FMO DATABASE

FMODB ID: G5821

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1767139.370666
FMO2-HF: Nuclear repulsion	1702709.102417
FMO2-HF: Total energy	-64430.268249
FMO2-MP2: Total energy	-64622.338704

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.
-12.545	-7.204	1.951	-3.144	-4.148	0.005

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 : -0.013 / q_NPA : -0.009

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	0.769	0.879	3.599	2.726	5.402	0.043	-1.360	-1.359	0.003
4	A	5	VAL	0	0.000	0.000	5.388	-0.513	-0.471	-0.001	-0.003	-0.038	0.000
5	A	6	ALA	0	0.028	0.024	9.164	0.120	0.120	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.013	-0.022	12.063	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.004	0.014	14.980	0.013	0.013	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.021	-0.022	18.274	0.002	0.002	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.027	0.022	20.892	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.020	-0.005	24.382	0.012	0.012	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.843	-0.915	26.972	0.002	0.002	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.038	0.020	21.877	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.849	-0.907	25.095	0.013	0.013	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.776	-0.885	23.567	0.042	0.042	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.082	0.034	21.400	0.007	0.007	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.044	-0.046	20.725	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	18	TYR	0	0.003	0.012	15.324	0.002	0.002	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.017	-0.021	16.984	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.005	0.021	16.407	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.028	-0.001	15.533	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.820	0.911	11.127	-0.425	-0.425	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.921	-0.964	11.522	0.170	0.170	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.033	-0.008	11.995	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.014	-0.012	9.077	-0.063	-0.063	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.755	-0.837	7.169	0.558	0.558	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.099	-0.065	7.677	-0.124	-0.124	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.060	-0.015	8.558	-0.045	-0.045	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.038	-0.010	4.820	-0.169	-0.169	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.089	-0.057	2.799	-3.732	-2.316	0.160	-0.692	-0.884	-0.007
30	A	31	ASN	0	0.011	0.004	2.339	-6.687	-5.467	1.750	-1.088	-1.882	0.009
31	A	32	THR	0	-0.041	-0.042	5.497	-0.496	-0.509	-0.001	-0.001	0.015	0.000
32	A	33	VAL	0	-0.003	0.001	8.308	0.062	0.062	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.037	-0.011	11.055	-0.083	-0.083	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.029	-0.018	13.050	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.094	0.033	16.726	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.813	-0.888	20.491	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.092	-0.056	22.256	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.049	0.056	18.319	0.009	0.009	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.086	-0.052	18.769	0.009	0.009	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.053	-0.019	20.542	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.814	-0.895	21.661	0.098	0.098	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.021	0.004	21.783	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.037	-0.028	24.204	0.010	0.010	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.016	0.025	25.447	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.803	0.872	26.227	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.106	-0.068	27.636	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.022	-0.002	28.437	0.001	0.001	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.857	-0.922	20.444	0.097	0.097	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.746	0.851	24.253	-0.081	-0.081	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.031	0.016	18.214	0.013	0.013	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.008	-0.007	17.859	-0.012	-0.012	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.006	0.008	17.855	0.013	0.013	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.823	-0.902	13.347	0.270	0.270	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.058	-0.041	12.967	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.024	0.014	16.144	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.030	-0.031	18.554	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.050	-0.016	20.146	-0.015	-0.015	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.860	-0.943	17.731	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.032	-0.008	15.393	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.804	0.889	13.952	0.203	0.203	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.028	0.014	13.410	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.810	-0.902	13.161	-0.317	-0.317	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.904	-0.938	9.090	-0.554	-0.554	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.041	-0.029	8.113	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.827	-0.916	6.149	-2.480	-2.480	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.030	-0.019	9.243	0.074	0.074	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.017	0.015	11.625	0.059	0.059	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.018	-0.007	14.355	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.004	-0.004	16.143	0.016	0.016	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.026	0.007	18.413	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.033	0.026	21.109	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.016	-0.013	24.885	0.008	0.008	0.000	0.000	0.000	0.000
73	A	74	PHE	0	-0.003	-0.025	27.792	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.014	0.037	23.658	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.009	-0.014	24.567	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.832	-0.914	26.189	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.057	-0.041	27.943	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.060	-0.028	22.477	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.732	0.830	26.347	0.039	0.039	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.010	0.008	29.199	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.836	-0.895	26.856	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.047	-0.055	29.494	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.916	-0.923	28.545	-0.041	-0.041	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.016	0.017	28.138	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.789	0.872	23.479	0.020	0.020	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.030	-0.015	21.012	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.056	0.036	22.123	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.039	-0.035	23.267	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.028	-0.018	14.380	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.038	0.003	18.789	-0.026	-0.026	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.840	0.928	20.117	0.111	0.111	0.000	0.000	0.000	0.000
92	A	93	TYR	0	-0.036	-0.006	14.598	0.009	0.009	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.013	0.001	12.619	-0.023	-0.023	0.000	0.000	0.000	0.000
94	A	95	THR	0	0.010	-0.015	17.824	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.868	0.938	21.326	0.209	0.209	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.106	-0.060	18.441	0.021	0.021	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.828	-0.904	18.556	-0.265	-0.265	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.014	0.023	13.449	-0.033	-0.033	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.014	0.002	12.543	0.070	0.070	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.010	-0.007	14.899	0.011	0.011	0.000	0.000	0.000	0.000
101	A	102	PHE	0	0.010	-0.007	12.387	0.010	0.010	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.007	0.003	18.128	0.017	0.017	0.000	0.000	0.000	0.000
103	A	104	ILE	0	0.002	0.003	21.122	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	105	CSO	0	0.000	-0.022	23.305	0.009	0.009	0.000	0.000	0.000	0.000
105	A	106	HIS	0	0.050	0.041	26.916	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.047	0.030	23.490	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	PRO	0	-0.023	-0.036	24.425	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.037	-0.033	26.009	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.030	0.023	22.418	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.009	0.003	21.245	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.025	0.006	25.068	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.799	-0.859	27.070	-0.061	-0.061	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.050	-0.030	23.222	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.927	-0.970	26.415	-0.091	-0.091	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.880	-0.928	24.982	-0.146	-0.146	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.020	0.005	25.820	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.940	0.977	28.774	0.079	0.079	0.000	0.000	0.000	0.000
118	A	119	GLY	0	-0.058	-0.032	31.620	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.752	0.872	22.696	0.172	0.172	0.000	0.000	0.000	0.000
120	A	121	THR	0	-0.050	-0.044	27.827	0.013	0.013	0.000	0.000	0.000	0.000
121	A	122	LEU	0	0.005	-0.001	25.721	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	123	THR	0	-0.029	-0.038	26.836	0.010	0.010	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.041	0.019	27.378	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.029	0.019	28.891	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.011	-0.014	30.950	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	ASN	0	-0.048	-0.041	33.901	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	128	VAL	0	0.073	0.051	29.892	0.001	0.001	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.765	0.875	31.651	0.038	0.038	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.855	0.926	34.054	0.042	0.042	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.825	-0.911	34.028	-0.042	-0.042	0.000	0.000	0.000	0.000
131	A	132	LEU	0	0.012	0.006	28.449	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.019	-0.007	32.555	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.072	-0.047	35.691	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	ALA	0	0.013	0.018	31.745	0.000	0.000	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.040	-0.019	33.150	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.032	0.033	30.551	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	138	HIS	0	-0.045	-0.030	31.752	0.011	0.011	0.000	0.000	0.000	0.000
138	A	139	VAL	0	-0.027	-0.015	31.652	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	140	VAL	0	-0.006	0.002	30.681	0.004	0.004	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.833	-0.883	32.151	-0.037	-0.037	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.895	-0.941	28.852	-0.055	-0.055	0.000	0.000	0.000	0.000
142	A	143	SER	0	-0.034	-0.038	26.742	0.000	0.000	0.000	0.000	0.000	0.000
143	A	144	VAL	0	-0.030	-0.003	21.531	0.000	0.000	0.000	0.000	0.000	0.000
144	A	145	VAL	0	-0.039	-0.001	24.563	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	146	VAL	0	-0.008	-0.015	20.209	-0.006	-0.006	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.799	-0.871	22.473	-0.135	-0.135	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.062	-0.037	20.445	-0.018	-0.018	0.000	0.000	0.000	0.000
148	A	149	ASN	0	0.065	0.049	17.655	0.011	0.011	0.000	0.000	0.000	0.000
149	A	150	ILE	0	0.001	0.009	18.093	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	151	VAL	0	0.001	0.000	17.766	0.005	0.005	0.000	0.000	0.000	0.000
151	A	152	THR	0	-0.014	-0.011	20.634	0.012	0.012	0.000	0.000	0.000	0.000
152	A	153	SER	0	0.033	-0.016	23.151	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	154	ARG	1	0.773	0.874	24.913	0.043	0.043	0.000	0.000	0.000	0.000
154	A	155	VAL	0	-0.012	-0.025	27.202	0.005	0.005	0.000	0.000	0.000	0.000
155	A	156	PRO	0	0.003	-0.016	24.996	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	157	ASP	-1	-0.927	-0.947	25.600	-0.013	-0.013	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.741	-0.851	25.155	-0.039	-0.039	0.000	0.000	0.000	0.000
158	A	159	LEU	0	-0.042	-0.012	20.155	-0.009	-0.009	0.000	0.000	0.000	0.000
159	A	160	ASP	-1	-0.846	-0.929	20.378	-0.016	-0.016	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.828	-0.886	20.265	-0.077	-0.077	0.000	0.000	0.000	0.000
161	A	162	PHE	0	-0.003	-0.013	17.995	-0.017	-0.017	0.000	0.000	0.000	0.000
162	A	163	ASN	0	0.026	-0.005	16.441	-0.016	-0.016	0.000	0.000	0.000	0.000
163	A	164	ARG	1	0.764	0.871	15.395	0.077	0.077	0.000	0.000	0.000	0.000
164	A	165	GLU	-1	-0.770	-0.867	16.015	-0.181	-0.181	0.000	0.000	0.000	0.000
165	A	166	ILE	0	0.018	0.015	13.695	-0.040	-0.040	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.005	0.019	10.889	-0.052	-0.052	0.000	0.000	0.000	0.000
167	A	168	LYS	1	0.823	0.893	11.528	0.081	0.081	0.000	0.000	0.000	0.000
168	A	169	GLN	0	-0.049	-0.045	13.268	-0.087	-0.087	0.000	0.000	0.000	0.000
169	A	170	LEU	0	0.010	0.020	7.908	-0.093	-0.093	0.000	0.000	0.000	0.000
170	A	171	GLN	0	-0.039	-0.010	8.407	-0.230	-0.230	0.000	0.000	0.000	0.000
171	A	172	LEU	0	-0.077	-0.017	10.038	-0.101	-0.101	0.000	0.000	0.000	0.000

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