FMO DATABASE

FMODB ID: 94LL2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-420491.483903
FMO2-HF: Nuclear repulsion	391525.511577
FMO2-HF: Total energy	-28965.972326
FMO2-MP2: Total energy	-29052.731389

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.
-10.977	-7.298	0.095	-1.13	-2.643	-0.001

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 : 1.029 / 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	-0.779	-0.872	3.717	-26.125	-24.316	-0.001	-0.678	-1.130	0.001
4	A	5	LEU	0	0.040	0.030	3.068	0.487	1.448	0.060	-0.225	-0.796	-0.001
5	A	6	ARG	1	0.885	0.935	3.101	37.717	38.508	0.037	-0.216	-0.612	-0.001
6	A	7	ARG	1	0.821	0.906	4.741	26.319	26.437	-0.001	-0.011	-0.105	0.000
7	A	8	ALA	0	0.054	0.027	7.856	2.285	2.285	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.013	-0.003	6.620	1.750	1.750	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.815	-0.898	8.433	-25.667	-25.667	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.871	-0.947	10.723	-16.430	-16.430	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.004	0.013	12.515	1.285	1.285	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.940	-0.972	13.224	-19.272	-19.272	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.841	0.915	14.112	18.935	18.935	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.047	0.027	16.925	0.903	0.903	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.022	0.004	16.689	0.790	0.790	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.918	0.965	16.154	16.751	16.751	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.867	-0.934	21.236	-11.384	-11.384	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.005	0.004	22.545	0.450	0.450	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.918	0.968	23.732	11.654	11.654	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.852	0.925	24.431	12.078	12.078	0.000	0.000	0.000	0.000
21	A	22	SER	0	0.010	0.002	27.176	0.484	0.484	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.023	-0.008	28.241	0.263	0.263	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.876	-0.944	29.470	-10.166	-10.166	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-1.005	-1.011	31.657	-8.656	-8.656	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.023	-0.010	32.729	0.278	0.278	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.927	-0.973	32.317	-9.266	-9.266	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.949	0.978	32.699	9.237	9.237	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.009	-0.004	37.516	0.303	0.303	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.006	0.003	38.546	0.211	0.211	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.923	-0.961	38.799	-7.826	-7.826	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.985	-1.002	42.001	-6.852	-6.852	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.060	-0.020	42.820	0.219	0.219	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.973	-1.000	43.427	-7.169	-7.169	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.863	0.944	44.879	7.141	7.141	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.075	-0.038	47.820	0.299	0.299	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.022	0.032	48.283	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.013	-0.027	48.671	0.143	0.143	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.919	-0.964	48.286	-6.234	-6.234	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.871	-0.936	47.215	-6.455	-6.455	0.000	0.000	0.000	0.000
40	A	41	ALA	0	-0.001	0.002	44.931	-0.174	-0.174	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.004	-0.005	43.497	-0.203	-0.203	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.016	-0.001	42.681	-0.217	-0.217	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.798	-0.871	39.554	-7.956	-7.956	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.064	0.030	39.117	-0.353	-0.353	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.033	-0.032	37.871	-0.296	-0.296	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.808	0.892	35.514	7.931	7.931	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.025	0.011	34.113	-0.295	-0.295	0.000	0.000	0.000	0.000
48	A	49	ASN	0	0.018	0.009	33.155	-0.572	-0.572	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.023	-0.013	32.680	-0.343	-0.343	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.906	-0.956	30.859	-9.807	-9.807	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.084	0.054	28.569	-0.548	-0.548	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.093	-0.062	27.775	-0.493	-0.493	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.900	0.957	27.517	9.211	9.211	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.013	0.011	23.183	-0.458	-0.458	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.014	0.008	23.168	-0.672	-0.672	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.008	-0.007	22.891	-0.550	-0.550	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.793	-0.861	19.542	-14.521	-14.521	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.001	-0.016	18.417	-0.888	-0.888	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.018	-0.010	18.042	-0.928	-0.928	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.814	0.888	16.123	14.563	14.563	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.029	-0.009	13.628	-0.799	-0.799	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.020	0.009	13.786	-1.418	-1.418	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.001	-0.006	14.158	-0.914	-0.914	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.950	-0.972	11.132	-19.165	-19.165	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.013	-0.012	8.905	-1.551	-1.551	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.029	-0.017	10.060	-1.610	-1.610	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.956	0.977	12.514	15.931	15.931	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.022	-0.006	5.779	-0.499	-0.499	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.018	-0.013	7.610	-3.996	-3.996	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.029	0.000	9.237	-0.109	-0.109	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.814	0.908	7.426	23.972	23.972	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.087	-0.045	6.602	-1.680	-1.680	0.000	0.000	0.000	0.000

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