FMO DATABASE

FMODB ID: N9NVQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-828299.180544
FMO2-HF: Nuclear repulsion	785135.202024
FMO2-HF: Total energy	-43163.97852
FMO2-MP2: Total energy	-43290.195887

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.
-2.037	0.602	0.352	-1.288	-1.701	-0.006

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 : -0.026 / q_NPA : -0.023

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	-0.003	-0.008	2.843	-3.329	-0.812	0.353	-1.283	-1.586	-0.006
4	R	9	LYS	1	0.970	0.984	4.718	0.772	0.894	-0.001	-0.005	-0.115	0.000
5	R	10	VAL	0	0.011	0.001	6.463	-0.038	-0.038	0.000	0.000	0.000	0.000
6	R	11	PRO	0	-0.020	0.000	9.504	0.060	0.060	0.000	0.000	0.000	0.000
7	R	12	ASP	-1	-0.781	-0.885	12.422	-0.057	-0.057	0.000	0.000	0.000	0.000
8	R	13	ASP	-1	-0.950	-0.969	16.050	-0.046	-0.046	0.000	0.000	0.000	0.000
9	R	14	LYS	1	0.862	0.905	18.024	0.006	0.006	0.000	0.000	0.000	0.000
10	R	15	SER	0	-0.023	-0.042	18.440	0.012	0.012	0.000	0.000	0.000	0.000
11	R	16	ARG	1	0.815	0.905	14.829	0.039	0.039	0.000	0.000	0.000	0.000
12	R	17	PHE	0	0.014	0.018	17.973	0.007	0.007	0.000	0.000	0.000	0.000
13	R	18	GLU	-1	-0.800	-0.885	21.095	0.021	0.021	0.000	0.000	0.000	0.000
14	R	19	ILE	0	-0.025	-0.012	17.962	0.008	0.008	0.000	0.000	0.000	0.000
15	R	20	GLU	-1	-0.752	-0.871	16.329	0.033	0.033	0.000	0.000	0.000	0.000
16	R	21	LEU	0	-0.006	0.014	20.511	0.004	0.004	0.000	0.000	0.000	0.000
17	R	22	GLU	-1	-0.859	-0.944	23.542	0.068	0.068	0.000	0.000	0.000	0.000
18	R	23	PHE	0	-0.044	-0.024	18.399	0.009	0.009	0.000	0.000	0.000	0.000
19	R	24	VAL	0	0.039	0.007	22.406	0.004	0.004	0.000	0.000	0.000	0.000
20	R	25	GLN	0	0.026	0.000	24.636	-0.003	-0.003	0.000	0.000	0.000	0.000
21	R	26	MET	0	-0.027	-0.011	23.422	-0.002	-0.002	0.000	0.000	0.000	0.000
22	R	27	LEU	0	-0.019	-0.010	22.053	0.002	0.002	0.000	0.000	0.000	0.000
23	R	28	SER	0	-0.019	-0.006	26.063	-0.006	-0.006	0.000	0.000	0.000	0.000
24	R	29	ASN	0	-0.047	-0.018	28.685	-0.001	-0.001	0.000	0.000	0.000	0.000
25	R	30	PRO	0	0.075	0.032	28.858	0.006	0.006	0.000	0.000	0.000	0.000
26	R	31	TRP	0	0.036	0.007	29.594	0.005	0.005	0.000	0.000	0.000	0.000
27	R	32	TYR	0	-0.007	0.003	20.762	0.009	0.009	0.000	0.000	0.000	0.000
28	R	33	LEU	0	0.040	0.017	24.870	0.014	0.014	0.000	0.000	0.000	0.000
29	R	34	ASN	0	0.006	0.012	25.656	0.013	0.013	0.000	0.000	0.000	0.000
30	R	35	PHE	0	-0.024	-0.012	21.265	0.008	0.008	0.000	0.000	0.000	0.000
31	R	36	LEU	0	-0.005	0.003	19.195	0.015	0.015	0.000	0.000	0.000	0.000
32	R	37	ALA	0	-0.003	-0.005	21.610	0.018	0.018	0.000	0.000	0.000	0.000
33	R	38	GLN	0	-0.058	-0.029	23.511	0.011	0.011	0.000	0.000	0.000	0.000
34	R	39	HIS	0	-0.110	-0.055	19.679	0.016	0.016	0.000	0.000	0.000	0.000
35	R	40	LYS	1	0.832	0.910	19.202	-0.151	-0.151	0.000	0.000	0.000	0.000
36	R	41	TYR	0	0.049	0.021	15.034	0.025	0.025	0.000	0.000	0.000	0.000
37	R	42	PHE	0	-0.042	-0.029	17.302	-0.002	-0.002	0.000	0.000	0.000	0.000
38	R	43	GLU	-1	-0.872	-0.927	17.658	0.170	0.170	0.000	0.000	0.000	0.000
39	R	44	ASP	-1	-0.886	-0.930	12.246	0.344	0.344	0.000	0.000	0.000	0.000
40	R	45	GLU	-1	-0.943	-0.970	12.856	0.052	0.052	0.000	0.000	0.000	0.000
41	R	46	ALA	0	0.000	-0.013	10.127	-0.037	-0.037	0.000	0.000	0.000	0.000
42	R	47	PHE	0	-0.019	-0.007	12.131	-0.036	-0.036	0.000	0.000	0.000	0.000
43	R	48	LEU	0	-0.019	-0.014	15.172	-0.029	-0.029	0.000	0.000	0.000	0.000
44	R	49	GLN	0	-0.030	-0.025	13.605	-0.012	-0.012	0.000	0.000	0.000	0.000
45	R	50	TYR	0	-0.076	-0.054	14.037	-0.010	-0.010	0.000	0.000	0.000	0.000
46	R	51	LEU	0	-0.004	0.001	15.761	-0.013	-0.013	0.000	0.000	0.000	0.000
47	R	52	GLU	-1	-0.929	-0.966	17.829	-0.005	-0.005	0.000	0.000	0.000	0.000
48	R	53	TYR	0	0.021	0.021	16.087	-0.020	-0.020	0.000	0.000	0.000	0.000
49	R	54	MET	0	-0.018	0.000	18.200	-0.005	-0.005	0.000	0.000	0.000	0.000
50	R	55	GLU	-1	-0.808	-0.877	20.999	0.032	0.032	0.000	0.000	0.000	0.000
51	R	56	TYR	0	-0.029	-0.004	19.907	-0.008	-0.008	0.000	0.000	0.000	0.000
52	R	57	TRP	0	-0.048	-0.034	19.866	-0.003	-0.003	0.000	0.000	0.000	0.000
53	R	58	ARG	1	0.811	0.881	25.271	-0.031	-0.031	0.000	0.000	0.000	0.000
54	R	59	GLU	-1	-0.917	-0.933	26.773	-0.004	-0.004	0.000	0.000	0.000	0.000
55	R	60	PRO	0	-0.005	0.010	28.777	0.003	0.003	0.000	0.000	0.000	0.000
56	R	61	GLU	-1	-0.877	-0.968	28.969	-0.007	-0.007	0.000	0.000	0.000	0.000
57	R	62	TYR	0	-0.033	-0.010	23.246	0.000	0.000	0.000	0.000	0.000	0.000
58	R	63	VAL	0	0.009	0.001	28.175	0.004	0.004	0.000	0.000	0.000	0.000
59	R	64	LYS	1	0.883	0.948	30.254	-0.004	-0.004	0.000	0.000	0.000	0.000
60	R	65	PHE	0	-0.087	-0.051	28.819	0.000	0.000	0.000	0.000	0.000	0.000
61	R	66	ILE	0	-0.047	-0.003	27.677	0.004	0.004	0.000	0.000	0.000	0.000
62	R	67	ILE	0	0.000	0.007	30.284	-0.002	-0.002	0.000	0.000	0.000	0.000
63	R	68	TYR	0	-0.005	-0.013	30.920	-0.002	-0.002	0.000	0.000	0.000	0.000
64	R	69	PRO	0	0.056	0.025	31.691	0.002	0.002	0.000	0.000	0.000	0.000
65	R	70	THR	0	0.009	-0.005	32.519	-0.001	-0.001	0.000	0.000	0.000	0.000
66	R	71	CYS	0	-0.002	0.033	27.519	-0.001	-0.001	0.000	0.000	0.000	0.000
67	R	72	LEU	0	0.054	0.027	28.775	0.002	0.002	0.000	0.000	0.000	0.000
68	R	73	HIS	0	0.025	0.012	29.616	-0.001	-0.001	0.000	0.000	0.000	0.000
69	R	74	MET	0	0.013	-0.006	28.820	0.001	0.001	0.000	0.000	0.000	0.000
70	R	75	LEU	0	-0.019	-0.002	23.697	0.005	0.005	0.000	0.000	0.000	0.000
71	R	76	THR	0	-0.049	-0.044	26.785	0.000	0.000	0.000	0.000	0.000	0.000
72	R	77	LEU	0	-0.030	-0.011	29.046	-0.001	-0.001	0.000	0.000	0.000	0.000
73	R	78	LEU	0	-0.015	0.010	22.899	0.002	0.002	0.000	0.000	0.000	0.000
74	R	79	LYS	1	0.861	0.919	24.135	-0.030	-0.030	0.000	0.000	0.000	0.000
75	R	80	ASN	0	-0.026	0.003	26.105	-0.001	-0.001	0.000	0.000	0.000	0.000
76	R	81	PRO	0	0.034	0.003	24.757	0.005	0.005	0.000	0.000	0.000	0.000
77	R	82	GLN	0	-0.035	-0.029	26.455	0.004	0.004	0.000	0.000	0.000	0.000
78	R	83	PHE	0	0.069	0.032	28.194	0.002	0.002	0.000	0.000	0.000	0.000
79	R	84	ARG	1	0.905	0.955	22.187	-0.091	-0.091	0.000	0.000	0.000	0.000
80	R	85	ASN	0	-0.055	-0.025	26.844	0.012	0.012	0.000	0.000	0.000	0.000
81	R	86	ASP	-1	-0.798	-0.898	28.182	0.074	0.074	0.000	0.000	0.000	0.000
82	R	87	ILE	0	-0.021	0.011	26.066	-0.002	-0.002	0.000	0.000	0.000	0.000
83	R	88	SER	0	0.024	0.001	26.773	0.007	0.007	0.000	0.000	0.000	0.000
84	R	89	ARG	1	0.786	0.904	28.572	-0.069	-0.069	0.000	0.000	0.000	0.000
85	R	90	ALA	0	0.026	0.011	32.352	0.000	0.000	0.000	0.000	0.000	0.000
86	R	91	ASP	-1	-0.884	-0.951	34.225	0.068	0.068	0.000	0.000	0.000	0.000
87	R	92	LEU	0	0.054	0.024	32.739	-0.003	-0.003	0.000	0.000	0.000	0.000
88	R	93	SER	0	0.030	0.018	32.375	-0.001	-0.001	0.000	0.000	0.000	0.000
89	R	94	LYS	1	0.809	0.881	34.051	-0.054	-0.054	0.000	0.000	0.000	0.000
90	R	95	GLN	0	-0.031	-0.014	37.487	-0.002	-0.002	0.000	0.000	0.000	0.000
91	R	96	VAL	0	0.067	0.041	33.391	-0.003	-0.003	0.000	0.000	0.000	0.000
92	R	97	ASN	0	-0.054	-0.031	35.799	-0.001	-0.001	0.000	0.000	0.000	0.000
93	R	98	ASP	-1	-0.853	-0.919	37.031	0.049	0.049	0.000	0.000	0.000	0.000
94	R	99	GLU	-1	-0.927	-0.962	38.468	0.043	0.043	0.000	0.000	0.000	0.000
95	R	100	ILE	0	-0.033	-0.008	36.191	-0.002	-0.002	0.000	0.000	0.000	0.000
96	R	101	TYR	0	-0.033	-0.013	39.307	-0.003	-0.003	0.000	0.000	0.000	0.000
97	R	102	TYR	0	-0.054	0.012	41.659	-0.003	-0.003	0.000	0.000	0.000	0.000
98	R	103	GLU	-1	-0.974	-0.975	40.813	0.029	0.029	0.000	0.000	0.000	0.000
99	R	104	TRP	0	-0.144	-0.113	40.070	-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)