FMO DATABASE

FMODB ID: 76MZK

Calculation Name: 4GHJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHJ

Chain ID: A

ChEMBL ID:

UniProt ID: A0A3Q0

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-417142.964598
FMO2-HF: Nuclear repulsion	389189.266722
FMO2-HF: Total energy	-27953.697876
FMO2-MP2: Total energy	-28035.591569

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.
-114.229	-117.072	30.664	-14.171	-13.651	-0.165

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 : 0.850 / q_NPA : 0.914

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	VAL	0	0.008	0.002	2.303	0.371	2.835	1.772	-1.540	-2.697	0.003
4	A	5	THR	0	0.036	0.019	4.504	0.551	0.582	-0.001	-0.005	-0.024	0.000
5	A	6	ALA	0	0.071	0.019	6.819	-3.814	-3.814	0.000	0.000	0.000	0.000
6	A	7	ALA	0	0.003	-0.002	8.449	-1.396	-1.396	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.034	0.018	7.466	0.231	0.231	0.000	0.000	0.000	0.000
8	A	9	LEU	0	0.008	0.006	1.940	-7.526	-9.616	6.346	-1.496	-2.761	-0.020
9	A	10	ALA	0	0.012	-0.003	5.094	-1.977	-1.930	-0.001	0.000	-0.046	0.000
10	A	11	GLU	-1	-0.950	-0.970	8.008	-24.967	-24.967	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.772	-0.849	1.797	-148.734	-152.893	22.462	-10.743	-7.561	-0.146
12	A	13	ILE	0	-0.043	-0.038	4.535	1.494	1.574	-0.001	-0.002	-0.076	0.000
13	A	14	GLY	0	0.046	0.030	7.223	3.744	3.744	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.849	-0.923	9.085	-23.717	-23.717	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.839	0.919	2.533	63.819	64.603	0.087	-0.385	-0.486	-0.002
16	A	17	LEU	0	0.008	0.014	9.457	2.364	2.364	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.860	0.912	12.532	23.912	23.912	0.000	0.000	0.000	0.000
18	A	19	GLN	0	-0.044	-0.029	12.088	0.998	0.998	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.002	-0.002	13.312	1.327	1.327	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.795	0.859	14.969	17.507	17.507	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.041	-0.024	16.588	1.017	1.017	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.006	0.002	15.565	0.697	0.697	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.845	0.920	16.488	17.288	17.288	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.924	-0.940	21.391	-12.262	-12.262	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.012	0.029	21.767	0.422	0.422	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.020	-0.053	22.238	-0.655	-0.655	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.061	-0.066	18.813	0.673	0.673	0.000	0.000	0.000	0.000
28	A	29	SER	0	-0.019	-0.027	22.764	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.733	-0.810	25.590	-11.472	-11.472	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.016	0.008	20.080	0.007	0.007	0.000	0.000	0.000	0.000
31	A	32	ALA	0	-0.073	-0.044	23.454	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.950	-0.966	25.143	-9.910	-9.910	0.000	0.000	0.000	0.000
33	A	34	ILE	0	-0.015	-0.002	25.186	0.207	0.207	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.022	-0.013	23.366	0.134	0.134	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.014	0.033	25.467	0.116	0.116	0.000	0.000	0.000	0.000
36	A	37	ILE	0	-0.066	-0.034	21.911	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.037	0.015	26.215	0.204	0.204	0.000	0.000	0.000	0.000
38	A	39	ARG	1	1.005	0.980	23.585	12.153	12.153	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.851	0.914	22.019	13.402	13.402	0.000	0.000	0.000	0.000
40	A	41	THR	0	0.034	0.012	20.896	-0.478	-0.478	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.084	0.053	19.292	-0.907	-0.907	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.072	-0.028	18.289	-0.971	-0.971	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.022	-0.020	17.823	-0.708	-0.708	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.096	0.054	15.394	-1.132	-1.132	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.783	-0.848	13.618	-19.577	-19.577	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.877	0.935	13.255	17.029	17.029	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.051	0.038	11.391	-1.017	-1.017	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.845	0.923	12.053	18.756	18.756	0.000	0.000	0.000	0.000
49	A	50	VAL	0	0.013	-0.014	13.741	1.141	1.141	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.042	-0.013	15.531	-0.729	-0.729	0.000	0.000	0.000	0.000
51	A	52	LEU	0	0.054	0.010	14.211	-0.200	-0.200	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.791	-0.887	16.713	-14.711	-14.711	0.000	0.000	0.000	0.000
53	A	54	ILE	0	-0.002	-0.005	19.290	0.136	0.136	0.000	0.000	0.000	0.000
54	A	55	MET	0	0.000	0.002	11.419	0.345	0.345	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.014	0.004	16.487	-0.330	-0.330	0.000	0.000	0.000	0.000
56	A	57	ALA	0	0.033	0.022	17.912	0.301	0.301	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.031	-0.024	17.261	0.333	0.333	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.010	-0.011	13.352	-0.050	-0.050	0.000	0.000	0.000	0.000
59	A	60	MET	0	-0.016	-0.004	17.642	0.285	0.285	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.010	0.006	21.178	0.475	0.475	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.082	-0.037	16.514	0.199	0.199	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.899	-0.929	19.933	-13.841	-13.841	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.069	-0.031	13.616	-0.583	-0.583	0.000	0.000	0.000	0.000
64	A	65	THR	0	0.060	0.004	16.237	-1.160	-1.160	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.897	-0.933	18.168	-14.170	-14.170	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.030	-0.035	12.969	0.909	0.909	0.000	0.000	0.000	0.000
67	A	68	ILE	0	-0.062	-0.035	13.697	-1.027	-1.027	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.848	-0.902	15.928	-15.037	-15.037	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.066	-0.051	14.765	0.303	0.303	0.000	0.000	0.000	0.000
70	A	71	PHE	0	-0.068	-0.027	9.583	-1.723	-1.723	0.000	0.000	0.000	0.000
71	A	72	ILE	0	-0.069	-0.041	12.323	0.929	0.929	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.070	0.074	14.961	0.982	0.982	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.897	0.934	18.362	15.992	15.992	0.000	0.000	0.000	0.000

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