FMO DATABASE

FMODB ID: ZV84N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1612034.22233
FMO2-HF: Nuclear repulsion	1550540.660677
FMO2-HF: Total energy	-61493.561653
FMO2-MP2: Total energy	-61675.968829

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.
-31.702	-21.434	3.651	-6.049	-7.871	-0.017

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 : -0.047 / q_NPA : -0.033

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	-0.017	0.018	2.610	-3.029	1.052	0.625	-1.962	-2.744	0.003
4	A	45	THR	0	-0.016	-0.009	2.537	-8.122	-6.078	1.097	-1.566	-1.575	-0.021
5	A	46	VAL	0	-0.032	-0.029	2.871	1.009	1.500	0.067	-0.128	-0.430	0.000
6	A	47	LEU	0	-0.033	-0.010	5.502	0.286	0.286	0.000	0.000	0.000	0.000
7	A	48	ASP	-1	-0.916	-0.955	9.185	-1.614	-1.614	0.000	0.000	0.000	0.000
8	A	49	LYS	1	0.859	0.922	11.331	1.210	1.210	0.000	0.000	0.000	0.000
9	A	50	PRO	0	-0.064	-0.028	11.953	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	51	PHE	0	0.026	0.022	13.792	0.173	0.173	0.000	0.000	0.000	0.000
11	A	52	GLU	-1	-0.830	-0.912	16.314	-0.703	-0.703	0.000	0.000	0.000	0.000
12	A	53	LYS	1	0.874	0.937	18.995	0.449	0.449	0.000	0.000	0.000	0.000
13	A	54	PRO	0	0.009	0.005	19.689	0.066	0.066	0.000	0.000	0.000	0.000
14	A	55	ASP	-1	-0.890	-0.936	22.883	-0.356	-0.356	0.000	0.000	0.000	0.000
15	A	56	LEU	0	-0.015	-0.001	23.948	0.019	0.019	0.000	0.000	0.000	0.000
16	A	57	VAL	0	0.007	-0.007	27.469	0.019	0.019	0.000	0.000	0.000	0.000
17	A	58	LEU	0	-0.012	0.007	26.975	0.003	0.003	0.000	0.000	0.000	0.000
18	A	59	THR	0	-0.039	-0.013	31.007	0.027	0.027	0.000	0.000	0.000	0.000
19	A	60	ASP	-1	-0.747	-0.877	30.358	-0.197	-0.197	0.000	0.000	0.000	0.000
20	A	61	THR	0	0.014	-0.007	29.565	0.013	0.013	0.000	0.000	0.000	0.000
21	A	62	GLN	0	-0.067	-0.020	32.335	0.024	0.024	0.000	0.000	0.000	0.000
22	A	63	GLY	0	-0.031	-0.019	34.829	0.012	0.012	0.000	0.000	0.000	0.000
23	A	64	LYS	1	0.823	0.913	34.950	0.136	0.136	0.000	0.000	0.000	0.000
24	A	65	LYS	1	0.972	0.997	33.984	0.198	0.198	0.000	0.000	0.000	0.000
25	A	66	TYR	0	0.048	0.013	25.100	0.019	0.019	0.000	0.000	0.000	0.000
26	A	67	ASP	-1	-0.845	-0.913	28.691	-0.327	-0.327	0.000	0.000	0.000	0.000
27	A	68	LEU	0	0.021	-0.005	22.028	0.010	0.010	0.000	0.000	0.000	0.000
28	A	69	ARG	1	0.859	0.939	23.643	0.472	0.472	0.000	0.000	0.000	0.000
29	A	70	GLU	-1	-0.893	-0.939	25.218	-0.196	-0.196	0.000	0.000	0.000	0.000
30	A	71	GLN	0	-0.037	-0.028	26.964	0.025	0.025	0.000	0.000	0.000	0.000
31	A	72	THR	0	-0.117	-0.069	21.590	0.008	0.008	0.000	0.000	0.000	0.000
32	A	73	ALA	0	0.005	0.015	21.793	-0.023	-0.023	0.000	0.000	0.000	0.000
33	A	74	GLY	0	0.015	0.001	20.880	0.046	0.046	0.000	0.000	0.000	0.000
34	A	75	LYS	1	0.755	0.870	20.063	0.258	0.258	0.000	0.000	0.000	0.000
35	A	76	PRO	0	-0.036	0.025	15.227	-0.069	-0.069	0.000	0.000	0.000	0.000
36	A	77	THR	0	0.011	-0.018	16.055	0.079	0.079	0.000	0.000	0.000	0.000
37	A	78	LEU	0	-0.019	-0.009	12.473	-0.112	-0.112	0.000	0.000	0.000	0.000
38	A	79	ILE	0	-0.032	-0.009	15.788	0.109	0.109	0.000	0.000	0.000	0.000
39	A	80	TYR	0	0.068	0.045	16.118	-0.090	-0.090	0.000	0.000	0.000	0.000
40	A	81	PHE	0	0.011	0.001	18.101	0.098	0.098	0.000	0.000	0.000	0.000
41	A	82	GLY	0	0.079	0.037	20.474	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	83	TYR	0	-0.013	-0.017	22.813	0.054	0.054	0.000	0.000	0.000	0.000
43	A	84	THR	0	-0.018	-0.049	25.743	0.004	0.004	0.000	0.000	0.000	0.000
44	A	85	HIS	0	-0.096	-0.055	27.626	0.037	0.037	0.000	0.000	0.000	0.000
45	A	86	CSD	-1	-0.823	-0.880	22.359	-0.473	-0.473	0.000	0.000	0.000	0.000
46	A	87	PRO	0	-0.051	-0.033	25.269	0.014	0.014	0.000	0.000	0.000	0.000
47	A	88	ASP	-1	-0.936	-0.970	19.999	-0.418	-0.418	0.000	0.000	0.000	0.000
48	A	89	VAL	0	0.086	0.042	16.935	0.010	0.010	0.000	0.000	0.000	0.000
49	A	90	ALA	0	-0.015	-0.004	18.685	-0.020	-0.020	0.000	0.000	0.000	0.000
50	A	91	PRO	0	-0.014	-0.010	20.480	0.015	0.015	0.000	0.000	0.000	0.000
51	A	92	LEU	0	0.028	0.032	15.640	0.063	0.063	0.000	0.000	0.000	0.000
52	A	93	THR	0	-0.012	-0.014	14.764	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	94	MET	0	-0.042	-0.020	16.406	0.058	0.058	0.000	0.000	0.000	0.000
54	A	95	ASN	0	0.007	0.007	18.528	0.086	0.086	0.000	0.000	0.000	0.000
55	A	96	ASN	0	-0.003	-0.004	12.996	0.202	0.202	0.000	0.000	0.000	0.000
56	A	97	ILE	0	0.029	0.013	13.827	0.135	0.135	0.000	0.000	0.000	0.000
57	A	98	ALA	0	-0.002	0.001	15.524	0.108	0.108	0.000	0.000	0.000	0.000
58	A	99	VAL	0	0.015	0.012	16.774	0.067	0.067	0.000	0.000	0.000	0.000
59	A	100	ALA	0	0.019	0.024	13.240	0.092	0.092	0.000	0.000	0.000	0.000
60	A	101	LYS	1	0.756	0.840	15.110	0.066	0.066	0.000	0.000	0.000	0.000
61	A	102	LYS	1	0.726	0.843	17.566	-0.085	-0.085	0.000	0.000	0.000	0.000
62	A	103	GLN	0	-0.043	-0.013	16.095	0.042	0.042	0.000	0.000	0.000	0.000
63	A	104	LEU	0	-0.059	0.000	15.222	0.038	0.038	0.000	0.000	0.000	0.000
64	A	105	SER	0	0.001	-0.026	19.126	-0.074	-0.074	0.000	0.000	0.000	0.000
65	A	106	GLN	0	-0.033	-0.041	22.148	0.001	0.001	0.000	0.000	0.000	0.000
66	A	107	ALA	0	0.031	0.012	24.091	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	108	GLU	-1	-0.876	-0.929	17.636	0.443	0.443	0.000	0.000	0.000	0.000
68	A	109	GLN	0	0.011	0.008	19.996	-0.092	-0.092	0.000	0.000	0.000	0.000
69	A	110	ASP	-1	-0.813	-0.890	21.324	0.005	0.005	0.000	0.000	0.000	0.000
70	A	111	LYS	1	0.869	0.953	19.706	-0.207	-0.207	0.000	0.000	0.000	0.000
71	A	112	LEU	0	-0.014	0.008	15.682	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	113	ARG	1	0.840	0.914	19.060	0.155	0.155	0.000	0.000	0.000	0.000
73	A	114	VAL	0	0.052	0.029	17.771	-0.067	-0.067	0.000	0.000	0.000	0.000
74	A	115	VAL	0	-0.005	-0.009	19.538	0.051	0.051	0.000	0.000	0.000	0.000
75	A	116	PHE	0	0.031	0.009	20.237	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	117	VAL	0	-0.020	-0.022	22.201	0.057	0.057	0.000	0.000	0.000	0.000
77	A	118	SER	0	-0.013	-0.058	23.855	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	119	THR	0	0.005	-0.009	23.778	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	120	ASP	-1	-0.811	-0.895	26.881	-0.298	-0.298	0.000	0.000	0.000	0.000
80	A	121	PRO	0	0.006	0.007	30.143	0.021	0.021	0.000	0.000	0.000	0.000
81	A	122	GLU	-1	-0.917	-0.950	32.313	-0.211	-0.211	0.000	0.000	0.000	0.000
82	A	123	ARG	1	0.793	0.879	31.266	0.288	0.288	0.000	0.000	0.000	0.000
83	A	124	ASP	-1	-0.797	-0.814	28.577	-0.287	-0.287	0.000	0.000	0.000	0.000
84	A	125	THR	0	0.054	0.017	32.090	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	126	PRO	0	0.052	0.014	32.831	0.000	0.000	0.000	0.000	0.000	0.000
86	A	127	ALA	0	0.016	-0.001	33.074	0.003	0.003	0.000	0.000	0.000	0.000
87	A	128	ALA	0	-0.047	-0.019	34.135	0.012	0.012	0.000	0.000	0.000	0.000
88	A	129	LEU	0	0.037	0.038	26.722	0.007	0.007	0.000	0.000	0.000	0.000
89	A	130	GLY	0	0.038	0.001	29.518	0.001	0.001	0.000	0.000	0.000	0.000
90	A	131	LYS	1	0.856	0.920	30.910	0.126	0.126	0.000	0.000	0.000	0.000
91	A	132	TRP	0	0.015	0.025	23.422	0.023	0.023	0.000	0.000	0.000	0.000
92	A	133	LEU	0	0.062	0.023	24.316	0.009	0.009	0.000	0.000	0.000	0.000
93	A	134	LYS	1	0.937	0.970	26.581	0.080	0.080	0.000	0.000	0.000	0.000
94	A	135	GLY	0	-0.087	-0.037	28.697	0.025	0.025	0.000	0.000	0.000	0.000
95	A	136	ILE	0	-0.016	0.010	21.940	0.010	0.010	0.000	0.000	0.000	0.000
96	A	137	ASP	-1	-0.733	-0.876	22.439	0.029	0.029	0.000	0.000	0.000	0.000
97	A	138	PRO	0	-0.051	-0.015	24.895	-0.028	-0.028	0.000	0.000	0.000	0.000
98	A	139	GLN	0	-0.022	-0.011	24.335	0.010	0.010	0.000	0.000	0.000	0.000
99	A	140	ILE	0	-0.063	-0.010	21.580	-0.020	-0.020	0.000	0.000	0.000	0.000
100	A	141	VAL	0	0.000	0.005	23.762	0.016	0.016	0.000	0.000	0.000	0.000
101	A	142	GLY	0	0.020	0.007	24.472	-0.036	-0.036	0.000	0.000	0.000	0.000
102	A	143	LEU	0	-0.069	-0.039	25.127	0.024	0.024	0.000	0.000	0.000	0.000
103	A	144	THR	0	0.003	-0.015	27.605	-0.025	-0.025	0.000	0.000	0.000	0.000
104	A	145	GLY	0	0.019	-0.006	30.187	0.011	0.011	0.000	0.000	0.000	0.000
105	A	146	GLU	-1	-0.868	-0.934	32.114	-0.278	-0.278	0.000	0.000	0.000	0.000
106	A	147	PHE	0	0.028	0.007	27.991	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	148	ASP	-1	-0.912	-0.943	29.499	-0.399	-0.399	0.000	0.000	0.000	0.000
108	A	149	THR	0	-0.014	-0.017	29.487	-0.020	-0.020	0.000	0.000	0.000	0.000
109	A	150	ILE	0	-0.014	-0.002	25.301	-0.035	-0.035	0.000	0.000	0.000	0.000
110	A	151	GLN	0	-0.046	-0.021	25.169	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	152	ALA	0	0.016	0.007	25.023	-0.055	-0.055	0.000	0.000	0.000	0.000
112	A	153	GLY	0	0.001	-0.005	24.497	-0.039	-0.039	0.000	0.000	0.000	0.000
113	A	154	ALA	0	0.032	0.024	20.920	-0.063	-0.063	0.000	0.000	0.000	0.000
114	A	155	ARG	1	0.944	0.962	20.251	0.741	0.741	0.000	0.000	0.000	0.000
115	A	156	THR	0	-0.141	-0.072	21.326	-0.053	-0.053	0.000	0.000	0.000	0.000
116	A	157	LEU	0	-0.030	-0.015	16.602	-0.040	-0.040	0.000	0.000	0.000	0.000
117	A	158	GLY	0	-0.021	-0.010	16.285	-0.156	-0.156	0.000	0.000	0.000	0.000
118	A	159	ILE	0	-0.042	-0.013	15.916	-0.059	-0.059	0.000	0.000	0.000	0.000
119	A	160	SER	0	-0.026	-0.016	18.745	0.081	0.081	0.000	0.000	0.000	0.000
120	A	161	ILE	0	0.019	0.022	20.876	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	162	ASP	-1	-0.889	-0.931	23.963	-0.523	-0.523	0.000	0.000	0.000	0.000
122	A	163	PRO	0	-0.013	-0.021	27.154	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	164	PRO	0	-0.033	0.003	28.133	0.007	0.007	0.000	0.000	0.000	0.000
124	A	177	GLY	0	0.035	0.014	14.363	0.053	0.053	0.000	0.000	0.000	0.000
125	A	178	THR	0	-0.042	-0.037	12.063	-0.215	-0.215	0.000	0.000	0.000	0.000
126	A	179	GLN	0	-0.017	-0.011	12.454	0.295	0.295	0.000	0.000	0.000	0.000
127	A	180	VAL	0	-0.036	-0.019	11.891	0.237	0.237	0.000	0.000	0.000	0.000
128	A	181	VAL	0	-0.007	0.013	11.508	-0.347	-0.347	0.000	0.000	0.000	0.000
129	A	182	ALA	0	-0.011	-0.012	10.477	0.289	0.289	0.000	0.000	0.000	0.000
130	A	183	PHE	0	-0.019	-0.019	12.231	-0.178	-0.178	0.000	0.000	0.000	0.000
131	A	184	SER	0	0.031	0.012	12.849	0.201	0.201	0.000	0.000	0.000	0.000
132	A	185	PRO	0	0.023	0.015	14.308	0.008	0.008	0.000	0.000	0.000	0.000
133	A	186	LYS	1	0.805	0.889	12.614	0.267	0.267	0.000	0.000	0.000	0.000
134	A	187	SER	0	-0.003	-0.012	15.460	0.018	0.018	0.000	0.000	0.000	0.000
135	A	188	ASP	-1	-0.801	-0.869	17.902	-0.414	-0.414	0.000	0.000	0.000	0.000
136	A	189	ALA	0	0.011	0.011	15.524	-0.018	-0.018	0.000	0.000	0.000	0.000
137	A	190	GLY	0	-0.013	-0.025	13.749	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	191	TYR	0	-0.031	-0.054	8.273	-0.070	-0.070	0.000	0.000	0.000	0.000
139	A	192	VAL	0	0.004	0.006	5.589	-0.558	-0.558	0.000	0.000	0.000	0.000
140	A	193	LEU	0	-0.021	0.005	7.639	0.769	0.769	0.000	0.000	0.000	0.000
141	A	194	TYR	0	-0.011	-0.036	5.831	-1.477	-1.477	0.000	0.000	0.000	0.000
142	A	195	GLY	0	0.103	0.052	8.535	0.515	0.515	0.000	0.000	0.000	0.000
143	A	196	GLU	-1	-0.902	-0.964	10.557	-0.948	-0.948	0.000	0.000	0.000	0.000
144	A	197	ASP	-1	-0.975	-0.972	6.752	-3.740	-3.740	0.000	0.000	0.000	0.000
145	A	198	ALA	0	-0.031	-0.006	7.377	0.121	0.121	0.000	0.000	0.000	0.000
146	A	199	THR	0	0.015	-0.023	7.943	0.537	0.537	0.000	0.000	0.000	0.000
147	A	200	VAL	0	0.019	-0.010	9.956	0.077	0.077	0.000	0.000	0.000	0.000
148	A	201	ASP	-1	-0.909	-0.936	9.323	1.008	1.008	0.000	0.000	0.000	0.000
149	A	202	ASP	-1	-0.827	-0.889	4.745	0.489	0.582	-0.001	-0.005	-0.087	0.000
150	A	203	TYR	0	0.024	-0.005	7.182	0.474	0.474	0.000	0.000	0.000	0.000
151	A	204	THR	0	-0.020	-0.035	9.835	0.089	0.089	0.000	0.000	0.000	0.000
152	A	205	LYS	1	0.897	0.958	6.695	-3.959	-3.959	0.000	0.000	0.000	0.000
153	A	206	ASP	-1	-0.742	-0.872	5.176	4.775	4.916	-0.001	-0.001	-0.140	0.000
154	A	207	LEU	0	0.006	0.015	7.964	-0.417	-0.417	0.000	0.000	0.000	0.000
155	A	208	PRO	0	0.034	0.016	10.912	-0.175	-0.175	0.000	0.000	0.000	0.000
156	A	209	LYS	1	0.777	0.895	5.640	-5.534	-5.534	0.000	0.000	0.000	0.000
157	A	210	LEU	0	0.009	0.008	7.825	-0.302	-0.302	0.000	0.000	0.000	0.000
158	A	211	ILE	0	-0.018	-0.010	10.648	-0.140	-0.140	0.000	0.000	0.000	0.000
159	A	212	LYS	1	0.851	0.911	12.598	-0.749	-0.749	0.000	0.000	0.000	0.000
160	A	213	GLY	0	0.035	0.024	11.891	-0.023	-0.023	0.000	0.000	0.000	0.000
161	A	214	GLU	-1	-0.925	-0.942	9.138	0.487	0.487	0.000	0.000	0.000	0.000
162	A	215	ASN	0	0.027	0.015	4.796	-0.125	-0.123	-0.001	0.000	-0.001	0.000
163	A	216	PRO	0	0.007	0.020	2.301	-11.858	-8.442	1.865	-2.387	-2.894	0.001

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