FMO DATABASE

FMODB ID: MN49Z

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	OptH
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	-801305.925172
FMO2-HF: Nuclear repulsion	760632.43465
FMO2-HF: Total energy	-40673.490521
FMO2-MP2: Total energy	-40795.370953

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.
-4.216	1.929	1.487	-3.718	-3.911	-0.013

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 : 0.034 / q_NPA : 0.026

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	0.807	0.894	3.623	-0.200	2.389	-0.007	-1.474	-1.107	0.006
4	A	5	HIS	1	0.891	0.928	6.242	0.865	0.865	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.046	-0.023	9.272	0.101	0.101	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.017	0.002	11.937	0.031	0.031	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.007	0.006	15.392	0.026	0.026	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.016	0.004	18.504	0.008	0.008	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.862	0.910	21.518	0.147	0.147	0.000	0.000	0.000	0.000
10	A	11	PHE	0	0.000	-0.004	22.946	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.864	0.925	27.025	0.128	0.128	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.862	-0.930	30.459	-0.103	-0.103	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-1.014	-1.003	33.100	-0.084	-0.084	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.056	-0.004	28.145	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.005	-0.007	31.545	0.002	0.002	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.870	-0.958	29.444	-0.090	-0.090	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.034	0.022	28.811	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	19	GLN	0	0.077	0.046	28.832	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.875	0.941	25.301	0.095	0.095	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.960	-0.975	24.207	-0.051	-0.051	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.862	-0.919	24.289	-0.070	-0.070	0.000	0.000	0.000	0.000
22	A	23	PHE	0	-0.031	-0.007	19.928	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	24	PHE	0	0.021	-0.009	18.759	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.954	0.990	19.450	0.021	0.021	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.026	-0.021	20.665	0.013	0.013	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.005	-0.022	13.546	-0.013	-0.013	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.006	-0.008	15.592	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.019	0.003	16.031	0.033	0.033	0.000	0.000	0.000	0.000
29	A	30	LEU	0	0.019	0.006	15.820	0.016	0.016	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.021	0.011	11.756	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	32	ASN	0	-0.087	-0.042	14.128	0.053	0.053	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.075	-0.030	16.783	0.010	0.010	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.050	-0.029	13.606	0.000	0.000	0.000	0.000	0.000	0.000
34	A	35	PRO	0	-0.011	-0.014	13.369	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.007	0.011	10.501	0.049	0.049	0.000	0.000	0.000	0.000
36	A	37	MET	0	-0.066	-0.007	8.667	-0.046	-0.046	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.954	0.984	4.896	-0.490	-0.490	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.902	-0.951	7.229	0.314	0.314	0.000	0.000	0.000	0.000
39	A	40	VAL	0	0.005	-0.008	8.441	-0.165	-0.165	0.000	0.000	0.000	0.000
40	A	41	TYR	0	-0.021	0.002	9.935	0.087	0.087	0.000	0.000	0.000	0.000
41	A	42	TRP	0	-0.001	0.000	13.124	-0.070	-0.070	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.027	0.019	16.039	0.032	0.032	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.940	0.968	18.667	0.081	0.081	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.758	-0.870	22.012	-0.166	-0.166	0.000	0.000	0.000	0.000
45	A	46	VAL	0	-0.031	-0.028	22.859	0.015	0.015	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.077	-0.051	24.164	0.014	0.014	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.020	-0.002	26.823	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.958	0.966	28.285	0.143	0.143	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.045	-0.023	24.590	0.000	0.000	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.870	0.947	27.842	0.098	0.098	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.940	-0.947	29.673	-0.097	-0.097	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.883	-0.939	31.540	-0.116	-0.116	0.000	0.000	0.000	0.000
53	A	54	GLY	0	-0.042	-0.020	27.587	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.033	-0.030	22.490	0.004	0.004	0.000	0.000	0.000	0.000
55	A	56	THR	0	0.006	0.009	23.742	0.006	0.006	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.029	-0.023	20.415	0.024	0.024	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.005	0.011	14.518	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.009	0.001	13.060	0.042	0.042	0.000	0.000	0.000	0.000
59	A	60	GLU	-1	-0.878	-0.935	9.311	-0.609	-0.609	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.037	0.015	8.272	0.115	0.115	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.022	-0.005	2.537	-0.629	-0.537	0.841	-0.275	-0.658	0.000
62	A	63	PHE	0	0.022	0.000	3.475	0.246	0.519	0.003	-0.079	-0.196	0.000
63	A	64	GLU	-1	-0.918	-0.957	2.696	-3.006	-1.061	0.619	-1.288	-1.276	-0.015
64	A	65	SER	0	0.007	-0.002	3.400	-1.440	-0.550	0.031	-0.487	-0.433	-0.004
65	A	66	VAL	0	0.045	-0.006	5.632	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.922	-0.946	8.574	-0.108	-0.108	0.000	0.000	0.000	0.000
67	A	68	THR	0	0.024	0.007	7.612	0.046	0.046	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.043	-0.016	7.641	0.036	0.036	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.026	0.008	10.091	0.062	0.062	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.852	-0.933	12.400	-0.137	-0.137	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.031	-0.018	11.653	0.048	0.048	0.000	0.000	0.000	0.000
72	A	73	ILE	0	-0.083	-0.027	13.623	0.038	0.038	0.000	0.000	0.000	0.000
73	A	74	ILE	0	-0.020	-0.005	15.903	0.031	0.031	0.000	0.000	0.000	0.000
74	A	75	HIS	0	0.065	0.053	16.513	0.023	0.023	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.029	0.002	18.502	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.019	0.009	19.033	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.043	-0.025	16.806	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.018	-0.012	18.913	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.051	0.030	21.951	0.003	0.003	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.013	-0.010	20.058	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.001	-0.015	21.753	0.000	0.000	0.000	0.000	0.000	0.000
82	A	83	ASP	-1	-0.918	-0.962	22.814	-0.117	-0.117	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.075	-0.036	25.863	0.006	0.006	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.038	-0.038	23.503	0.004	0.004	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.925	0.961	24.570	0.152	0.152	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.068	-0.030	25.469	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.073	0.033	25.576	0.002	0.002	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.025	0.027	21.540	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.845	-0.904	26.152	-0.134	-0.134	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.903	0.948	25.466	0.180	0.180	0.000	0.000	0.000	0.000
91	A	92	LEU	0	-0.012	-0.012	19.508	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.029	-0.004	19.230	0.004	0.004	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.024	0.013	14.373	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	95	PHE	0	-0.024	-0.013	13.385	0.018	0.018	0.000	0.000	0.000	0.000
95	A	96	ASP	-1	-0.746	-0.843	10.158	-0.968	-0.968	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.028	-0.023	8.620	0.045	0.045	0.000	0.000	0.000	0.000
97	A	98	THR	0	0.052	0.031	3.628	-0.689	-0.527	0.001	-0.064	-0.099	0.000
98	A	99	PRO	0	-0.023	-0.004	3.994	0.918	1.112	-0.001	-0.051	-0.142	0.000
99	A	100	ARG	1	0.923	0.961	5.363	1.011	1.011	0.000	0.000	0.000	0.000
100	A	101	LYS	1	1.005	1.008	7.956	0.054	0.054	0.000	0.000	0.000	0.000

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