-0.026	0.004	25.210	0.015	0.015	0.000	0.000	0.000	0.000
146	A	163	PHE	0	0.017	-0.006	22.826	-0.017	-0.017	0.000	0.000	0.000	0.000
147	A	164	GLU	-1	-0.764	-0.854	22.528	0.094	0.094	0.000	0.000	0.000	0.000
148	A	165	LEU	0	0.021	-0.006	16.859	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	166	ASN	0	-0.065	-0.023	18.207	0.011	0.011	0.000	0.000	0.000	0.000
150	A	167	ILE	0	0.030	0.009	13.841	-0.031	-0.031	0.000	0.000	0.000	0.000
151	A	168	ASN	0	-0.023	-0.004	12.915	0.065	0.065	0.000	0.000	0.000	0.000
152	A	169	ASP	-1	-0.774	-0.842	10.159	0.476	0.476	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:18:SER)