FMO DATABASE

FMODB ID: VQVG1

Calculation Name: 4Y1G-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-hydroxycysteine

ligand 3-letter code: CSO

PDB ID: 4Y1G

Chain ID: A

ChEMBL ID:

UniProt ID: P0A0K0

Base Structure: X-ray

Registration Date: 2023-09-22

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	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	171
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1761393.952201
FMO2-HF: Nuclear repulsion	1696965.075334
FMO2-HF: Total energy	-64428.876866
FMO2-MP2: Total energy	-64620.976223

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-3.936	-0.712	0	-1.337	-1.885	0.004

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.020

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	4	LYS	1	0.899	0.950	3.765	1.918	4.436	-0.001	-1.223	-1.293	0.004
4	A	5	VAL	0	0.008	0.006	5.936	-0.372	-0.372	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.014	0.012	9.675	0.041	0.041	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.007	-0.012	12.399	0.008	0.008	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.007	0.010	15.450	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.016	-0.021	18.646	0.009	0.009	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.016	0.021	21.215	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.018	-0.009	24.686	0.005	0.005	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.883	-0.929	27.314	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.023	0.022	22.413	0.000	0.000	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.908	-0.965	25.524	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.723	-0.868	23.888	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.036	0.012	22.207	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.053	-0.047	21.383	0.000	0.000	0.000	0.000	0.000	0.000
17	A	18	TYR	0	0.020	0.020	15.690	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.053	0.015	17.422	0.011	0.011	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.017	0.021	17.224	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.009	-0.005	16.342	0.010	0.010	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.877	0.951	12.590	0.004	0.004	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.938	-0.972	12.202	0.052	0.052	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.050	-0.020	13.059	0.009	0.009	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.035	-0.027	9.663	0.020	0.020	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.783	-0.874	8.062	0.182	0.182	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.047	-0.017	8.533	-0.070	-0.070	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.095	-0.039	9.657	-0.023	-0.023	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.039	-0.014	5.956	0.087	0.087	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.062	-0.037	3.841	-0.203	0.154	0.001	-0.071	-0.287	0.000
30	A	31	ASN	0	0.047	0.016	4.004	-1.518	-1.169	0.000	-0.043	-0.305	0.000
31	A	32	THR	0	-0.056	-0.038	5.911	-0.050	-0.050	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.010	-0.002	8.652	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.017	-0.008	11.473	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.020	-0.011	13.325	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.088	0.026	16.930	0.008	0.008	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.867	-0.907	20.686	-0.068	-0.068	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.058	-0.034	22.958	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.035	0.049	18.667	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.041	-0.042	19.096	0.006	0.006	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.091	-0.050	21.037	0.005	0.005	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.897	-0.961	22.189	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.026	-0.003	22.195	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.040	-0.038	24.283	0.003	0.003	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.027	0.030	25.803	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.862	0.919	26.592	0.018	0.018	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.137	-0.066	28.453	0.001	0.001	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.022	-0.008	29.028	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.902	-0.953	20.705	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.863	0.942	24.136	0.017	0.017	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.035	0.020	18.298	0.002	0.002	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.009	-0.006	18.433	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.026	0.001	17.986	0.002	0.002	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.825	-0.900	13.620	-0.033	-0.033	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.051	-0.033	13.040	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.026	0.020	16.229	0.007	0.007	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.011	-0.015	18.867	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.071	-0.046	20.370	-0.010	-0.010	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.924	-0.971	17.897	-0.109	-0.109	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.026	0.006	15.646	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.937	0.971	13.686	0.239	0.239	0.000	0.000	0.000	0.000
61	A	62	PRO	0	-0.003	0.005	13.146	-0.049	-0.049	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.920	-0.980	12.858	-0.366	-0.366	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.945	-0.967	9.084	-0.646	-0.646	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.105	-0.057	7.784	-0.168	-0.168	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.821	-0.912	6.064	-2.342	-2.342	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.030	-0.023	9.305	0.120	0.120	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.020	0.020	12.056	0.018	0.018	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.005	-0.008	14.730	0.014	0.014	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.009	-0.012	16.244	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.007	-0.007	18.501	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.012	0.012	21.305	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.006	-0.018	25.109	0.000	0.000	0.000	0.000	0.000	0.000
73	A	74	PHE	0	0.004	-0.025	28.088	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.016	0.042	23.850	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.002	-0.009	24.809	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.951	-0.975	26.747	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.014	-0.031	28.186	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.045	-0.013	22.741	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.782	0.870	26.722	0.051	0.051	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.005	0.018	29.260	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.821	-0.890	27.452	-0.072	-0.072	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.010	-0.012	29.523	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.980	-0.983	28.658	-0.065	-0.065	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.013	0.019	28.403	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.826	0.870	23.645	0.073	0.073	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.015	-0.019	20.796	-0.015	-0.015	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.056	0.036	22.364	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.038	-0.028	22.862	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.021	-0.007	14.395	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.043	0.010	18.998	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.935	0.977	20.502	0.111	0.111	0.000	0.000	0.000	0.000
92	A	93	TYR	0	-0.046	-0.011	14.482	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.015	-0.002	12.935	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.041	-0.053	18.014	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.917	0.965	21.466	0.160	0.160	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.097	-0.045	17.485	0.017	0.017	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.942	-0.961	17.574	-0.204	-0.204	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.007	0.006	12.943	-0.019	-0.019	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.017	0.002	12.329	0.057	0.057	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.003	-0.008	15.052	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.006	-0.007	12.580	0.015	0.015	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.025	0.006	18.265	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	ILE	0	0.009	0.018	21.243	0.003	0.003	0.000	0.000	0.000	0.000
104	A	105	CSO	0	0.006	0.001	23.423	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	106	HIS	0	0.041	0.015	26.992	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.035	0.028	23.723	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	PRO	0	-0.017	-0.027	24.655	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	109	GLN	0	0.008	-0.009	26.035	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.031	0.023	22.812	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.018	0.006	21.820	-0.006	-0.006	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.045	-0.007	25.498	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.812	-0.883	27.109	-0.065	-0.065	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.099	-0.055	23.483	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.950	-0.970	26.604	-0.075	-0.075	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.870	-0.904	25.180	-0.118	-0.118	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.025	-0.022	26.511	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.953	0.977	29.170	0.056	0.056	0.000	0.000	0.000	0.000
118	A	119	GLY	0	-0.085	-0.040	30.962	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.852	0.937	22.453	0.103	0.103	0.000	0.000	0.000	0.000
120	A	121	THR	0	-0.039	-0.038	27.845	0.007	0.007	0.000	0.000	0.000	0.000
121	A	122	LEU	0	0.009	0.002	25.980	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	123	THR	0	-0.036	-0.034	27.004	0.005	0.005	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.039	0.013	27.683	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.018	0.015	29.108	0.003	0.003	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.003	-0.006	31.193	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	ASN	0	-0.050	-0.038	33.953	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	128	VAL	0	0.068	0.041	29.994	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.881	0.956	32.497	0.021	0.021	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.925	0.969	34.338	0.027	0.027	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.873	-0.941	34.090	-0.037	-0.037	0.000	0.000	0.000	0.000
131	A	132	LEU	0	0.026	0.007	28.803	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.052	-0.019	32.861	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.052	-0.039	35.822	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	ALA	0	-0.003	0.018	32.245	0.000	0.000	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.057	-0.028	33.267	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.021	0.021	30.707	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	138	HIS	0	-0.044	-0.027	31.863	0.006	0.006	0.000	0.000	0.000	0.000
138	A	139	VAL	0	-0.022	-0.018	31.753	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	140	VAL	0	0.013	0.011	30.727	0.003	0.003	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.929	-0.958	32.330	-0.018	-0.018	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.908	-0.962	29.320	-0.016	-0.016	0.000	0.000	0.000	0.000
142	A	143	SER	0	-0.074	-0.053	27.625	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.003	0.014	22.137	0.000	0.000	0.000	0.000	0.000	0.000
144	A	145	VAL	0	-0.023	0.009	24.729	0.001	0.001	0.000	0.000	0.000	0.000
145	A	146	VAL	0	-0.004	-0.007	20.370	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.834	-0.892	22.856	-0.071	-0.071	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.027	-0.026	20.192	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	149	ASN	0	0.080	0.044	17.476	0.027	0.027	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.017	0.001	18.040	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	VAL	0	0.007	0.012	17.943	0.011	0.011	0.000	0.000	0.000	0.000
151	A	152	THR	0	0.001	0.001	20.799	0.001	0.001	0.000	0.000	0.000	0.000
152	A	153	SER	0	0.028	-0.022	23.530	0.004	0.004	0.000	0.000	0.000	0.000
153	A	154	ARG	1	0.722	0.848	25.179	0.010	0.010	0.000	0.000	0.000	0.000
154	A	155	VAL	0	0.011	-0.015	27.719	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	156	PRO	0	0.025	-0.010	25.613	0.001	0.001	0.000	0.000	0.000	0.000
156	A	157	ASP	-1	-0.919	-0.956	25.915	0.003	0.003	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.690	-0.823	25.821	-0.009	-0.009	0.000	0.000	0.000	0.000
158	A	159	LEU	0	-0.030	-0.020	20.777	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	160	ASP	-1	-0.891	-0.929	21.132	0.026	0.026	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.872	-0.922	21.442	0.011	0.011	0.000	0.000	0.000	0.000
161	A	162	PHE	0	-0.018	-0.020	18.362	-0.001	-0.001	0.000	0.000	0.000	0.000
162	A	163	ASN	0	0.033	-0.006	17.245	0.000	0.000	0.000	0.000	0.000	0.000
163	A	164	ARG	1	0.846	0.940	16.348	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	165	GLU	-1	-0.891	-0.967	16.850	-0.006	-0.006	0.000	0.000	0.000	0.000
165	A	166	ILE	0	-0.006	0.007	14.119	-0.012	-0.012	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.016	0.017	11.625	-0.001	-0.001	0.000	0.000	0.000	0.000
167	A	168	LYS	1	0.927	0.965	11.904	0.011	0.011	0.000	0.000	0.000	0.000
168	A	169	GLN	0	-0.006	-0.014	13.497	-0.044	-0.044	0.000	0.000	0.000	0.000
169	A	170	LEU	0	0.034	0.039	7.647	-0.077	-0.077	0.000	0.000	0.000	0.000
170	A	171	GLN	0	-0.096	-0.047	8.700	-0.148	-0.148	0.000	0.000	0.000	0.000
171	A	172	LEU	0	-0.079	-0.012	10.216	-0.047	-0.047	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)