FMO DATABASE

FMODB ID: NN2NQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1493375.672564
FMO2-HF: Nuclear repulsion	1429759.033125
FMO2-HF: Total energy	-63616.639439
FMO2-MP2: Total energy	-63800.012697

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.
-16.631	-12.565	2.868	-3.174	-3.762	0.008

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 : 0.026 / 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	5	GLN	0	0.014	0.025	3.856	-0.484	2.130	-0.030	-1.414	-1.171	-0.001
4	A	6	ARG	1	0.830	0.892	7.317	-1.052	-1.052	0.000	0.000	0.000	0.000
5	A	7	ALA	0	0.064	0.014	10.272	0.119	0.119	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.770	-0.857	13.066	0.605	0.605	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.029	0.016	12.527	-0.024	-0.024	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.027	0.006	12.033	0.067	0.067	0.000	0.000	0.000	0.000
9	A	11	MET	0	-0.057	-0.009	13.867	-0.203	-0.203	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.016	-0.053	15.444	0.111	0.111	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.918	-0.971	17.408	0.731	0.731	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.024	0.006	18.233	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.745	-0.823	19.438	0.630	0.630	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.033	-0.009	14.329	0.011	0.011	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.016	0.010	18.590	-0.035	-0.035	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.844	-0.911	21.446	0.387	0.387	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.043	0.002	17.982	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	20	VAL	0	-0.007	-0.008	18.902	-0.030	-0.030	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.030	-0.013	21.491	-0.065	-0.065	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.034	-0.020	24.755	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.036	-0.004	22.229	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.947	0.980	24.470	-0.233	-0.233	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.011	-0.001	23.669	-0.021	-0.021	0.000	0.000	0.000	0.000
24	A	26	GLY	0	0.073	0.057	20.041	0.034	0.034	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.036	-0.013	17.679	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.024	-0.003	17.355	0.061	0.061	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.003	-0.005	15.057	-0.057	-0.057	0.000	0.000	0.000	0.000
28	A	30	THR	0	0.004	0.003	16.778	0.022	0.022	0.000	0.000	0.000	0.000
29	A	31	ILE	0	0.007	0.004	14.820	-0.032	-0.032	0.000	0.000	0.000	0.000
30	A	32	GLY	0	0.036	0.032	18.549	0.014	0.014	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.039	-0.038	21.138	-0.021	-0.021	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.876	-0.940	22.439	-0.150	-0.150	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.018	-0.011	18.575	-0.039	-0.039	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.055	-0.015	17.140	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.022	0.008	14.790	0.042	0.042	0.000	0.000	0.000	0.000
36	A	38	HIS	0	-0.006	0.011	17.347	0.021	0.021	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.037	0.012	16.361	0.038	0.038	0.000	0.000	0.000	0.000
38	A	40	THR	0	-0.025	-0.018	20.304	-0.028	-0.028	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.046	0.033	21.743	0.033	0.033	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.064	-0.034	22.815	-0.039	-0.039	0.000	0.000	0.000	0.000
41	A	43	TRP	0	0.028	0.015	24.185	0.019	0.019	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.076	-0.081	22.878	0.000	0.000	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.047	0.040	25.823	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.015	-0.023	23.853	0.036	0.036	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.021	-0.016	25.332	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.880	-0.936	25.490	0.308	0.308	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.019	-0.005	23.089	0.022	0.022	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.814	-0.867	20.654	0.493	0.493	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.001	0.001	18.285	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	52	TRP	0	0.018	-0.001	21.711	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.030	-0.012	21.359	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.780	-0.875	25.384	0.151	0.151	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.020	0.007	26.813	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.884	0.950	29.461	-0.101	-0.101	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.067	0.032	30.842	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.946	0.958	31.421	-0.046	-0.046	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.014	-0.002	28.409	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.053	0.011	25.463	0.000	0.000	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.908	0.959	23.441	-0.162	-0.162	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.040	0.022	24.222	0.007	0.007	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.025	-0.017	26.481	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.020	-0.027	21.944	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.015	-0.011	19.641	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.877	0.954	22.807	-0.077	-0.077	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.819	0.927	19.825	0.054	0.054	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.767	-0.872	18.056	-0.081	-0.081	0.000	0.000	0.000	0.000
67	A	69	PRO	0	0.047	0.026	18.970	0.015	0.015	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.803	0.882	13.295	0.202	0.202	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.003	0.009	14.857	-0.052	-0.052	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.003	-0.013	11.189	0.046	0.046	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.016	-0.015	13.436	-0.141	-0.141	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.023	-0.003	12.408	0.179	0.179	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.021	0.016	15.304	-0.112	-0.112	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.925	-0.989	16.627	0.539	0.539	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.789	-0.847	18.662	0.367	0.367	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.066	0.029	20.722	0.035	0.035	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.920	-0.955	22.747	0.225	0.225	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.075	-0.058	24.346	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.026	0.001	17.440	0.044	0.044	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.760	-0.874	20.620	0.284	0.284	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.022	-0.042	22.712	0.029	0.029	0.000	0.000	0.000	0.000
82	A	84	LEU	0	-0.055	0.009	17.589	0.025	0.025	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.813	0.857	17.560	-0.408	-0.408	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.049	0.017	15.899	-0.076	-0.076	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.018	-0.009	13.065	0.157	0.157	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.000	0.013	9.750	-0.289	-0.289	0.000	0.000	0.000	0.000
87	A	89	PHE	0	-0.006	-0.013	10.211	0.464	0.464	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.849	-0.910	6.573	2.247	2.247	0.000	0.000	0.000	0.000
89	A	91	GLY	0	0.009	-0.021	10.579	0.157	0.157	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.040	-0.012	13.094	-0.122	-0.122	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.021	0.010	16.584	0.049	0.049	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.898	-0.929	19.875	0.209	0.209	0.000	0.000	0.000	0.000
93	A	95	ILE	0	-0.046	-0.030	23.286	0.006	0.006	0.000	0.000	0.000	0.000
94	A	96	VAL	0	0.028	0.023	26.414	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.951	-1.000	29.209	0.098	0.098	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.843	-0.916	32.511	0.143	0.143	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.021	0.006	34.188	0.008	0.008	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.817	-0.908	35.845	0.164	0.164	0.000	0.000	0.000	0.000
99	A	101	ALA	0	-0.002	-0.002	30.593	0.009	0.009	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.056	-0.025	31.546	0.011	0.011	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.008	-0.003	33.293	0.001	0.001	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.943	0.958	31.218	-0.193	-0.193	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.021	-0.005	28.464	0.012	0.012	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.038	-0.011	30.943	0.005	0.005	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.023	0.000	34.006	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.046	0.039	29.520	0.007	0.007	0.000	0.000	0.000	0.000
107	A	109	VAL	0	-0.016	-0.019	29.460	0.007	0.007	0.000	0.000	0.000	0.000
108	A	110	TRP	0	-0.048	-0.037	31.638	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.833	-0.927	33.975	0.184	0.184	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.741	0.884	25.956	-0.317	-0.317	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.127	-0.083	26.675	0.009	0.009	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.076	-0.026	33.401	-0.013	-0.013	0.000	0.000	0.000	0.000
113	A	115	GLY	0	-0.005	-0.005	37.006	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.012	0.006	37.896	0.006	0.006	0.000	0.000	0.000	0.000
115	A	117	TYR	0	0.006	0.005	38.281	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.047	-0.054	40.162	0.001	0.001	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.870	-0.934	43.612	0.117	0.117	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.892	-0.928	45.302	0.100	0.100	0.000	0.000	0.000	0.000
119	A	121	CSO	0	-0.045	-0.011	41.899	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	122	LYS	1	0.864	0.936	41.661	-0.113	-0.113	0.000	0.000	0.000	0.000
121	A	123	PRO	0	0.019	0.002	42.481	0.001	0.001	0.000	0.000	0.000	0.000
122	A	124	MET	0	-0.036	-0.011	41.906	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	125	VAL	0	0.038	0.028	36.865	0.002	0.002	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.835	-0.914	38.335	0.113	0.113	0.000	0.000	0.000	0.000
125	A	127	GLN	0	-0.092	-0.048	39.985	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.019	0.008	34.495	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	129	MET	0	0.022	0.019	31.637	0.000	0.000	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.069	0.055	36.056	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.827	0.892	37.294	-0.076	-0.076	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.786	0.894	32.163	-0.139	-0.139	0.000	0.000	0.000	0.000
131	A	133	VAL	0	0.000	0.007	28.605	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.061	0.031	28.489	0.005	0.005	0.000	0.000	0.000	0.000
133	A	135	VAL	0	-0.078	-0.056	22.160	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	136	ARG	1	0.817	0.889	21.872	-0.337	-0.337	0.000	0.000	0.000	0.000
135	A	137	ILE	0	-0.013	-0.017	16.702	-0.006	-0.006	0.000	0.000	0.000	0.000
136	A	138	VAL	0	0.019	0.014	16.928	0.037	0.037	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.011	0.011	12.747	0.009	0.009	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.870	0.925	10.637	-0.721	-0.721	0.000	0.000	0.000	0.000
139	A	141	ARG	1	0.837	0.906	1.990	-13.644	-12.446	2.895	-1.708	-2.385	0.009
140	A	142	THR	0	0.068	0.032	8.540	-0.293	-0.293	0.000	0.000	0.000	0.000
141	A	143	ARG	1	0.792	0.901	4.428	-5.563	-5.309	0.003	-0.052	-0.206	0.000
142	A	144	SER	0	0.076	0.036	8.819	-0.371	-0.371	0.000	0.000	0.000	0.000
143	A	145	TRP	0	-0.047	-0.007	11.533	0.245	0.245	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.714	-0.840	14.342	0.442	0.442	0.000	0.000	0.000	0.000
145	A	147	HIS	0	-0.063	-0.042	15.884	0.068	0.068	0.000	0.000	0.000	0.000
146	A	148	ARG	1	0.910	0.937	19.248	-0.469	-0.469	0.000	0.000	0.000	0.000
147	A	149	LYS	1	0.728	0.851	18.030	-0.729	-0.729	0.000	0.000	0.000	0.000
148	A	150	LEU	0	-0.049	-0.017	17.384	-0.004	-0.004	0.000	0.000	0.000	0.000
149	A	151	GLY	0	-0.023	0.005	21.123	-0.033	-0.033	0.000	0.000	0.000	0.000
150	A	152	LEU	0	-0.040	-0.023	21.878	-0.028	-0.028	0.000	0.000	0.000	0.000
151	A	153	PRO	0	-0.020	-0.002	25.306	0.003	0.003	0.000	0.000	0.000	0.000
152	A	154	HIS	0	-0.066	-0.039	27.565	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	155	MET	0	-0.025	-0.002	24.186	-0.020	-0.020	0.000	0.000	0.000	0.000
154	A	156	SER	0	0.037	0.024	29.260	0.008	0.008	0.000	0.000	0.000	0.000
155	A	157	VAL	0	0.016	0.002	28.404	-0.003	-0.003	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.015	0.001	29.379	-0.011	-0.011	0.000	0.000	0.000	0.000
157	A	159	GLY	0	-0.006	-0.007	29.861	0.003	0.003	0.000	0.000	0.000	0.000
158	A	160	SER	0	-0.006	-0.021	31.330	0.006	0.006	0.000	0.000	0.000	0.000
159	A	161	THR	0	-0.003	0.002	27.912	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	162	ALA	0	-0.033	0.011	30.728	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)