FMO DATABASE

FMODB ID: V5ZV1

Calculation Name: 2BSE-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BSE

Chain ID: D

ChEMBL ID:

UniProt ID: Q71AW2

Base Structure: X-ray

Registration Date: 2023-06-26

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	121
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1002144.154933
FMO2-HF: Nuclear repulsion	954325.919242
FMO2-HF: Total energy	-47818.235691
FMO2-MP2: Total energy	-47954.847473

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(D:2:VAL)

Summations of interaction energy for fragment #1(D:2:VAL)

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.
-15.3	-5.707	4.348	-5.394	-8.55	-0.031

Interaction energy analysis for fragmet #1(D:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.012

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

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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	D	4	LEU	0	0.011	0.005	3.213	1.091	2.869	0.030	-0.718	-1.090	0.002
4	D	5	GLN	0	-0.015	-0.007	5.529	0.036	0.036	0.000	0.000	0.000	0.000
5	D	6	GLU	-1	-0.760	-0.887	9.250	-0.758	-0.758	0.000	0.000	0.000	0.000
6	D	7	SER	0	-0.012	-0.006	11.922	0.067	0.067	0.000	0.000	0.000	0.000
7	D	8	GLY	0	0.038	0.021	15.578	-0.011	-0.011	0.000	0.000	0.000	0.000
8	D	9	GLY	0	0.015	0.010	18.471	-0.032	-0.032	0.000	0.000	0.000	0.000
9	D	10	GLY	0	-0.001	-0.008	20.446	0.027	0.027	0.000	0.000	0.000	0.000
10	D	11	LEU	0	-0.017	-0.014	23.590	-0.010	-0.010	0.000	0.000	0.000	0.000
11	D	12	VAL	0	-0.004	0.005	26.178	0.010	0.010	0.000	0.000	0.000	0.000
12	D	13	GLN	0	-0.006	0.000	28.470	0.000	0.000	0.000	0.000	0.000	0.000
13	D	14	ALA	0	0.034	0.003	30.825	-0.003	-0.003	0.000	0.000	0.000	0.000
14	D	15	GLY	0	-0.048	-0.022	31.726	0.008	0.008	0.000	0.000	0.000	0.000
15	D	16	GLY	0	0.005	0.009	30.736	0.006	0.006	0.000	0.000	0.000	0.000
16	D	17	SER	0	-0.025	-0.046	26.692	-0.007	-0.007	0.000	0.000	0.000	0.000
17	D	18	LEU	0	-0.036	-0.005	22.280	0.005	0.005	0.000	0.000	0.000	0.000
18	D	19	ARG	1	0.901	0.965	17.965	0.013	0.013	0.000	0.000	0.000	0.000
19	D	20	LEU	0	0.005	0.010	15.672	0.000	0.000	0.000	0.000	0.000	0.000
20	D	21	SER	0	-0.012	-0.017	14.346	0.034	0.034	0.000	0.000	0.000	0.000
21	D	22	CYS	0	-0.114	-0.028	8.471	-0.087	-0.087	0.000	0.000	0.000	0.000
22	D	23	THR	0	-0.005	0.004	8.441	0.147	0.147	0.000	0.000	0.000	0.000
23	D	24	ALA	0	0.058	0.022	3.374	-0.622	-0.446	0.008	-0.063	-0.122	0.000
24	D	25	SER	0	-0.043	-0.017	3.731	1.433	2.026	0.024	-0.248	-0.370	0.000
25	D	26	ARG	1	0.953	0.975	2.908	-5.875	-4.368	0.346	-0.508	-1.344	0.000
26	D	27	ARG	1	0.890	0.938	4.418	-1.169	-0.985	0.000	-0.026	-0.157	0.000
27	D	28	THR	0	-0.081	-0.075	2.723	-0.226	0.397	0.663	-0.265	-1.021	0.000
28	D	29	GLY	0	0.039	0.021	5.150	-0.001	0.007	-0.001	-0.002	-0.005	0.000
29	D	30	SER	0	0.009	0.018	8.966	-0.016	-0.016	0.000	0.000	0.000	0.000
30	D	31	ASN	0	0.015	0.012	11.448	-0.108	-0.108	0.000	0.000	0.000	0.000
31	D	32	TRP	0	0.030	0.026	3.010	-0.464	0.051	0.070	-0.153	-0.434	0.001
32	D	33	CYS	0	-0.069	-0.016	9.232	0.135	0.135	0.000	0.000	0.000	0.000
33	D	34	MET	0	-0.002	0.001	6.599	-0.286	-0.286	0.000	0.000	0.000	0.000
34	D	35	GLY	0	-0.001	-0.003	9.261	0.177	0.177	0.000	0.000	0.000	0.000
35	D	36	TRP	0	0.014	0.007	10.880	-0.121	-0.121	0.000	0.000	0.000	0.000
36	D	37	PHE	0	0.012	0.016	11.736	0.068	0.068	0.000	0.000	0.000	0.000
37	D	38	ARG	1	0.797	0.889	15.257	0.284	0.284	0.000	0.000	0.000	0.000
38	D	39	GLN	0	0.047	0.005	17.725	-0.035	-0.035	0.000	0.000	0.000	0.000
39	D	40	LEU	0	0.011	0.009	19.873	0.018	0.018	0.000	0.000	0.000	0.000
40	D	41	ALA	0	0.016	-0.003	23.683	-0.013	-0.013	0.000	0.000	0.000	0.000
41	D	42	GLY	0	0.016	0.018	24.906	0.018	0.018	0.000	0.000	0.000	0.000
42	D	43	LYS	1	0.798	0.885	22.886	0.305	0.305	0.000	0.000	0.000	0.000
43	D	44	GLU	-1	-0.734	-0.845	19.621	-0.472	-0.472	0.000	0.000	0.000	0.000
44	D	45	PRO	0	-0.046	-0.008	16.669	0.027	0.027	0.000	0.000	0.000	0.000
45	D	46	GLU	-1	-0.804	-0.868	18.826	-0.274	-0.274	0.000	0.000	0.000	0.000
46	D	47	LEU	0	-0.005	0.010	13.441	-0.004	-0.004	0.000	0.000	0.000	0.000
47	D	48	VAL	0	-0.023	-0.015	16.696	0.056	0.056	0.000	0.000	0.000	0.000
48	D	49	VAL	0	-0.005	-0.010	15.862	0.052	0.052	0.000	0.000	0.000	0.000
49	D	50	ALA	0	0.006	0.003	13.359	-0.078	-0.078	0.000	0.000	0.000	0.000
50	D	51	LEU	0	0.000	0.006	13.192	0.062	0.062	0.000	0.000	0.000	0.000
51	D	52	ASN	0	0.037	-0.006	12.459	-0.022	-0.022	0.000	0.000	0.000	0.000
52	D	53	PHE	0	0.013	-0.020	10.865	0.081	0.081	0.000	0.000	0.000	0.000
53	D	54	ASP	-1	-0.843	-0.903	12.558	0.210	0.210	0.000	0.000	0.000	0.000
54	D	55	TYR	0	-0.031	-0.023	15.299	0.001	0.001	0.000	0.000	0.000	0.000
55	D	56	ASP	-1	-0.822	-0.893	17.153	0.047	0.047	0.000	0.000	0.000	0.000
56	D	57	MET	0	-0.038	0.009	18.166	-0.015	-0.015	0.000	0.000	0.000	0.000
57	D	58	THR	0	-0.009	-0.025	17.244	-0.020	-0.020	0.000	0.000	0.000	0.000
58	D	59	TYR	0	-0.016	0.002	17.651	0.020	0.020	0.000	0.000	0.000	0.000
59	D	60	TYR	0	0.057	0.028	18.670	-0.020	-0.020	0.000	0.000	0.000	0.000
60	D	61	ALA	0	0.060	0.039	21.069	0.014	0.014	0.000	0.000	0.000	0.000
61	D	62	ASP	-1	-0.820	-0.920	22.842	-0.155	-0.155	0.000	0.000	0.000	0.000
62	D	63	SER	0	-0.009	0.010	24.743	0.012	0.012	0.000	0.000	0.000	0.000
63	D	64	VAL	0	0.001	-0.006	21.439	0.008	0.008	0.000	0.000	0.000	0.000
64	D	65	LYS	1	0.838	0.908	24.734	0.176	0.176	0.000	0.000	0.000	0.000
65	D	66	GLY	0	-0.012	0.012	25.678	0.008	0.008	0.000	0.000	0.000	0.000
66	D	67	ARG	1	0.715	0.811	26.303	0.153	0.153	0.000	0.000	0.000	0.000
67	D	68	PHE	0	0.017	-0.005	20.670	0.003	0.003	0.000	0.000	0.000	0.000
68	D	69	THR	0	-0.049	-0.030	21.732	0.010	0.010	0.000	0.000	0.000	0.000
69	D	70	VAL	0	0.003	0.001	15.250	0.000	0.000	0.000	0.000	0.000	0.000
70	D	71	SER	0	-0.029	-0.007	17.024	0.026	0.026	0.000	0.000	0.000	0.000
71	D	72	ARG	1	0.863	0.919	14.373	-0.166	-0.166	0.000	0.000	0.000	0.000
72	D	73	ASP	-1	-0.751	-0.833	14.360	0.215	0.215	0.000	0.000	0.000	0.000
73	D	74	SER	0	-0.005	-0.018	15.775	0.005	0.005	0.000	0.000	0.000	0.000
74	D	75	GLY	0	-0.014	-0.001	14.611	0.053	0.053	0.000	0.000	0.000	0.000
75	D	76	LYS	1	0.869	0.905	13.207	-0.214	-0.214	0.000	0.000	0.000	0.000
76	D	77	ASN	0	-0.042	-0.008	5.943	-0.431	-0.431	0.000	0.000	0.000	0.000
77	D	78	THR	0	0.018	-0.001	8.549	0.033	0.033	0.000	0.000	0.000	0.000
78	D	79	VAL	0	-0.025	-0.009	10.343	-0.005	-0.005	0.000	0.000	0.000	0.000
79	D	80	TYR	0	-0.022	-0.049	12.445	-0.016	-0.016	0.000	0.000	0.000	0.000
80	D	81	LEU	0	0.017	0.010	15.512	-0.011	-0.011	0.000	0.000	0.000	0.000
81	D	82	GLN	0	-0.021	-0.007	17.543	0.009	0.009	0.000	0.000	0.000	0.000
82	D	83	MET	0	-0.009	0.004	20.610	-0.021	-0.021	0.000	0.000	0.000	0.000
83	D	84	ASN	0	0.075	0.037	23.305	0.017	0.017	0.000	0.000	0.000	0.000
84	D	85	SER	0	0.014	0.013	27.121	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	86	LEU	0	-0.024	0.013	24.265	-0.007	-0.007	0.000	0.000	0.000	0.000
86	D	87	LYS	1	0.861	0.910	28.128	0.135	0.135	0.000	0.000	0.000	0.000
87	D	88	PRO	0	0.036	0.002	28.669	-0.010	-0.010	0.000	0.000	0.000	0.000
88	D	89	GLU	-1	-0.796	-0.885	28.869	-0.143	-0.143	0.000	0.000	0.000	0.000
89	D	90	ASP	-1	-0.761	-0.834	24.471	-0.180	-0.180	0.000	0.000	0.000	0.000
90	D	91	THR	0	-0.069	-0.036	23.786	-0.019	-0.019	0.000	0.000	0.000	0.000
91	D	92	ALA	0	0.007	-0.005	21.291	-0.005	-0.005	0.000	0.000	0.000	0.000
92	D	93	ILE	0	-0.012	0.012	17.051	0.017	0.017	0.000	0.000	0.000	0.000
93	D	94	TYR	0	-0.038	-0.036	16.192	-0.021	-0.021	0.000	0.000	0.000	0.000
94	D	95	TYR	0	0.027	0.008	11.928	0.033	0.033	0.000	0.000	0.000	0.000
95	D	97	ALA	0	0.019	0.004	7.467	-0.243	-0.243	0.000	0.000	0.000	0.000
96	D	98	ALA	0	0.002	-0.011	3.883	0.309	0.404	-0.001	-0.018	-0.077	0.000
97	D	99	ARG	1	0.812	0.896	5.526	0.138	0.138	0.000	0.000	0.000	0.000
98	D	100	SER	0	-0.049	-0.009	6.891	0.404	0.404	0.000	0.000	0.000	0.000
99	D	101	GLY	0	0.011	0.000	8.699	-0.088	-0.088	0.000	0.000	0.000	0.000
100	D	102	GLY	0	0.011	-0.008	12.203	0.006	0.006	0.000	0.000	0.000	0.000
101	D	103	PHE	0	-0.003	-0.015	12.573	-0.110	-0.110	0.000	0.000	0.000	0.000
102	D	104	SER	0	0.023	0.021	12.845	0.068	0.068	0.000	0.000	0.000	0.000
103	D	105	SER	0	0.040	0.017	14.602	-0.053	-0.053	0.000	0.000	0.000	0.000
104	D	106	ASN	0	0.004	0.015	14.995	-0.010	-0.010	0.000	0.000	0.000	0.000
105	D	107	ARG	1	0.857	0.896	12.394	0.547	0.547	0.000	0.000	0.000	0.000
106	D	108	GLU	-1	-0.937	-0.968	10.912	-0.874	-0.874	0.000	0.000	0.000	0.000
107	D	109	LEU	0	0.001	-0.016	7.835	0.047	0.047	0.000	0.000	0.000	0.000
108	D	110	TYR	0	-0.031	-0.007	6.993	0.234	0.234	0.000	0.000	0.000	0.000
109	D	111	ASP	-1	-0.810	-0.887	2.568	-2.584	-1.810	0.290	-0.312	-0.752	-0.001
110	D	112	GLY	0	0.005	0.001	2.431	-7.841	-4.567	2.860	-3.171	-2.963	-0.033
111	D	113	TRP	0	-0.025	-0.018	3.326	1.400	1.466	0.059	0.090	-0.215	0.000
112	D	114	GLY	0	0.000	0.009	6.962	-0.112	-0.112	0.000	0.000	0.000	0.000
113	D	115	GLN	0	-0.030	-0.028	9.328	0.089	0.089	0.000	0.000	0.000	0.000
114	D	116	GLY	0	-0.013	-0.005	12.134	0.064	0.064	0.000	0.000	0.000	0.000
115	D	117	THR	0	-0.062	-0.033	14.267	0.071	0.071	0.000	0.000	0.000	0.000
116	D	118	GLN	0	0.033	0.024	17.184	-0.009	-0.009	0.000	0.000	0.000	0.000
117	D	119	VAL	0	0.024	0.018	19.928	0.023	0.023	0.000	0.000	0.000	0.000
118	D	120	THR	0	0.011	0.011	22.643	0.000	0.000	0.000	0.000	0.000	0.000
119	D	121	VAL	0	-0.005	0.001	26.348	0.013	0.013	0.000	0.000	0.000	0.000
120	D	122	SER	0	-0.034	-0.016	28.706	0.003	0.003	0.000	0.000	0.000	0.000
121	D	123	SER	0	0.043	0.024	32.230	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:2:VAL)