FMO DATABASE

FMODB ID: 72YYK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-422190.991517
FMO2-HF: Nuclear repulsion	393224.317131
FMO2-HF: Total energy	-28966.674385
FMO2-MP2: Total energy	-29053.423653

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.
-10.309	-7.473	0.017	-0.933	-1.921	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 : 1.042 / 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	-0.781	-0.869	3.765	-26.054	-24.296	-0.003	-0.706	-1.049	0.001
4	A	5	LEU	0	0.052	0.037	3.382	1.764	2.445	0.020	-0.141	-0.560	-0.001
5	A	6	ARG	1	0.851	0.900	3.870	34.436	34.833	0.000	-0.086	-0.312	0.000
6	A	7	ARG	1	0.764	0.854	5.687	25.918	25.918	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.040	0.016	8.323	2.011	2.011	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.021	0.003	6.607	1.579	1.579	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.763	-0.851	9.216	-24.573	-24.573	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.802	-0.865	11.534	-16.965	-16.965	0.000	0.000	0.000	0.000
11	A	12	LEU	0	0.008	0.017	13.313	1.185	1.185	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.830	-0.887	13.631	-17.186	-17.186	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.822	0.882	14.667	18.534	18.534	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.022	0.012	17.728	0.835	0.835	0.000	0.000	0.000	0.000
15	A	16	LEU	0	0.014	0.000	17.118	0.755	0.755	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.828	0.887	16.713	16.756	16.756	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.852	-0.902	22.162	-11.584	-11.584	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.007	0.006	23.002	0.453	0.453	0.000	0.000	0.000	0.000
19	A	20	LYS	1	0.785	0.881	24.496	10.824	10.824	0.000	0.000	0.000	0.000
20	A	21	LYS	1	0.841	0.902	24.843	12.121	12.121	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.028	-0.020	27.909	0.514	0.514	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.016	-0.006	28.532	0.318	0.318	0.000	0.000	0.000	0.000
23	A	24	ASP	-1	-0.826	-0.917	29.525	-10.153	-10.153	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.911	-0.942	32.182	-8.494	-8.494	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.000	0.000	33.053	0.270	0.270	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.847	-0.920	31.847	-9.563	-9.563	0.000	0.000	0.000	0.000
27	A	28	ARG	1	0.851	0.907	33.239	9.205	9.205	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.032	-0.025	38.003	0.280	0.280	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.010	0.001	38.827	0.195	0.195	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.819	-0.899	40.364	-7.420	-7.420	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.856	-0.915	42.219	-6.727	-6.727	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.061	-0.024	42.729	0.194	0.194	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.955	-0.991	43.179	-7.190	-7.190	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.690	0.817	43.991	7.282	7.282	0.000	0.000	0.000	0.000
35	A	36	ASN	0	-0.088	-0.040	48.188	0.306	0.306	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.004	0.013	48.684	-0.039	-0.039	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.001	-0.011	48.884	0.124	0.124	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.928	-0.969	48.456	-6.225	-6.225	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.889	-0.947	47.336	-6.394	-6.394	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.021	0.012	45.042	-0.183	-0.183	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.010	-0.004	43.677	-0.209	-0.209	0.000	0.000	0.000	0.000
42	A	43	VAL	0	-0.025	-0.012	42.918	-0.203	-0.203	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.759	-0.836	39.849	-8.023	-8.023	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.051	0.039	39.362	-0.339	-0.339	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.027	-0.023	38.124	-0.369	-0.369	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.790	0.866	35.331	8.034	8.034	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.000	0.001	34.639	-0.314	-0.314	0.000	0.000	0.000	0.000
48	A	49	ASN	0	0.039	0.016	33.438	-0.576	-0.576	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.017	0.002	32.891	-0.313	-0.313	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.836	-0.901	31.314	-9.674	-9.674	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.065	0.045	29.126	-0.591	-0.591	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.059	-0.047	27.960	-0.574	-0.574	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.790	0.879	27.591	9.225	9.225	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.006	0.001	23.681	-0.449	-0.449	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.009	0.007	23.394	-0.665	-0.665	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.006	-0.002	23.095	-0.527	-0.527	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.762	-0.838	19.222	-14.647	-14.647	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.004	-0.008	18.983	-0.887	-0.887	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.001	-0.003	18.167	-0.918	-0.918	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.800	0.872	15.916	14.510	14.510	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.040	-0.018	13.763	-0.822	-0.822	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.005	0.002	13.862	-1.419	-1.419	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.014	0.004	14.419	-0.876	-0.876	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.858	-0.905	11.540	-18.087	-18.087	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.010	-0.004	9.320	-1.614	-1.614	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.005	0.006	10.070	-1.727	-1.727	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.853	0.906	12.107	16.318	16.318	0.000	0.000	0.000	0.000
68	A	69	ILE	0	-0.045	-0.020	5.769	-0.499	-0.499	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.045	-0.033	7.790	-3.757	-3.757	0.000	0.000	0.000	0.000
70	A	71	ALA	0	-0.001	0.010	9.004	-0.099	-0.099	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.807	0.887	7.340	24.722	24.722	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.113	-0.047	6.306	-2.049	-2.049	0.000	0.000	0.000	0.000

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