FMO DATABASE

FMODB ID: MVRRZ

Calculation Name: 5J0H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J0H

Chain ID: A

ChEMBL ID:

UniProt ID:

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-420882.125783
FMO2-HF: Nuclear repulsion	391915.512394
FMO2-HF: Total energy	-28966.613389
FMO2-MP2: Total energy	-29053.398598

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
-8.697	-5.168	0.065	-1.103	-2.491	0

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.027 / q_NPA : 1.002

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	A	4	GLU	-1	-0.791	-0.871	3.723	-26.226	-24.336	-0.002	-0.732	-1.156	0.001
4	A	5	LEU	0	0.051	0.033	3.080	1.303	2.193	0.051	-0.198	-0.743	-0.001
5	A	6	ARG	1	0.856	0.907	3.261	35.491	36.129	0.017	-0.167	-0.488	0.000
6	A	7	ARG	1	0.772	0.856	5.075	26.076	26.187	-0.001	-0.006	-0.104	0.000
7	A	8	ALA	0	0.043	0.023	8.166	2.242	2.242	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.017	0.000	6.523	1.716	1.716	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.776	-0.859	8.738	-24.948	-24.948	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.793	-0.866	11.029	-16.994	-16.994	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.004	0.012	12.873	1.254	1.254	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.842	-0.908	13.524	-17.835	-17.835	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.816	0.878	14.306	18.798	18.798	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.019	0.018	17.260	0.895	0.895	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.019	0.002	16.895	0.772	0.772	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.836	0.905	15.961	17.245	17.245	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.857	-0.909	21.556	-11.455	-11.455	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.011	0.000	22.889	0.472	0.472	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.865	0.931	24.079	11.075	11.075	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.857	0.915	24.716	12.023	12.023	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.025	-0.024	27.511	0.509	0.509	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.029	-0.013	28.370	0.299	0.299	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.839	-0.913	29.558	-10.163	-10.163	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.926	-0.966	31.992	-8.573	-8.573	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.017	-0.007	32.884	0.283	0.283	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.904	-0.966	32.094	-9.404	-9.404	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.866	0.935	33.018	9.234	9.234	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.020	-0.022	37.860	0.297	0.297	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.007	0.003	38.725	0.196	0.196	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.833	-0.915	40.205	-7.489	-7.489	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.908	-0.952	42.303	-6.824	-6.824	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.053	-0.018	42.856	0.208	0.208	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.966	-0.997	43.314	-7.172	-7.172	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.713	0.858	43.878	7.333	7.333	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.083	-0.043	48.168	0.303	0.303	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.019	0.029	48.647	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.004	-0.020	49.032	0.131	0.131	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.925	-0.967	48.637	-6.225	-6.225	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.890	-0.946	47.547	-6.408	-6.408	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.016	0.009	45.281	-0.179	-0.179	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.005	-0.002	43.854	-0.209	-0.209	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.022	-0.008	42.946	-0.216	-0.216	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.770	-0.842	39.796	-8.002	-8.002	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.053	0.039	39.477	-0.342	-0.342	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.020	-0.026	38.170	-0.343	-0.343	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.791	0.871	35.455	7.959	7.959	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.011	0.002	34.411	-0.309	-0.309	0.000	0.000	0.000	0.000
48	A	49	ASN	0	0.029	0.012	33.505	-0.573	-0.573	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.015	-0.003	32.791	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.825	-0.893	31.249	-9.756	-9.756	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.069	0.051	28.828	-0.554	-0.554	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.075	-0.056	27.899	-0.533	-0.533	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.809	0.891	27.558	9.248	9.248	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.002	0.004	23.545	-0.453	-0.453	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.016	0.010	23.262	-0.677	-0.677	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.005	-0.005	22.912	-0.544	-0.544	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.768	-0.840	19.507	-14.669	-14.669	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.003	-0.014	18.621	-0.881	-0.881	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.011	-0.008	18.065	-0.920	-0.920	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.795	0.869	16.020	14.581	14.581	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.034	-0.013	13.676	-0.849	-0.849	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.011	0.005	13.822	-1.419	-1.419	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.012	0.003	14.206	-0.925	-0.925	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.865	-0.916	11.540	-18.261	-18.261	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.000	-0.007	9.045	-1.573	-1.573	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.022	-0.013	10.126	-1.607	-1.607	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.861	0.915	12.527	16.686	16.686	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.041	-0.018	5.868	-0.516	-0.516	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.013	-0.014	7.619	-3.988	-3.988	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.004	0.013	9.322	-0.101	-0.101	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.815	0.897	7.443	24.838	24.838	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.118	-0.051	6.523	-1.659	-1.659	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)