FMO DATABASE

FMODB ID: 2N9LR

Calculation Name: 5B08-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B08

Chain ID: A

ChEMBL ID:

UniProt ID: I6WU39

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-800647.760215
FMO2-HF: Nuclear repulsion	759973.632741
FMO2-HF: Total energy	-40674.127474
FMO2-MP2: Total energy	-40796.05865

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-4.235	2.371	0.989	-3.798	-3.797	-0.018

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.028

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	4	LYS	1	0.822	0.903	3.578	-0.382	2.064	0.000	-1.412	-1.034	0.004
4	A	5	HIS	1	0.907	0.948	6.224	0.791	0.791	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.046	-0.023	9.455	0.080	0.080	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.004	0.003	12.186	0.020	0.020	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.001	0.006	15.782	0.020	0.020	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.014	-0.004	18.860	0.006	0.006	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.841	0.901	22.006	0.126	0.126	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.038	0.004	23.430	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.841	0.911	27.345	0.113	0.113	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.830	-0.908	30.878	-0.100	-0.100	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.939	-0.968	33.354	-0.081	-0.081	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.076	-0.010	28.723	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.026	-0.023	31.967	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.806	-0.919	29.329	-0.089	-0.089	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.006	0.010	28.862	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.102	0.073	28.946	0.002	0.002	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.831	0.924	25.627	0.085	0.085	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.837	-0.897	24.334	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.857	-0.912	24.324	-0.068	-0.068	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.005	0.005	20.273	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.003	-0.015	19.064	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.807	0.895	19.570	0.036	0.036	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.014	-0.020	20.782	0.011	0.011	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.003	-0.019	13.955	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.015	-0.012	15.789	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.013	0.003	16.269	0.029	0.029	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.014	0.010	15.956	0.015	0.015	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.048	0.014	12.022	0.002	0.002	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.091	-0.044	14.411	0.049	0.049	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.055	-0.023	16.996	0.008	0.008	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.042	-0.013	13.711	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.006	-0.012	13.286	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.001	0.016	10.770	0.062	0.062	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.054	-0.018	8.739	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.851	0.930	4.941	-0.348	-0.348	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.857	-0.907	7.494	0.239	0.239	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.004	-0.001	8.520	-0.161	-0.161	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.070	-0.048	9.694	0.044	0.044	0.000	0.000	0.000	0.000
41	A	42	TRP	0	-0.012	-0.010	13.282	-0.056	-0.056	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.028	0.021	16.251	0.025	0.025	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.887	0.939	19.243	0.079	0.079	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.766	-0.854	22.672	-0.152	-0.152	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.036	0.012	23.830	0.013	0.013	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.055	-0.051	24.690	0.014	0.014	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.036	0.012	27.398	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.951	0.972	29.158	0.134	0.134	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.023	-0.022	25.289	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.768	0.875	28.338	0.094	0.094	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.949	-0.943	30.271	-0.084	-0.084	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.880	-0.938	31.988	-0.108	-0.108	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.024	-0.006	28.154	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.030	-0.019	22.796	0.005	0.005	0.000	0.000	0.000	0.000
55	A	56	THR	0	0.005	-0.002	24.216	0.005	0.005	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.017	-0.020	21.062	0.024	0.024	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.012	0.007	15.233	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.003	-0.005	13.841	0.040	0.040	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.866	-0.921	9.798	-0.643	-0.643	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.027	0.009	8.466	0.111	0.111	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.010	-0.007	2.953	-0.666	-0.384	0.148	-0.111	-0.319	0.000
62	A	63	PHE	0	0.017	0.001	3.556	0.274	0.507	0.001	-0.056	-0.178	0.000
63	A	64	GLU	-1	-0.845	-0.914	2.696	-2.861	-0.755	0.752	-1.408	-1.451	-0.016
64	A	65	SER	0	-0.003	-0.008	3.166	-1.749	-0.504	0.090	-0.727	-0.608	-0.006
65	A	66	VAL	0	0.063	0.009	5.515	0.042	0.042	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.940	-0.952	8.499	-0.100	-0.100	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.016	-0.005	7.207	0.040	0.040	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.033	-0.009	7.610	0.035	0.035	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.024	0.009	10.464	0.059	0.059	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.872	-0.941	12.583	-0.108	-0.108	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.063	-0.051	11.894	0.029	0.029	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.065	-0.028	13.912	0.034	0.034	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.006	-0.001	16.243	0.030	0.030	0.000	0.000	0.000	0.000
74	A	75	HIS	0	0.045	0.049	16.964	0.018	0.018	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.023	-0.004	18.913	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.007	0.006	19.434	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.007	0.006	17.139	-0.022	-0.022	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.031	-0.008	19.257	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.062	0.037	22.311	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.016	-0.009	20.531	0.002	0.002	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.002	-0.011	22.260	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.911	-0.965	23.316	-0.107	-0.107	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.039	-0.009	26.324	0.007	0.007	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.018	-0.032	23.706	0.003	0.003	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.848	0.929	25.163	0.144	0.144	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.071	-0.039	25.979	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.051	0.031	26.011	0.001	0.001	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.041	0.026	21.975	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.794	-0.862	26.743	-0.131	-0.131	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.784	0.871	25.975	0.149	0.149	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.014	-0.018	19.863	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.028	-0.002	19.697	0.006	0.006	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.020	0.003	14.839	0.000	0.000	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.014	-0.007	13.597	0.020	0.020	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.764	-0.864	10.379	-0.926	-0.926	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.019	-0.006	8.982	0.007	0.007	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.074	0.038	3.968	-0.266	-0.147	-0.001	-0.044	-0.074	0.000
98	A	99	PRO	0	0.008	0.011	4.401	0.762	0.937	-0.001	-0.040	-0.133	0.000
99	A	100	ARG	1	0.890	0.940	5.979	1.050	1.050	0.000	0.000	0.000	0.000
100	A	101	LYS	1	0.999	1.010	8.452	0.175	0.175	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)