FMO DATABASE

FMODB ID: R9Q88

Calculation Name: 5D90-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D90

Chain ID: B

ChEMBL ID:

UniProt ID: P44558

Base Structure: X-ray

Registration Date: 2023-06-22

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-943566.029753
FMO2-HF: Nuclear repulsion	892976.835378
FMO2-HF: Total energy	-50589.194375
FMO2-MP2: Total energy	-50735.879028

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(B:0:GLY)

Summations of interaction energy for fragment #1(B:0:GLY)

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.
-4.314	-1.129	0.1	-1.666	-1.618	-0.004

Interaction energy analysis for fragmet #1(B:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.005

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	B	2	THR	0	-0.070	-0.033	3.146	-2.018	-0.089	0.006	-1.040	-0.894	0.002
4	B	3	TYR	0	-0.011	-0.005	3.109	-1.731	-0.475	0.094	-0.626	-0.724	-0.006
5	B	4	THR	0	0.042	0.005	5.526	0.033	0.033	0.000	0.000	0.000	0.000
6	B	5	THR	0	0.066	0.012	9.007	-0.134	-0.134	0.000	0.000	0.000	0.000
7	B	6	ALA	0	-0.005	-0.003	11.530	-0.067	-0.067	0.000	0.000	0.000	0.000
8	B	7	LYS	1	0.890	0.922	6.269	0.048	0.048	0.000	0.000	0.000	0.000
9	B	8	ALA	0	0.010	0.010	7.832	-0.247	-0.247	0.000	0.000	0.000	0.000
10	B	9	ALA	0	-0.024	-0.018	8.689	-0.024	-0.024	0.000	0.000	0.000	0.000
11	B	10	GLU	-1	-0.818	-0.888	8.125	-0.330	-0.330	0.000	0.000	0.000	0.000
12	B	11	LYS	1	0.882	0.965	5.266	1.960	1.960	0.000	0.000	0.000	0.000
13	B	12	ILE	0	-0.029	-0.016	9.312	0.007	0.007	0.000	0.000	0.000	0.000
14	B	13	GLY	0	0.014	0.028	12.336	0.064	0.064	0.000	0.000	0.000	0.000
15	B	14	ILE	0	-0.064	-0.033	14.379	0.057	0.057	0.000	0.000	0.000	0.000
16	B	15	SER	0	0.032	0.019	15.265	0.006	0.006	0.000	0.000	0.000	0.000
17	B	16	ALA	0	0.071	0.000	15.443	-0.015	-0.015	0.000	0.000	0.000	0.000
18	B	17	TYR	0	-0.018	-0.004	16.523	0.002	0.002	0.000	0.000	0.000	0.000
19	B	18	THR	0	0.032	0.014	18.991	0.005	0.005	0.000	0.000	0.000	0.000
20	B	19	LEU	0	0.001	0.021	12.656	0.008	0.008	0.000	0.000	0.000	0.000
21	B	20	ARG	1	0.981	0.972	16.474	0.049	0.049	0.000	0.000	0.000	0.000
22	B	21	PHE	0	-0.008	0.014	18.966	0.011	0.011	0.000	0.000	0.000	0.000
23	B	22	TYR	0	0.006	-0.032	18.017	0.015	0.015	0.000	0.000	0.000	0.000
24	B	23	ASP	-1	-0.826	-0.896	18.153	-0.144	-0.144	0.000	0.000	0.000	0.000
25	B	24	LYS	1	0.927	0.971	19.978	0.077	0.077	0.000	0.000	0.000	0.000
26	B	25	GLU	-1	-0.877	-0.924	23.401	-0.090	-0.090	0.000	0.000	0.000	0.000
27	B	26	GLY	0	-0.014	0.000	23.345	0.003	0.003	0.000	0.000	0.000	0.000
28	B	27	LEU	0	-0.014	-0.003	21.374	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	28	LEU	0	-0.059	-0.027	15.782	-0.034	-0.034	0.000	0.000	0.000	0.000
30	B	29	PRO	0	0.013	0.056	18.297	0.001	0.001	0.000	0.000	0.000	0.000
31	B	30	ASN	0	0.011	-0.028	17.723	-0.009	-0.009	0.000	0.000	0.000	0.000
32	B	31	VAL	0	-0.029	-0.006	12.645	-0.009	-0.009	0.000	0.000	0.000	0.000
33	B	32	GLY	0	0.068	0.037	13.899	0.052	0.052	0.000	0.000	0.000	0.000
34	B	33	ARG	1	0.854	0.904	14.167	0.032	0.032	0.000	0.000	0.000	0.000
35	B	34	ASP	-1	-0.849	-0.931	12.446	0.199	0.199	0.000	0.000	0.000	0.000
36	B	35	GLU	-1	-0.915	-0.978	14.255	0.064	0.064	0.000	0.000	0.000	0.000
37	B	36	TYR	0	-0.026	-0.005	15.806	0.015	0.015	0.000	0.000	0.000	0.000
38	B	37	GLY	0	0.019	0.023	17.647	-0.016	-0.016	0.000	0.000	0.000	0.000
39	B	38	ASN	0	-0.060	-0.015	14.485	-0.070	-0.070	0.000	0.000	0.000	0.000
40	B	39	ARG	1	0.804	0.873	13.535	0.166	0.166	0.000	0.000	0.000	0.000
41	B	40	ARG	1	0.909	0.961	8.733	-0.165	-0.165	0.000	0.000	0.000	0.000
42	B	41	PHE	0	-0.009	0.001	8.235	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	42	THR	0	0.018	-0.036	6.952	-0.223	-0.223	0.000	0.000	0.000	0.000
44	B	43	ASP	-1	-0.765	-0.902	5.647	-3.000	-3.000	0.000	0.000	0.000	0.000
45	B	44	LYS	1	0.904	0.955	8.227	0.713	0.713	0.000	0.000	0.000	0.000
46	B	45	ASP	-1	-0.797	-0.871	10.813	-0.493	-0.493	0.000	0.000	0.000	0.000
47	B	46	LEU	0	0.006	0.011	6.747	0.124	0.124	0.000	0.000	0.000	0.000
48	B	47	GLN	0	0.016	0.019	10.970	0.143	0.143	0.000	0.000	0.000	0.000
49	B	48	TRP	0	0.016	0.016	13.696	0.063	0.063	0.000	0.000	0.000	0.000
50	B	49	LEU	0	0.009	-0.003	11.837	0.055	0.055	0.000	0.000	0.000	0.000
51	B	50	SER	0	-0.031	-0.030	13.528	0.043	0.043	0.000	0.000	0.000	0.000
52	B	51	LEU	0	-0.027	-0.002	16.003	0.048	0.048	0.000	0.000	0.000	0.000
53	B	52	LEU	0	0.027	0.011	18.195	0.037	0.037	0.000	0.000	0.000	0.000
54	B	53	GLN	0	0.037	0.020	17.646	0.045	0.045	0.000	0.000	0.000	0.000
55	B	54	CYS	0	-0.018	0.002	19.989	0.029	0.029	0.000	0.000	0.000	0.000
56	B	55	LEU	0	0.017	0.027	21.776	0.025	0.025	0.000	0.000	0.000	0.000
57	B	56	LYS	1	0.972	0.994	22.766	0.172	0.172	0.000	0.000	0.000	0.000
58	B	57	ASN	0	-0.070	-0.048	21.334	0.025	0.025	0.000	0.000	0.000	0.000
59	B	58	THR	0	-0.005	-0.005	25.004	0.012	0.012	0.000	0.000	0.000	0.000
60	B	59	GLY	0	0.003	0.003	27.603	0.010	0.010	0.000	0.000	0.000	0.000
61	B	60	MET	0	-0.035	0.009	27.145	0.009	0.009	0.000	0.000	0.000	0.000
62	B	61	SER	0	-0.034	-0.058	28.369	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	62	LEU	0	0.055	0.007	25.964	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	63	LYS	1	0.886	0.920	28.307	0.087	0.087	0.000	0.000	0.000	0.000
65	B	64	ASP	-1	-0.764	-0.836	30.594	-0.103	-0.103	0.000	0.000	0.000	0.000
66	B	65	ILE	0	-0.012	0.005	23.875	-0.006	-0.006	0.000	0.000	0.000	0.000
67	B	66	LYS	1	0.838	0.897	26.049	0.097	0.097	0.000	0.000	0.000	0.000
68	B	67	ARG	1	0.800	0.875	27.387	0.098	0.098	0.000	0.000	0.000	0.000
69	B	68	PHE	0	0.033	0.009	22.884	-0.002	-0.002	0.000	0.000	0.000	0.000
70	B	69	ALA	0	0.000	-0.013	23.780	-0.005	-0.005	0.000	0.000	0.000	0.000
71	B	70	GLU	-1	-0.878	-0.926	25.141	-0.103	-0.103	0.000	0.000	0.000	0.000
72	B	71	CYS	0	-0.025	-0.014	28.077	0.005	0.005	0.000	0.000	0.000	0.000
73	B	72	THR	0	-0.070	-0.042	23.903	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	73	ILE	0	-0.077	-0.029	24.409	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	74	ILE	0	-0.034	-0.009	26.585	0.006	0.006	0.000	0.000	0.000	0.000
76	B	75	GLY	0	0.043	0.037	28.931	0.006	0.006	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.917	-0.985	29.762	-0.134	-0.134	0.000	0.000	0.000	0.000
78	B	77	ASP	-1	-0.909	-0.939	32.009	-0.084	-0.084	0.000	0.000	0.000	0.000
79	B	78	THR	0	-0.029	-0.018	31.229	0.000	0.000	0.000	0.000	0.000	0.000
80	B	79	ILE	0	-0.028	-0.014	29.988	-0.007	-0.007	0.000	0.000	0.000	0.000
81	B	80	GLU	-1	-0.892	-0.949	32.592	-0.089	-0.089	0.000	0.000	0.000	0.000
82	B	81	GLU	-1	-0.791	-0.858	33.499	-0.103	-0.103	0.000	0.000	0.000	0.000
83	B	82	ARG	1	0.898	0.932	26.779	0.148	0.148	0.000	0.000	0.000	0.000
84	B	83	LEU	0	-0.003	0.008	30.365	-0.008	-0.008	0.000	0.000	0.000	0.000
85	B	84	SER	0	0.018	0.009	32.195	0.000	0.000	0.000	0.000	0.000	0.000
86	B	85	LEU	0	-0.015	-0.007	28.711	0.001	0.001	0.000	0.000	0.000	0.000
87	B	86	PHE	0	-0.006	-0.014	24.517	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	87	GLU	-1	-0.930	-0.939	30.084	-0.099	-0.099	0.000	0.000	0.000	0.000
89	B	88	ASN	0	-0.005	-0.014	33.396	0.007	0.007	0.000	0.000	0.000	0.000
90	B	89	GLN	0	0.037	0.015	28.269	0.012	0.012	0.000	0.000	0.000	0.000
91	B	90	THR	0	-0.033	-0.038	29.012	0.002	0.002	0.000	0.000	0.000	0.000
92	B	91	LYS	1	0.919	0.967	31.154	0.092	0.092	0.000	0.000	0.000	0.000
93	B	92	ASN	0	0.002	0.008	32.397	0.009	0.009	0.000	0.000	0.000	0.000
94	B	93	VAL	0	0.060	0.024	28.261	0.003	0.003	0.000	0.000	0.000	0.000
95	B	94	LYS	1	0.920	0.959	31.500	0.121	0.121	0.000	0.000	0.000	0.000
96	B	95	CYS	0	-0.026	-0.011	33.735	0.006	0.006	0.000	0.000	0.000	0.000
97	B	96	GLN	0	-0.038	-0.018	31.108	0.001	0.001	0.000	0.000	0.000	0.000
98	B	97	ILE	0	-0.012	-0.009	29.405	0.003	0.003	0.000	0.000	0.000	0.000
99	B	98	ALA	0	-0.028	-0.013	33.448	0.004	0.004	0.000	0.000	0.000	0.000
100	B	99	GLU	-1	-0.765	-0.858	37.060	-0.065	-0.065	0.000	0.000	0.000	0.000
101	B	100	LEU	0	-0.016	-0.009	31.777	0.004	0.004	0.000	0.000	0.000	0.000
102	B	101	LYS	1	0.951	0.971	33.640	0.098	0.098	0.000	0.000	0.000	0.000
103	B	102	ARG	1	0.871	0.931	37.134	0.067	0.067	0.000	0.000	0.000	0.000
104	B	103	TYR	0	-0.064	-0.051	37.949	0.006	0.006	0.000	0.000	0.000	0.000
105	B	104	LEU	0	-0.017	-0.008	34.752	0.002	0.002	0.000	0.000	0.000	0.000
106	B	105	ASP	-1	-0.848	-0.909	38.322	-0.060	-0.060	0.000	0.000	0.000	0.000
107	B	106	LEU	0	-0.058	-0.025	41.596	0.004	0.004	0.000	0.000	0.000	0.000
108	B	107	LEU	0	-0.026	-0.021	37.560	0.003	0.003	0.000	0.000	0.000	0.000
109	B	108	GLU	-1	-0.879	-0.946	37.208	-0.064	-0.064	0.000	0.000	0.000	0.000
110	B	109	TYR	0	-0.002	0.009	41.241	0.004	0.004	0.000	0.000	0.000	0.000
111	B	110	LYS	1	0.906	0.951	44.168	0.040	0.040	0.000	0.000	0.000	0.000
112	B	111	LEU	0	-0.006	0.004	38.848	0.003	0.003	0.000	0.000	0.000	0.000
113	B	112	ALA	0	0.046	0.022	43.003	0.002	0.002	0.000	0.000	0.000	0.000
114	B	113	PHE	0	-0.071	-0.039	45.186	0.003	0.003	0.000	0.000	0.000	0.000
115	B	114	TYR	0	0.026	-0.014	45.254	0.002	0.002	0.000	0.000	0.000	0.000
116	B	115	GLN	0	-0.002	0.007	40.801	0.002	0.002	0.000	0.000	0.000	0.000
117	B	116	LYS	1	0.984	0.998	45.990	0.032	0.032	0.000	0.000	0.000	0.000
118	B	117	ALA	0	-0.023	-0.012	49.538	0.002	0.002	0.000	0.000	0.000	0.000
119	B	118	LYS	1	0.968	0.990	43.895	0.030	0.030	0.000	0.000	0.000	0.000
120	B	119	ALA	0	-0.032	-0.010	49.202	0.001	0.001	0.000	0.000	0.000	0.000
121	B	120	LEU	0	-0.060	-0.044	50.651	0.001	0.001	0.000	0.000	0.000	0.000
122	B	121	GLY	0	0.048	0.038	52.796	0.001	0.001	0.000	0.000	0.000	0.000
123	B	122	SER	0	0.004	-0.003	53.998	0.001	0.001	0.000	0.000	0.000	0.000
124	B	123	VAL	0	-0.031	-0.011	52.276	-0.001	-0.001	0.000	0.000	0.000	0.000
125	B	124	LYS	1	0.925	0.979	54.797	0.025	0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:GLY)