FMO DATABASE

FMODB ID: QYY1Y

Calculation Name: 4D2K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D2K

Chain ID: A

ChEMBL ID:

UniProt ID: Q7K304

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	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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-561980.809304
FMO2-HF: Nuclear repulsion	529828.560389
FMO2-HF: Total energy	-32152.248915
FMO2-MP2: Total energy	-32248.128884

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:7:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
33.296	35.672	0.182	-1.182	-1.377	0.004

Interaction energy analysis for fragmet #1(A:7:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.970 / q_NPA : 0.971

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	9	LYS	1	0.870	0.931	3.808	26.363	28.038	-0.024	-0.816	-0.835	0.002
4	A	10	ARG	1	0.938	0.988	3.451	21.696	22.397	0.206	-0.366	-0.542	0.002
5	A	11	PRO	0	-0.016	0.003	6.582	2.435	2.435	0.000	0.000	0.000	0.000
6	A	12	LEU	0	0.035	0.020	8.973	-0.594	-0.594	0.000	0.000	0.000	0.000
7	A	13	LYS	1	0.928	0.971	11.973	15.980	15.980	0.000	0.000	0.000	0.000
8	A	14	ILE	0	0.006	0.018	15.764	0.093	0.093	0.000	0.000	0.000	0.000
9	A	15	TRP	0	0.027	-0.007	18.097	0.313	0.313	0.000	0.000	0.000	0.000
10	A	16	ASP	-1	-0.736	-0.861	21.671	-10.178	-10.178	0.000	0.000	0.000	0.000
11	A	17	SER	0	0.025	-0.004	24.737	-0.047	-0.047	0.000	0.000	0.000	0.000
12	A	18	TRP	0	0.011	0.018	26.588	0.107	0.107	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.707	0.832	24.638	10.490	10.490	0.000	0.000	0.000	0.000
14	A	20	ASN	0	-0.003	0.002	26.196	0.034	0.034	0.000	0.000	0.000	0.000
15	A	21	VAL	0	-0.040	-0.018	24.328	-0.203	-0.203	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.869	0.927	22.259	10.676	10.676	0.000	0.000	0.000	0.000
17	A	23	LYS	1	0.919	0.964	19.949	11.582	11.582	0.000	0.000	0.000	0.000
18	A	24	GLY	0	0.013	0.021	16.299	-0.343	-0.343	0.000	0.000	0.000	0.000
19	A	25	VAL	0	-0.047	-0.028	12.835	0.390	0.390	0.000	0.000	0.000	0.000
20	A	26	VAL	0	0.021	-0.007	9.492	-0.912	-0.912	0.000	0.000	0.000	0.000
21	A	27	VAL	0	-0.001	0.006	9.537	0.538	0.538	0.000	0.000	0.000	0.000
22	A	28	GLY	0	-0.021	-0.009	6.812	-2.086	-2.086	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.004	0.009	6.877	-0.386	-0.386	0.000	0.000	0.000	0.000
24	A	30	PHE	0	0.095	0.055	9.616	0.144	0.144	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.843	-0.933	12.445	-15.730	-15.730	0.000	0.000	0.000	0.000
26	A	32	GLU	-1	-0.864	-0.951	11.365	-20.172	-20.172	0.000	0.000	0.000	0.000
27	A	33	LEU	0	-0.022	-0.010	12.355	0.266	0.266	0.000	0.000	0.000	0.000
28	A	34	LEU	0	0.029	0.018	14.008	0.683	0.683	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.017	-0.008	17.272	0.550	0.550	0.000	0.000	0.000	0.000
30	A	36	ARG	1	0.899	0.949	15.221	15.622	15.622	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.030	0.025	17.350	0.268	0.268	0.000	0.000	0.000	0.000
32	A	38	LYS	1	0.916	0.954	18.639	11.902	11.902	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.936	-0.958	20.800	-11.862	-11.862	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.889	0.947	17.986	14.823	14.823	0.000	0.000	0.000	0.000
35	A	41	LEU	0	-0.058	-0.040	21.263	0.267	0.267	0.000	0.000	0.000	0.000
36	A	42	GLY	0	-0.013	0.014	24.083	0.399	0.399	0.000	0.000	0.000	0.000
37	A	43	VAL	0	-0.054	-0.025	24.693	0.403	0.403	0.000	0.000	0.000	0.000
38	A	44	PRO	0	0.026	0.005	25.816	-0.272	-0.272	0.000	0.000	0.000	0.000
39	A	45	ALA	0	0.038	0.010	24.471	-0.104	-0.104	0.000	0.000	0.000	0.000
40	A	46	SER	0	-0.033	-0.021	24.820	-0.279	-0.279	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.819	-0.879	27.114	-9.328	-9.328	0.000	0.000	0.000	0.000
42	A	48	PRO	0	-0.007	-0.007	25.188	-0.421	-0.421	0.000	0.000	0.000	0.000
43	A	49	VAL	0	-0.027	-0.019	21.552	0.196	0.196	0.000	0.000	0.000	0.000
44	A	50	ARG	1	0.873	0.925	22.132	9.863	9.863	0.000	0.000	0.000	0.000
45	A	51	VAL	0	0.013	0.008	16.325	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.005	0.007	19.462	0.005	0.005	0.000	0.000	0.000	0.000
47	A	53	LEU	0	0.011	-0.004	15.239	-0.477	-0.477	0.000	0.000	0.000	0.000
48	A	54	GLU	-1	-0.858	-0.914	18.723	-11.107	-11.107	0.000	0.000	0.000	0.000
49	A	55	CYS	0	-0.029	-0.009	19.851	0.369	0.369	0.000	0.000	0.000	0.000
50	A	56	ASP	-1	-0.805	-0.902	21.466	-11.718	-11.718	0.000	0.000	0.000	0.000
51	A	57	GLY	0	0.013	0.009	22.631	0.293	0.293	0.000	0.000	0.000	0.000
52	A	58	THR	0	-0.044	-0.032	18.930	0.186	0.186	0.000	0.000	0.000	0.000
53	A	59	GLN	0	-0.024	-0.021	19.847	-0.346	-0.346	0.000	0.000	0.000	0.000
54	A	60	ILE	0	-0.043	-0.021	13.820	-0.391	-0.391	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.970	-0.992	17.125	-11.323	-11.323	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.804	-0.900	15.096	-14.444	-14.444	0.000	0.000	0.000	0.000
57	A	63	GLY	0	-0.011	-0.025	11.264	-0.693	-0.693	0.000	0.000	0.000	0.000
58	A	64	GLU	-1	-0.922	-0.966	10.065	-17.317	-17.317	0.000	0.000	0.000	0.000
59	A	65	TYR	0	0.083	0.041	10.509	-1.145	-1.145	0.000	0.000	0.000	0.000
60	A	66	PHE	0	-0.010	0.012	7.232	-0.857	-0.857	0.000	0.000	0.000	0.000
61	A	67	ARG	1	0.860	0.930	6.124	19.418	19.418	0.000	0.000	0.000	0.000
62	A	68	THR	0	-0.070	-0.041	6.381	-1.989	-1.989	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.014	0.009	8.882	-0.052	-0.052	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.033	0.022	7.495	-2.206	-2.206	0.000	0.000	0.000	0.000
65	A	71	ASN	0	0.031	0.007	6.331	0.514	0.514	0.000	0.000	0.000	0.000
66	A	72	ASN	0	-0.103	-0.077	8.828	1.808	1.808	0.000	0.000	0.000	0.000
67	A	73	THR	0	0.043	0.010	11.163	1.263	1.263	0.000	0.000	0.000	0.000
68	A	74	VAL	0	-0.047	-0.022	13.379	-0.177	-0.177	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.011	0.013	13.233	0.183	0.183	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.011	0.000	17.507	0.196	0.196	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.018	-0.006	20.013	-0.215	-0.215	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.044	-0.016	21.836	0.402	0.402	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.900	0.916	25.143	9.267	9.267	0.000	0.000	0.000	0.000
74	A	80	GLN	0	-0.018	-0.021	27.588	0.178	0.178	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.002	0.009	30.644	0.166	0.166	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.816	-0.894	28.197	-9.378	-9.378	0.000	0.000	0.000	0.000
77	A	83	ARG	1	0.931	0.962	28.548	8.244	8.244	0.000	0.000	0.000	0.000
78	A	84	TRP	0	0.003	0.016	23.954	0.149	0.149	0.000	0.000	0.000	0.000
79	A	85	LEU	0	0.015	0.006	27.153	0.298	0.298	0.000	0.000	0.000	0.000
80	A	86	GLU	-1	-0.896	-0.931	27.769	-8.988	-8.988	0.000	0.000	0.000	0.000
81	A	87	HIS	0	-0.010	-0.003	27.945	0.028	0.028	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:ARG)