FMO DATABASE

FMODB ID: R8278

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1616219.321936
FMO2-HF: Nuclear repulsion	1554725.429882
FMO2-HF: Total energy	-61493.892054
FMO2-MP2: Total energy	-61676.317522

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.
-52.835	-50.207	20.894	-11.09	-12.435	-0.006

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 : -0.030 / 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	44	ALA	0	-0.044	-0.013	2.592	-1.895	1.242	2.003	-1.945	-3.196	0.004
4	A	45	THR	0	0.008	0.005	2.160	-15.573	-13.405	3.059	-2.475	-2.752	-0.037
5	A	46	VAL	0	-0.042	-0.029	2.955	2.238	2.729	0.082	-0.103	-0.471	0.000
6	A	47	LEU	0	-0.027	-0.005	5.450	0.337	0.337	0.000	0.000	0.000	0.000
7	A	48	ASP	-1	-0.928	-0.962	9.164	-1.518	-1.518	0.000	0.000	0.000	0.000
8	A	49	LYS	1	0.817	0.889	11.817	1.254	1.254	0.000	0.000	0.000	0.000
9	A	50	PRO	0	-0.028	-0.015	11.884	-0.082	-0.082	0.000	0.000	0.000	0.000
10	A	51	PHE	0	0.033	0.030	13.278	0.212	0.212	0.000	0.000	0.000	0.000
11	A	52	GLU	-1	-0.821	-0.901	16.186	-0.721	-0.721	0.000	0.000	0.000	0.000
12	A	53	LYS	1	0.820	0.900	18.417	0.435	0.435	0.000	0.000	0.000	0.000
13	A	54	PRO	0	0.030	0.018	19.487	0.078	0.078	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.830	-0.910	22.708	-0.402	-0.402	0.000	0.000	0.000	0.000
15	A	56	LEU	0	-0.028	-0.019	23.090	0.022	0.022	0.000	0.000	0.000	0.000
16	A	57	VAL	0	-0.038	-0.020	26.739	0.023	0.023	0.000	0.000	0.000	0.000
17	A	58	LEU	0	-0.017	0.002	26.576	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	59	THR	0	-0.047	-0.019	30.546	0.037	0.037	0.000	0.000	0.000	0.000
19	A	60	ASP	-1	-0.735	-0.868	29.976	-0.215	-0.215	0.000	0.000	0.000	0.000
20	A	61	THR	0	0.011	0.000	28.489	0.008	0.008	0.000	0.000	0.000	0.000
21	A	62	GLN	0	-0.075	-0.033	31.423	0.034	0.034	0.000	0.000	0.000	0.000
22	A	63	GLY	0	-0.016	0.013	34.506	0.013	0.013	0.000	0.000	0.000	0.000
23	A	64	LYS	1	0.802	0.884	34.635	0.158	0.158	0.000	0.000	0.000	0.000
24	A	65	LYS	1	0.971	0.992	33.662	0.211	0.211	0.000	0.000	0.000	0.000
25	A	66	TYR	0	0.049	0.018	24.523	0.030	0.030	0.000	0.000	0.000	0.000
26	A	67	ASP	-1	-0.824	-0.909	28.198	-0.342	-0.342	0.000	0.000	0.000	0.000
27	A	68	LEU	0	0.020	0.006	21.488	0.013	0.013	0.000	0.000	0.000	0.000
28	A	69	ARG	1	0.815	0.929	23.617	0.483	0.483	0.000	0.000	0.000	0.000
29	A	70	GLU	-1	-0.850	-0.928	24.674	-0.172	-0.172	0.000	0.000	0.000	0.000
30	A	71	GLN	0	-0.047	-0.034	26.480	0.028	0.028	0.000	0.000	0.000	0.000
31	A	72	THR	0	-0.108	-0.079	21.057	0.013	0.013	0.000	0.000	0.000	0.000
32	A	73	ALA	0	0.013	0.020	21.380	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	74	GLY	0	-0.002	0.000	20.807	0.049	0.049	0.000	0.000	0.000	0.000
34	A	75	LYS	1	0.769	0.881	20.038	0.240	0.240	0.000	0.000	0.000	0.000
35	A	76	PRO	0	-0.022	0.021	15.243	-0.079	-0.079	0.000	0.000	0.000	0.000
36	A	77	THR	0	0.011	0.000	15.813	0.048	0.048	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.006	-0.006	11.626	-0.113	-0.113	0.000	0.000	0.000	0.000
38	A	79	ILE	0	-0.027	-0.007	15.330	0.126	0.126	0.000	0.000	0.000	0.000
39	A	80	TYR	0	0.055	0.033	15.914	-0.120	-0.120	0.000	0.000	0.000	0.000
40	A	81	PHE	0	0.012	-0.002	17.954	0.118	0.118	0.000	0.000	0.000	0.000
41	A	82	GLY	0	0.070	0.033	20.525	-0.068	-0.068	0.000	0.000	0.000	0.000
42	A	83	TYR	0	-0.020	-0.013	22.704	0.065	0.065	0.000	0.000	0.000	0.000
43	A	84	THR	0	-0.014	-0.051	25.220	0.005	0.005	0.000	0.000	0.000	0.000
44	A	85	HIS	0	-0.098	-0.057	27.164	0.039	0.039	0.000	0.000	0.000	0.000
45	A	86	CSD	-1	-0.805	-0.874	21.930	-0.620	-0.620	0.000	0.000	0.000	0.000
46	A	87	PRO	0	-0.054	-0.035	24.690	0.018	0.018	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.930	-0.972	19.460	-0.583	-0.583	0.000	0.000	0.000	0.000
48	A	89	VAL	0	0.076	0.045	16.562	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	90	ALA	0	0.010	0.014	17.870	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	91	PRO	0	-0.033	-0.023	19.606	0.017	0.017	0.000	0.000	0.000	0.000
51	A	92	LEU	0	0.009	0.017	14.690	0.069	0.069	0.000	0.000	0.000	0.000
52	A	93	THR	0	-0.011	-0.015	13.918	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	94	MET	0	-0.053	-0.019	15.300	0.078	0.078	0.000	0.000	0.000	0.000
54	A	95	ASN	0	0.011	0.007	16.943	0.124	0.124	0.000	0.000	0.000	0.000
55	A	96	ASN	0	-0.018	-0.014	11.720	0.280	0.280	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.031	0.015	12.533	0.182	0.182	0.000	0.000	0.000	0.000
57	A	98	ALA	0	0.002	0.006	14.295	0.149	0.149	0.000	0.000	0.000	0.000
58	A	99	VAL	0	-0.004	-0.008	15.988	0.096	0.096	0.000	0.000	0.000	0.000
59	A	100	ALA	0	0.032	0.035	12.106	0.125	0.125	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.745	0.840	14.005	0.080	0.080	0.000	0.000	0.000	0.000
61	A	102	LYS	1	0.740	0.855	16.593	-0.133	-0.133	0.000	0.000	0.000	0.000
62	A	103	GLN	0	-0.041	-0.016	15.000	0.056	0.056	0.000	0.000	0.000	0.000
63	A	104	LEU	0	-0.039	0.009	14.583	0.075	0.075	0.000	0.000	0.000	0.000
64	A	105	SER	0	-0.016	-0.041	18.210	-0.111	-0.111	0.000	0.000	0.000	0.000
65	A	106	GLN	0	-0.007	-0.030	21.438	0.000	0.000	0.000	0.000	0.000	0.000
66	A	107	ALA	0	0.043	0.024	23.645	-0.033	-0.033	0.000	0.000	0.000	0.000
67	A	108	GLU	-1	-0.892	-0.911	17.677	0.690	0.690	0.000	0.000	0.000	0.000
68	A	109	GLN	0	0.046	0.024	19.443	-0.116	-0.116	0.000	0.000	0.000	0.000
69	A	110	ASP	-1	-0.784	-0.881	20.777	0.067	0.067	0.000	0.000	0.000	0.000
70	A	111	LYS	1	0.795	0.897	19.410	-0.373	-0.373	0.000	0.000	0.000	0.000
71	A	112	LEU	0	-0.004	0.006	15.337	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	113	ARG	1	0.832	0.910	18.479	0.095	0.095	0.000	0.000	0.000	0.000
73	A	114	VAL	0	0.046	0.029	16.701	-0.079	-0.079	0.000	0.000	0.000	0.000
74	A	115	VAL	0	-0.026	-0.016	18.774	0.061	0.061	0.000	0.000	0.000	0.000
75	A	116	PHE	0	0.025	0.006	19.701	-0.093	-0.093	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.011	-0.013	21.767	0.073	0.073	0.000	0.000	0.000	0.000
77	A	118	SER	0	-0.013	-0.046	23.922	-0.045	-0.045	0.000	0.000	0.000	0.000
78	A	119	THR	0	0.015	-0.003	24.037	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	120	ASP	-1	-0.802	-0.897	27.060	-0.364	-0.364	0.000	0.000	0.000	0.000
80	A	121	PRO	0	0.006	0.015	30.239	0.026	0.026	0.000	0.000	0.000	0.000
81	A	122	GLU	-1	-0.925	-0.954	32.480	-0.257	-0.257	0.000	0.000	0.000	0.000
82	A	123	ARG	1	0.783	0.872	30.894	0.359	0.359	0.000	0.000	0.000	0.000
83	A	124	ASP	-1	-0.769	-0.812	27.901	-0.363	-0.363	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.041	0.005	31.383	0.001	0.001	0.000	0.000	0.000	0.000
85	A	126	PRO	0	0.009	-0.005	32.550	0.004	0.004	0.000	0.000	0.000	0.000
86	A	127	ALA	0	0.027	0.010	32.499	0.003	0.003	0.000	0.000	0.000	0.000
87	A	128	ALA	0	-0.044	-0.007	33.187	0.013	0.013	0.000	0.000	0.000	0.000
88	A	129	LEU	0	0.043	0.030	26.094	0.007	0.007	0.000	0.000	0.000	0.000
89	A	130	GLY	0	0.039	0.004	28.445	0.000	0.000	0.000	0.000	0.000	0.000
90	A	131	LYS	1	0.851	0.917	29.694	0.156	0.156	0.000	0.000	0.000	0.000
91	A	132	TRP	0	0.019	0.024	22.492	0.029	0.029	0.000	0.000	0.000	0.000
92	A	133	LEU	0	0.081	0.052	23.078	0.011	0.011	0.000	0.000	0.000	0.000
93	A	134	LYS	1	0.875	0.933	25.368	0.098	0.098	0.000	0.000	0.000	0.000
94	A	135	GLY	0	-0.032	-0.014	27.262	0.033	0.033	0.000	0.000	0.000	0.000
95	A	136	ILE	0	-0.030	0.003	20.781	0.010	0.010	0.000	0.000	0.000	0.000
96	A	137	ASP	-1	-0.753	-0.879	21.390	0.059	0.059	0.000	0.000	0.000	0.000
97	A	138	PRO	0	-0.051	-0.025	23.520	-0.033	-0.033	0.000	0.000	0.000	0.000
98	A	139	GLN	0	-0.022	-0.006	23.162	0.022	0.022	0.000	0.000	0.000	0.000
99	A	140	ILE	0	-0.030	0.003	20.277	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	141	VAL	0	-0.013	-0.001	22.821	0.016	0.016	0.000	0.000	0.000	0.000
101	A	142	GLY	0	0.026	0.001	23.895	-0.052	-0.052	0.000	0.000	0.000	0.000
102	A	143	LEU	0	-0.053	-0.034	24.523	0.032	0.032	0.000	0.000	0.000	0.000
103	A	144	THR	0	-0.001	-0.013	27.327	-0.037	-0.037	0.000	0.000	0.000	0.000
104	A	145	GLY	0	0.010	-0.014	30.098	0.020	0.020	0.000	0.000	0.000	0.000
105	A	146	GLU	-1	-0.869	-0.940	32.093	-0.332	-0.332	0.000	0.000	0.000	0.000
106	A	147	PHE	0	0.017	0.015	28.103	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	148	ASP	-1	-0.863	-0.933	29.352	-0.460	-0.460	0.000	0.000	0.000	0.000
108	A	149	THR	0	-0.011	-0.004	29.131	-0.027	-0.027	0.000	0.000	0.000	0.000
109	A	150	ILE	0	-0.021	-0.004	25.067	-0.037	-0.037	0.000	0.000	0.000	0.000
110	A	151	GLN	0	-0.048	-0.020	24.872	-0.033	-0.033	0.000	0.000	0.000	0.000
111	A	152	ALA	0	0.004	-0.006	24.835	-0.065	-0.065	0.000	0.000	0.000	0.000
112	A	153	GLY	0	0.006	-0.007	23.983	-0.042	-0.042	0.000	0.000	0.000	0.000
113	A	154	ALA	0	0.020	0.017	20.577	-0.069	-0.069	0.000	0.000	0.000	0.000
114	A	155	ARG	1	0.903	0.950	19.973	0.889	0.889	0.000	0.000	0.000	0.000
115	A	156	THR	0	-0.128	-0.071	20.981	-0.056	-0.056	0.000	0.000	0.000	0.000
116	A	157	LEU	0	-0.026	-0.008	16.193	-0.036	-0.036	0.000	0.000	0.000	0.000
117	A	158	GLY	0	-0.021	-0.011	15.858	-0.204	-0.204	0.000	0.000	0.000	0.000
118	A	159	ILE	0	-0.015	0.003	16.233	-0.012	-0.012	0.000	0.000	0.000	0.000
119	A	160	SER	0	-0.036	-0.021	18.470	0.106	0.106	0.000	0.000	0.000	0.000
120	A	161	ILE	0	0.014	0.014	20.795	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	162	ASP	-1	-0.888	-0.939	23.788	-0.636	-0.636	0.000	0.000	0.000	0.000
122	A	163	PRO	0	-0.017	-0.016	27.174	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	164	PRO	0	-0.040	0.003	27.597	0.014	0.014	0.000	0.000	0.000	0.000
124	A	177	GLY	0	0.044	0.022	13.706	0.060	0.060	0.000	0.000	0.000	0.000
125	A	178	THR	0	-0.059	-0.047	12.234	-0.288	-0.288	0.000	0.000	0.000	0.000
126	A	179	GLN	0	0.004	-0.006	12.789	0.402	0.402	0.000	0.000	0.000	0.000
127	A	180	VAL	0	-0.049	-0.027	11.764	0.303	0.303	0.000	0.000	0.000	0.000
128	A	181	VAL	0	-0.003	0.007	11.543	-0.440	-0.440	0.000	0.000	0.000	0.000
129	A	182	ALA	0	-0.004	-0.002	9.961	0.365	0.365	0.000	0.000	0.000	0.000
130	A	183	PHE	0	-0.029	-0.020	11.804	-0.196	-0.196	0.000	0.000	0.000	0.000
131	A	184	SER	0	0.035	0.025	12.546	0.243	0.243	0.000	0.000	0.000	0.000
132	A	185	PRO	0	0.017	0.003	13.997	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	186	LYS	1	0.806	0.894	12.865	-0.126	-0.126	0.000	0.000	0.000	0.000
134	A	187	SER	0	-0.027	-0.023	15.336	0.004	0.004	0.000	0.000	0.000	0.000
135	A	188	ASP	-1	-0.797	-0.861	17.787	-0.388	-0.388	0.000	0.000	0.000	0.000
136	A	189	ALA	0	0.032	0.021	15.606	-0.044	-0.044	0.000	0.000	0.000	0.000
137	A	190	GLY	0	-0.005	-0.021	13.590	0.009	0.009	0.000	0.000	0.000	0.000
138	A	191	TYR	0	-0.029	-0.053	8.188	-0.148	-0.148	0.000	0.000	0.000	0.000
139	A	192	VAL	0	-0.010	-0.004	5.057	-0.555	-0.555	0.000	0.000	0.000	0.000
140	A	193	LEU	0	-0.015	0.004	7.113	0.985	0.985	0.000	0.000	0.000	0.000
141	A	194	TYR	0	-0.014	-0.034	4.991	-1.765	-1.765	0.000	0.000	0.000	0.000
142	A	195	GLY	0	0.093	0.048	8.721	0.676	0.676	0.000	0.000	0.000	0.000
143	A	196	GLU	-1	-0.896	-0.951	10.665	-1.479	-1.479	0.000	0.000	0.000	0.000
144	A	197	ASP	-1	-0.949	-0.966	6.803	-4.809	-4.809	0.000	0.000	0.000	0.000
145	A	198	ALA	0	-0.027	-0.009	6.782	0.029	0.029	0.000	0.000	0.000	0.000
146	A	199	THR	0	0.019	-0.013	6.552	0.887	0.887	0.000	0.000	0.000	0.000
147	A	200	VAL	0	0.025	-0.003	8.905	0.032	0.032	0.000	0.000	0.000	0.000
148	A	201	ASP	-1	-0.897	-0.933	8.117	0.955	0.955	0.000	0.000	0.000	0.000
149	A	202	ASP	-1	-0.820	-0.890	3.320	-2.187	-1.299	0.050	-0.444	-0.494	-0.003
150	A	203	TYR	0	0.050	0.010	6.068	0.795	0.795	0.000	0.000	0.000	0.000
151	A	204	THR	0	-0.041	-0.045	8.604	0.224	0.224	0.000	0.000	0.000	0.000
152	A	205	LYS	1	0.882	0.957	5.996	-4.725	-4.725	0.000	0.000	0.000	0.000
153	A	206	ASP	-1	-0.728	-0.853	4.450	6.298	6.506	-0.001	-0.016	-0.192	0.000
154	A	207	LEU	0	0.013	0.014	7.596	-0.371	-0.371	0.000	0.000	0.000	0.000
155	A	208	PRO	0	0.024	0.004	10.587	-0.196	-0.196	0.000	0.000	0.000	0.000
156	A	209	LYS	1	0.781	0.900	4.883	-9.103	-9.031	-0.001	-0.001	-0.070	0.000
157	A	210	LEU	0	0.021	0.013	7.533	-0.353	-0.353	0.000	0.000	0.000	0.000
158	A	211	ILE	0	-0.006	-0.018	10.612	-0.204	-0.204	0.000	0.000	0.000	0.000
159	A	212	LYS	1	0.817	0.901	12.738	-1.367	-1.367	0.000	0.000	0.000	0.000
160	A	213	GLY	0	0.030	0.023	11.988	-0.021	-0.021	0.000	0.000	0.000	0.000
161	A	214	GLU	-1	-0.901	-0.934	9.330	1.225	1.225	0.000	0.000	0.000	0.000
162	A	215	ASN	0	0.046	0.021	4.954	-0.378	-0.378	0.000	0.000	0.000	0.000
163	A	216	PRO	0	-0.028	-0.002	1.802	-20.912	-25.248	15.702	-6.106	-5.260	0.030

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