FMO DATABASE

FMODB ID: 2J4RR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-463678.847368
FMO2-HF: Nuclear repulsion	433505.392312
FMO2-HF: Total energy	-30173.455056
FMO2-MP2: Total energy	-30263.07369

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.
0.677	2.052	-0.009	-0.803	-0.563	0.003

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 : -0.014 / q_NPA : -0.027

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	0.018	0.027	3.808	-0.089	1.286	-0.009	-0.803	-0.563	0.003
4	A	2	ALA	0	0.028	0.011	6.311	0.196	0.196	0.000	0.000	0.000	0.000
5	A	3	TYR	0	-0.006	-0.008	8.110	0.055	0.055	0.000	0.000	0.000	0.000
6	A	4	SER	0	0.014	0.007	11.518	0.044	0.044	0.000	0.000	0.000	0.000
7	A	5	LYS	1	0.932	0.954	13.922	0.233	0.233	0.000	0.000	0.000	0.000
8	A	6	ILE	0	0.052	0.027	17.537	0.012	0.012	0.000	0.000	0.000	0.000
9	A	7	ARG	1	0.938	0.968	19.885	0.119	0.119	0.000	0.000	0.000	0.000
10	A	8	GLN	0	0.043	0.027	22.303	0.005	0.005	0.000	0.000	0.000	0.000
11	A	9	PRO	0	-0.022	-0.002	25.769	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	10	LYS	1	0.991	0.993	26.433	0.117	0.117	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.039	0.019	30.571	0.005	0.005	0.000	0.000	0.000	0.000
14	A	12	SER	0	-0.016	-0.038	33.721	0.003	0.003	0.000	0.000	0.000	0.000
15	A	13	ASP	-1	-0.826	-0.915	31.101	-0.077	-0.077	0.000	0.000	0.000	0.000
16	A	14	VAL	0	-0.052	-0.026	32.618	0.004	0.004	0.000	0.000	0.000	0.000
17	A	15	ILE	0	-0.033	-0.020	35.190	0.004	0.004	0.000	0.000	0.000	0.000
18	A	16	GLU	-1	-0.840	-0.922	37.510	-0.052	-0.052	0.000	0.000	0.000	0.000
19	A	17	GLN	0	0.004	-0.003	33.409	0.002	0.002	0.000	0.000	0.000	0.000
20	A	18	GLN	0	0.009	0.018	38.458	0.002	0.002	0.000	0.000	0.000	0.000
21	A	19	LEU	0	-0.013	-0.025	40.655	0.003	0.003	0.000	0.000	0.000	0.000
22	A	20	GLU	-1	-0.849	-0.915	40.054	-0.041	-0.041	0.000	0.000	0.000	0.000
23	A	21	PHE	0	0.000	0.008	41.339	0.002	0.002	0.000	0.000	0.000	0.000
24	A	22	LEU	0	0.001	-0.003	43.350	0.002	0.002	0.000	0.000	0.000	0.000
25	A	23	ILE	0	-0.025	-0.019	46.294	0.002	0.002	0.000	0.000	0.000	0.000
26	A	24	LEU	0	-0.047	-0.021	43.371	0.002	0.002	0.000	0.000	0.000	0.000
27	A	25	GLU	-1	-0.931	-0.959	45.618	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	26	GLY	0	-0.067	-0.017	48.358	0.002	0.002	0.000	0.000	0.000	0.000
29	A	27	THR	0	-0.028	-0.015	49.138	0.001	0.001	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.038	-0.006	48.218	0.000	0.000	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.886	0.936	51.826	0.025	0.025	0.000	0.000	0.000	0.000
32	A	30	PRO	0	0.031	-0.006	54.520	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	31	GLY	0	-0.031	-0.010	55.498	0.001	0.001	0.000	0.000	0.000	0.000
34	A	32	GLU	-1	-0.912	-0.954	53.946	-0.030	-0.030	0.000	0.000	0.000	0.000
35	A	33	LYS	1	0.913	0.969	54.359	0.031	0.031	0.000	0.000	0.000	0.000
36	A	34	LEU	0	0.043	0.024	48.088	0.000	0.000	0.000	0.000	0.000	0.000
37	A	35	PRO	0	0.015	0.004	50.431	0.001	0.001	0.000	0.000	0.000	0.000
38	A	36	PRO	0	0.001	-0.001	50.995	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	37	GLU	-1	-0.708	-0.814	45.996	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	38	ARG	1	0.828	0.894	47.563	0.040	0.040	0.000	0.000	0.000	0.000
41	A	39	GLU	-1	-0.770	-0.863	48.567	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	40	LEU	0	0.056	0.029	46.119	0.000	0.000	0.000	0.000	0.000	0.000
43	A	41	ALA	0	-0.007	-0.009	44.015	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	42	LYS	1	0.889	0.939	44.305	0.039	0.039	0.000	0.000	0.000	0.000
45	A	43	GLN	0	-0.054	-0.028	46.093	0.000	0.000	0.000	0.000	0.000	0.000
46	A	44	PHE	0	-0.021	-0.032	42.181	0.000	0.000	0.000	0.000	0.000	0.000
47	A	45	ASP	-1	-0.920	-0.929	41.602	-0.060	-0.060	0.000	0.000	0.000	0.000
48	A	46	VAL	0	-0.018	-0.003	38.560	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	47	SER	0	-0.024	-0.021	38.083	0.001	0.001	0.000	0.000	0.000	0.000
50	A	48	ARG	1	0.912	0.910	40.089	0.054	0.054	0.000	0.000	0.000	0.000
51	A	49	PRO	0	0.002	-0.008	38.395	0.002	0.002	0.000	0.000	0.000	0.000
52	A	50	SER	0	0.068	0.054	36.578	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	51	LEU	0	0.030	0.019	38.363	0.001	0.001	0.000	0.000	0.000	0.000
54	A	52	ARG	1	0.834	0.886	41.520	0.060	0.060	0.000	0.000	0.000	0.000
55	A	53	GLU	-1	-0.829	-0.881	35.811	-0.076	-0.076	0.000	0.000	0.000	0.000
56	A	54	ALA	0	0.035	0.019	39.211	0.001	0.001	0.000	0.000	0.000	0.000
57	A	55	ILE	0	-0.042	-0.026	40.280	0.003	0.003	0.000	0.000	0.000	0.000
58	A	56	GLN	0	0.001	0.006	41.899	0.000	0.000	0.000	0.000	0.000	0.000
59	A	57	ARG	1	0.874	0.933	35.811	0.069	0.069	0.000	0.000	0.000	0.000
60	A	58	LEU	0	0.026	0.012	41.246	0.002	0.002	0.000	0.000	0.000	0.000
61	A	59	GLU	-1	-0.826	-0.912	43.822	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	60	ALA	0	-0.054	-0.014	42.567	0.002	0.002	0.000	0.000	0.000	0.000
63	A	61	LYS	1	0.779	0.872	38.694	0.049	0.049	0.000	0.000	0.000	0.000
64	A	62	GLY	0	-0.010	0.013	44.568	0.002	0.002	0.000	0.000	0.000	0.000
65	A	63	LEU	0	-0.004	0.001	44.195	0.002	0.002	0.000	0.000	0.000	0.000
66	A	64	LEU	0	-0.036	-0.022	46.319	0.001	0.001	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.039	0.024	49.389	0.000	0.000	0.000	0.000	0.000	0.000
68	A	66	ARG	1	0.798	0.884	47.513	0.044	0.044	0.000	0.000	0.000	0.000
69	A	67	ARG	1	0.930	0.979	52.653	0.030	0.030	0.000	0.000	0.000	0.000
70	A	68	GLN	0	0.034	0.005	54.004	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	69	GLY	0	-0.012	0.007	56.789	0.000	0.000	0.000	0.000	0.000	0.000
72	A	70	GLY	0	0.025	0.005	56.416	0.000	0.000	0.000	0.000	0.000	0.000
73	A	71	GLY	0	-0.059	-0.029	54.710	0.001	0.001	0.000	0.000	0.000	0.000
74	A	72	THR	0	0.013	-0.005	49.120	0.000	0.000	0.000	0.000	0.000	0.000
75	A	73	PHE	0	-0.055	-0.037	52.543	0.000	0.000	0.000	0.000	0.000	0.000
76	A	74	VAL	0	0.055	0.039	50.363	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	75	GLN	0	0.012	0.016	51.394	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)