FMO DATABASE

FMODB ID: 6NZ7Z

Calculation Name: 5KVR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KVR

Chain ID: A

ChEMBL ID:

UniProt ID: P0ACL9

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	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	77
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-464202.748857
FMO2-HF: Nuclear repulsion	434029.155575
FMO2-HF: Total energy	-30173.593282
FMO2-MP2: Total energy	-30263.191436

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(A:-1:ASN)

Summations of interaction energy for fragment #1(A:-1:ASN)

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.
0.555	1.994	-0.013	-0.797	-0.629	0.002

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.014

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	A	1	MET	0	0.005	0.004	3.857	-0.219	1.220	-0.013	-0.797	-0.629	0.002
4	A	2	ALA	0	0.047	0.023	6.053	0.291	0.291	0.000	0.000	0.000	0.000
5	A	3	TYR	0	-0.014	-0.024	7.623	0.023	0.023	0.000	0.000	0.000	0.000
6	A	4	SER	0	-0.008	0.011	11.208	0.059	0.059	0.000	0.000	0.000	0.000
7	A	5	LYS	1	0.933	0.958	13.323	0.188	0.188	0.000	0.000	0.000	0.000
8	A	6	ILE	0	0.056	0.025	16.956	0.012	0.012	0.000	0.000	0.000	0.000
9	A	7	ARG	1	0.946	0.977	19.421	0.102	0.102	0.000	0.000	0.000	0.000
10	A	8	GLN	0	0.036	0.026	21.857	0.008	0.008	0.000	0.000	0.000	0.000
11	A	9	PRO	0	-0.021	-0.004	25.202	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	10	LYS	1	0.906	0.942	25.090	0.094	0.094	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.041	0.012	30.399	0.004	0.004	0.000	0.000	0.000	0.000
14	A	12	SER	0	-0.001	-0.038	33.604	0.003	0.003	0.000	0.000	0.000	0.000
15	A	13	ASP	-1	-0.765	-0.878	30.388	-0.064	-0.064	0.000	0.000	0.000	0.000
16	A	14	VAL	0	-0.048	-0.002	32.397	0.004	0.004	0.000	0.000	0.000	0.000
17	A	15	ILE	0	-0.010	-0.005	35.004	0.003	0.003	0.000	0.000	0.000	0.000
18	A	16	GLU	-1	-0.868	-0.938	36.951	-0.042	-0.042	0.000	0.000	0.000	0.000
19	A	17	GLN	0	0.010	-0.015	32.755	0.004	0.004	0.000	0.000	0.000	0.000
20	A	18	GLN	0	-0.018	0.005	38.125	0.002	0.002	0.000	0.000	0.000	0.000
21	A	19	LEU	0	-0.002	-0.015	40.322	0.002	0.002	0.000	0.000	0.000	0.000
22	A	20	GLU	-1	-0.850	-0.918	39.331	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	21	PHE	0	0.004	0.005	40.956	0.002	0.002	0.000	0.000	0.000	0.000
24	A	22	LEU	0	0.005	-0.001	42.944	0.002	0.002	0.000	0.000	0.000	0.000
25	A	23	ILE	0	-0.025	-0.012	45.836	0.001	0.001	0.000	0.000	0.000	0.000
26	A	24	LEU	0	-0.039	-0.016	42.855	0.002	0.002	0.000	0.000	0.000	0.000
27	A	25	GLU	-1	-0.940	-0.962	45.328	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	26	GLY	0	-0.050	-0.013	48.069	0.001	0.001	0.000	0.000	0.000	0.000
29	A	27	THR	0	-0.041	-0.011	48.756	0.001	0.001	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.033	-0.007	47.580	0.000	0.000	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.868	0.908	51.269	0.020	0.020	0.000	0.000	0.000	0.000
32	A	30	PRO	0	0.024	0.001	53.732	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	31	GLY	0	-0.024	-0.006	55.073	0.001	0.001	0.000	0.000	0.000	0.000
34	A	32	GLU	-1	-0.885	-0.936	53.829	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	33	LYS	1	0.838	0.922	54.380	0.026	0.026	0.000	0.000	0.000	0.000
36	A	34	LEU	0	0.038	0.023	47.711	0.000	0.000	0.000	0.000	0.000	0.000
37	A	35	PRO	0	0.024	0.009	50.302	0.000	0.000	0.000	0.000	0.000	0.000
38	A	36	PRO	0	0.003	0.007	50.490	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	37	GLU	-1	-0.732	-0.830	45.549	-0.048	-0.048	0.000	0.000	0.000	0.000
40	A	38	ARG	1	0.822	0.880	46.852	0.036	0.036	0.000	0.000	0.000	0.000
41	A	39	GLU	-1	-0.790	-0.860	48.504	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	40	LEU	0	0.076	0.035	45.786	0.000	0.000	0.000	0.000	0.000	0.000
43	A	41	ALA	0	-0.007	-0.008	43.364	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	42	LYS	1	0.881	0.927	43.720	0.036	0.036	0.000	0.000	0.000	0.000
45	A	43	GLN	0	-0.043	-0.033	46.132	0.000	0.000	0.000	0.000	0.000	0.000
46	A	44	PHE	0	-0.020	-0.017	41.674	0.001	0.001	0.000	0.000	0.000	0.000
47	A	45	ASP	-1	-0.925	-0.931	41.071	-0.056	-0.056	0.000	0.000	0.000	0.000
48	A	46	VAL	0	-0.001	0.006	38.319	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.030	-0.028	37.446	0.001	0.001	0.000	0.000	0.000	0.000
50	A	48	ARG	1	0.907	0.912	39.459	0.049	0.049	0.000	0.000	0.000	0.000
51	A	49	PRO	0	-0.001	-0.006	38.000	0.002	0.002	0.000	0.000	0.000	0.000
52	A	50	SER	0	0.075	0.058	35.983	0.000	0.000	0.000	0.000	0.000	0.000
53	A	51	LEU	0	0.024	0.022	37.840	0.002	0.002	0.000	0.000	0.000	0.000
54	A	52	ARG	1	0.839	0.892	41.197	0.052	0.052	0.000	0.000	0.000	0.000
55	A	53	GLU	-1	-0.805	-0.859	35.285	-0.061	-0.061	0.000	0.000	0.000	0.000
56	A	54	ALA	0	0.027	0.012	38.723	0.002	0.002	0.000	0.000	0.000	0.000
57	A	55	ILE	0	-0.020	-0.014	39.849	0.003	0.003	0.000	0.000	0.000	0.000
58	A	56	GLN	0	0.006	-0.005	41.546	0.000	0.000	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.845	0.918	34.902	0.055	0.055	0.000	0.000	0.000	0.000
60	A	58	LEU	0	0.036	0.015	40.606	0.002	0.002	0.000	0.000	0.000	0.000
61	A	59	GLU	-1	-0.823	-0.899	43.296	-0.034	-0.034	0.000	0.000	0.000	0.000
62	A	60	ALA	0	-0.048	-0.018	41.808	0.002	0.002	0.000	0.000	0.000	0.000
63	A	61	LYS	1	0.775	0.871	37.983	0.038	0.038	0.000	0.000	0.000	0.000
64	A	62	GLY	0	-0.008	0.011	43.865	0.002	0.002	0.000	0.000	0.000	0.000
65	A	63	LEU	0	0.008	0.006	43.578	0.001	0.001	0.000	0.000	0.000	0.000
66	A	64	LEU	0	-0.040	-0.018	45.708	0.000	0.000	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.034	0.012	48.731	0.000	0.000	0.000	0.000	0.000	0.000
68	A	66	ARG	1	0.790	0.879	46.932	0.037	0.037	0.000	0.000	0.000	0.000
69	A	67	ARG	1	0.950	0.988	52.122	0.024	0.024	0.000	0.000	0.000	0.000
70	A	68	GLN	0	0.022	-0.012	53.092	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	69	GLY	0	0.017	0.023	56.011	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	70	GLY	0	-0.006	-0.006	57.032	0.000	0.000	0.000	0.000	0.000	0.000
73	A	71	GLY	0	-0.018	-0.006	53.609	0.001	0.001	0.000	0.000	0.000	0.000
74	A	72	THR	0	0.001	0.001	48.581	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	PHE	0	-0.035	-0.027	51.969	0.000	0.000	0.000	0.000	0.000	0.000
76	A	74	VAL	0	0.065	0.041	50.065	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.001	0.008	50.669	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:ASN)