FMO DATABASE

FMODB ID: 76QMK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-802149.974373
FMO2-HF: Nuclear repulsion	761475.974586
FMO2-HF: Total energy	-40673.999787
FMO2-MP2: Total energy	-40795.93779

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.
-3.564	2.52	1.246	-3.536	-3.792	-0.01

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 : 0.032 / q_NPA : 0.024

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	0.823	0.896	3.691	-0.093	2.428	-0.012	-1.414	-1.095	0.006
4	A	5	HIS	1	0.900	0.937	6.301	0.861	0.861	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.054	-0.024	9.338	0.092	0.092	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.011	0.002	11.990	0.037	0.037	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.006	0.005	15.444	0.024	0.024	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.013	-0.001	18.551	0.011	0.011	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.857	0.904	21.565	0.140	0.140	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.003	0.001	23.168	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.849	0.910	27.068	0.129	0.129	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.815	-0.902	30.506	-0.110	-0.110	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.976	-0.986	32.967	-0.090	-0.090	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.062	-0.001	28.189	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.024	-0.018	31.581	0.000	0.000	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.836	-0.944	29.395	-0.102	-0.102	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.021	0.016	28.829	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.102	0.072	28.851	0.000	0.000	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.843	0.925	25.410	0.099	0.099	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.879	-0.925	24.230	-0.061	-0.061	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.875	-0.922	24.304	-0.079	-0.079	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.010	-0.002	19.998	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.008	-0.012	18.792	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.855	0.928	19.466	0.046	0.046	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.015	-0.013	20.678	0.011	0.011	0.000	0.000	0.000	0.000
26	A	27	TYR	0	0.002	-0.014	13.667	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.009	-0.010	15.606	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.009	0.009	16.040	0.029	0.029	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.016	0.007	15.792	0.016	0.016	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.015	0.008	11.730	0.001	0.001	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.085	-0.043	14.140	0.050	0.050	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.071	-0.029	16.795	0.011	0.011	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.047	-0.027	13.563	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	PRO	0	-0.006	-0.011	13.394	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	36	ALA	0	-0.008	0.003	10.633	0.043	0.043	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.065	-0.011	8.701	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.891	0.943	4.770	-0.468	-0.414	-0.001	-0.003	-0.050	0.000
38	A	39	ASP	-1	-0.859	-0.922	7.239	0.197	0.197	0.000	0.000	0.000	0.000
39	A	40	VAL	0	-0.007	-0.013	8.447	-0.163	-0.163	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.065	-0.027	9.461	0.058	0.058	0.000	0.000	0.000	0.000
41	A	42	TRP	0	-0.001	-0.001	13.159	-0.064	-0.064	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.027	0.020	16.080	0.030	0.030	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.887	0.948	18.704	0.091	0.091	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.745	-0.848	22.051	-0.178	-0.178	0.000	0.000	0.000	0.000
45	A	46	VAL	0	0.003	-0.005	22.897	0.016	0.016	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.059	-0.058	24.195	0.016	0.016	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.035	0.008	26.857	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.963	0.974	28.471	0.147	0.147	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.038	-0.029	24.549	0.005	0.005	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.798	0.908	27.913	0.108	0.108	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.963	-0.955	29.719	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.878	-0.941	31.595	-0.118	-0.118	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.033	-0.015	27.640	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.027	-0.026	22.543	0.007	0.007	0.000	0.000	0.000	0.000
55	A	56	THR	0	0.013	0.000	23.815	0.005	0.005	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.025	-0.014	20.552	0.023	0.023	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.000	0.013	14.599	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.004	-0.004	13.269	0.040	0.040	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.877	-0.922	9.414	-0.740	-0.740	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.028	0.009	8.264	0.108	0.108	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.018	-0.004	2.590	-0.669	-0.531	0.743	-0.254	-0.626	0.000
62	A	63	PHE	0	0.025	0.004	3.540	0.259	0.511	0.002	-0.071	-0.183	0.000
63	A	64	GLU	-1	-0.849	-0.914	2.765	-2.581	-0.691	0.483	-1.207	-1.165	-0.013
64	A	65	SER	0	-0.002	-0.008	3.407	-1.270	-0.411	0.030	-0.469	-0.420	-0.003
65	A	66	VAL	0	0.064	0.003	5.643	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.933	-0.952	8.588	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.019	0.005	7.630	0.042	0.042	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.045	-0.018	7.583	0.032	0.032	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.029	0.010	10.165	0.055	0.055	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.864	-0.936	12.463	-0.106	-0.106	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.060	-0.047	11.674	0.031	0.031	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.083	-0.027	13.683	0.035	0.035	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.004	0.000	15.972	0.029	0.029	0.000	0.000	0.000	0.000
74	A	75	HIS	0	0.065	0.051	16.562	0.022	0.022	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.028	0.000	18.557	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.019	0.012	19.100	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.022	0.000	16.855	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.022	-0.013	18.966	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.057	0.033	22.011	0.002	0.002	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.017	-0.013	19.981	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.001	-0.013	21.804	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.918	-0.963	22.872	-0.116	-0.116	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.070	-0.032	25.902	0.007	0.007	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.028	-0.041	23.547	0.005	0.005	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.914	0.963	24.637	0.154	0.154	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.055	-0.023	25.526	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.061	0.036	25.639	0.002	0.002	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.039	0.029	21.578	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.800	-0.878	26.203	-0.141	-0.141	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.788	0.890	25.696	0.169	0.169	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.015	-0.020	19.468	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.033	-0.004	19.381	0.005	0.005	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.024	0.013	14.512	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.020	-0.013	13.390	0.021	0.021	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.752	-0.852	10.228	-0.961	-0.961	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.022	-0.016	8.780	0.036	0.036	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.066	0.036	3.544	-0.448	-0.274	0.002	-0.066	-0.110	0.000
98	A	99	PRO	0	-0.001	0.011	3.958	0.889	1.085	-0.001	-0.052	-0.143	0.000
99	A	100	ARG	1	0.899	0.945	5.418	1.029	1.029	0.000	0.000	0.000	0.000
100	A	101	LYS	1	1.007	1.011	8.004	0.101	0.101	0.000	0.000	0.000	0.000

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