FMO DATABASE

FMODB ID: JQ2Q9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1495118.631001
FMO2-HF: Nuclear repulsion	1431501.570904
FMO2-HF: Total energy	-63617.060097
FMO2-MP2: Total energy	-63800.497383

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.
-14.523	-15.83	9.851	-4.181	-4.362	0.012

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 : 0.030 / q_NPA : 0.019

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	0.025	-0.013	3.916	4.305	5.832	-0.006	-0.805	-0.715	0.003
4	A	6	ARG	1	0.839	0.912	7.102	-1.417	-1.417	0.000	0.000	0.000	0.000
5	A	7	ALA	0	0.046	0.012	10.502	0.060	0.060	0.000	0.000	0.000	0.000
6	A	8	ASP	-1	-0.774	-0.859	13.100	0.747	0.747	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.005	0.002	12.417	-0.056	-0.056	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.026	0.005	11.876	0.039	0.039	0.000	0.000	0.000	0.000
9	A	11	MET	0	-0.059	0.007	13.790	-0.217	-0.217	0.000	0.000	0.000	0.000
10	A	12	SER	0	-0.003	-0.049	15.022	0.144	0.144	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.918	-0.971	17.241	0.756	0.756	0.000	0.000	0.000	0.000
12	A	14	ALA	0	0.049	0.025	18.016	-0.033	-0.033	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.748	-0.822	19.048	0.730	0.730	0.000	0.000	0.000	0.000
14	A	16	ILE	0	-0.029	-0.013	13.937	0.004	0.004	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.023	0.018	18.287	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.842	-0.915	21.286	0.403	0.403	0.000	0.000	0.000	0.000
17	A	19	PHE	0	-0.062	-0.006	17.602	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	20	VAL	0	-0.001	-0.004	18.524	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	21	ASN	0	-0.031	-0.017	21.181	-0.072	-0.072	0.000	0.000	0.000	0.000
20	A	22	SER	0	-0.035	-0.026	24.570	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.042	-0.009	21.935	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.893	0.967	24.181	-0.230	-0.230	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.011	-0.002	23.795	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	26	GLY	0	0.085	0.051	20.088	0.038	0.038	0.000	0.000	0.000	0.000
25	A	27	THR	0	-0.050	-0.021	17.615	-0.087	-0.087	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.013	0.003	17.078	0.063	0.063	0.000	0.000	0.000	0.000
27	A	29	ALA	0	0.000	-0.006	14.689	-0.058	-0.058	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.004	-0.006	16.769	0.021	0.021	0.000	0.000	0.000	0.000
29	A	31	ILE	0	0.015	0.017	14.495	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	32	GLY	0	0.051	0.039	18.334	0.019	0.019	0.000	0.000	0.000	0.000
31	A	33	PRO	0	-0.053	-0.043	21.170	-0.024	-0.024	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.850	-0.933	22.287	-0.197	-0.197	0.000	0.000	0.000	0.000
33	A	35	GLY	0	-0.017	-0.009	18.530	-0.041	-0.041	0.000	0.000	0.000	0.000
34	A	36	GLN	0	-0.049	-0.014	17.019	-0.047	-0.047	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.027	-0.004	14.490	0.044	0.044	0.000	0.000	0.000	0.000
36	A	38	HIS	0	-0.004	0.017	16.983	0.038	0.038	0.000	0.000	0.000	0.000
37	A	39	LEU	0	0.020	0.008	15.950	0.037	0.037	0.000	0.000	0.000	0.000
38	A	40	THR	0	-0.040	-0.033	19.826	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.058	0.042	21.614	0.034	0.034	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.064	-0.035	22.548	-0.042	-0.042	0.000	0.000	0.000	0.000
41	A	43	TRP	0	0.022	0.011	24.142	0.016	0.016	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.064	-0.070	22.403	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	45	ALA	0	0.051	0.047	25.540	0.001	0.001	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.021	-0.015	23.553	0.033	0.033	0.000	0.000	0.000	0.000
45	A	47	ILE	0	0.008	0.002	25.061	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	48	ASP	-1	-0.895	-0.944	25.113	0.307	0.307	0.000	0.000	0.000	0.000
47	A	49	GLY	0	-0.005	0.005	22.891	0.015	0.015	0.000	0.000	0.000	0.000
48	A	50	GLU	-1	-0.832	-0.872	20.528	0.463	0.463	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.008	0.003	17.868	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.004	-0.015	21.387	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.018	-0.011	21.307	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.792	-0.872	25.097	0.132	0.132	0.000	0.000	0.000	0.000
53	A	55	THR	0	0.053	0.014	27.057	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	56	LYS	1	0.885	0.952	29.514	-0.087	-0.087	0.000	0.000	0.000	0.000
55	A	57	ALA	0	0.057	0.023	31.030	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.937	0.969	31.658	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.001	0.005	28.523	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	60	GLN	0	0.048	0.005	25.027	0.003	0.003	0.000	0.000	0.000	0.000
59	A	61	LYS	1	0.922	0.964	23.269	-0.147	-0.147	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.040	0.021	24.369	0.005	0.005	0.000	0.000	0.000	0.000
61	A	63	VAL	0	-0.030	-0.004	27.057	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.006	-0.015	21.671	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	65	LEU	0	-0.015	-0.004	19.407	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	66	ARG	1	0.826	0.905	22.672	-0.050	-0.050	0.000	0.000	0.000	0.000
65	A	67	ARG	1	0.783	0.897	19.630	0.129	0.129	0.000	0.000	0.000	0.000
66	A	68	ASP	-1	-0.760	-0.856	17.877	-0.196	-0.196	0.000	0.000	0.000	0.000
67	A	69	PRO	0	0.036	0.024	19.297	0.009	0.009	0.000	0.000	0.000	0.000
68	A	70	ARG	1	0.805	0.877	13.186	0.346	0.346	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.003	0.000	14.687	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.017	-0.018	11.412	0.032	0.032	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.008	-0.007	13.288	-0.132	-0.132	0.000	0.000	0.000	0.000
72	A	74	LEU	0	-0.012	0.005	12.168	0.183	0.183	0.000	0.000	0.000	0.000
73	A	75	LEU	0	0.025	0.019	15.018	-0.117	-0.117	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.910	-0.970	16.530	0.578	0.578	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.794	-0.853	18.516	0.395	0.395	0.000	0.000	0.000	0.000
76	A	78	GLY	0	0.070	0.024	20.654	0.047	0.047	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.931	-0.960	22.846	0.248	0.248	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.047	-0.039	24.443	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	81	TYR	0	0.019	0.002	17.779	0.055	0.055	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.733	-0.853	20.976	0.325	0.325	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.028	-0.049	22.940	0.034	0.034	0.000	0.000	0.000	0.000
82	A	84	LEU	0	-0.072	-0.004	17.737	0.031	0.031	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.816	0.859	17.254	-0.439	-0.439	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.044	0.012	15.879	-0.079	-0.079	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.026	-0.017	12.804	0.179	0.179	0.000	0.000	0.000	0.000
86	A	88	SER	0	0.000	0.007	9.557	-0.316	-0.316	0.000	0.000	0.000	0.000
87	A	89	PHE	0	-0.002	-0.003	10.220	0.463	0.463	0.000	0.000	0.000	0.000
88	A	90	GLU	-1	-0.827	-0.902	6.301	2.290	2.290	0.000	0.000	0.000	0.000
89	A	91	GLY	0	-0.001	-0.020	10.419	0.155	0.155	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.014	0.002	12.734	-0.140	-0.140	0.000	0.000	0.000	0.000
91	A	93	ALA	0	0.014	0.009	16.385	0.065	0.065	0.000	0.000	0.000	0.000
92	A	94	GLU	-1	-0.878	-0.922	19.693	0.182	0.182	0.000	0.000	0.000	0.000
93	A	95	ILE	0	-0.044	-0.022	23.229	0.011	0.011	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.001	0.007	26.175	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.859	-0.957	28.949	0.078	0.078	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.813	-0.894	32.234	0.137	0.137	0.000	0.000	0.000	0.000
97	A	99	PRO	0	0.023	0.002	33.881	0.008	0.008	0.000	0.000	0.000	0.000
98	A	100	GLU	-1	-0.802	-0.889	36.046	0.157	0.157	0.000	0.000	0.000	0.000
99	A	101	ALA	0	0.010	0.013	30.434	0.010	0.010	0.000	0.000	0.000	0.000
100	A	102	LEU	0	-0.071	-0.029	31.600	0.010	0.010	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.003	-0.011	33.290	0.002	0.002	0.000	0.000	0.000	0.000
102	A	104	ARG	1	0.885	0.927	31.180	-0.178	-0.178	0.000	0.000	0.000	0.000
103	A	105	VAL	0	-0.020	-0.010	28.217	0.013	0.013	0.000	0.000	0.000	0.000
104	A	106	GLY	0	0.049	0.003	30.740	0.006	0.006	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.011	0.006	33.755	0.000	0.000	0.000	0.000	0.000	0.000
106	A	108	SER	0	0.021	0.012	28.988	0.006	0.006	0.000	0.000	0.000	0.000
107	A	109	VAL	0	-0.028	-0.029	29.319	0.009	0.009	0.000	0.000	0.000	0.000
108	A	110	TRP	0	-0.048	-0.044	31.381	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.835	-0.927	33.785	0.185	0.185	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.773	0.889	25.472	-0.326	-0.326	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.129	-0.071	26.242	0.008	0.008	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.055	-0.021	32.879	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	115	GLY	0	0.007	0.000	36.717	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	116	PRO	0	0.013	0.001	37.802	0.003	0.003	0.000	0.000	0.000	0.000
115	A	117	TYR	0	-0.031	-0.035	38.196	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	118	THR	0	-0.038	-0.050	40.054	0.000	0.000	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.831	-0.901	43.331	0.118	0.118	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.897	-0.931	45.055	0.098	0.098	0.000	0.000	0.000	0.000
119	A	121	CSO	0	-0.037	-0.004	41.825	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	122	LYS	1	0.861	0.943	41.161	-0.110	-0.110	0.000	0.000	0.000	0.000
121	A	123	PRO	0	0.007	-0.004	42.139	0.000	0.000	0.000	0.000	0.000	0.000
122	A	124	MET	0	-0.029	-0.009	41.556	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	125	VAL	0	0.035	0.032	36.665	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	ASP	-1	-0.810	-0.902	37.988	0.109	0.109	0.000	0.000	0.000	0.000
125	A	127	GLN	0	-0.093	-0.052	39.873	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	128	MET	0	-0.024	0.000	34.752	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	129	MET	0	0.012	0.022	31.594	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	130	ASN	0	0.063	0.050	36.121	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.837	0.902	37.364	-0.065	-0.065	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.742	0.849	32.050	-0.129	-0.129	0.000	0.000	0.000	0.000
131	A	133	VAL	0	-0.009	0.000	28.675	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.054	0.028	28.307	0.006	0.006	0.000	0.000	0.000	0.000
133	A	135	VAL	0	-0.056	-0.048	22.075	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	136	ARG	1	0.815	0.894	21.638	-0.300	-0.300	0.000	0.000	0.000	0.000
135	A	137	ILE	0	-0.012	-0.018	16.488	-0.019	-0.019	0.000	0.000	0.000	0.000
136	A	138	VAL	0	0.021	0.014	16.795	0.057	0.057	0.000	0.000	0.000	0.000
137	A	139	ALA	0	0.019	0.013	12.627	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.824	0.904	10.635	-0.716	-0.716	0.000	0.000	0.000	0.000
139	A	141	ARG	1	0.831	0.896	1.818	-13.983	-17.189	9.853	-3.240	-3.406	0.008
140	A	142	THR	0	0.071	0.034	8.242	-0.306	-0.306	0.000	0.000	0.000	0.000
141	A	143	ARG	1	0.784	0.891	3.966	-7.820	-7.448	0.004	-0.136	-0.241	0.001
142	A	144	SER	0	0.061	0.035	8.753	-0.376	-0.376	0.000	0.000	0.000	0.000
143	A	145	TRP	0	-0.034	0.002	11.396	0.299	0.299	0.000	0.000	0.000	0.000
144	A	146	ASP	-1	-0.723	-0.838	14.088	0.485	0.485	0.000	0.000	0.000	0.000
145	A	147	HIS	0	-0.041	-0.034	16.256	0.089	0.089	0.000	0.000	0.000	0.000
146	A	148	ARG	1	0.877	0.919	19.371	-0.516	-0.516	0.000	0.000	0.000	0.000
147	A	149	LYS	1	0.750	0.853	17.791	-0.832	-0.832	0.000	0.000	0.000	0.000
148	A	150	LEU	0	-0.057	-0.017	17.890	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	151	GLY	0	-0.016	0.002	21.453	-0.038	-0.038	0.000	0.000	0.000	0.000
150	A	152	LEU	0	-0.038	-0.018	22.164	-0.033	-0.033	0.000	0.000	0.000	0.000
151	A	153	PRO	0	-0.030	-0.012	25.337	0.001	0.001	0.000	0.000	0.000	0.000
152	A	154	HIS	0	-0.058	-0.038	27.927	-0.009	-0.009	0.000	0.000	0.000	0.000
153	A	155	MET	0	-0.046	-0.018	24.821	-0.023	-0.023	0.000	0.000	0.000	0.000
154	A	156	SER	0	0.016	0.022	29.500	0.008	0.008	0.000	0.000	0.000	0.000
155	A	157	VAL	0	0.033	0.006	28.355	-0.004	-0.004	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.008	-0.003	29.478	-0.012	-0.012	0.000	0.000	0.000	0.000
157	A	159	GLY	0	0.011	0.007	29.948	0.002	0.002	0.000	0.000	0.000	0.000
158	A	160	SER	0	-0.001	-0.014	31.433	0.005	0.005	0.000	0.000	0.000	0.000
159	A	161	THR	0	-0.002	-0.003	27.571	-0.005	-0.005	0.000	0.000	0.000	0.000
160	A	162	ALA	0	-0.058	-0.001	30.722	0.008	0.008	0.000	0.000	0.000	0.000

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