FMO DATABASE

FMODB ID: 72YNK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-463859.937084
FMO2-HF: Nuclear repulsion	433686.777991
FMO2-HF: Total energy	-30173.159093
FMO2-MP2: Total energy	-30262.770607

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.
0.779	2.083	0	-0.705	-0.598	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 : -0.006 / q_NPA : -0.018

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

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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].	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	0.025	0.028	3.808	0.037	1.341	-0.705	-0.598	0.003
4	A	2	ALA	0	0.020	0.010	6.310	0.158	0.158	0.000	0.000	0.000
5	A	3	TYR	0	-0.007	-0.008	8.108	0.074	0.074	0.000	0.000	0.000
6	A	4	SER	0	0.002	0.001	11.517	0.051	0.051	0.000	0.000	0.000
7	A	5	LYS	1	0.936	0.956	13.921	0.217	0.217	0.000	0.000	0.000
8	A	6	ILE	0	0.058	0.031	17.535	0.016	0.016	0.000	0.000	0.000
9	A	7	ARG	1	0.937	0.966	19.883	0.103	0.103	0.000	0.000	0.000
10	A	8	GLN	0	0.040	0.026	22.301	0.005	0.005	0.000	0.000	0.000
11	A	9	PRO	0	-0.018	0.000	25.768	-0.002	-0.002	0.000	0.000	0.000
12	A	10	LYS	1	0.995	0.987	26.621	0.111	0.111	0.000	0.000	0.000
13	A	11	LEU	0	0.053	0.025	30.569	0.005	0.005	0.000	0.000	0.000
14	A	12	SER	0	0.008	-0.001	33.719	0.004	0.004	0.000	0.000	0.000
15	A	13	ASP	-1	-0.810	-0.897	31.663	-0.065	-0.065	0.000	0.000	0.000
16	A	14	VAL	0	-0.062	-0.032	32.643	0.004	0.004	0.000	0.000	0.000
17	A	15	ILE	0	-0.033	-0.020	35.188	0.004	0.004	0.000	0.000	0.000
18	A	16	GLU	-1	-0.862	-0.936	37.252	-0.045	-0.045	0.000	0.000	0.000
19	A	17	GLN	0	-0.006	-0.010	33.503	0.002	0.002	0.000	0.000	0.000
20	A	18	GLN	0	0.023	0.027	38.457	0.003	0.003	0.000	0.000	0.000
21	A	19	LEU	0	-0.020	-0.029	40.654	0.003	0.003	0.000	0.000	0.000
22	A	20	GLU	-1	-0.826	-0.896	40.828	-0.032	-0.032	0.000	0.000	0.000
23	A	21	PHE	0	0.006	0.007	41.358	0.002	0.002	0.000	0.000	0.000
24	A	22	LEU	0	0.000	-0.005	43.348	0.002	0.002	0.000	0.000	0.000
25	A	23	ILE	0	-0.034	-0.022	46.289	0.002	0.002	0.000	0.000	0.000
26	A	24	LEU	0	-0.058	-0.025	43.384	0.002	0.002	0.000	0.000	0.000
27	A	25	GLU	-1	-0.934	-0.964	45.659	-0.021	-0.021	0.000	0.000	0.000
28	A	26	GLY	0	-0.068	-0.015	48.357	0.001	0.001	0.000	0.000	0.000
29	A	27	THR	0	-0.036	-0.025	49.105	0.000	0.000	0.000	0.000	0.000
30	A	28	LEU	0	-0.033	-0.007	48.404	0.000	0.000	0.000	0.000	0.000
31	A	29	ARG	1	0.924	0.964	51.825	0.022	0.022	0.000	0.000	0.000
32	A	30	PRO	0	0.025	-0.006	54.438	-0.001	-0.001	0.000	0.000	0.000
33	A	31	GLY	0	-0.028	-0.008	55.495	0.001	0.001	0.000	0.000	0.000
34	A	32	GLU	-1	-0.935	-0.967	53.395	-0.028	-0.028	0.000	0.000	0.000
35	A	33	LYS	1	0.904	0.967	54.357	0.030	0.030	0.000	0.000	0.000
36	A	34	LEU	0	0.041	0.020	48.081	0.000	0.000	0.000	0.000	0.000
37	A	35	PRO	0	0.021	0.008	50.446	0.000	0.000	0.000	0.000	0.000
38	A	36	PRO	0	0.005	-0.001	50.993	-0.001	-0.001	0.000	0.000	0.000
39	A	37	GLU	-1	-0.685	-0.815	45.611	-0.056	-0.056	0.000	0.000	0.000
40	A	38	ARG	1	0.882	0.942	47.415	0.043	0.043	0.000	0.000	0.000
41	A	39	GLU	-1	-0.896	-0.953	48.378	-0.043	-0.043	0.000	0.000	0.000
42	A	40	LEU	0	0.053	0.026	46.105	0.000	0.000	0.000	0.000	0.000
43	A	41	ALA	0	-0.004	-0.008	43.796	-0.001	-0.001	0.000	0.000	0.000
44	A	42	LYS	1	0.949	0.983	44.303	0.043	0.043	0.000	0.000	0.000
45	A	43	GLN	0	-0.052	-0.030	46.091	0.000	0.000	0.000	0.000	0.000
46	A	44	PHE	0	-0.016	-0.025	42.138	0.000	0.000	0.000	0.000	0.000
47	A	45	ASP	-1	-0.930	-0.936	41.380	-0.066	-0.066	0.000	0.000	0.000
48	A	46	VAL	0	-0.008	0.004	38.565	-0.004	-0.004	0.000	0.000	0.000
49	A	47	SER	0	0.000	-0.003	37.224	0.003	0.003	0.000	0.000	0.000
50	A	48	ARG	1	0.935	0.939	39.869	0.056	0.056	0.000	0.000	0.000
51	A	49	PRO	0	-0.016	-0.017	38.194	0.002	0.002	0.000	0.000	0.000
52	A	50	SER	0	0.020	0.016	36.636	0.001	0.001	0.000	0.000	0.000
53	A	51	LEU	0	0.062	0.034	38.173	0.002	0.002	0.000	0.000	0.000
54	A	52	ARG	1	0.783	0.859	41.507	0.062	0.062	0.000	0.000	0.000
55	A	53	GLU	-1	-0.929	-0.967	35.598	-0.071	-0.071	0.000	0.000	0.000
56	A	54	ALA	0	0.042	0.022	39.262	0.002	0.002	0.000	0.000	0.000
57	A	55	ILE	0	-0.040	-0.027	40.278	0.003	0.003	0.000	0.000	0.000
58	A	56	GLN	0	0.008	0.011	41.349	0.001	0.001	0.000	0.000	0.000
59	A	57	ARG	1	0.934	0.974	35.878	0.060	0.060	0.000	0.000	0.000
60	A	58	LEU	0	0.026	0.010	41.244	0.003	0.003	0.000	0.000	0.000
61	A	59	GLU	-1	-0.906	-0.965	43.820	-0.038	-0.038	0.000	0.000	0.000
62	A	60	ALA	0	-0.059	-0.019	42.565	0.002	0.002	0.000	0.000	0.000
63	A	61	LYS	1	0.785	0.874	38.538	0.040	0.040	0.000	0.000	0.000
64	A	62	GLY	0	-0.009	0.015	44.566	0.002	0.002	0.000	0.000	0.000
65	A	63	LEU	0	0.004	0.002	44.210	0.001	0.001	0.000	0.000	0.000
66	A	64	LEU	0	-0.041	-0.023	46.361	0.000	0.000	0.000	0.000	0.000
67	A	65	LEU	0	0.042	0.027	49.387	0.000	0.000	0.000	0.000	0.000
68	A	66	ARG	1	0.876	0.942	47.419	0.042	0.042	0.000	0.000	0.000
69	A	67	ARG	1	0.939	0.981	52.651	0.028	0.028	0.000	0.000	0.000
70	A	68	GLN	0	0.029	0.001	53.739	-0.001	-0.001	0.000	0.000	0.000
71	A	69	GLY	0	-0.011	0.008	56.580	-0.001	-0.001	0.000	0.000	0.000
72	A	70	GLY	0	0.021	0.003	56.205	-0.001	-0.001	0.000	0.000	0.000
73	A	71	GLY	0	-0.062	-0.032	54.709	0.001	0.001	0.000	0.000	0.000
74	A	72	THR	0	0.012	-0.006	49.132	0.000	0.000	0.000	0.000	0.000
75	A	73	PHE	0	-0.055	-0.035	52.541	0.000	0.000	0.000	0.000	0.000
76	A	74	VAL	0	0.052	0.040	50.385	-0.001	-0.001	0.000	0.000	0.000
77	A	75	GLN	0	0.019	0.017	51.394	0.001	0.001	0.000	0.000	0.000

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