FMO DATABASE

FMODB ID: QYV7Y

Calculation Name: 5N9J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: B

ChEMBL ID:

UniProt ID: P87310

Base Structure: X-ray

Registration Date: 2023-06-21

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-852782.64794
FMO2-HF: Nuclear repulsion	800376.38577
FMO2-HF: Total energy	-52406.26217
FMO2-MP2: Total energy	-52561.928482

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:8:THR)

Summations of interaction energy for fragment #1(B:8:THR)

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.
-8.148	-4.253	12.162	-6.723	-9.333	-0.004

Interaction energy analysis for fragmet #1(B:8:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : -0.011

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	B	10	GLU	-1	-0.895	-0.955	2.599	-9.085	-5.784	0.478	-1.502	-2.277	-0.013
4	B	11	MET	0	-0.028	-0.009	2.028	-0.434	-0.563	8.479	-4.043	-4.307	0.004
5	B	12	LYS	1	0.930	0.971	2.267	-0.381	0.241	3.206	-1.168	-2.659	0.005
6	B	13	SER	0	-0.015	0.003	4.777	0.735	0.836	-0.001	-0.010	-0.090	0.000
7	B	14	LEU	0	0.002	0.004	6.934	0.396	0.396	0.000	0.000	0.000	0.000
8	B	15	ALA	0	0.007	-0.009	7.515	0.246	0.246	0.000	0.000	0.000	0.000
9	B	16	SER	0	-0.001	0.020	8.703	0.112	0.112	0.000	0.000	0.000	0.000
10	B	17	ARG	1	0.931	0.954	10.533	0.546	0.546	0.000	0.000	0.000	0.000
11	B	18	LEU	0	-0.017	-0.027	11.728	0.070	0.070	0.000	0.000	0.000	0.000
12	B	19	GLU	-1	-0.951	-0.977	12.197	0.028	0.028	0.000	0.000	0.000	0.000
13	B	20	ASP	-1	-0.876	-0.944	14.507	-0.271	-0.271	0.000	0.000	0.000	0.000
14	B	21	THR	0	-0.015	-0.013	16.457	0.016	0.016	0.000	0.000	0.000	0.000
15	B	22	THR	0	-0.105	-0.035	16.817	0.032	0.032	0.000	0.000	0.000	0.000
16	B	23	GLN	0	0.005	0.001	18.774	0.030	0.030	0.000	0.000	0.000	0.000
17	B	24	ALA	0	0.055	0.040	20.555	0.009	0.009	0.000	0.000	0.000	0.000
18	B	25	PHE	0	-0.068	-0.046	22.358	0.007	0.007	0.000	0.000	0.000	0.000
19	B	26	TYR	0	-0.038	-0.009	23.357	0.014	0.014	0.000	0.000	0.000	0.000
20	B	27	ASP	-1	-0.869	-0.943	24.301	-0.056	-0.056	0.000	0.000	0.000	0.000
21	B	28	LEU	0	-0.026	-0.007	26.468	0.005	0.005	0.000	0.000	0.000	0.000
22	B	29	ALA	0	-0.021	-0.023	28.141	0.005	0.005	0.000	0.000	0.000	0.000
23	B	30	LEU	0	-0.034	-0.009	29.137	0.007	0.007	0.000	0.000	0.000	0.000
24	B	31	ILE	0	-0.007	-0.004	29.833	0.002	0.002	0.000	0.000	0.000	0.000
25	B	32	VAL	0	-0.054	-0.026	32.562	0.002	0.002	0.000	0.000	0.000	0.000
26	B	33	TYR	0	-0.077	-0.032	33.829	0.005	0.005	0.000	0.000	0.000	0.000
27	B	34	ASN	0	-0.041	-0.035	34.081	0.001	0.001	0.000	0.000	0.000	0.000
28	B	35	LEU	0	-0.003	0.022	36.738	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	36	GLU	-1	-0.944	-0.986	38.840	-0.014	-0.014	0.000	0.000	0.000	0.000
30	B	37	ASP	-1	-0.899	-0.893	41.012	-0.029	-0.029	0.000	0.000	0.000	0.000
31	B	38	THR	0	-0.073	-0.049	41.006	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	39	THR	0	-0.059	-0.066	37.076	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	40	PRO	0	0.025	0.013	35.932	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	41	SER	0	0.072	0.021	36.766	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	42	ASP	-1	-0.941	-0.987	35.879	-0.076	-0.076	0.000	0.000	0.000	0.000
36	B	43	ALA	0	0.005	0.004	32.858	-0.007	-0.007	0.000	0.000	0.000	0.000
37	B	44	ILE	0	-0.006	0.007	31.649	-0.004	-0.004	0.000	0.000	0.000	0.000
38	B	45	PRO	0	-0.051	-0.046	31.575	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	46	GLU	-1	-0.870	-0.904	28.686	-0.118	-0.118	0.000	0.000	0.000	0.000
40	B	47	SER	0	0.012	0.020	26.955	-0.013	-0.013	0.000	0.000	0.000	0.000
41	B	48	LEU	0	0.034	0.030	26.709	-0.014	-0.014	0.000	0.000	0.000	0.000
42	B	49	ASP	-1	-0.914	-0.960	27.062	-0.156	-0.156	0.000	0.000	0.000	0.000
43	B	50	THR	0	-0.144	-0.115	23.335	-0.023	-0.023	0.000	0.000	0.000	0.000
44	B	51	LEU	0	0.097	0.052	22.504	-0.027	-0.027	0.000	0.000	0.000	0.000
45	B	52	ILE	0	-0.026	-0.012	22.420	-0.029	-0.029	0.000	0.000	0.000	0.000
46	B	53	ARG	1	0.926	0.958	21.545	0.200	0.200	0.000	0.000	0.000	0.000
47	B	54	ASP	-1	-0.822	-0.896	18.737	-0.327	-0.327	0.000	0.000	0.000	0.000
48	B	55	LEU	0	-0.004	0.017	18.053	-0.061	-0.061	0.000	0.000	0.000	0.000
49	B	56	LYS	1	0.850	0.934	19.639	0.242	0.242	0.000	0.000	0.000	0.000
50	B	57	SER	0	-0.076	-0.055	15.694	-0.048	-0.048	0.000	0.000	0.000	0.000
51	B	58	LEU	0	0.060	0.024	13.918	-0.106	-0.106	0.000	0.000	0.000	0.000
52	B	59	PRO	0	-0.009	-0.013	13.895	-0.099	-0.099	0.000	0.000	0.000	0.000
53	B	60	ASP	-1	-0.880	-0.944	14.459	-0.629	-0.629	0.000	0.000	0.000	0.000
54	B	61	ILE	0	-0.006	-0.006	8.986	-0.131	-0.131	0.000	0.000	0.000	0.000
55	B	62	SER	0	0.010	0.007	9.602	-0.293	-0.293	0.000	0.000	0.000	0.000
56	B	63	ARG	1	0.845	0.922	10.676	0.499	0.499	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.901	0.957	7.494	1.277	1.277	0.000	0.000	0.000	0.000
58	B	65	VAL	0	-0.043	0.008	5.299	-0.281	-0.281	0.000	0.000	0.000	0.000
59	B	66	ASN	0	0.016	0.005	6.759	-0.079	-0.079	0.000	0.000	0.000	0.000
60	B	67	ASN	0	-0.024	-0.015	5.413	-0.165	-0.165	0.000	0.000	0.000	0.000
61	B	68	LEU	0	0.013	0.001	8.963	0.099	0.099	0.000	0.000	0.000	0.000
62	B	69	ILE	0	-0.012	-0.001	11.061	0.066	0.066	0.000	0.000	0.000	0.000
63	B	70	PRO	0	-0.024	-0.010	13.842	-0.012	-0.012	0.000	0.000	0.000	0.000
64	B	71	GLN	0	0.077	0.033	17.017	-0.007	-0.007	0.000	0.000	0.000	0.000
65	B	72	ASP	-1	-0.860	-0.938	20.155	0.021	0.021	0.000	0.000	0.000	0.000
66	B	73	VAL	0	-0.040	-0.017	14.611	0.027	0.027	0.000	0.000	0.000	0.000
67	B	74	LEU	0	0.015	0.009	17.297	0.013	0.013	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.889	-0.942	18.983	0.005	0.005	0.000	0.000	0.000	0.000
69	B	76	TYR	0	-0.127	-0.103	19.551	0.011	0.011	0.000	0.000	0.000	0.000
70	B	77	ILE	0	-0.048	-0.031	15.525	0.019	0.019	0.000	0.000	0.000	0.000
71	B	78	GLU	-1	-0.915	-0.931	19.728	-0.042	-0.042	0.000	0.000	0.000	0.000
72	B	79	GLN	0	-0.062	-0.044	22.665	0.000	0.000	0.000	0.000	0.000	0.000
73	B	80	GLY	0	-0.014	0.008	22.500	0.007	0.007	0.000	0.000	0.000	0.000
74	B	81	ARG	1	0.869	0.942	22.100	-0.105	-0.105	0.000	0.000	0.000	0.000
75	B	82	ASN	0	0.034	0.009	17.204	0.025	0.025	0.000	0.000	0.000	0.000
76	B	83	PRO	0	0.095	0.041	14.617	-0.013	-0.013	0.000	0.000	0.000	0.000
77	B	84	ASP	-1	-0.865	-0.938	13.863	0.624	0.624	0.000	0.000	0.000	0.000
78	B	85	VAL	0	-0.124	-0.067	15.916	-0.013	-0.013	0.000	0.000	0.000	0.000
79	B	86	TYR	0	0.065	0.043	16.285	-0.017	-0.017	0.000	0.000	0.000	0.000
80	B	87	ALA	0	0.031	0.014	14.085	-0.015	-0.015	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.932	0.968	16.090	-0.317	-0.317	0.000	0.000	0.000	0.000
82	B	89	GLN	0	0.063	0.038	18.952	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	90	PHE	0	0.035	0.023	18.170	-0.021	-0.021	0.000	0.000	0.000	0.000
84	B	91	SER	0	-0.049	-0.016	17.323	-0.010	-0.010	0.000	0.000	0.000	0.000
85	B	92	GLU	-1	-0.935	-0.977	19.240	0.187	0.187	0.000	0.000	0.000	0.000
86	B	93	LEU	0	-0.039	-0.014	22.539	-0.016	-0.016	0.000	0.000	0.000	0.000
87	B	94	VAL	0	0.017	0.014	19.491	-0.017	-0.017	0.000	0.000	0.000	0.000
88	B	95	GLN	0	-0.002	0.006	22.845	0.001	0.001	0.000	0.000	0.000	0.000
89	B	96	LYS	1	0.943	0.963	24.828	-0.137	-0.137	0.000	0.000	0.000	0.000
90	B	97	ASP	-1	-0.856	-0.946	26.396	0.072	0.072	0.000	0.000	0.000	0.000
91	B	98	ASN	0	-0.072	-0.013	25.168	-0.022	-0.022	0.000	0.000	0.000	0.000
92	B	99	GLN	0	-0.019	-0.022	27.806	0.002	0.002	0.000	0.000	0.000	0.000
93	B	100	TYR	0	0.007	0.011	30.754	-0.013	-0.013	0.000	0.000	0.000	0.000
94	B	101	VAL	0	0.026	0.004	30.109	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	102	ASN	0	0.007	0.015	31.433	-0.011	-0.011	0.000	0.000	0.000	0.000
96	B	103	GLY	0	0.038	0.011	33.242	-0.004	-0.004	0.000	0.000	0.000	0.000
97	B	104	LYS	1	0.895	0.943	35.682	-0.054	-0.054	0.000	0.000	0.000	0.000
98	B	105	LEU	0	-0.001	0.002	33.848	-0.005	-0.005	0.000	0.000	0.000	0.000
99	B	106	TYR	0	0.020	0.006	35.577	-0.001	-0.001	0.000	0.000	0.000	0.000
100	B	107	ALA	0	-0.036	-0.010	39.455	-0.003	-0.003	0.000	0.000	0.000	0.000
101	B	108	ILE	0	-0.002	-0.011	41.162	-0.003	-0.003	0.000	0.000	0.000	0.000
102	B	109	GLU	-1	-0.912	-0.949	40.081	0.045	0.045	0.000	0.000	0.000	0.000
103	B	110	GLY	0	-0.026	-0.009	43.072	-0.002	-0.002	0.000	0.000	0.000	0.000
104	B	111	PHE	0	-0.030	-0.007	45.463	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	112	GLN	0	0.022	0.009	45.865	-0.001	-0.001	0.000	0.000	0.000	0.000
106	B	113	LYS	1	0.921	0.950	43.741	-0.048	-0.048	0.000	0.000	0.000	0.000
107	B	114	ALA	0	0.045	0.026	49.099	-0.001	-0.001	0.000	0.000	0.000	0.000
108	B	115	PHE	0	-0.017	-0.004	50.960	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	116	ALA	0	0.010	-0.001	51.469	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	117	GLU	-1	-0.967	-0.984	52.807	0.033	0.033	0.000	0.000	0.000	0.000
111	B	118	GLU	-1	-0.904	-0.962	55.274	0.026	0.026	0.000	0.000	0.000	0.000
112	B	119	ILE	0	-0.019	-0.012	54.695	-0.002	-0.002	0.000	0.000	0.000	0.000
113	B	120	LYS	1	0.806	0.898	54.049	-0.028	-0.028	0.000	0.000	0.000	0.000
114	B	121	GLN	0	-0.072	-0.032	58.937	-0.002	-0.002	0.000	0.000	0.000	0.000
115	B	122	ALA	0	-0.025	-0.003	60.875	-0.001	-0.001	0.000	0.000	0.000	0.000
116	B	123	TYR	0	-0.071	-0.040	60.914	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	124	PRO	0	0.025	0.027	61.406	0.000	0.000	0.000	0.000	0.000	0.000
118	B	125	GLU	-1	-0.920	-0.971	62.113	0.015	0.015	0.000	0.000	0.000	0.000
119	B	126	VAL	0	-0.022	-0.017	59.084	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	127	SER	0	0.030	0.015	57.614	0.001	0.001	0.000	0.000	0.000	0.000
121	B	128	SER	0	-0.031	-0.014	56.359	0.001	0.001	0.000	0.000	0.000	0.000
122	B	129	VAL	0	-0.001	0.001	55.123	0.000	0.000	0.000	0.000	0.000	0.000
123	B	130	VAL	0	0.056	0.018	53.257	0.000	0.000	0.000	0.000	0.000	0.000
124	B	131	ASP	-1	-0.812	-0.892	51.592	0.026	0.026	0.000	0.000	0.000	0.000
125	B	132	LYS	1	0.904	0.934	50.617	-0.013	-0.013	0.000	0.000	0.000	0.000
126	B	133	ILE	0	-0.019	0.000	48.722	0.000	0.000	0.000	0.000	0.000	0.000
127	B	134	LEU	0	-0.019	-0.004	46.867	0.001	0.001	0.000	0.000	0.000	0.000
128	B	135	ASN	0	-0.099	-0.061	45.648	0.003	0.003	0.000	0.000	0.000	0.000
129	B	136	GLU	-1	-0.974	-0.976	45.559	0.018	0.018	0.000	0.000	0.000	0.000
130	B	137	GLY	0	0.058	0.052	42.981	-0.001	-0.001	0.000	0.000	0.000	0.000
131	B	138	LYS	1	0.856	0.928	40.370	-0.037	-0.037	0.000	0.000	0.000	0.000
132	B	139	VAL	0	-0.001	0.000	36.029	-0.003	-0.003	0.000	0.000	0.000	0.000
133	B	140	GLU	-1	-0.981	-0.982	39.387	0.018	0.018	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:8:THR)