FMO DATABASE

FMODB ID: Z6VYN

Calculation Name: 5VJI-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VJI

Chain ID: C

ChEMBL ID:

UniProt ID: Q8R0W1

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	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	62
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-272134.452099
FMO2-HF: Nuclear repulsion	247882.266929
FMO2-HF: Total energy	-24252.18517
FMO2-MP2: Total energy	-24323.799259

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(C:2:ASN)

Summations of interaction energy for fragment #1(C:2: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.
-5.939	-2.116	0.501	-1.418	-2.905	0.006

Interaction energy analysis for fragmet #1(C:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.013

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].	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	C	4	LEU	0	0.038	0.026	3.885	-3.228	-1.840	-0.002	-0.568	-0.818	0.001
4	C	5	VAL	0	0.027	0.005	2.890	-1.150	-0.128	0.153	-0.293	-0.882	0.000
5	C	6	VAL	0	-0.006	0.000	2.964	-1.658	-0.366	0.351	-0.553	-1.090	0.005
6	C	7	LEU	0	0.023	0.024	5.775	-0.734	-0.613	-0.001	-0.004	-0.115	0.000
7	C	8	HIS	0	0.014	0.007	8.044	-0.169	-0.169	0.000	0.000	0.000	0.000
8	C	9	LYS	1	0.925	0.959	5.530	1.964	1.964	0.000	0.000	0.000	0.000
9	C	10	SER	0	-0.028	-0.017	9.558	-0.078	-0.078	0.000	0.000	0.000	0.000
10	C	11	GLY	0	0.027	0.016	11.630	-0.009	-0.009	0.000	0.000	0.000	0.000
11	C	12	LEU	0	0.032	0.005	11.403	-0.008	-0.008	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.007	0.018	10.231	0.026	0.026	0.000	0.000	0.000	0.000
13	C	14	GLU	-1	-0.816	-0.895	13.259	0.194	0.194	0.000	0.000	0.000	0.000
14	C	15	ILE	0	0.077	0.033	16.430	-0.020	-0.020	0.000	0.000	0.000	0.000
15	C	16	THR	0	-0.027	-0.014	15.394	-0.002	-0.002	0.000	0.000	0.000	0.000
16	C	17	LEU	0	-0.061	-0.035	15.036	-0.024	-0.024	0.000	0.000	0.000	0.000
17	C	18	LYS	1	0.857	0.915	18.439	-0.246	-0.246	0.000	0.000	0.000	0.000
18	C	19	THR	0	-0.004	-0.008	20.641	-0.029	-0.029	0.000	0.000	0.000	0.000
19	C	20	LYS	1	0.930	0.957	17.499	-0.695	-0.695	0.000	0.000	0.000	0.000
20	C	21	GLU	-1	-0.762	-0.820	22.167	0.237	0.237	0.000	0.000	0.000	0.000
21	C	22	LEU	0	0.025	0.017	24.382	-0.021	-0.021	0.000	0.000	0.000	0.000
22	C	23	ILE	0	-0.012	-0.008	23.675	-0.014	-0.014	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.838	0.885	25.797	-0.269	-0.269	0.000	0.000	0.000	0.000
24	C	25	GLN	0	-0.070	-0.051	27.756	-0.024	-0.024	0.000	0.000	0.000	0.000
25	C	26	ASN	0	0.017	0.011	30.136	-0.022	-0.022	0.000	0.000	0.000	0.000
26	C	27	GLN	0	-0.039	-0.033	27.835	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	28	ALA	0	-0.018	0.000	32.014	-0.009	-0.009	0.000	0.000	0.000	0.000
28	C	29	THR	0	0.045	-0.002	33.902	-0.007	-0.007	0.000	0.000	0.000	0.000
29	C	30	GLN	0	-0.108	-0.056	35.294	-0.007	-0.007	0.000	0.000	0.000	0.000
30	C	31	ALA	0	0.015	0.007	36.398	-0.009	-0.009	0.000	0.000	0.000	0.000
31	C	32	GLU	-1	-0.907	-0.938	37.470	0.144	0.144	0.000	0.000	0.000	0.000
32	C	33	LEU	0	-0.012	-0.012	39.170	-0.010	-0.010	0.000	0.000	0.000	0.000
33	C	34	ASP	-1	-0.829	-0.893	39.855	0.170	0.170	0.000	0.000	0.000	0.000
34	C	35	GLN	0	0.021	0.012	42.298	-0.009	-0.009	0.000	0.000	0.000	0.000
35	C	36	LEU	0	0.019	0.012	44.111	-0.008	-0.008	0.000	0.000	0.000	0.000
36	C	37	LYS	1	0.849	0.926	42.613	-0.164	-0.164	0.000	0.000	0.000	0.000
37	C	38	GLU	-1	-0.905	-0.949	45.599	0.131	0.131	0.000	0.000	0.000	0.000
38	C	39	GLN	0	-0.029	-0.017	46.914	-0.008	-0.008	0.000	0.000	0.000	0.000
39	C	40	THR	0	-0.024	-0.021	49.553	-0.007	-0.007	0.000	0.000	0.000	0.000
40	C	41	GLN	0	-0.036	-0.024	49.881	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	42	MET	0	0.040	0.039	52.166	-0.005	-0.005	0.000	0.000	0.000	0.000
42	C	43	PHE	0	0.032	0.014	54.633	-0.005	-0.005	0.000	0.000	0.000	0.000
43	C	44	ILE	0	0.002	0.001	55.601	-0.005	-0.005	0.000	0.000	0.000	0.000
44	C	45	GLU	-1	-0.809	-0.893	54.980	0.095	0.095	0.000	0.000	0.000	0.000
45	C	46	ALA	0	-0.016	-0.003	58.908	-0.003	-0.003	0.000	0.000	0.000	0.000
46	C	47	THR	0	-0.012	-0.020	60.144	-0.003	-0.003	0.000	0.000	0.000	0.000
47	C	48	LYS	1	0.844	0.933	60.158	-0.081	-0.081	0.000	0.000	0.000	0.000
48	C	49	SER	0	-0.021	-0.009	62.566	0.001	0.001	0.000	0.000	0.000	0.000
49	C	50	ARG	1	0.860	0.911	65.027	-0.067	-0.067	0.000	0.000	0.000	0.000
50	C	51	ALA	0	0.025	0.040	66.802	-0.001	-0.001	0.000	0.000	0.000	0.000
51	C	52	PRO	0	0.014	-0.002	68.746	-0.001	-0.001	0.000	0.000	0.000	0.000
52	C	53	GLN	0	0.009	-0.017	64.989	0.000	0.000	0.000	0.000	0.000	0.000
53	C	54	ALA	0	-0.036	0.000	65.369	0.001	0.001	0.000	0.000	0.000	0.000
54	C	55	TRP	0	0.102	0.029	59.795	0.001	0.001	0.000	0.000	0.000	0.000
55	C	56	ALA	0	0.012	0.007	61.697	0.001	0.001	0.000	0.000	0.000	0.000
56	C	57	LYS	1	0.814	0.898	55.301	-0.093	-0.093	0.000	0.000	0.000	0.000
57	C	58	LEU	0	0.058	0.030	57.039	0.003	0.003	0.000	0.000	0.000	0.000
58	C	59	GLN	0	0.025	0.015	57.293	0.000	0.000	0.000	0.000	0.000	0.000
59	C	60	ALA	0	-0.016	0.003	56.412	0.000	0.000	0.000	0.000	0.000	0.000
60	C	61	SER	0	-0.045	-0.029	52.915	0.002	0.002	0.000	0.000	0.000	0.000
61	C	62	LEU	0	-0.023	-0.006	53.181	0.001	0.001	0.000	0.000	0.000	0.000
62	C	63	THR	0	-0.066	-0.025	54.301	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:ASN)