FMO DATABASE

FMODB ID: 8598Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-828713.837644
FMO2-HF: Nuclear repulsion	785551.139662
FMO2-HF: Total energy	-43162.697982
FMO2-MP2: Total energy	-43289.022086

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.
-1.267	1.124	0.155	-1.07	-1.476	-0.001

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 : -0.016 / q_NPA : -0.019

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	-0.017	-0.018	3.083	-2.717	-0.454	0.156	-1.065	-1.354	-0.001
4	R	9	LYS	1	0.980	0.992	4.781	0.767	0.895	-0.001	-0.005	-0.122	0.000
5	R	10	VAL	0	0.007	-0.001	6.638	-0.059	-0.059	0.000	0.000	0.000	0.000
6	R	11	PRO	0	-0.020	-0.005	9.595	0.059	0.059	0.000	0.000	0.000	0.000
7	R	12	ASP	-1	-0.775	-0.831	12.541	-0.051	-0.051	0.000	0.000	0.000	0.000
8	R	13	ASP	-1	-0.926	-0.969	16.180	-0.031	-0.031	0.000	0.000	0.000	0.000
9	R	14	LYS	1	0.982	0.985	18.112	0.012	0.012	0.000	0.000	0.000	0.000
10	R	15	SER	0	-0.030	-0.083	18.493	0.010	0.010	0.000	0.000	0.000	0.000
11	R	16	ARG	1	0.867	0.948	13.879	0.031	0.031	0.000	0.000	0.000	0.000
12	R	17	PHE	0	0.023	0.020	17.974	0.008	0.008	0.000	0.000	0.000	0.000
13	R	18	GLU	-1	-0.893	-0.954	21.064	0.030	0.030	0.000	0.000	0.000	0.000
14	R	19	ILE	0	-0.033	-0.012	17.722	0.008	0.008	0.000	0.000	0.000	0.000
15	R	20	GLU	-1	-0.811	-0.915	16.572	0.058	0.058	0.000	0.000	0.000	0.000
16	R	21	LEU	0	-0.026	0.010	20.407	0.003	0.003	0.000	0.000	0.000	0.000
17	R	22	GLU	-1	-0.871	-0.951	23.538	0.080	0.080	0.000	0.000	0.000	0.000
18	R	23	PHE	0	-0.021	-0.017	18.700	0.009	0.009	0.000	0.000	0.000	0.000
19	R	24	VAL	0	0.039	0.007	22.262	0.004	0.004	0.000	0.000	0.000	0.000
20	R	25	GLN	0	0.072	0.017	24.458	-0.006	-0.006	0.000	0.000	0.000	0.000
21	R	26	MET	0	-0.026	0.023	23.145	-0.002	-0.002	0.000	0.000	0.000	0.000
22	R	27	LEU	0	-0.036	-0.011	22.009	0.002	0.002	0.000	0.000	0.000	0.000
23	R	28	SER	0	-0.052	-0.060	25.957	-0.007	-0.007	0.000	0.000	0.000	0.000
24	R	29	ASN	0	-0.025	0.003	28.773	-0.002	-0.002	0.000	0.000	0.000	0.000
25	R	30	PRO	0	0.070	0.032	28.878	0.007	0.007	0.000	0.000	0.000	0.000
26	R	31	TRP	0	0.017	0.007	29.619	0.006	0.006	0.000	0.000	0.000	0.000
27	R	32	TYR	0	-0.005	0.005	21.015	0.011	0.011	0.000	0.000	0.000	0.000
28	R	33	LEU	0	0.036	0.018	25.095	0.016	0.016	0.000	0.000	0.000	0.000
29	R	34	ASN	0	0.034	0.024	25.681	0.015	0.015	0.000	0.000	0.000	0.000
30	R	35	PHE	0	-0.037	-0.020	21.078	0.008	0.008	0.000	0.000	0.000	0.000
31	R	36	LEU	0	-0.007	0.003	19.509	0.017	0.017	0.000	0.000	0.000	0.000
32	R	37	ALA	0	-0.007	-0.014	21.639	0.020	0.020	0.000	0.000	0.000	0.000
33	R	38	GLN	0	-0.057	-0.027	23.541	0.011	0.011	0.000	0.000	0.000	0.000
34	R	39	HIS	0	-0.105	-0.057	19.654	0.017	0.017	0.000	0.000	0.000	0.000
35	R	40	LYS	1	0.919	0.966	19.239	-0.171	-0.171	0.000	0.000	0.000	0.000
36	R	41	TYR	0	0.036	0.020	15.391	0.029	0.029	0.000	0.000	0.000	0.000
37	R	42	PHE	0	-0.031	-0.014	17.319	0.001	0.001	0.000	0.000	0.000	0.000
38	R	43	GLU	-1	-0.944	-0.974	17.424	0.186	0.186	0.000	0.000	0.000	0.000
39	R	44	ASP	-1	-0.915	-0.943	12.259	0.424	0.424	0.000	0.000	0.000	0.000
40	R	45	GLU	-1	-0.919	-0.963	12.450	0.092	0.092	0.000	0.000	0.000	0.000
41	R	46	ALA	0	-0.012	-0.017	10.567	-0.042	-0.042	0.000	0.000	0.000	0.000
42	R	47	PHE	0	-0.044	-0.016	12.415	-0.032	-0.032	0.000	0.000	0.000	0.000
43	R	48	LEU	0	-0.025	-0.019	15.379	-0.033	-0.033	0.000	0.000	0.000	0.000
44	R	49	GLN	0	0.048	0.017	13.853	-0.009	-0.009	0.000	0.000	0.000	0.000
45	R	50	TYR	0	-0.086	-0.035	14.026	-0.013	-0.013	0.000	0.000	0.000	0.000
46	R	51	LEU	0	-0.014	0.000	15.679	-0.015	-0.015	0.000	0.000	0.000	0.000
47	R	52	GLU	-1	-0.963	-1.003	17.960	0.012	0.012	0.000	0.000	0.000	0.000
48	R	53	TYR	0	-0.001	0.003	15.992	-0.022	-0.022	0.000	0.000	0.000	0.000
49	R	54	MET	0	-0.010	0.001	18.136	-0.008	-0.008	0.000	0.000	0.000	0.000
50	R	55	GLU	-1	-0.857	-0.914	20.945	0.045	0.045	0.000	0.000	0.000	0.000
51	R	56	TYR	0	-0.029	-0.010	19.450	-0.009	-0.009	0.000	0.000	0.000	0.000
52	R	57	TRP	0	-0.032	-0.032	20.102	-0.005	-0.005	0.000	0.000	0.000	0.000
53	R	58	ARG	1	0.803	0.877	25.245	-0.043	-0.043	0.000	0.000	0.000	0.000
54	R	59	GLU	-1	-0.886	-0.917	26.763	0.003	0.003	0.000	0.000	0.000	0.000
55	R	60	PRO	0	-0.026	-0.002	28.745	0.003	0.003	0.000	0.000	0.000	0.000
56	R	61	GLU	-1	-0.882	-0.969	29.158	0.001	0.001	0.000	0.000	0.000	0.000
57	R	62	TYR	0	-0.027	-0.010	23.101	-0.001	-0.001	0.000	0.000	0.000	0.000
58	R	63	VAL	0	0.013	0.004	28.177	0.004	0.004	0.000	0.000	0.000	0.000
59	R	64	LYS	1	0.870	0.942	30.243	-0.007	-0.007	0.000	0.000	0.000	0.000
60	R	65	PHE	0	-0.076	-0.046	28.754	-0.001	-0.001	0.000	0.000	0.000	0.000
61	R	66	ILE	0	-0.058	-0.005	27.619	0.003	0.003	0.000	0.000	0.000	0.000
62	R	67	ILE	0	0.013	0.001	30.161	-0.003	-0.003	0.000	0.000	0.000	0.000
63	R	68	TYR	0	-0.020	-0.014	30.852	-0.003	-0.003	0.000	0.000	0.000	0.000
64	R	69	PRO	0	0.049	0.022	31.514	0.003	0.003	0.000	0.000	0.000	0.000
65	R	70	THR	0	0.010	-0.004	32.325	-0.001	-0.001	0.000	0.000	0.000	0.000
66	R	71	CYS	0	0.010	0.043	27.374	-0.001	-0.001	0.000	0.000	0.000	0.000
67	R	72	LEU	0	0.064	0.026	28.530	0.003	0.003	0.000	0.000	0.000	0.000
68	R	73	HIS	0	0.034	0.019	29.485	-0.001	-0.001	0.000	0.000	0.000	0.000
69	R	74	MET	0	0.020	0.007	28.496	0.001	0.001	0.000	0.000	0.000	0.000
70	R	75	LEU	0	-0.027	0.000	23.784	0.006	0.006	0.000	0.000	0.000	0.000
71	R	76	THR	0	-0.079	-0.061	26.940	0.000	0.000	0.000	0.000	0.000	0.000
72	R	77	LEU	0	-0.022	-0.011	29.218	-0.001	-0.001	0.000	0.000	0.000	0.000
73	R	78	LEU	0	-0.001	-0.004	22.888	0.002	0.002	0.000	0.000	0.000	0.000
74	R	79	LYS	1	0.840	0.924	24.337	-0.044	-0.044	0.000	0.000	0.000	0.000
75	R	80	ASN	0	-0.017	0.006	26.375	-0.001	-0.001	0.000	0.000	0.000	0.000
76	R	81	PRO	0	0.021	-0.007	25.017	0.005	0.005	0.000	0.000	0.000	0.000
77	R	82	GLN	0	-0.037	-0.023	26.695	0.004	0.004	0.000	0.000	0.000	0.000
78	R	83	PHE	0	0.062	0.043	28.098	0.002	0.002	0.000	0.000	0.000	0.000
79	R	84	ARG	1	0.948	0.991	22.778	-0.112	-0.112	0.000	0.000	0.000	0.000
80	R	85	ASN	0	0.004	-0.011	26.857	0.012	0.012	0.000	0.000	0.000	0.000
81	R	86	ASP	-1	-0.877	-0.949	28.200	0.081	0.081	0.000	0.000	0.000	0.000
82	R	87	ILE	0	-0.026	-0.009	25.909	-0.003	-0.003	0.000	0.000	0.000	0.000
83	R	88	SER	0	-0.008	-0.012	27.060	0.010	0.010	0.000	0.000	0.000	0.000
84	R	89	ARG	1	0.839	0.945	28.599	-0.079	-0.079	0.000	0.000	0.000	0.000
85	R	90	ALA	0	0.022	0.010	32.380	0.000	0.000	0.000	0.000	0.000	0.000
86	R	91	ASP	-1	-0.877	-0.951	34.256	0.075	0.075	0.000	0.000	0.000	0.000
87	R	92	LEU	0	0.046	0.026	32.414	-0.003	-0.003	0.000	0.000	0.000	0.000
88	R	93	SER	0	0.032	0.013	32.429	0.000	0.000	0.000	0.000	0.000	0.000
89	R	94	LYS	1	0.876	0.921	34.076	-0.060	-0.060	0.000	0.000	0.000	0.000
90	R	95	GLN	0	-0.044	-0.016	37.513	-0.002	-0.002	0.000	0.000	0.000	0.000
91	R	96	VAL	0	0.073	0.043	33.329	-0.003	-0.003	0.000	0.000	0.000	0.000
92	R	97	ASN	0	-0.035	-0.030	35.802	-0.003	-0.003	0.000	0.000	0.000	0.000
93	R	98	ASP	-1	-0.896	-0.955	37.053	0.054	0.054	0.000	0.000	0.000	0.000
94	R	99	GLU	-1	-0.941	-0.973	38.600	0.049	0.049	0.000	0.000	0.000	0.000
95	R	100	ILE	0	-0.034	-0.006	36.136	-0.003	-0.003	0.000	0.000	0.000	0.000
96	R	101	TYR	0	-0.080	-0.041	39.322	-0.004	-0.004	0.000	0.000	0.000	0.000
97	R	102	TYR	0	-0.061	-0.029	41.678	-0.003	-0.003	0.000	0.000	0.000	0.000
98	R	103	GLU	-1	-0.986	-0.984	40.589	0.034	0.034	0.000	0.000	0.000	0.000
99	R	104	TRP	0	-0.093	-0.040	39.745	-0.004	-0.004	0.000	0.000	0.000	0.000

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