FMO DATABASE

FMODB ID: 9G5K2

Calculation Name: 2DX5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DX5

Chain ID: A

ChEMBL ID:

UniProt ID: P0CH28

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	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	101
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-834510.03337
FMO2-HF: Nuclear repulsion	792130.320785
FMO2-HF: Total energy	-42379.712585
FMO2-MP2: Total energy	-42503.001924

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:10:LEU)

Summations of interaction energy for fragment #1(A:10:LEU)

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.
-8.917	-4.663	1.284	-1.879	-3.661	0

Interaction energy analysis for fragmet #1(A:10:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.025

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	12	GLU	-1	-0.847	-0.903	3.826	-4.002	-1.640	-0.031	-1.145	-1.186	-0.002
4	A	13	ILE	0	0.041	0.007	6.827	0.245	0.245	0.000	0.000	0.000	0.000
5	A	14	ASN	0	-0.081	-0.046	9.982	0.061	0.061	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.736	-0.805	6.653	-0.557	-0.557	0.000	0.000	0.000	0.000
7	A	16	THR	0	-0.012	-0.016	8.539	-0.090	-0.090	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.028	-0.019	6.623	0.113	0.113	0.000	0.000	0.000	0.000
9	A	18	VAL	0	0.023	0.026	8.991	-0.111	-0.111	0.000	0.000	0.000	0.000
10	A	19	ILE	0	0.001	-0.014	11.760	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	20	GLN	0	0.001	0.012	7.713	0.000	0.000	0.000	0.000	0.000	0.000
12	A	21	GLN	0	-0.028	-0.017	11.646	-0.115	-0.115	0.000	0.000	0.000	0.000
13	A	22	ARG	1	0.900	0.938	13.808	-0.436	-0.436	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.011	0.006	15.670	-0.061	-0.061	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.037	-0.011	14.654	-0.055	-0.055	0.000	0.000	0.000	0.000
16	A	25	ARG	1	0.901	0.954	16.171	-0.225	-0.225	0.000	0.000	0.000	0.000
17	A	26	VAL	0	0.073	0.023	13.868	0.002	0.002	0.000	0.000	0.000	0.000
18	A	27	TYR	0	-0.080	-0.034	17.326	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	28	ASP	-1	-0.801	-0.878	20.091	0.114	0.114	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.034	0.022	21.677	0.000	0.000	0.000	0.000	0.000	0.000
21	A	30	GLU	-1	-0.818	-0.900	24.972	0.118	0.118	0.000	0.000	0.000	0.000
22	A	31	GLU	-1	-0.840	-0.931	22.673	0.092	0.092	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.965	0.993	25.901	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	33	ILE	0	-0.036	-0.055	24.281	0.010	0.010	0.000	0.000	0.000	0.000
25	A	34	LYS	1	0.803	0.891	20.902	-0.119	-0.119	0.000	0.000	0.000	0.000
26	A	35	PHE	0	-0.039	0.001	19.199	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.774	-0.877	14.497	0.215	0.215	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.062	-0.028	16.099	0.024	0.024	0.000	0.000	0.000	0.000
29	A	38	GLY	0	0.031	0.002	12.528	0.006	0.006	0.000	0.000	0.000	0.000
30	A	39	THR	0	-0.090	-0.053	9.947	-0.120	-0.120	0.000	0.000	0.000	0.000
31	A	40	LEU	0	0.020	0.027	10.006	0.200	0.200	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.057	-0.031	5.444	0.125	0.125	0.000	0.000	0.000	0.000
33	A	42	LEU	0	0.012	0.019	8.747	0.030	0.030	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.039	-0.069	8.216	0.121	0.121	0.000	0.000	0.000	0.000
35	A	44	THR	0	0.074	0.009	10.221	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	45	HIS	0	-0.030	0.005	10.556	-0.037	-0.037	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.790	0.867	3.123	1.424	2.014	0.013	-0.220	-0.384	0.000
38	A	47	LEU	0	0.013	-0.001	9.734	0.131	0.131	0.000	0.000	0.000	0.000
39	A	48	ILE	0	0.020	0.009	3.890	-0.239	0.035	0.001	-0.043	-0.232	0.000
40	A	49	TRP	0	0.017	0.010	6.903	0.067	0.067	0.000	0.000	0.000	0.000
41	A	50	ARG	1	0.928	0.967	3.659	-5.317	-4.849	0.004	-0.139	-0.333	0.001
42	A	51	ASP	-1	-0.735	-0.868	6.964	0.304	0.304	0.000	0.000	0.000	0.000
43	A	52	GLN	0	-0.021	-0.022	9.929	0.051	0.051	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.793	0.880	12.564	-0.274	-0.274	0.000	0.000	0.000	0.000
45	A	54	ASN	0	0.010	-0.015	9.026	-0.043	-0.043	0.000	0.000	0.000	0.000
46	A	55	ASN	0	0.016	0.019	8.365	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	56	GLU	-1	-0.913	-0.954	8.624	0.107	0.107	0.000	0.000	0.000	0.000
48	A	57	CYS	0	-0.071	-0.019	5.551	0.197	0.197	0.000	0.000	0.000	0.000
49	A	58	CYS	0	-0.118	-0.060	2.506	-0.182	0.238	1.298	-0.321	-1.397	0.001
50	A	59	MET	0	0.052	0.026	4.442	-0.521	-0.381	-0.001	-0.011	-0.129	0.000
51	A	60	ALA	0	-0.015	-0.003	6.892	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	61	ILE	0	0.045	0.003	5.787	0.184	0.184	0.000	0.000	0.000	0.000
53	A	62	PRO	0	-0.026	-0.008	9.005	-0.090	-0.090	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.048	-0.006	12.134	-0.050	-0.050	0.000	0.000	0.000	0.000
55	A	64	SER	0	0.064	0.023	13.942	-0.052	-0.052	0.000	0.000	0.000	0.000
56	A	65	GLN	0	-0.044	-0.005	15.721	0.009	0.009	0.000	0.000	0.000	0.000
57	A	66	ILE	0	-0.049	-0.006	15.751	0.005	0.005	0.000	0.000	0.000	0.000
58	A	67	VAL	0	0.021	0.021	18.603	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	68	PHE	0	-0.007	-0.009	22.341	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.023	-0.015	19.141	0.010	0.010	0.000	0.000	0.000	0.000
61	A	70	GLU	-1	-0.850	-0.914	22.551	0.080	0.080	0.000	0.000	0.000	0.000
62	A	71	GLU	-1	-0.877	-0.945	23.979	0.174	0.174	0.000	0.000	0.000	0.000
63	A	72	GLN	0	-0.019	-0.003	26.267	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	73	ALA	0	-0.004	-0.002	27.841	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.885	0.951	23.167	-0.165	-0.165	0.000	0.000	0.000	0.000
66	A	82	ILE	0	-0.003	-0.006	19.089	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	83	VAL	0	0.010	0.007	20.813	0.018	0.018	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.014	-0.007	16.962	0.002	0.002	0.000	0.000	0.000	0.000
69	A	85	HIS	0	-0.002	-0.005	20.288	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	86	LEU	0	0.014	-0.025	16.171	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	87	HIS	0	-0.012	0.012	19.123	-0.030	-0.030	0.000	0.000	0.000	0.000
72	A	101	SER	0	-0.009	-0.014	30.410	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.963	0.976	24.832	0.010	0.010	0.000	0.000	0.000	0.000
74	A	103	ASN	0	-0.029	-0.009	21.715	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	104	SER	0	0.030	0.008	24.074	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	105	TYR	0	-0.036	-0.017	21.714	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.032	0.040	15.967	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.764	0.853	20.166	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	108	LEU	0	0.034	0.012	15.699	0.017	0.017	0.000	0.000	0.000	0.000
80	A	109	SER	0	-0.059	-0.030	19.235	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	110	PHE	0	0.051	0.024	16.780	0.015	0.015	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.912	0.971	20.800	-0.256	-0.256	0.000	0.000	0.000	0.000
83	A	112	GLU	-1	-0.881	-0.927	19.086	0.375	0.375	0.000	0.000	0.000	0.000
84	A	113	HIS	0	0.039	0.013	21.009	0.015	0.015	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.082	0.016	19.826	0.024	0.024	0.000	0.000	0.000	0.000
86	A	115	GLN	0	0.032	0.026	20.027	0.045	0.045	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.056	-0.039	22.279	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	117	GLU	-1	-0.929	-0.947	20.294	0.252	0.252	0.000	0.000	0.000	0.000
89	A	118	PHE	0	0.018	-0.014	12.974	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	119	TYR	0	0.034	0.019	18.783	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	120	ARG	1	0.856	0.927	21.232	-0.165	-0.165	0.000	0.000	0.000	0.000
92	A	121	ARG	1	0.912	0.934	16.754	-0.232	-0.232	0.000	0.000	0.000	0.000
93	A	122	LEU	0	-0.008	-0.002	15.682	0.002	0.002	0.000	0.000	0.000	0.000
94	A	123	SER	0	0.008	0.000	17.814	-0.029	-0.029	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.840	-0.901	20.293	0.140	0.140	0.000	0.000	0.000	0.000
96	A	125	GLU	-1	-0.902	-0.940	14.599	0.119	0.119	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.037	0.003	17.343	-0.034	-0.034	0.000	0.000	0.000	0.000
98	A	127	THR	0	0.026	-0.014	18.225	-0.025	-0.025	0.000	0.000	0.000	0.000
99	A	128	GLN	0	-0.038	0.003	20.751	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.915	0.987	14.460	0.088	0.088	0.000	0.000	0.000	0.000
101	A	130	ARG	1	0.860	0.935	18.773	-0.026	-0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:LEU)