FMO DATABASE

FMODB ID: 39RNL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1496992.157279
FMO2-HF: Nuclear repulsion	1436101.198073
FMO2-HF: Total energy	-60890.959206
FMO2-MP2: Total energy	-61065.229454

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.
1.6	3.751	-0.015	-1.041	-1.094	0.006

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 : 0.051 / q_NPA : 0.024

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	0.013	0.011	3.820	-0.395	1.566	-0.016	-0.979	-0.966	0.006
4	A	21	LYS	1	0.936	0.961	6.098	1.180	1.180	0.000	0.000	0.000	0.000
5	A	22	PRO	0	0.032	0.024	8.504	0.044	0.044	0.000	0.000	0.000	0.000
6	A	23	ILE	0	-0.022	-0.006	9.236	-0.172	-0.172	0.000	0.000	0.000	0.000
7	A	24	THR	0	0.008	-0.010	11.853	0.060	0.060	0.000	0.000	0.000	0.000
8	A	25	GLY	0	0.004	0.000	15.645	-0.009	-0.009	0.000	0.000	0.000	0.000
9	A	26	THR	0	-0.031	0.005	18.646	0.002	0.002	0.000	0.000	0.000	0.000
10	A	27	ILE	0	0.031	0.021	19.132	0.015	0.015	0.000	0.000	0.000	0.000
11	A	28	ASN	0	-0.027	-0.006	22.668	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	29	ASP	-1	-0.733	-0.838	25.400	0.074	0.074	0.000	0.000	0.000	0.000
13	A	30	LEU	0	0.034	0.003	27.663	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	31	ASN	0	-0.081	-0.018	29.969	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	32	GLN	0	-0.036	-0.029	28.033	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	33	GLN	0	-0.063	-0.044	30.976	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	34	VAL	0	-0.033	-0.027	26.311	0.009	0.009	0.000	0.000	0.000	0.000
18	A	35	TRP	0	0.020	0.003	21.995	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	36	THR	0	-0.008	-0.001	26.861	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	37	LEU	0	0.021	0.010	27.239	0.006	0.006	0.000	0.000	0.000	0.000
21	A	38	GLN	0	0.013	0.015	29.489	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	39	GLY	0	0.011	0.000	33.211	0.003	0.003	0.000	0.000	0.000	0.000
23	A	40	GLN	0	-0.040	-0.033	30.046	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	41	ASN	0	0.004	0.016	30.443	0.007	0.007	0.000	0.000	0.000	0.000
25	A	42	LEU	0	0.031	0.020	24.312	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	43	VAL	0	0.007	0.004	28.954	0.005	0.005	0.000	0.000	0.000	0.000
27	A	44	ALA	0	0.008	0.020	30.207	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	45	VAL	0	0.034	0.011	31.191	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	46	PRO	0	0.019	0.020	32.107	0.002	0.002	0.000	0.000	0.000	0.000
30	A	47	ARG	1	0.906	0.946	25.156	-0.030	-0.030	0.000	0.000	0.000	0.000
31	A	48	SER	0	-0.009	-0.002	32.571	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	49	ASP	-1	-0.847	-0.895	35.476	0.008	0.008	0.000	0.000	0.000	0.000
33	A	50	SER	0	-0.052	-0.025	34.038	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	51	VAL	0	-0.008	0.013	31.932	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	52	THR	0	0.007	-0.004	28.336	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	53	PRO	0	-0.044	-0.024	25.567	0.004	0.004	0.000	0.000	0.000	0.000
37	A	54	VAL	0	-0.003	-0.002	23.485	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	55	THR	0	-0.041	-0.021	19.407	0.001	0.001	0.000	0.000	0.000	0.000
39	A	56	VAL	0	-0.006	-0.013	17.734	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	57	ALA	0	0.001	-0.008	15.179	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	58	VAL	0	0.021	0.010	11.673	0.033	0.033	0.000	0.000	0.000	0.000
42	A	59	ILE	0	-0.025	-0.025	6.959	-0.071	-0.071	0.000	0.000	0.000	0.000
43	A	60	THR	0	0.016	0.009	7.250	-0.199	-0.199	0.000	0.000	0.000	0.000
44	A	61	CYS	0	-0.046	-0.005	7.692	0.187	0.187	0.000	0.000	0.000	0.000
45	A	62	LYS	1	0.886	0.932	5.168	0.596	0.596	0.000	0.000	0.000	0.000
46	A	63	TYR	0	-0.025	-0.020	7.242	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	64	PRO	0	-0.002	0.006	9.335	-0.095	-0.095	0.000	0.000	0.000	0.000
48	A	65	GLU	-1	-0.856	-0.931	11.203	0.418	0.418	0.000	0.000	0.000	0.000
49	A	66	ALA	0	-0.014	0.000	13.943	-0.062	-0.062	0.000	0.000	0.000	0.000
50	A	67	LEU	0	-0.099	-0.048	14.501	-0.051	-0.051	0.000	0.000	0.000	0.000
51	A	68	GLU	-1	-0.913	-0.945	17.386	0.224	0.224	0.000	0.000	0.000	0.000
52	A	69	GLN	0	-0.059	-0.041	15.727	0.085	0.085	0.000	0.000	0.000	0.000
53	A	70	GLY	0	-0.021	-0.021	18.871	-0.032	-0.032	0.000	0.000	0.000	0.000
54	A	71	ARG	1	0.831	0.890	19.579	-0.229	-0.229	0.000	0.000	0.000	0.000
55	A	72	GLY	0	-0.010	0.001	17.236	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	73	ASP	-1	-0.924	-0.961	11.823	0.750	0.750	0.000	0.000	0.000	0.000
57	A	74	PRO	0	-0.005	0.013	12.271	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	75	ILE	0	-0.048	-0.036	11.584	0.148	0.148	0.000	0.000	0.000	0.000
59	A	76	TYR	0	0.049	0.022	11.317	-0.076	-0.076	0.000	0.000	0.000	0.000
60	A	77	LEU	0	0.000	-0.008	14.161	0.017	0.017	0.000	0.000	0.000	0.000
61	A	78	GLY	0	0.051	0.022	16.873	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	79	ILE	0	-0.056	-0.013	18.646	0.006	0.006	0.000	0.000	0.000	0.000
63	A	80	GLN	0	0.038	0.005	16.686	-0.012	-0.012	0.000	0.000	0.000	0.000
64	A	81	ASN	0	-0.086	-0.017	21.230	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	82	PRO	0	0.061	0.022	24.510	0.004	0.004	0.000	0.000	0.000	0.000
66	A	83	GLU	-1	-0.861	-0.946	17.518	-0.087	-0.087	0.000	0.000	0.000	0.000
67	A	84	MET	0	-0.023	0.001	21.414	0.002	0.002	0.000	0.000	0.000	0.000
68	A	85	CYS	0	-0.037	-0.010	18.043	0.012	0.012	0.000	0.000	0.000	0.000
69	A	86	LEU	0	-0.009	-0.012	20.099	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	87	TYR	0	-0.005	-0.006	20.682	0.013	0.013	0.000	0.000	0.000	0.000
71	A	88	CYS	0	-0.024	0.037	22.845	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	89	GLU	-1	-0.834	-0.909	25.439	0.030	0.030	0.000	0.000	0.000	0.000
73	A	90	LYS	1	0.847	0.910	28.366	-0.055	-0.055	0.000	0.000	0.000	0.000
74	A	91	VAL	0	0.029	0.019	30.909	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	92	GLY	0	0.021	0.023	34.040	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	93	GLU	-1	-0.898	-0.955	35.311	0.056	0.056	0.000	0.000	0.000	0.000
77	A	94	GLN	0	-0.031	-0.018	33.967	0.005	0.005	0.000	0.000	0.000	0.000
78	A	95	PRO	0	-0.008	0.012	28.583	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	96	THR	0	-0.008	-0.004	29.974	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	97	LEU	0	-0.022	-0.009	24.114	0.003	0.003	0.000	0.000	0.000	0.000
81	A	98	GLN	0	-0.017	-0.011	26.361	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	99	LEU	0	0.019	0.002	23.948	0.010	0.010	0.000	0.000	0.000	0.000
83	A	100	LYS	1	0.836	0.909	23.263	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	101	GLU	-1	-0.924	-0.962	23.187	-0.054	-0.054	0.000	0.000	0.000	0.000
85	A	102	GLN	0	-0.044	-0.041	17.725	0.002	0.002	0.000	0.000	0.000	0.000
86	A	103	LYS	1	0.956	0.982	16.944	0.156	0.156	0.000	0.000	0.000	0.000
87	A	104	ILE	0	0.088	0.026	13.055	0.010	0.010	0.000	0.000	0.000	0.000
88	A	105	MET	0	-0.035	-0.027	8.528	0.083	0.083	0.000	0.000	0.000	0.000
89	A	106	ASP	-1	-0.916	-0.934	12.172	-0.107	-0.107	0.000	0.000	0.000	0.000
90	A	107	LEU	0	0.025	0.018	13.927	0.003	0.003	0.000	0.000	0.000	0.000
91	A	108	TYR	0	-0.056	-0.044	3.894	-0.274	-0.084	0.001	-0.062	-0.128	0.000
92	A	109	GLY	0	-0.024	-0.015	9.279	-0.023	-0.023	0.000	0.000	0.000	0.000
93	A	110	GLN	0	-0.020	0.002	11.016	-0.053	-0.053	0.000	0.000	0.000	0.000
94	A	111	PRO	0	-0.021	0.000	11.820	0.020	0.020	0.000	0.000	0.000	0.000
95	A	112	GLU	-1	-0.914	-0.950	13.141	0.075	0.075	0.000	0.000	0.000	0.000
96	A	113	PRO	0	-0.023	-0.016	13.568	0.004	0.004	0.000	0.000	0.000	0.000
97	A	114	VAL	0	0.031	0.019	14.659	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	115	LYS	1	1.006	0.983	17.412	-0.176	-0.176	0.000	0.000	0.000	0.000
99	A	116	PRO	0	0.013	0.011	19.303	0.012	0.012	0.000	0.000	0.000	0.000
100	A	117	PHE	0	0.007	-0.010	17.785	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	118	LEU	0	-0.040	-0.007	13.483	0.025	0.025	0.000	0.000	0.000	0.000
102	A	119	PHE	0	0.006	-0.013	16.704	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	120	TYR	0	0.063	0.036	16.548	0.066	0.066	0.000	0.000	0.000	0.000
104	A	121	ARG	1	0.830	0.873	13.457	-0.399	-0.399	0.000	0.000	0.000	0.000
105	A	122	ALA	0	0.029	0.022	16.725	0.052	0.052	0.000	0.000	0.000	0.000
106	A	123	LYS	1	0.866	0.928	12.725	-0.511	-0.511	0.000	0.000	0.000	0.000
107	A	124	THR	0	0.019	0.002	19.510	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	125	GLY	0	-0.006	-0.002	22.764	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	126	ARG	1	0.858	0.912	21.546	-0.080	-0.080	0.000	0.000	0.000	0.000
110	A	127	THR	0	-0.027	0.001	22.380	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	128	SER	0	-0.020	-0.026	18.756	0.038	0.038	0.000	0.000	0.000	0.000
112	A	129	THR	0	0.021	0.037	20.997	-0.016	-0.016	0.000	0.000	0.000	0.000
113	A	130	LEU	0	0.012	-0.011	18.307	0.028	0.028	0.000	0.000	0.000	0.000
114	A	131	GLU	-1	-0.779	-0.860	21.129	0.181	0.181	0.000	0.000	0.000	0.000
115	A	132	SER	0	-0.014	-0.043	21.091	0.024	0.024	0.000	0.000	0.000	0.000
116	A	133	VAL	0	-0.016	-0.003	17.448	0.001	0.001	0.000	0.000	0.000	0.000
117	A	134	ALA	0	-0.057	-0.022	20.921	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	135	PHE	0	-0.036	-0.026	23.446	-0.015	-0.015	0.000	0.000	0.000	0.000
119	A	136	PRO	0	0.051	0.019	25.188	0.001	0.001	0.000	0.000	0.000	0.000
120	A	137	ASP	-1	-0.881	-0.946	26.202	0.143	0.143	0.000	0.000	0.000	0.000
121	A	138	TRP	0	-0.014	0.009	27.102	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	139	PHE	0	-0.023	-0.024	24.887	0.016	0.016	0.000	0.000	0.000	0.000
123	A	140	ILE	0	-0.009	0.000	21.941	-0.016	-0.016	0.000	0.000	0.000	0.000
124	A	141	ALA	0	-0.005	-0.011	25.967	0.006	0.006	0.000	0.000	0.000	0.000
125	A	142	SER	0	0.001	-0.004	28.793	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	143	SER	0	0.044	0.000	30.862	0.002	0.002	0.000	0.000	0.000	0.000
127	A	144	LYS	1	0.930	0.978	34.497	-0.041	-0.041	0.000	0.000	0.000	0.000
128	A	145	ARG	1	0.842	0.875	35.822	-0.014	-0.014	0.000	0.000	0.000	0.000
129	A	146	ASP	-1	-0.819	-0.907	35.539	0.014	0.014	0.000	0.000	0.000	0.000
130	A	147	GLN	0	-0.093	-0.032	35.406	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	148	PRO	0	0.027	-0.002	32.590	0.001	0.001	0.000	0.000	0.000	0.000
132	A	149	ILE	0	-0.042	-0.010	26.325	0.004	0.004	0.000	0.000	0.000	0.000
133	A	150	ILE	0	-0.031	-0.013	29.788	-0.003	-0.003	0.000	0.000	0.000	0.000
134	A	151	LEU	0	0.010	0.000	25.418	0.009	0.009	0.000	0.000	0.000	0.000
135	A	152	THR	0	-0.019	-0.013	29.313	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	153	SER	0	0.065	0.033	30.242	0.008	0.008	0.000	0.000	0.000	0.000
137	A	154	GLU	-1	-0.895	-0.924	32.247	0.068	0.068	0.000	0.000	0.000	0.000
138	A	155	LEU	0	0.022	0.009	28.517	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	156	GLY	0	-0.010	-0.014	32.625	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	157	LYS	1	0.820	0.901	34.403	-0.070	-0.070	0.000	0.000	0.000	0.000
141	A	158	SER	0	-0.053	-0.025	37.017	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	159	TYR	0	0.003	0.001	32.295	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	160	ASN	0	-0.034	-0.011	30.449	0.005	0.005	0.000	0.000	0.000	0.000
144	A	161	THR	0	0.050	0.010	27.071	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	162	ALA	0	-0.021	0.007	25.287	0.015	0.015	0.000	0.000	0.000	0.000
146	A	163	PHE	0	0.008	-0.013	22.605	-0.017	-0.017	0.000	0.000	0.000	0.000
147	A	164	GLU	-1	-0.771	-0.865	22.282	0.101	0.101	0.000	0.000	0.000	0.000
148	A	165	LEU	0	0.015	-0.008	16.651	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	166	ASN	0	-0.072	-0.027	18.322	0.009	0.009	0.000	0.000	0.000	0.000
150	A	167	ILE	0	0.026	0.008	13.716	-0.034	-0.034	0.000	0.000	0.000	0.000
151	A	168	ASN	0	-0.010	-0.004	12.747	0.061	0.061	0.000	0.000	0.000	0.000
152	A	169	ASP	-1	-0.797	-0.855	9.941	0.357	0.357	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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