FMO DATABASE

FMODB ID: 1N5LZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1763016.312161
FMO2-HF: Nuclear repulsion	1698586.339503
FMO2-HF: Total energy	-64429.972658
FMO2-MP2: Total energy	-64622.047699

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.
-7.121	-2.993	0.063	-1.84	-2.351	0.007

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 : -0.019 / q_NPA : -0.014

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	0.797	0.887	3.862	2.270	4.744	-0.009	-1.221	-1.244	0.004
4	A	5	VAL	0	0.010	0.007	5.674	-0.375	-0.375	0.000	0.000	0.000	0.000
5	A	6	ALA	0	0.009	0.010	9.483	0.085	0.085	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.003	-0.012	12.151	-0.004	-0.004	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.005	0.012	15.142	0.003	0.003	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.019	-0.022	18.367	0.007	0.007	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.017	0.020	20.883	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.019	-0.009	24.357	0.008	0.008	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.874	-0.935	27.012	-0.019	-0.019	0.000	0.000	0.000	0.000
12	A	13	PHE	0	0.025	0.019	22.525	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.841	-0.899	25.603	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.733	-0.867	24.009	0.008	0.008	0.000	0.000	0.000	0.000
15	A	16	ILE	0	0.064	0.025	22.281	0.004	0.004	0.000	0.000	0.000	0.000
16	A	17	ASN	0	-0.062	-0.047	21.463	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	18	TYR	0	0.015	0.019	15.829	0.000	0.000	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.051	0.014	17.510	0.009	0.009	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.011	0.008	17.342	0.008	0.008	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.015	-0.003	16.295	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.842	0.917	12.454	-0.174	-0.174	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.914	-0.958	12.299	0.106	0.106	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.049	-0.014	12.987	0.002	0.002	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.032	-0.023	9.727	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.764	-0.847	8.082	0.346	0.346	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.085	-0.049	8.415	-0.080	-0.080	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.083	-0.029	9.238	-0.049	-0.049	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.036	-0.012	5.485	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	30	PHE	0	-0.065	-0.039	3.539	-0.860	-0.382	0.005	-0.149	-0.334	-0.001
30	A	31	ASN	0	0.004	0.001	3.118	-3.534	-2.358	0.067	-0.470	-0.773	0.004
31	A	32	THR	0	-0.032	-0.033	6.053	-0.311	-0.311	0.000	0.000	0.000	0.000
32	A	33	VAL	0	0.005	0.007	8.317	0.012	0.012	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.018	-0.008	11.121	-0.054	-0.054	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.025	-0.016	12.980	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.093	0.031	16.682	0.003	0.003	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.861	-0.893	20.433	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.073	-0.050	22.691	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.040	0.045	18.479	0.007	0.007	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.066	-0.053	18.865	0.010	0.010	0.000	0.000	0.000	0.000
40	A	41	SER	0	-0.064	-0.024	20.842	0.003	0.003	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.815	-0.902	21.854	0.027	0.027	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.017	-0.001	21.787	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	44	VAL	0	-0.038	-0.034	24.199	0.007	0.007	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.029	0.032	26.005	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.818	0.881	26.734	0.011	0.011	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.150	-0.093	28.308	0.000	0.000	0.000	0.000	0.000	0.000
47	A	48	GLY	0	-0.025	-0.010	29.267	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.884	-0.947	20.926	0.040	0.040	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.768	0.872	24.442	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.038	0.021	18.345	0.008	0.008	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.023	-0.011	18.241	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.018	0.005	17.619	0.009	0.009	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.821	-0.893	13.328	0.099	0.099	0.000	0.000	0.000	0.000
54	A	55	VAL	0	-0.067	-0.045	12.869	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	56	GLY	0	0.029	0.018	16.044	0.003	0.003	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.019	-0.021	18.764	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.064	-0.036	20.283	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	59	GLU	-1	-0.883	-0.944	17.883	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	60	ALA	0	-0.032	0.004	15.618	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.800	0.885	13.687	0.268	0.268	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.036	0.024	13.220	-0.057	-0.057	0.000	0.000	0.000	0.000
62	A	63	GLU	-1	-0.818	-0.913	12.930	-0.378	-0.378	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.906	-0.937	9.140	-0.755	-0.755	0.000	0.000	0.000	0.000
64	A	65	TYR	0	-0.060	-0.037	7.868	-0.180	-0.180	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.833	-0.916	6.227	-2.725	-2.725	0.000	0.000	0.000	0.000
66	A	67	ALA	0	-0.028	-0.024	9.301	0.116	0.116	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.030	0.014	11.883	0.029	0.029	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.005	-0.005	14.599	0.009	0.009	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.000	-0.009	16.334	0.005	0.005	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.018	0.001	18.699	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.022	0.013	21.390	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.005	-0.016	25.191	0.004	0.004	0.000	0.000	0.000	0.000
73	A	74	PHE	0	0.002	-0.026	28.173	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	75	SER	0	0.008	0.039	23.593	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.000	-0.007	24.710	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.879	-0.941	26.457	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.043	-0.031	27.928	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.039	-0.010	22.569	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.779	0.856	26.483	0.054	0.054	0.000	0.000	0.000	0.000
80	A	81	GLY	0	-0.002	0.015	29.058	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.820	-0.876	27.254	-0.065	-0.065	0.000	0.000	0.000	0.000
82	A	83	THR	0	-0.054	-0.045	29.360	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.925	-0.940	28.524	-0.058	-0.058	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.021	0.020	28.312	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.827	0.867	23.568	0.059	0.059	0.000	0.000	0.000	0.000
86	A	87	TYR	0	0.006	-0.037	20.743	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.055	0.037	22.243	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.044	-0.036	23.145	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.023	-0.012	14.289	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	91	ALA	0	0.040	0.006	18.968	-0.027	-0.027	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.839	0.927	20.433	0.116	0.116	0.000	0.000	0.000	0.000
92	A	93	TYR	0	-0.035	-0.008	14.384	0.020	0.020	0.000	0.000	0.000	0.000
93	A	94	PHE	0	0.002	-0.011	12.817	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	95	THR	0	-0.003	-0.020	18.020	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.916	0.968	21.464	0.183	0.183	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.105	-0.055	17.486	0.026	0.026	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.898	-0.944	17.488	-0.235	-0.235	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.021	-0.006	12.812	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	100	PRO	0	-0.001	0.009	12.238	0.065	0.065	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.015	-0.013	15.052	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.002	-0.007	12.560	0.015	0.015	0.000	0.000	0.000	0.000
102	A	103	ALA	0	0.022	0.006	18.324	0.008	0.008	0.000	0.000	0.000	0.000
103	A	104	ILE	0	0.010	0.016	21.368	0.001	0.001	0.000	0.000	0.000	0.000
104	A	105	CSO	0	0.003	-0.003	23.466	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	HIS	0	0.038	0.016	27.041	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	107	GLY	0	0.034	0.030	23.814	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	108	PRO	0	-0.019	-0.030	24.705	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	109	GLN	0	-0.030	-0.028	26.069	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.029	0.018	22.467	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	111	LEU	0	0.010	0.004	21.607	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.032	0.000	25.349	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	113	ASP	-1	-0.805	-0.866	27.028	-0.070	-0.070	0.000	0.000	0.000	0.000
113	A	114	THR	0	-0.090	-0.052	23.406	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.931	-0.970	26.552	-0.085	-0.085	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.853	-0.899	25.244	-0.138	-0.138	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.012	-0.002	26.429	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.944	0.972	29.170	0.070	0.070	0.000	0.000	0.000	0.000
118	A	119	GLY	0	-0.074	-0.030	30.888	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.795	0.907	22.460	0.139	0.139	0.000	0.000	0.000	0.000
120	A	121	THR	0	-0.051	-0.035	27.892	0.010	0.010	0.000	0.000	0.000	0.000
121	A	122	LEU	0	0.011	0.005	25.914	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	123	THR	0	-0.038	-0.040	27.033	0.008	0.008	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.051	0.019	27.725	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.016	0.013	29.150	0.003	0.003	0.000	0.000	0.000	0.000
125	A	126	LEU	0	0.014	-0.004	31.232	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	ASN	0	-0.063	-0.045	34.022	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	128	VAL	0	0.072	0.043	30.179	0.000	0.000	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.789	0.892	32.272	0.032	0.032	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.910	0.960	34.401	0.035	0.035	0.000	0.000	0.000	0.000
130	A	131	ASP	-1	-0.855	-0.930	34.045	-0.044	-0.044	0.000	0.000	0.000	0.000
131	A	132	LEU	0	0.016	0.003	28.699	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.044	-0.018	32.860	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.066	-0.048	35.858	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	ALA	0	0.010	0.024	32.125	0.000	0.000	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.052	-0.025	33.180	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.016	0.019	30.752	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	138	HIS	0	-0.034	-0.023	31.869	0.008	0.008	0.000	0.000	0.000	0.000
138	A	139	VAL	0	-0.023	-0.018	31.747	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	140	VAL	0	0.015	0.010	30.777	0.004	0.004	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.850	-0.888	32.342	-0.032	-0.032	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.898	-0.952	29.428	-0.037	-0.037	0.000	0.000	0.000	0.000
142	A	143	SER	0	-0.037	-0.035	27.424	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	144	VAL	0	-0.015	0.003	22.137	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	145	VAL	0	-0.029	0.008	24.729	0.001	0.001	0.000	0.000	0.000	0.000
145	A	146	VAL	0	-0.006	-0.011	20.338	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	147	ASP	-1	-0.803	-0.880	22.857	-0.103	-0.103	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.034	-0.024	20.227	-0.014	-0.014	0.000	0.000	0.000	0.000
148	A	149	ASN	0	0.077	0.048	17.461	0.024	0.024	0.000	0.000	0.000	0.000
149	A	150	ILE	0	-0.006	0.009	18.028	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	151	VAL	0	0.002	0.008	17.999	0.012	0.012	0.000	0.000	0.000	0.000
151	A	152	THR	0	0.003	0.001	20.801	0.005	0.005	0.000	0.000	0.000	0.000
152	A	153	SER	0	0.027	-0.022	23.553	0.001	0.001	0.000	0.000	0.000	0.000
153	A	154	ARG	1	0.739	0.845	25.180	0.028	0.028	0.000	0.000	0.000	0.000
154	A	155	VAL	0	0.010	-0.017	27.722	0.001	0.001	0.000	0.000	0.000	0.000
155	A	156	PRO	0	0.027	0.001	25.577	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	157	ASP	-1	-0.919	-0.954	25.829	-0.009	-0.009	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.728	-0.833	25.857	-0.028	-0.028	0.000	0.000	0.000	0.000
158	A	159	LEU	0	-0.013	-0.011	20.871	-0.005	-0.005	0.000	0.000	0.000	0.000
159	A	160	ASP	-1	-0.896	-0.939	20.947	-0.001	-0.001	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.819	-0.887	21.128	-0.033	-0.033	0.000	0.000	0.000	0.000
161	A	162	PHE	0	-0.021	-0.019	18.363	-0.008	-0.008	0.000	0.000	0.000	0.000
162	A	163	ASN	0	0.023	-0.013	17.067	-0.009	-0.009	0.000	0.000	0.000	0.000
163	A	164	ARG	1	0.770	0.878	16.127	0.038	0.038	0.000	0.000	0.000	0.000
164	A	165	GLU	-1	-0.781	-0.880	16.863	-0.083	-0.083	0.000	0.000	0.000	0.000
165	A	166	ILE	0	0.008	0.014	14.253	-0.024	-0.024	0.000	0.000	0.000	0.000
166	A	167	VAL	0	0.008	0.015	11.470	-0.027	-0.027	0.000	0.000	0.000	0.000
167	A	168	LYS	1	0.826	0.895	11.909	0.050	0.050	0.000	0.000	0.000	0.000
168	A	169	GLN	0	-0.030	-0.033	13.485	-0.057	-0.057	0.000	0.000	0.000	0.000
169	A	170	LEU	0	0.020	0.030	7.836	-0.084	-0.084	0.000	0.000	0.000	0.000
170	A	171	GLN	0	-0.066	-0.025	8.681	-0.156	-0.156	0.000	0.000	0.000	0.000
171	A	172	LEU	0	-0.080	-0.013	10.202	-0.041	-0.041	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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