FMO DATABASE

FMODB ID: 4JJJN

Calculation Name: 4DPO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DPO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PWK2

Base Structure: X-ray

Registration Date: 2023-09-21

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816816.2321
FMO2-HF: Nuclear repulsion	773543.61613
FMO2-HF: Total energy	-43272.61597
FMO2-MP2: Total energy	-43396.240487

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:-5:ASN)

Summations of interaction energy for fragment #1(A:-5:ASN)

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.
-19.997	-13.994	8.753	-5.499	-9.26	0.038

Interaction energy analysis for fragmet #1(A:-5:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.004

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

Sort

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	-3	TYR	0	-0.005	0.003	2.036	-11.639	-9.209	7.919	-4.271	-6.079	0.040
4	A	-2	PHE	0	0.021	-0.014	2.472	-8.102	-4.959	0.834	-1.169	-2.809	-0.002
5	A	-1	GLN	0	0.027	0.010	4.135	0.346	0.776	0.000	-0.059	-0.372	0.000
6	A	0	SER	0	-0.017	0.008	6.332	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	1	MET	0	-0.093	-0.049	7.002	-0.437	-0.437	0.000	0.000	0.000	0.000
8	A	2	LEU	0	-0.042	-0.014	8.829	-0.135	-0.135	0.000	0.000	0.000	0.000
9	A	3	ALA	0	0.022	0.028	10.408	0.011	0.011	0.000	0.000	0.000	0.000
10	A	4	ILE	0	-0.027	-0.014	12.340	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	5	ARG	1	0.928	0.964	15.468	-0.472	-0.472	0.000	0.000	0.000	0.000
12	A	6	VAL	0	0.005	0.012	18.992	-0.045	-0.045	0.000	0.000	0.000	0.000
13	A	7	VAL	0	-0.029	-0.009	22.494	0.038	0.038	0.000	0.000	0.000	0.000
14	A	8	ALA	0	0.028	-0.002	25.585	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	9	LYS	1	0.996	1.008	28.522	-0.081	-0.081	0.000	0.000	0.000	0.000
16	A	10	ASN	0	0.019	0.005	31.742	-0.030	-0.030	0.000	0.000	0.000	0.000
17	A	11	GLN	0	-0.036	-0.018	34.832	0.008	0.008	0.000	0.000	0.000	0.000
18	A	12	VAL	0	-0.004	0.000	37.633	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	13	LYS	1	0.986	1.007	40.370	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	14	PRO	0	0.020	0.014	43.826	0.003	0.003	0.000	0.000	0.000	0.000
21	A	15	GLU	-1	-0.932	-0.967	45.296	0.066	0.066	0.000	0.000	0.000	0.000
22	A	16	LYS	1	0.764	0.863	42.613	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	17	VAL	0	0.045	0.033	39.852	0.003	0.003	0.000	0.000	0.000	0.000
24	A	18	GLN	0	0.009	0.010	40.088	0.009	0.009	0.000	0.000	0.000	0.000
25	A	19	GLU	-1	-0.814	-0.902	40.546	0.061	0.061	0.000	0.000	0.000	0.000
26	A	20	PHE	0	0.063	0.023	33.900	0.001	0.001	0.000	0.000	0.000	0.000
27	A	21	MET	0	0.002	0.000	35.702	0.007	0.007	0.000	0.000	0.000	0.000
28	A	22	ASN	0	-0.091	-0.060	35.748	0.001	0.001	0.000	0.000	0.000	0.000
29	A	23	LEU	0	0.023	0.016	35.777	0.003	0.003	0.000	0.000	0.000	0.000
30	A	24	CYS	0	0.020	0.005	31.557	0.001	0.001	0.000	0.000	0.000	0.000
31	A	25	LYS	1	0.911	0.980	31.173	-0.107	-0.107	0.000	0.000	0.000	0.000
32	A	26	SER	0	-0.017	-0.042	31.517	0.011	0.011	0.000	0.000	0.000	0.000
33	A	27	LEU	0	0.028	0.037	28.411	0.000	0.000	0.000	0.000	0.000	0.000
34	A	28	ILE	0	-0.013	0.010	26.260	0.002	0.002	0.000	0.000	0.000	0.000
35	A	29	GLU	-1	-0.887	-0.921	26.306	0.187	0.187	0.000	0.000	0.000	0.000
36	A	30	GLU	-1	-0.869	-0.940	26.837	0.118	0.118	0.000	0.000	0.000	0.000
37	A	31	THR	0	-0.041	-0.033	22.813	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	32	LEU	0	-0.007	-0.023	21.605	0.006	0.006	0.000	0.000	0.000	0.000
39	A	33	LYS	1	0.715	0.861	21.268	-0.110	-0.110	0.000	0.000	0.000	0.000
40	A	34	GLU	-1	-0.842	-0.923	20.678	0.035	0.035	0.000	0.000	0.000	0.000
41	A	35	GLU	-1	-0.908	-0.950	14.493	0.224	0.224	0.000	0.000	0.000	0.000
42	A	36	GLY	0	-0.007	-0.017	14.233	-0.058	-0.058	0.000	0.000	0.000	0.000
43	A	37	CYS	0	-0.048	-0.012	15.314	0.036	0.036	0.000	0.000	0.000	0.000
44	A	38	ILE	0	-0.086	-0.042	11.951	0.068	0.068	0.000	0.000	0.000	0.000
45	A	39	ASP	-1	-0.869	-0.945	16.083	0.536	0.536	0.000	0.000	0.000	0.000
46	A	40	TYR	0	-0.013	-0.027	19.512	-0.062	-0.062	0.000	0.000	0.000	0.000
47	A	41	GLY	0	0.013	0.030	22.850	0.011	0.011	0.000	0.000	0.000	0.000
48	A	42	VAL	0	-0.017	-0.021	26.095	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	43	TYR	0	-0.017	-0.005	24.248	0.016	0.016	0.000	0.000	0.000	0.000
50	A	44	GLN	0	0.026	0.008	30.525	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	45	GLU	-1	-0.985	-0.972	33.372	0.148	0.148	0.000	0.000	0.000	0.000
52	A	46	LEU	0	-0.004	-0.017	33.294	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	47	GLU	-1	-0.957	-0.966	36.100	0.143	0.143	0.000	0.000	0.000	0.000
54	A	48	ASN	0	-0.082	-0.059	37.699	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	49	PRO	0	0.073	0.025	38.324	0.002	0.002	0.000	0.000	0.000	0.000
56	A	50	GLU	-1	-0.878	-0.935	39.363	0.093	0.093	0.000	0.000	0.000	0.000
57	A	51	ILE	0	-0.082	-0.031	34.286	-0.009	-0.009	0.000	0.000	0.000	0.000
58	A	52	LEU	0	0.033	0.008	34.119	0.014	0.014	0.000	0.000	0.000	0.000
59	A	53	THR	0	-0.050	-0.035	28.196	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	54	MET	0	-0.008	0.000	26.952	0.010	0.010	0.000	0.000	0.000	0.000
61	A	55	LEU	0	-0.074	-0.025	23.652	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	56	GLU	-1	-0.792	-0.912	21.358	0.131	0.131	0.000	0.000	0.000	0.000
63	A	57	GLU	-1	-1.001	-1.010	13.977	0.746	0.746	0.000	0.000	0.000	0.000
64	A	58	TRP	0	0.031	0.025	15.992	0.021	0.021	0.000	0.000	0.000	0.000
65	A	59	LYS	1	0.918	0.956	8.092	-0.540	-0.540	0.000	0.000	0.000	0.000
66	A	60	ASP	-1	-0.864	-0.912	11.358	-0.514	-0.514	0.000	0.000	0.000	0.000
67	A	61	GLU	-1	-0.904	-0.962	13.498	-0.299	-0.299	0.000	0.000	0.000	0.000
68	A	62	GLY	0	0.010	0.005	15.959	0.045	0.045	0.000	0.000	0.000	0.000
69	A	63	SER	0	0.025	-0.031	14.850	0.059	0.059	0.000	0.000	0.000	0.000
70	A	64	LEU	0	-0.023	0.008	17.489	0.039	0.039	0.000	0.000	0.000	0.000
71	A	65	ASP	-1	-0.860	-0.905	19.927	-0.181	-0.181	0.000	0.000	0.000	0.000
72	A	66	GLN	0	-0.003	-0.026	18.181	0.045	0.045	0.000	0.000	0.000	0.000
73	A	67	HIS	1	0.888	0.959	21.571	-0.041	-0.041	0.000	0.000	0.000	0.000
74	A	68	ILE	0	-0.040	-0.019	23.341	0.010	0.010	0.000	0.000	0.000	0.000
75	A	69	ARG	1	0.761	0.862	24.744	0.156	0.156	0.000	0.000	0.000	0.000
76	A	70	SER	0	0.026	0.021	25.431	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	71	ASP	-1	-0.856	-0.934	27.386	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	72	HIS	0	0.055	0.035	25.590	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	73	PHE	0	-0.010	0.016	27.710	0.004	0.004	0.000	0.000	0.000	0.000
80	A	74	LYS	1	0.832	0.903	29.803	0.026	0.026	0.000	0.000	0.000	0.000
81	A	75	GLU	-1	-0.960	-0.984	32.402	0.025	0.025	0.000	0.000	0.000	0.000
82	A	76	ILE	0	-0.020	-0.026	32.247	0.004	0.004	0.000	0.000	0.000	0.000
83	A	77	PHE	0	-0.016	0.003	31.793	0.003	0.003	0.000	0.000	0.000	0.000
84	A	78	PRO	0	-0.033	-0.025	33.751	0.002	0.002	0.000	0.000	0.000	0.000
85	A	79	LEU	0	0.030	0.023	37.241	0.002	0.002	0.000	0.000	0.000	0.000
86	A	80	LEU	0	-0.013	-0.022	32.524	0.004	0.004	0.000	0.000	0.000	0.000
87	A	81	SER	0	0.020	0.002	35.906	0.003	0.003	0.000	0.000	0.000	0.000
88	A	82	GLU	-1	-0.962	-0.951	38.100	0.027	0.027	0.000	0.000	0.000	0.000
89	A	83	CYS	0	-0.148	-0.076	39.351	0.003	0.003	0.000	0.000	0.000	0.000
90	A	84	LEU	0	-0.007	0.002	36.055	0.006	0.006	0.000	0.000	0.000	0.000
91	A	85	ASP	-1	-0.946	-0.964	40.546	0.044	0.044	0.000	0.000	0.000	0.000
92	A	86	LYS	1	0.827	0.900	35.354	-0.049	-0.049	0.000	0.000	0.000	0.000
93	A	87	GLU	-1	-0.849	-0.926	35.657	0.007	0.007	0.000	0.000	0.000	0.000
94	A	88	THR	0	-0.026	0.002	32.046	0.006	0.006	0.000	0.000	0.000	0.000
95	A	89	GLU	-1	-0.982	-0.998	31.291	0.038	0.038	0.000	0.000	0.000	0.000
96	A	90	ILE	0	0.000	-0.002	26.500	0.016	0.016	0.000	0.000	0.000	0.000
97	A	91	ASN	0	-0.036	-0.009	25.374	-0.037	-0.037	0.000	0.000	0.000	0.000
98	A	92	ILE	0	0.043	0.021	20.055	0.027	0.027	0.000	0.000	0.000	0.000
99	A	93	TYR	0	-0.048	-0.022	19.493	-0.027	-0.027	0.000	0.000	0.000	0.000
100	A	94	ARG	1	0.970	0.975	13.596	0.398	0.398	0.000	0.000	0.000	0.000
101	A	95	LYS	1	0.946	0.993	11.583	-0.962	-0.962	0.000	0.000	0.000	0.000
102	A	96	LYS	1	0.976	0.993	13.196	0.139	0.139	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-5:ASN)