FMO DATABASE

FMODB ID: 6Y21Z

Calculation Name: 4BPY-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4BPY

Chain ID: A

ChEMBL ID:

UniProt ID: Q93J40

Base Structure: X-ray

Registration Date: 2023-09-23

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	163
LigandCharge	CSD=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1611005.965181
FMO2-HF: Nuclear repulsion	1549513.541372
FMO2-HF: Total energy	-61492.423809
FMO2-MP2: Total energy	-61674.750515

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:42:GLN)

Summations of interaction energy for fragment #1(A:42:GLN)

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.
-21.422	-16.906	7.104	-5.223	-6.397	-0.037

Interaction energy analysis for fragmet #1(A:42:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.067 / q_NPA : -0.053

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	44	ALA	0	-0.016	0.016	2.902	-2.012	0.869	0.163	-1.259	-1.785	0.002
4	A	45	THR	0	-0.016	-0.008	2.557	-6.765	-4.984	0.859	-1.323	-1.317	-0.019
5	A	46	VAL	0	-0.032	-0.026	3.296	0.781	1.101	0.008	-0.062	-0.266	0.000
6	A	47	LEU	0	-0.033	-0.016	5.937	0.398	0.398	0.000	0.000	0.000	0.000
7	A	48	ASP	-1	-0.899	-0.947	9.631	-2.011	-2.011	0.000	0.000	0.000	0.000
8	A	49	LYS	1	0.915	0.954	11.644	1.327	1.327	0.000	0.000	0.000	0.000
9	A	50	PRO	0	-0.062	-0.032	12.249	0.028	0.028	0.000	0.000	0.000	0.000
10	A	51	PHE	0	0.012	0.015	13.938	0.174	0.174	0.000	0.000	0.000	0.000
11	A	52	GLU	-1	-0.882	-0.935	16.723	-0.787	-0.787	0.000	0.000	0.000	0.000
12	A	53	LYS	1	0.919	0.956	19.399	0.645	0.645	0.000	0.000	0.000	0.000
13	A	54	PRO	0	0.015	0.013	20.166	0.069	0.069	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.926	-0.969	23.268	-0.416	-0.416	0.000	0.000	0.000	0.000
15	A	56	LEU	0	-0.024	0.000	24.080	0.027	0.027	0.000	0.000	0.000	0.000
16	A	57	VAL	0	0.027	0.003	27.771	0.012	0.012	0.000	0.000	0.000	0.000
17	A	58	LEU	0	-0.026	-0.003	27.193	0.010	0.010	0.000	0.000	0.000	0.000
18	A	59	THR	0	-0.044	-0.013	31.209	0.021	0.021	0.000	0.000	0.000	0.000
19	A	60	ASP	-1	-0.757	-0.887	30.695	-0.223	-0.223	0.000	0.000	0.000	0.000
20	A	61	THR	0	0.005	-0.007	29.942	0.016	0.016	0.000	0.000	0.000	0.000
21	A	62	GLN	0	-0.058	-0.018	32.628	0.024	0.024	0.000	0.000	0.000	0.000
22	A	63	GLY	0	-0.032	-0.021	35.168	0.012	0.012	0.000	0.000	0.000	0.000
23	A	64	LYS	1	0.835	0.924	35.169	0.155	0.155	0.000	0.000	0.000	0.000
24	A	65	LYS	1	0.978	1.000	34.227	0.232	0.232	0.000	0.000	0.000	0.000
25	A	66	TYR	0	0.026	0.004	25.304	0.014	0.014	0.000	0.000	0.000	0.000
26	A	67	ASP	-1	-0.845	-0.921	29.124	-0.389	-0.389	0.000	0.000	0.000	0.000
27	A	68	LEU	0	0.012	-0.007	22.222	0.001	0.001	0.000	0.000	0.000	0.000
28	A	69	ARG	1	0.881	0.946	23.976	0.553	0.553	0.000	0.000	0.000	0.000
29	A	70	GLU	-1	-0.945	-0.964	25.390	-0.292	-0.292	0.000	0.000	0.000	0.000
30	A	71	GLN	0	0.026	0.008	27.070	0.012	0.012	0.000	0.000	0.000	0.000
31	A	72	THR	0	-0.106	-0.055	21.739	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	73	ALA	0	0.005	0.016	22.017	-0.048	-0.048	0.000	0.000	0.000	0.000
33	A	74	GLY	0	0.008	-0.007	21.204	0.050	0.050	0.000	0.000	0.000	0.000
34	A	75	LYS	1	0.763	0.889	20.304	0.392	0.392	0.000	0.000	0.000	0.000
35	A	76	PRO	0	-0.030	0.022	15.424	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	77	THR	0	0.010	-0.013	16.288	0.126	0.126	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.021	-0.012	12.738	-0.147	-0.147	0.000	0.000	0.000	0.000
38	A	79	ILE	0	-0.030	-0.008	16.035	0.127	0.127	0.000	0.000	0.000	0.000
39	A	80	TYR	0	0.058	0.036	16.430	-0.094	-0.094	0.000	0.000	0.000	0.000
40	A	81	PHE	0	0.001	0.000	18.492	0.073	0.073	0.000	0.000	0.000	0.000
41	A	82	GLY	0	0.080	0.041	20.911	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	83	TYR	0	0.000	-0.011	23.270	0.032	0.032	0.000	0.000	0.000	0.000
43	A	84	THR	0	-0.027	-0.044	25.844	0.017	0.017	0.000	0.000	0.000	0.000
44	A	85	HIS	0	-0.085	-0.045	27.707	0.037	0.037	0.000	0.000	0.000	0.000
45	A	86	CSD	-1	-0.830	-0.888	22.486	-0.252	-0.252	0.000	0.000	0.000	0.000
46	A	87	PRO	0	-0.046	-0.040	25.357	0.010	0.010	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.936	-0.966	19.983	-0.090	-0.090	0.000	0.000	0.000	0.000
48	A	89	VAL	0	0.082	0.042	17.043	0.013	0.013	0.000	0.000	0.000	0.000
49	A	90	ALA	0	-0.022	-0.004	18.760	-0.024	-0.024	0.000	0.000	0.000	0.000
50	A	91	PRO	0	-0.020	-0.012	20.526	0.000	0.000	0.000	0.000	0.000	0.000
51	A	92	LEU	0	0.025	0.029	15.587	0.049	0.049	0.000	0.000	0.000	0.000
52	A	93	THR	0	-0.013	-0.013	14.790	0.005	0.005	0.000	0.000	0.000	0.000
53	A	94	MET	0	-0.037	-0.016	16.384	0.008	0.008	0.000	0.000	0.000	0.000
54	A	95	ASN	0	0.013	0.008	18.984	0.016	0.016	0.000	0.000	0.000	0.000
55	A	96	ASN	0	0.010	-0.003	13.415	0.162	0.162	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.030	0.020	13.807	0.083	0.083	0.000	0.000	0.000	0.000
57	A	98	ALA	0	-0.010	-0.009	15.591	0.055	0.055	0.000	0.000	0.000	0.000
58	A	99	VAL	0	-0.002	-0.007	16.874	0.033	0.033	0.000	0.000	0.000	0.000
59	A	100	ALA	0	0.029	0.036	13.500	0.059	0.059	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.762	0.850	15.372	0.107	0.107	0.000	0.000	0.000	0.000
61	A	102	LYS	1	0.749	0.873	17.756	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	103	GLN	0	-0.051	-0.022	16.489	0.043	0.043	0.000	0.000	0.000	0.000
63	A	104	LEU	0	-0.051	0.004	15.111	0.017	0.017	0.000	0.000	0.000	0.000
64	A	105	SER	0	0.039	0.017	19.189	-0.029	-0.029	0.000	0.000	0.000	0.000
65	A	106	GLN	0	0.008	-0.015	21.975	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	107	ALA	0	0.032	0.016	23.801	-0.030	-0.030	0.000	0.000	0.000	0.000
67	A	108	GLU	-1	-0.951	-0.989	16.402	0.048	0.048	0.000	0.000	0.000	0.000
68	A	109	GLN	0	-0.017	-0.007	19.904	-0.092	-0.092	0.000	0.000	0.000	0.000
69	A	110	ASP	-1	-0.819	-0.895	21.206	-0.113	-0.113	0.000	0.000	0.000	0.000
70	A	111	LYS	1	0.879	0.947	19.693	0.121	0.121	0.000	0.000	0.000	0.000
71	A	112	LEU	0	-0.003	0.015	16.043	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	113	ARG	1	0.838	0.915	19.255	0.332	0.332	0.000	0.000	0.000	0.000
73	A	114	VAL	0	0.057	0.032	17.893	-0.084	-0.084	0.000	0.000	0.000	0.000
74	A	115	VAL	0	-0.012	-0.011	19.863	0.062	0.062	0.000	0.000	0.000	0.000
75	A	116	PHE	0	0.032	0.012	20.590	-0.064	-0.064	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.015	-0.022	22.510	0.046	0.046	0.000	0.000	0.000	0.000
77	A	118	SER	0	-0.014	-0.053	24.242	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	119	THR	0	0.011	-0.007	24.200	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	120	ASP	-1	-0.823	-0.905	27.276	-0.210	-0.210	0.000	0.000	0.000	0.000
80	A	121	PRO	0	0.002	0.007	30.583	0.020	0.020	0.000	0.000	0.000	0.000
81	A	122	GLU	-1	-0.916	-0.952	32.715	-0.176	-0.176	0.000	0.000	0.000	0.000
82	A	123	ARG	1	0.796	0.885	31.476	0.195	0.195	0.000	0.000	0.000	0.000
83	A	124	ASP	-1	-0.804	-0.827	29.029	-0.215	-0.215	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.051	0.016	32.421	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	126	PRO	0	0.058	0.010	33.187	0.002	0.002	0.000	0.000	0.000	0.000
86	A	127	ALA	0	0.015	0.002	33.304	0.002	0.002	0.000	0.000	0.000	0.000
87	A	128	ALA	0	-0.047	-0.019	34.220	0.012	0.012	0.000	0.000	0.000	0.000
88	A	129	LEU	0	0.033	0.037	26.921	0.011	0.011	0.000	0.000	0.000	0.000
89	A	130	GLY	0	0.034	-0.002	29.565	0.002	0.002	0.000	0.000	0.000	0.000
90	A	131	LYS	1	0.878	0.928	30.856	0.089	0.089	0.000	0.000	0.000	0.000
91	A	132	TRP	0	0.019	0.020	23.506	0.015	0.015	0.000	0.000	0.000	0.000
92	A	133	LEU	0	0.053	0.022	24.241	0.014	0.014	0.000	0.000	0.000	0.000
93	A	134	LYS	1	0.936	0.967	26.591	0.073	0.073	0.000	0.000	0.000	0.000
94	A	135	GLY	0	-0.084	-0.036	28.776	0.018	0.018	0.000	0.000	0.000	0.000
95	A	136	ILE	0	-0.013	0.014	22.013	0.018	0.018	0.000	0.000	0.000	0.000
96	A	137	ASP	-1	-0.738	-0.892	22.556	-0.034	-0.034	0.000	0.000	0.000	0.000
97	A	138	PRO	0	-0.043	-0.013	24.972	-0.029	-0.029	0.000	0.000	0.000	0.000
98	A	139	GLN	0	-0.029	-0.009	24.413	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	140	ILE	0	-0.062	-0.012	21.561	-0.033	-0.033	0.000	0.000	0.000	0.000
100	A	141	VAL	0	-0.007	0.002	23.954	0.023	0.023	0.000	0.000	0.000	0.000
101	A	142	GLY	0	0.024	0.011	24.796	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	143	LEU	0	-0.063	-0.037	25.391	0.017	0.017	0.000	0.000	0.000	0.000
103	A	144	THR	0	-0.003	-0.016	27.958	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	145	GLY	0	0.026	0.000	30.523	0.001	0.001	0.000	0.000	0.000	0.000
105	A	146	GLU	-1	-0.891	-0.947	32.418	-0.242	-0.242	0.000	0.000	0.000	0.000
106	A	147	PHE	0	0.040	0.011	28.058	-0.023	-0.023	0.000	0.000	0.000	0.000
107	A	148	ASP	-1	-0.913	-0.943	29.736	-0.376	-0.376	0.000	0.000	0.000	0.000
108	A	149	THR	0	0.011	-0.004	29.565	-0.026	-0.026	0.000	0.000	0.000	0.000
109	A	150	ILE	0	-0.028	-0.009	25.585	-0.042	-0.042	0.000	0.000	0.000	0.000
110	A	151	GLN	0	-0.047	-0.022	25.360	-0.038	-0.038	0.000	0.000	0.000	0.000
111	A	152	ALA	0	0.018	0.007	25.168	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	153	GLY	0	-0.002	-0.006	24.580	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	154	ALA	0	0.038	0.024	21.075	-0.072	-0.072	0.000	0.000	0.000	0.000
114	A	155	ARG	1	0.956	0.976	20.348	0.640	0.640	0.000	0.000	0.000	0.000
115	A	156	THR	0	-0.146	-0.074	21.324	-0.064	-0.064	0.000	0.000	0.000	0.000
116	A	157	LEU	0	-0.029	-0.015	16.680	-0.060	-0.060	0.000	0.000	0.000	0.000
117	A	158	GLY	0	-0.030	-0.015	16.316	-0.137	-0.137	0.000	0.000	0.000	0.000
118	A	159	ILE	0	-0.045	-0.011	16.054	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	160	SER	0	-0.034	-0.023	18.922	0.058	0.058	0.000	0.000	0.000	0.000
120	A	161	ILE	0	0.030	0.022	21.406	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	162	ASP	-1	-0.892	-0.934	24.271	-0.412	-0.412	0.000	0.000	0.000	0.000
122	A	163	PRO	0	-0.020	-0.028	27.537	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	164	PRO	0	-0.027	0.010	28.448	0.014	0.014	0.000	0.000	0.000	0.000
124	A	177	GLY	0	0.009	-0.014	14.043	0.051	0.051	0.000	0.000	0.000	0.000
125	A	178	THR	0	-0.003	-0.007	12.308	-0.145	-0.145	0.000	0.000	0.000	0.000
126	A	179	GLN	0	0.019	0.018	12.848	0.271	0.271	0.000	0.000	0.000	0.000
127	A	180	VAL	0	-0.033	-0.018	12.357	0.169	0.169	0.000	0.000	0.000	0.000
128	A	181	VAL	0	0.000	0.013	11.793	-0.339	-0.339	0.000	0.000	0.000	0.000
129	A	182	ALA	0	-0.013	-0.008	10.657	0.289	0.289	0.000	0.000	0.000	0.000
130	A	183	PHE	0	-0.030	-0.024	12.444	-0.202	-0.202	0.000	0.000	0.000	0.000
131	A	184	SER	0	0.030	0.014	13.068	0.179	0.179	0.000	0.000	0.000	0.000
132	A	185	PRO	0	0.022	0.011	14.525	0.054	0.054	0.000	0.000	0.000	0.000
133	A	186	LYS	1	0.891	0.931	13.933	0.886	0.886	0.000	0.000	0.000	0.000
134	A	187	SER	0	-0.023	-0.015	15.574	0.044	0.044	0.000	0.000	0.000	0.000
135	A	188	ASP	-1	-0.820	-0.884	18.115	-0.593	-0.593	0.000	0.000	0.000	0.000
136	A	189	ALA	0	0.018	0.008	15.509	0.006	0.006	0.000	0.000	0.000	0.000
137	A	190	GLY	0	-0.028	-0.035	14.019	-0.067	-0.067	0.000	0.000	0.000	0.000
138	A	191	TYR	0	-0.027	-0.049	8.677	0.039	0.039	0.000	0.000	0.000	0.000
139	A	192	VAL	0	0.009	0.011	6.158	-0.677	-0.677	0.000	0.000	0.000	0.000
140	A	193	LEU	0	-0.025	0.001	7.775	0.814	0.814	0.000	0.000	0.000	0.000
141	A	194	TYR	0	-0.023	-0.043	5.877	-1.279	-1.279	0.000	0.000	0.000	0.000
142	A	195	GLY	0	0.091	0.042	8.867	0.389	0.389	0.000	0.000	0.000	0.000
143	A	196	GLU	-1	-0.921	-0.981	10.740	-0.430	-0.430	0.000	0.000	0.000	0.000
144	A	197	ASP	-1	-0.990	-0.977	6.643	-2.207	-2.207	0.000	0.000	0.000	0.000
145	A	198	ALA	0	-0.018	0.001	7.465	0.288	0.288	0.000	0.000	0.000	0.000
146	A	199	THR	0	0.008	0.003	8.039	0.239	0.239	0.000	0.000	0.000	0.000
147	A	200	VAL	0	0.011	-0.016	9.960	-0.038	-0.038	0.000	0.000	0.000	0.000
148	A	201	ASP	-1	-0.914	-0.942	9.419	1.324	1.324	0.000	0.000	0.000	0.000
149	A	202	ASP	-1	-0.824	-0.912	5.200	2.022	2.132	-0.001	-0.002	-0.107	0.000
150	A	203	TYR	0	0.018	-0.004	7.345	0.032	0.032	0.000	0.000	0.000	0.000
151	A	204	THR	0	-0.027	-0.038	10.010	-0.110	-0.110	0.000	0.000	0.000	0.000
152	A	205	LYS	1	0.886	0.954	6.793	-3.894	-3.894	0.000	0.000	0.000	0.000
153	A	206	ASP	-1	-0.799	-0.903	5.355	1.540	1.540	0.000	0.000	0.000	0.000
154	A	207	LEU	0	-0.008	0.003	8.095	-0.518	-0.518	0.000	0.000	0.000	0.000
155	A	208	PRO	0	0.037	0.018	10.796	-0.175	-0.175	0.000	0.000	0.000	0.000
156	A	209	LYS	1	0.853	0.935	6.252	-1.846	-1.846	0.000	0.000	0.000	0.000
157	A	210	LEU	0	0.027	0.011	8.172	-0.179	-0.179	0.000	0.000	0.000	0.000
158	A	211	ILE	0	-0.025	-0.010	10.737	-0.037	-0.037	0.000	0.000	0.000	0.000
159	A	212	LYS	1	0.917	0.962	12.510	0.061	0.061	0.000	0.000	0.000	0.000
160	A	213	GLY	0	-0.001	0.002	12.149	0.021	0.021	0.000	0.000	0.000	0.000
161	A	214	GLU	-1	-1.012	-0.998	9.208	-0.543	-0.543	0.000	0.000	0.000	0.000
162	A	215	ASN	0	0.022	0.008	5.109	0.018	0.018	0.000	0.000	0.000	0.000
163	A	216	PRO	0	0.012	0.029	2.010	-8.158	-8.734	6.075	-2.577	-2.922	-0.020

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:GLN)