FMO DATABASE

FMODB ID: LR6M9

Calculation Name: 6ERD-A-Xray547

Preferred Name:

Target Type:

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

Ligand 3-letter code: CME

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6ERD

Chain ID: A

ChEMBL ID:

UniProt ID: Q81D84

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	171
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1865681.497143
FMO2-HF: Nuclear repulsion	1796334.295414
FMO2-HF: Total energy	-69347.201729
FMO2-MP2: Total energy	-69550.113626

3D Structure Molmil

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:41:LYS)

Summations of interaction energy for fragment #1(A:41:LYS)

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.
-140.476	-137.165	1.185	-1.347	-3.149	-0.011

Interaction energy analysis for fragmet #1(A:41:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.806 / q_NPA : 1.886

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	43	VAL	0	-0.008	-0.011	2.483	-6.706	-4.182	1.146	-1.126	-2.545	-0.010
4	A	44	ILE	0	0.038	0.027	4.885	6.388	6.521	-0.001	-0.015	-0.116	0.000
102	A	142	HIS	0	-0.053	-0.024	2.884	5.346	6.000	0.040	-0.206	-0.488	-0.001
5	A	45	LYS	1	0.856	0.918	8.513	48.882	48.882	0.000	0.000	0.000	0.000
6	A	46	LEU	0	-0.012	0.004	11.477	1.317	1.317	0.000	0.000	0.000	0.000
7	A	47	GLU	-1	-0.885	-0.943	14.738	-34.218	-34.218	0.000	0.000	0.000	0.000
8	A	48	SER	0	-0.015	-0.018	17.872	0.747	0.747	0.000	0.000	0.000	0.000
9	A	49	PHE	0	0.000	0.002	21.561	0.104	0.104	0.000	0.000	0.000	0.000
10	A	50	LYS	1	0.935	0.953	23.054	24.531	24.531	0.000	0.000	0.000	0.000
11	A	51	LYS	1	0.880	0.919	26.013	18.557	18.557	0.000	0.000	0.000	0.000
12	A	52	SER	0	-0.030	-0.016	24.595	0.449	0.449	0.000	0.000	0.000	0.000
13	A	53	ASP	-1	-0.751	-0.870	22.657	-27.391	-27.391	0.000	0.000	0.000	0.000
14	A	54	PHE	0	-0.021	-0.007	24.497	-0.170	-0.170	0.000	0.000	0.000	0.000
15	A	55	LYS	1	0.930	0.954	27.427	19.128	19.128	0.000	0.000	0.000	0.000
16	A	56	GLN	0	0.011	0.011	19.458	0.321	0.321	0.000	0.000	0.000	0.000
17	A	57	LEU	0	0.001	0.000	23.024	-0.254	-0.254	0.000	0.000	0.000	0.000
18	A	58	ILE	0	-0.022	-0.020	25.001	0.184	0.184	0.000	0.000	0.000	0.000
19	A	59	ASN	0	-0.043	-0.010	24.618	1.002	1.002	0.000	0.000	0.000	0.000
20	A	60	TRP	0	-0.023	-0.012	18.544	0.167	0.167	0.000	0.000	0.000	0.000
21	A	61	ILE	0	-0.041	-0.004	24.240	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	62	ASN	0	0.035	0.007	27.052	0.500	0.500	0.000	0.000	0.000	0.000
23	A	63	SER	0	-0.006	-0.011	29.269	0.759	0.759	0.000	0.000	0.000	0.000
24	A	64	GLU	-1	-0.892	-0.948	30.595	-17.381	-17.381	0.000	0.000	0.000	0.000
25	A	65	GLU	-1	-0.887	-0.952	30.789	-19.004	-19.004	0.000	0.000	0.000	0.000
26	A	66	PHE	0	-0.014	0.003	22.146	-0.591	-0.591	0.000	0.000	0.000	0.000
27	A	67	LEU	0	0.028	0.009	27.200	-0.754	-0.754	0.000	0.000	0.000	0.000
28	A	68	ILE	0	-0.003	0.017	28.763	-0.365	-0.365	0.000	0.000	0.000	0.000
29	A	69	GLN	0	-0.039	-0.036	25.707	-0.813	-0.813	0.000	0.000	0.000	0.000
30	A	70	TRP	0	-0.030	0.006	22.386	-0.156	-0.156	0.000	0.000	0.000	0.000
31	A	71	SER	0	-0.075	-0.059	24.844	-0.408	-0.408	0.000	0.000	0.000	0.000
32	A	72	GLY	0	0.028	0.015	27.597	0.445	0.445	0.000	0.000	0.000	0.000
33	A	73	ASN	0	-0.016	-0.035	30.431	0.666	0.666	0.000	0.000	0.000	0.000
34	A	74	ALA	0	-0.044	-0.013	30.002	0.409	0.409	0.000	0.000	0.000	0.000
35	A	75	PHE	0	-0.039	-0.019	27.831	-0.151	-0.151	0.000	0.000	0.000	0.000
36	A	76	THR	0	-0.024	-0.012	33.182	0.395	0.395	0.000	0.000	0.000	0.000
37	A	77	PHE	0	0.020	0.031	31.792	-0.442	-0.442	0.000	0.000	0.000	0.000
38	A	78	PRO	0	-0.007	-0.007	33.854	0.477	0.477	0.000	0.000	0.000	0.000
39	A	79	LEU	0	0.016	0.010	28.270	0.115	0.115	0.000	0.000	0.000	0.000
40	A	80	ASP	-1	-0.810	-0.896	32.553	-17.277	-17.277	0.000	0.000	0.000	0.000
41	A	81	GLU	-1	-0.877	-0.961	32.835	-19.029	-19.029	0.000	0.000	0.000	0.000
42	A	82	GLN	0	0.009	0.010	33.599	-0.222	-0.222	0.000	0.000	0.000	0.000
43	A	83	GLN	0	-0.014	-0.025	33.163	-0.334	-0.334	0.000	0.000	0.000	0.000
44	A	84	LEU	0	-0.007	-0.004	27.905	-0.493	-0.493	0.000	0.000	0.000	0.000
45	A	85	GLU	-1	-0.831	-0.899	30.317	-18.928	-18.928	0.000	0.000	0.000	0.000
46	A	86	LYS	1	1.002	0.996	32.367	16.485	16.485	0.000	0.000	0.000	0.000
47	A	87	TYR	0	-0.042	-0.044	23.874	-0.049	-0.049	0.000	0.000	0.000	0.000
48	A	88	ILE	0	-0.048	-0.018	26.731	-0.485	-0.485	0.000	0.000	0.000	0.000
49	A	89	GLU	-1	-0.953	-0.966	29.060	-18.026	-18.026	0.000	0.000	0.000	0.000
50	A	90	SER	0	-0.105	-0.052	30.048	0.359	0.359	0.000	0.000	0.000	0.000
51	A	91	ALA	0	0.043	0.010	30.597	-0.520	-0.520	0.000	0.000	0.000	0.000
52	A	92	ASN	0	-0.050	-0.027	29.422	-0.203	-0.203	0.000	0.000	0.000	0.000
53	A	93	THR	0	-0.022	-0.002	26.566	-0.506	-0.506	0.000	0.000	0.000	0.000
54	A	94	LEU	0	0.005	0.022	21.422	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	95	ALA	0	0.033	0.022	23.081	-0.353	-0.353	0.000	0.000	0.000	0.000
56	A	96	PHE	0	0.004	-0.010	17.754	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	97	LYS	1	0.822	0.915	18.282	29.685	29.685	0.000	0.000	0.000	0.000
58	A	98	VAL	0	-0.009	-0.011	12.481	-1.401	-1.401	0.000	0.000	0.000	0.000
59	A	99	VAL	0	0.013	0.007	13.251	1.372	1.372	0.000	0.000	0.000	0.000
60	A	100	ASP	-1	-0.823	-0.903	9.208	-59.685	-59.685	0.000	0.000	0.000	0.000
61	A	101	GLU	-1	-0.854	-0.922	6.916	-57.125	-57.125	0.000	0.000	0.000	0.000
62	A	102	GLU	-1	-1.032	-1.007	7.933	-59.758	-59.758	0.000	0.000	0.000	0.000
63	A	103	THR	0	-0.016	-0.044	9.778	4.145	4.145	0.000	0.000	0.000	0.000
64	A	104	SER	0	-0.043	-0.012	12.570	3.197	3.197	0.000	0.000	0.000	0.000
65	A	105	ASP	-1	-0.898	-0.933	14.354	-32.327	-32.327	0.000	0.000	0.000	0.000
66	A	106	VAL	0	-0.045	-0.025	14.590	-2.262	-2.262	0.000	0.000	0.000	0.000
67	A	107	ILE	0	-0.024	-0.024	11.149	1.312	1.312	0.000	0.000	0.000	0.000
68	A	108	GLY	0	0.013	0.002	15.464	0.285	0.285	0.000	0.000	0.000	0.000
69	A	109	HIS	0	-0.028	0.009	17.229	1.160	1.160	0.000	0.000	0.000	0.000
70	A	110	ILE	0	0.026	0.017	16.210	-0.642	-0.642	0.000	0.000	0.000	0.000
71	A	111	SER	0	-0.049	-0.023	19.322	0.956	0.956	0.000	0.000	0.000	0.000
72	A	112	LEU	0	0.028	0.015	20.265	-0.533	-0.533	0.000	0.000	0.000	0.000
73	A	113	GLY	0	0.059	0.028	22.563	0.670	0.670	0.000	0.000	0.000	0.000
74	A	114	GLN	0	-0.037	-0.038	26.338	-0.463	-0.463	0.000	0.000	0.000	0.000
75	A	115	ILE	0	0.020	0.009	24.218	0.073	0.073	0.000	0.000	0.000	0.000
76	A	116	ASP	-1	-0.818	-0.874	27.766	-18.077	-18.077	0.000	0.000	0.000	0.000
77	A	117	ASN	0	0.005	-0.025	28.268	-0.755	-0.755	0.000	0.000	0.000	0.000
78	A	118	ILE	0	-0.047	-0.011	30.566	0.211	0.211	0.000	0.000	0.000	0.000
79	A	119	ASN	0	-0.077	-0.066	32.165	0.305	0.305	0.000	0.000	0.000	0.000
80	A	120	LYS	1	0.874	0.957	26.468	21.435	21.435	0.000	0.000	0.000	0.000
81	A	121	SER	0	0.013	0.004	26.377	-0.585	-0.585	0.000	0.000	0.000	0.000
82	A	122	ALA	0	0.049	0.027	23.782	0.190	0.190	0.000	0.000	0.000	0.000
83	A	123	ARG	1	0.767	0.858	24.782	21.814	21.814	0.000	0.000	0.000	0.000
84	A	124	ILE	0	0.015	0.009	17.882	-0.225	-0.225	0.000	0.000	0.000	0.000
85	A	125	GLY	0	0.009	-0.002	21.992	0.953	0.953	0.000	0.000	0.000	0.000
86	A	126	LYS	1	0.913	0.964	21.849	22.199	22.199	0.000	0.000	0.000	0.000
87	A	127	VAL	0	0.022	0.024	17.019	-0.784	-0.784	0.000	0.000	0.000	0.000
88	A	128	LEU	0	-0.023	-0.008	18.525	0.797	0.797	0.000	0.000	0.000	0.000
89	A	129	VAL	0	0.044	-0.003	14.055	-1.426	-1.426	0.000	0.000	0.000	0.000
90	A	130	GLY	0	0.042	0.031	15.620	-1.291	-1.291	0.000	0.000	0.000	0.000
91	A	131	ASN	0	0.044	0.012	16.181	1.259	1.259	0.000	0.000	0.000	0.000
92	A	132	THR	0	0.088	0.055	10.359	-2.652	-2.652	0.000	0.000	0.000	0.000
93	A	133	LYS	0	-0.069	-0.030	10.645	-3.645	-3.645	0.000	0.000	0.000	0.000
94	A	134	MET	0	-0.023	-0.003	11.629	1.208	1.208	0.000	0.000	0.000	0.000
95	A	135	ARG	0	0.091	-0.003	10.346	-3.413	-3.413	0.000	0.000	0.000	0.000
96	A	136	GLY	0	-0.023	-0.017	10.420	-2.256	-2.256	0.000	0.000	0.000	0.000
97	A	137	ARG	1	0.878	0.935	6.216	53.528	53.528	0.000	0.000	0.000	0.000
98	A	138	SER	0	-0.024	-0.034	5.994	-6.349	-6.349	0.000	0.000	0.000	0.000
99	A	139	ILE	0	0.048	0.052	5.811	-0.565	-0.565	0.000	0.000	0.000	0.000
100	A	140	GLY	0	0.075	0.035	8.235	0.887	0.887	0.000	0.000	0.000	0.000
101	A	141	LYS	1	0.815	0.858	8.434	47.315	47.315	0.000	0.000	0.000	0.000
103	A	143	MET	0	-0.008	0.017	8.153	1.926	1.926	0.000	0.000	0.000	0.000
104	A	144	MET	0	0.044	0.025	11.618	2.011	2.011	0.000	0.000	0.000	0.000
105	A	145	LYS	1	0.953	0.971	8.912	55.145	55.145	0.000	0.000	0.000	0.000
106	A	146	ALA	0	-0.007	0.010	10.622	0.991	0.991	0.000	0.000	0.000	0.000
107	A	147	VAL	0	0.034	0.011	12.015	2.164	2.164	0.000	0.000	0.000	0.000
108	A	148	LEU	0	0.000	-0.001	14.083	1.690	1.690	0.000	0.000	0.000	0.000
109	A	149	HIS	0	-0.069	-0.032	12.122	1.067	1.067	0.000	0.000	0.000	0.000
110	A	150	ILE	0	0.048	0.028	14.263	1.972	1.972	0.000	0.000	0.000	0.000
111	A	151	ALA	0	0.005	0.002	17.027	1.870	1.870	0.000	0.000	0.000	0.000
112	A	152	PHE	0	0.003	-0.008	17.383	1.391	1.391	0.000	0.000	0.000	0.000
113	A	153	ASP	-1	-0.845	-0.896	14.258	-36.083	-36.083	0.000	0.000	0.000	0.000
114	A	154	GLU	-1	-0.912	-0.958	15.442	-33.729	-33.729	0.000	0.000	0.000	0.000
115	A	155	LEU	0	-0.031	-0.021	18.892	1.494	1.494	0.000	0.000	0.000	0.000
116	A	156	LYS	1	0.808	0.922	19.200	29.813	29.813	0.000	0.000	0.000	0.000
117	A	157	LEU	0	-0.001	0.002	22.539	1.340	1.340	0.000	0.000	0.000	0.000
118	A	158	HIS	0	-0.061	-0.046	23.163	-0.434	-0.434	0.000	0.000	0.000	0.000
119	A	159	ARG	1	0.798	0.850	24.761	21.081	21.081	0.000	0.000	0.000	0.000
120	A	160	VAL	0	-0.007	0.005	20.082	0.207	0.207	0.000	0.000	0.000	0.000
121	A	161	THR	0	-0.038	-0.028	23.127	0.461	0.461	0.000	0.000	0.000	0.000
122	A	162	LEU	0	0.011	0.008	19.617	-0.742	-0.742	0.000	0.000	0.000	0.000
123	A	163	GLY	0	0.025	0.014	23.718	0.850	0.850	0.000	0.000	0.000	0.000
124	A	164	VAL	0	-0.006	0.002	22.545	-0.498	-0.498	0.000	0.000	0.000	0.000
125	A	165	TYR	0	0.013	-0.005	25.249	0.631	0.631	0.000	0.000	0.000	0.000
126	A	166	ASP	-1	-0.825	-0.917	26.593	-19.980	-19.980	0.000	0.000	0.000	0.000
127	A	167	PHE	0	-0.011	0.001	27.451	-0.495	-0.495	0.000	0.000	0.000	0.000
128	A	168	ASN	0	-0.002	0.006	21.616	-0.816	-0.816	0.000	0.000	0.000	0.000
129	A	169	THR	0	0.034	0.003	22.893	-1.202	-1.202	0.000	0.000	0.000	0.000
130	A	170	SER	0	-0.019	0.002	18.485	-0.464	-0.464	0.000	0.000	0.000	0.000
131	A	171	ALA	0	0.053	0.024	18.096	-1.415	-1.415	0.000	0.000	0.000	0.000
132	A	172	ILE	0	0.021	0.015	18.626	-0.990	-0.990	0.000	0.000	0.000	0.000
133	A	173	SER	0	-0.005	-0.018	18.829	-0.249	-0.249	0.000	0.000	0.000	0.000
134	A	174	CYS	-1	-0.886	-0.855	13.728	-42.623	-42.623	0.000	0.000	0.000	0.000
135	A	175	TYR	-1	-0.827	-0.944	15.328	-32.887	-32.887	0.000	0.000	0.000	0.000
136	A	176	GLU	-1	-0.804	-0.881	17.474	-25.769	-25.769	0.000	0.000	0.000	0.000
137	A	177	LYS	1	0.815	0.912	13.901	34.652	34.652	0.000	0.000	0.000	0.000
138	A	178	ILE	0	-0.108	-0.056	12.269	-2.749	-2.749	0.000	0.000	0.000	0.000
139	A	179	GLY	0	0.030	0.024	14.620	-0.745	-0.745	0.000	0.000	0.000	0.000
140	A	180	PHE	0	-0.023	-0.018	17.449	0.771	0.771	0.000	0.000	0.000	0.000
141	A	181	VAL	0	0.032	0.021	20.518	0.209	0.209	0.000	0.000	0.000	0.000
142	A	182	LYS	1	0.807	0.888	24.065	24.032	24.032	0.000	0.000	0.000	0.000
143	A	183	GLU	-1	-0.766	-0.811	26.647	-20.794	-20.794	0.000	0.000	0.000	0.000
144	A	184	GLY	0	-0.005	-0.011	29.767	0.792	0.792	0.000	0.000	0.000	0.000
145	A	185	LEU	0	-0.039	-0.004	30.736	-0.496	-0.496	0.000	0.000	0.000	0.000
146	A	186	LEU	0	0.005	0.001	32.060	0.782	0.782	0.000	0.000	0.000	0.000
147	A	187	ARG	1	0.963	0.971	34.379	15.166	15.166	0.000	0.000	0.000	0.000
148	A	188	GLU	-1	-0.940	-0.979	36.737	-14.929	-14.929	0.000	0.000	0.000	0.000
149	A	189	SER	0	-0.045	-0.020	34.239	0.122	0.122	0.000	0.000	0.000	0.000
150	A	190	LYS	1	0.821	0.922	33.213	17.479	17.479	0.000	0.000	0.000	0.000
151	A	191	ARG	1	0.897	0.963	35.736	14.364	14.364	0.000	0.000	0.000	0.000
152	A	192	VAL	0	0.009	-0.001	33.998	-0.276	-0.276	0.000	0.000	0.000	0.000
153	A	193	GLY	0	0.019	0.016	37.412	0.124	0.124	0.000	0.000	0.000	0.000
154	A	194	GLU	-1	-0.873	-0.945	40.542	-13.653	-13.653	0.000	0.000	0.000	0.000
155	A	195	THR	0	-0.031	-0.002	37.253	0.255	0.255	0.000	0.000	0.000	0.000
156	A	196	TYR	0	0.024	0.001	37.846	-0.016	-0.016	0.000	0.000	0.000	0.000
157	A	197	TRP	0	-0.034	-0.010	30.168	-0.383	-0.383	0.000	0.000	0.000	0.000
158	A	198	ASN	0	0.004	-0.009	32.753	0.632	0.632	0.000	0.000	0.000	0.000
159	A	199	LEU	0	-0.021	0.003	27.863	-0.609	-0.609	0.000	0.000	0.000	0.000
160	A	200	TRP	0	0.004	-0.006	26.581	0.608	0.608	0.000	0.000	0.000	0.000
161	A	201	GLU	-1	-0.754	-0.838	27.219	-21.952	-21.952	0.000	0.000	0.000	0.000
162	A	202	MET	0	-0.040	-0.028	21.638	0.179	0.179	0.000	0.000	0.000	0.000
163	A	203	SER	0	-0.055	-0.053	24.309	-0.329	-0.329	0.000	0.000	0.000	0.000
164	A	204	MET	0	0.045	0.041	16.591	-1.330	-1.330	0.000	0.000	0.000	0.000
165	A	205	LEU	0	0.015	0.002	22.220	0.535	0.535	0.000	0.000	0.000	0.000
166	A	206	GLU	-1	-0.836	-0.914	21.045	-24.976	-24.976	0.000	0.000	0.000	0.000
167	A	207	TYR	0	-0.067	-0.041	20.706	-1.025	-1.025	0.000	0.000	0.000	0.000
168	A	208	GLU	-1	-0.895	-0.949	21.032	-25.370	-25.370	0.000	0.000	0.000	0.000
169	A	209	TRP	0	-0.044	-0.023	12.100	-2.457	-2.457	0.000	0.000	0.000	0.000
170	A	210	LYS	1	0.765	0.860	13.665	35.309	35.309	0.000	0.000	0.000	0.000
171	A	211	LYS	0	0.005	0.029	17.953	-3.296	-3.296	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:41:LYS)