FMO DATABASE

FMODB ID: JLQ69

Calculation Name: 5N9J-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5N9J

Chain ID: R

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	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	99
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-827611.121233
FMO2-HF: Nuclear repulsion	784446.563986
FMO2-HF: Total energy	-43164.557248
FMO2-MP2: Total energy	-43290.574826

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(R:6:LEU)

Summations of interaction energy for fragment #1(R:6:LEU)

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.
-1.86	0.746	0.399	-1.319	-1.685	-0.007

Interaction energy analysis for fragmet #1(R:6:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.020

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	R	8	SER	0	-0.007	-0.012	2.824	-3.106	-0.625	0.400	-1.315	-1.566	-0.007
4	R	9	LYS	1	0.972	0.989	4.798	0.757	0.882	-0.001	-0.004	-0.119	0.000
5	R	10	VAL	0	0.003	-0.006	6.511	-0.029	-0.029	0.000	0.000	0.000	0.000
6	R	11	PRO	0	0.001	0.011	9.710	0.060	0.060	0.000	0.000	0.000	0.000
7	R	12	ASP	-1	-0.775	-0.876	12.664	-0.068	-0.068	0.000	0.000	0.000	0.000
8	R	13	ASP	-1	-0.861	-0.927	16.259	-0.061	-0.061	0.000	0.000	0.000	0.000
9	R	14	LYS	1	0.827	0.893	17.632	0.015	0.015	0.000	0.000	0.000	0.000
10	R	15	SER	0	-0.020	-0.047	18.584	0.011	0.011	0.000	0.000	0.000	0.000
11	R	16	ARG	1	0.728	0.861	14.561	0.061	0.061	0.000	0.000	0.000	0.000
12	R	17	PHE	0	0.041	0.026	17.709	0.010	0.010	0.000	0.000	0.000	0.000
13	R	18	GLU	-1	-0.814	-0.883	20.715	0.012	0.012	0.000	0.000	0.000	0.000
14	R	19	ILE	0	-0.002	-0.007	17.881	0.009	0.009	0.000	0.000	0.000	0.000
15	R	20	GLU	-1	-0.743	-0.846	16.153	0.010	0.010	0.000	0.000	0.000	0.000
16	R	21	LEU	0	-0.001	0.012	20.281	0.005	0.005	0.000	0.000	0.000	0.000
17	R	22	GLU	-1	-0.865	-0.947	23.430	0.058	0.058	0.000	0.000	0.000	0.000
18	R	23	PHE	0	-0.066	-0.029	18.152	0.010	0.010	0.000	0.000	0.000	0.000
19	R	24	VAL	0	0.032	0.004	22.223	0.005	0.005	0.000	0.000	0.000	0.000
20	R	25	GLN	0	0.012	-0.002	24.538	-0.001	-0.001	0.000	0.000	0.000	0.000
21	R	26	MET	0	-0.012	-0.006	24.029	-0.002	-0.002	0.000	0.000	0.000	0.000
22	R	27	LEU	0	-0.005	-0.005	22.299	0.004	0.004	0.000	0.000	0.000	0.000
23	R	28	SER	0	-0.025	-0.017	26.153	-0.006	-0.006	0.000	0.000	0.000	0.000
24	R	29	ASN	0	-0.032	-0.008	28.753	-0.002	-0.002	0.000	0.000	0.000	0.000
25	R	30	PRO	0	0.061	0.024	28.945	0.008	0.008	0.000	0.000	0.000	0.000
26	R	31	TRP	0	0.041	0.010	29.963	0.005	0.005	0.000	0.000	0.000	0.000
27	R	32	TYR	0	-0.010	0.004	20.913	0.008	0.008	0.000	0.000	0.000	0.000
28	R	33	LEU	0	0.035	0.009	24.906	0.014	0.014	0.000	0.000	0.000	0.000
29	R	34	ASN	0	0.001	0.008	25.694	0.014	0.014	0.000	0.000	0.000	0.000
30	R	35	PHE	0	-0.011	-0.006	21.608	0.009	0.009	0.000	0.000	0.000	0.000
31	R	36	LEU	0	-0.014	-0.002	19.222	0.017	0.017	0.000	0.000	0.000	0.000
32	R	37	ALA	0	-0.007	-0.003	21.435	0.019	0.019	0.000	0.000	0.000	0.000
33	R	38	GLN	0	-0.053	-0.034	23.479	0.012	0.012	0.000	0.000	0.000	0.000
34	R	39	HIS	0	-0.115	-0.061	19.829	0.015	0.015	0.000	0.000	0.000	0.000
35	R	40	LYS	1	0.802	0.880	19.089	-0.155	-0.155	0.000	0.000	0.000	0.000
36	R	41	TYR	0	0.047	0.031	14.887	0.011	0.011	0.000	0.000	0.000	0.000
37	R	42	PHE	0	-0.018	-0.020	17.338	-0.003	-0.003	0.000	0.000	0.000	0.000
38	R	43	GLU	-1	-0.864	-0.908	18.382	0.174	0.174	0.000	0.000	0.000	0.000
39	R	44	ASP	-1	-0.849	-0.911	12.210	0.357	0.357	0.000	0.000	0.000	0.000
40	R	45	GLU	-1	-0.946	-0.975	12.855	0.048	0.048	0.000	0.000	0.000	0.000
41	R	46	ALA	0	-0.009	-0.008	9.910	-0.040	-0.040	0.000	0.000	0.000	0.000
42	R	47	PHE	0	-0.029	-0.025	11.912	-0.043	-0.043	0.000	0.000	0.000	0.000
43	R	48	LEU	0	-0.017	-0.018	14.931	-0.033	-0.033	0.000	0.000	0.000	0.000
44	R	49	GLN	0	-0.056	-0.031	13.463	-0.014	-0.014	0.000	0.000	0.000	0.000
45	R	50	TYR	0	-0.081	-0.058	13.863	-0.011	-0.011	0.000	0.000	0.000	0.000
46	R	51	LEU	0	-0.013	-0.003	15.657	-0.013	-0.013	0.000	0.000	0.000	0.000
47	R	52	GLU	-1	-0.914	-0.955	17.573	-0.014	-0.014	0.000	0.000	0.000	0.000
48	R	53	TYR	0	0.000	-0.004	16.325	-0.015	-0.015	0.000	0.000	0.000	0.000
49	R	54	MET	0	-0.018	-0.006	18.389	-0.005	-0.005	0.000	0.000	0.000	0.000
50	R	55	GLU	-1	-0.788	-0.869	20.899	0.027	0.027	0.000	0.000	0.000	0.000
51	R	56	TYR	0	-0.015	0.005	20.097	-0.007	-0.007	0.000	0.000	0.000	0.000
52	R	57	TRP	0	-0.049	-0.033	19.896	-0.001	-0.001	0.000	0.000	0.000	0.000
53	R	58	ARG	1	0.795	0.869	25.634	-0.025	-0.025	0.000	0.000	0.000	0.000
54	R	59	GLU	-1	-0.906	-0.935	26.684	-0.011	-0.011	0.000	0.000	0.000	0.000
55	R	60	PRO	0	-0.009	-0.005	28.678	0.002	0.002	0.000	0.000	0.000	0.000
56	R	61	GLU	-1	-0.914	-0.979	28.611	-0.014	-0.014	0.000	0.000	0.000	0.000
57	R	62	TYR	0	-0.036	-0.011	23.546	0.000	0.000	0.000	0.000	0.000	0.000
58	R	63	VAL	0	0.025	0.018	28.066	0.005	0.005	0.000	0.000	0.000	0.000
59	R	64	LYS	1	0.880	0.954	30.464	0.000	0.000	0.000	0.000	0.000	0.000
60	R	65	PHE	0	-0.092	-0.057	28.828	-0.001	-0.001	0.000	0.000	0.000	0.000
61	R	66	ILE	0	-0.025	0.008	27.888	0.004	0.004	0.000	0.000	0.000	0.000
62	R	67	ILE	0	-0.022	-0.008	30.423	-0.002	-0.002	0.000	0.000	0.000	0.000
63	R	68	TYR	0	0.021	0.003	30.955	-0.002	-0.002	0.000	0.000	0.000	0.000
64	R	69	PRO	0	0.055	0.022	31.875	0.003	0.003	0.000	0.000	0.000	0.000
65	R	70	THR	0	0.009	-0.002	32.631	-0.002	-0.002	0.000	0.000	0.000	0.000
66	R	71	CYS	0	-0.022	0.008	27.592	0.000	0.000	0.000	0.000	0.000	0.000
67	R	72	LEU	0	0.046	0.020	28.366	0.002	0.002	0.000	0.000	0.000	0.000
68	R	73	HIS	0	0.007	0.013	29.768	-0.002	-0.002	0.000	0.000	0.000	0.000
69	R	74	MET	0	0.011	0.007	28.456	0.001	0.001	0.000	0.000	0.000	0.000
70	R	75	LEU	0	-0.025	0.001	23.103	0.006	0.006	0.000	0.000	0.000	0.000
71	R	76	THR	0	-0.022	-0.029	26.218	-0.001	-0.001	0.000	0.000	0.000	0.000
72	R	77	LEU	0	-0.026	-0.005	28.845	0.000	0.000	0.000	0.000	0.000	0.000
73	R	78	LEU	0	-0.017	0.007	23.224	0.002	0.002	0.000	0.000	0.000	0.000
74	R	79	LYS	1	0.888	0.934	23.416	-0.026	-0.026	0.000	0.000	0.000	0.000
75	R	80	ASN	0	-0.012	0.002	25.767	0.001	0.001	0.000	0.000	0.000	0.000
76	R	81	PRO	0	0.017	-0.001	24.743	0.006	0.006	0.000	0.000	0.000	0.000
77	R	82	GLN	0	-0.042	-0.038	26.281	0.005	0.005	0.000	0.000	0.000	0.000
78	R	83	PHE	0	0.055	0.021	28.217	0.004	0.004	0.000	0.000	0.000	0.000
79	R	84	ARG	1	0.897	0.951	22.066	-0.089	-0.089	0.000	0.000	0.000	0.000
80	R	85	ASN	0	-0.045	-0.017	26.507	0.014	0.014	0.000	0.000	0.000	0.000
81	R	86	ASP	-1	-0.774	-0.874	28.001	0.078	0.078	0.000	0.000	0.000	0.000
82	R	87	ILE	0	0.017	0.019	25.879	-0.002	-0.002	0.000	0.000	0.000	0.000
83	R	88	SER	0	-0.011	-0.011	27.112	0.007	0.007	0.000	0.000	0.000	0.000
84	R	89	ARG	1	0.718	0.860	28.797	-0.069	-0.069	0.000	0.000	0.000	0.000
85	R	90	ALA	0	0.035	0.012	32.600	-0.002	-0.002	0.000	0.000	0.000	0.000
86	R	91	ASP	-1	-0.837	-0.915	34.529	0.069	0.069	0.000	0.000	0.000	0.000
87	R	92	LEU	0	0.047	0.026	32.791	-0.003	-0.003	0.000	0.000	0.000	0.000
88	R	93	SER	0	0.022	0.010	32.322	-0.001	-0.001	0.000	0.000	0.000	0.000
89	R	94	LYS	1	0.754	0.852	33.988	-0.055	-0.055	0.000	0.000	0.000	0.000
90	R	95	GLN	0	-0.023	-0.010	37.589	-0.001	-0.001	0.000	0.000	0.000	0.000
91	R	96	VAL	0	0.066	0.035	33.416	-0.002	-0.002	0.000	0.000	0.000	0.000
92	R	97	ASN	0	-0.063	-0.035	36.083	-0.001	-0.001	0.000	0.000	0.000	0.000
93	R	98	ASP	-1	-0.803	-0.887	37.233	0.047	0.047	0.000	0.000	0.000	0.000
94	R	99	GLU	-1	-0.931	-0.963	38.051	0.043	0.043	0.000	0.000	0.000	0.000
95	R	100	ILE	0	-0.009	-0.001	36.240	-0.002	-0.002	0.000	0.000	0.000	0.000
96	R	101	TYR	0	-0.043	-0.020	39.270	-0.002	-0.002	0.000	0.000	0.000	0.000
97	R	102	TYR	0	-0.058	-0.024	41.826	-0.002	-0.002	0.000	0.000	0.000	0.000
98	R	103	GLU	-1	-0.962	-0.966	40.662	0.027	0.027	0.000	0.000	0.000	0.000
99	R	104	TRP	0	-0.134	-0.069	40.625	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:6:LEU)