FMO DATABASE

FMODB ID: 89N9Y

Calculation Name: 1RFE-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-oxy cysteine

ligand 3-letter code: CSX

PDB ID: 1RFE

Chain ID: A

ChEMBL ID:

UniProt ID: O53240

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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1491990.401714
FMO2-HF: Nuclear repulsion	1428374.88512
FMO2-HF: Total energy	-63615.516595
FMO2-MP2: Total energy	-63798.928021

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:3:THR)

Summations of interaction energy for fragment #1(A:3: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.
-22.354	-16.244	0.946	-3.242	-3.815	0.016

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.010

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	5	GLN	0	0.010	0.022	3.856	-0.940	1.845	-0.031	-1.510	-1.245	-0.001
4	A	6	ARG	1	0.897	0.959	7.317	-1.075	-1.075	0.000	0.000	0.000	0.000
5	A	7	ALA	0	0.067	0.016	10.272	0.122	0.122	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.821	-0.915	13.066	0.630	0.630	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.015	0.008	12.310	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.026	0.010	12.075	0.068	0.068	0.000	0.000	0.000	0.000
9	A	11	MET	0	-0.042	0.010	13.867	-0.214	-0.214	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.011	-0.006	15.401	0.120	0.120	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.909	-0.970	17.404	0.781	0.781	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.018	0.004	18.233	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.779	-0.891	19.448	0.646	0.646	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.033	-0.014	14.425	0.010	0.010	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.008	0.005	18.590	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.874	-0.930	21.446	0.409	0.409	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.030	0.000	18.247	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	20	VAL	0	-0.013	-0.008	18.905	-0.032	-0.032	0.000	0.000	0.000	0.000
19	A	21	ASN	0	0.013	0.006	21.516	-0.062	-0.062	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.038	-0.017	24.789	-0.047	-0.047	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.048	-0.014	22.256	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.995	1.002	24.497	-0.238	-0.238	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.017	0.029	23.586	-0.022	-0.022	0.000	0.000	0.000	0.000
24	A	26	GLY	0	0.064	0.051	20.065	0.035	0.035	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.044	-0.017	17.527	-0.083	-0.083	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.016	-0.001	17.372	0.065	0.065	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.014	0.003	14.999	-0.060	-0.060	0.000	0.000	0.000	0.000
28	A	30	THR	0	0.004	0.003	16.781	0.022	0.022	0.000	0.000	0.000	0.000
29	A	31	ILE	0	0.010	0.007	14.991	-0.034	-0.034	0.000	0.000	0.000	0.000
30	A	32	GLY	0	0.034	0.024	18.510	0.016	0.016	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.049	-0.043	21.114	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.892	-0.946	22.478	-0.163	-0.163	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.018	-0.010	18.560	-0.040	-0.040	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.044	-0.012	17.119	-0.022	-0.022	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.011	0.008	14.729	0.042	0.042	0.000	0.000	0.000	0.000
36	A	38	HIS	0	0.016	0.028	17.301	0.019	0.019	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.028	0.005	16.284	0.038	0.038	0.000	0.000	0.000	0.000
38	A	40	THR	0	-0.050	-0.029	20.233	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.041	0.027	21.659	0.034	0.034	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.071	-0.034	22.840	-0.037	-0.037	0.000	0.000	0.000	0.000
41	A	43	TRP	0	0.026	0.017	24.221	0.020	0.020	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.076	-0.077	22.643	0.003	0.003	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.059	0.043	25.841	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.021	-0.023	23.825	0.037	0.037	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.023	-0.018	25.344	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.902	-0.942	25.502	0.316	0.316	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.020	-0.008	23.095	0.022	0.022	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.892	-0.937	20.623	0.525	0.525	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.005	0.003	18.256	-0.045	-0.045	0.000	0.000	0.000	0.000
50	A	52	TRP	0	0.028	0.003	21.721	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.028	-0.014	21.303	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.821	-0.909	25.394	0.163	0.163	0.000	0.000	0.000	0.000
53	A	55	THR	0	-0.041	-0.047	26.971	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.892	0.958	29.468	-0.099	-0.099	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.078	0.043	30.843	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.977	0.970	31.419	-0.048	-0.048	0.000	0.000	0.000	0.000
57	A	59	SER	0	0.005	0.035	28.776	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.019	-0.009	25.464	0.003	0.003	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.931	0.978	23.406	-0.131	-0.131	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.049	0.023	24.220	0.006	0.006	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.021	-0.012	26.477	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.011	-0.038	21.879	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.019	-0.011	19.901	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.876	0.949	22.801	-0.076	-0.076	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.867	0.950	20.204	0.059	0.059	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.810	-0.920	18.026	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	69	PRO	0	0.046	0.034	18.846	0.016	0.016	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.819	0.912	12.788	0.222	0.222	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.004	0.004	14.846	-0.055	-0.055	0.000	0.000	0.000	0.000
70	A	72	SER	0	0.028	-0.001	11.074	0.041	0.041	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.025	-0.019	13.447	-0.143	-0.143	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.014	0.004	12.537	0.183	0.183	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.012	0.005	15.327	-0.117	-0.117	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.948	-1.007	16.657	0.518	0.518	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.787	-0.869	18.609	0.390	0.390	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.041	0.017	20.658	0.035	0.035	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.902	-0.947	22.688	0.226	0.226	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.072	-0.059	24.272	-0.021	-0.021	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.025	0.000	17.311	0.044	0.044	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.783	-0.894	20.572	0.291	0.291	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.028	-0.035	22.659	0.029	0.029	0.000	0.000	0.000	0.000
82	A	84	LEU	0	-0.047	0.004	17.405	0.023	0.023	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.860	0.916	17.546	-0.423	-0.423	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.030	0.018	15.925	-0.077	-0.077	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.012	-0.007	13.138	0.167	0.167	0.000	0.000	0.000	0.000
86	A	88	SER	0	-0.032	0.002	9.771	-0.229	-0.229	0.000	0.000	0.000	0.000
87	A	89	PHE	0	0.014	-0.003	10.234	0.479	0.479	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.945	-0.970	7.048	1.323	1.323	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.011	-0.023	10.584	0.167	0.167	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.048	-0.013	13.092	-0.127	-0.127	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.034	0.015	16.578	0.050	0.050	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.922	-0.953	19.873	0.202	0.202	0.000	0.000	0.000	0.000
93	A	95	ILE	0	-0.071	-0.042	23.282	0.005	0.005	0.000	0.000	0.000	0.000
94	A	96	VAL	0	0.039	0.035	26.411	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.959	-1.007	29.208	0.097	0.097	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.855	-0.931	32.503	0.146	0.146	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.012	0.001	34.190	0.009	0.009	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.895	-0.947	35.669	0.161	0.161	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.014	-0.014	30.600	0.010	0.010	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.046	-0.023	31.564	0.011	0.011	0.000	0.000	0.000	0.000
101	A	103	HIS	0	0.034	0.023	33.300	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.979	0.992	31.496	-0.200	-0.200	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.022	-0.002	28.471	0.012	0.012	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.051	-0.006	30.955	0.005	0.005	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.013	-0.004	34.019	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.055	0.046	29.484	0.008	0.008	0.000	0.000	0.000	0.000
107	A	109	VAL	0	-0.002	-0.009	29.414	0.008	0.008	0.000	0.000	0.000	0.000
108	A	110	TRP	0	-0.028	-0.030	31.655	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.871	-0.952	33.888	0.193	0.193	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.736	0.882	25.932	-0.325	-0.325	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.166	-0.129	26.665	0.011	0.011	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.089	-0.026	33.423	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.002	-0.005	37.044	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.017	0.007	37.917	0.006	0.006	0.000	0.000	0.000	0.000
115	A	117	TYR	0	0.028	0.021	38.247	-0.010	-0.010	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.011	-0.009	40.181	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.872	-0.935	43.628	0.119	0.119	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.917	-0.961	45.317	0.100	0.100	0.000	0.000	0.000	0.000
119	A	121	CSO	0	-0.070	-0.033	41.907	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	122	LYS	1	0.910	0.966	41.688	-0.113	-0.113	0.000	0.000	0.000	0.000
121	A	123	PRO	0	0.017	0.002	42.493	0.001	0.001	0.000	0.000	0.000	0.000
122	A	124	MET	0	-0.039	-0.015	41.947	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	125	VAL	0	0.034	0.026	36.868	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.862	-0.932	38.347	0.113	0.113	0.000	0.000	0.000	0.000
125	A	127	GLN	0	-0.096	-0.052	39.994	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.033	0.004	34.557	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	129	MET	0	0.013	0.015	31.629	0.000	0.000	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.036	0.032	36.071	-0.005	-0.005	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.858	0.910	37.297	-0.073	-0.073	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.885	0.948	32.081	-0.133	-0.133	0.000	0.000	0.000	0.000
131	A	133	VAL	0	0.007	0.015	28.492	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.067	0.033	28.495	0.005	0.005	0.000	0.000	0.000	0.000
133	A	135	VAL	0	-0.076	-0.049	22.087	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	136	ARG	1	0.917	0.973	21.908	-0.337	-0.337	0.000	0.000	0.000	0.000
135	A	137	ILE	0	-0.017	-0.021	16.776	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	138	VAL	0	0.030	0.023	16.629	0.035	0.035	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.005	0.006	12.758	0.007	0.007	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.889	0.934	10.606	-0.697	-0.697	0.000	0.000	0.000	0.000
139	A	141	ARG	1	0.903	0.962	2.408	-13.809	-11.528	0.625	-1.187	-1.719	0.011
140	A	142	THR	0	0.070	0.032	8.546	-0.299	-0.299	0.000	0.000	0.000	0.000
141	A	143	ARG	1	0.815	0.921	3.010	-10.026	-8.982	0.352	-0.545	-0.851	0.006
142	A	144	SER	0	0.073	0.037	8.849	-0.378	-0.378	0.000	0.000	0.000	0.000
143	A	145	TRP	0	-0.064	-0.026	11.411	0.264	0.264	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.778	-0.902	14.377	0.474	0.474	0.000	0.000	0.000	0.000
145	A	147	HIS	0	-0.081	-0.042	15.824	0.070	0.070	0.000	0.000	0.000	0.000
146	A	148	ARG	1	1.011	1.011	19.248	-0.449	-0.449	0.000	0.000	0.000	0.000
147	A	149	LYS	1	0.724	0.844	17.687	-0.779	-0.779	0.000	0.000	0.000	0.000
148	A	150	LEU	0	-0.045	-0.020	17.371	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	151	GLY	0	-0.025	0.007	21.123	-0.034	-0.034	0.000	0.000	0.000	0.000
150	A	152	LEU	0	-0.039	-0.025	21.384	-0.029	-0.029	0.000	0.000	0.000	0.000
151	A	153	PRO	0	-0.023	-0.004	25.280	0.004	0.004	0.000	0.000	0.000	0.000
152	A	154	HIS	0	-0.040	-0.014	27.532	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	155	MET	0	-0.027	-0.005	24.070	-0.020	-0.020	0.000	0.000	0.000	0.000
154	A	156	SER	0	0.018	0.011	29.182	0.006	0.006	0.000	0.000	0.000	0.000
155	A	157	VAL	0	0.018	0.009	28.401	-0.004	-0.004	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.025	0.006	29.336	-0.011	-0.011	0.000	0.000	0.000	0.000
157	A	159	GLY	0	-0.006	-0.007	29.820	0.002	0.002	0.000	0.000	0.000	0.000
158	A	160	SER	0	-0.021	-0.029	31.256	0.006	0.006	0.000	0.000	0.000	0.000
159	A	161	THR	0	0.019	0.010	27.751	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	162	ALA	0	-0.043	0.011	30.648	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)