FMO DATABASE

FMODB ID: LJ599

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

Total energy (hartree)

FMO2-HF: Electronic energy	-834260.825007
FMO2-HF: Nuclear repulsion	791882.290853
FMO2-HF: Total energy	-42378.534155
FMO2-MP2: Total energy	-42501.949012

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.
-4.2	-0.103	1.559	-1.805	-3.849	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 : -0.026 / q_NPA : -0.027

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	12	GLU	-1	-0.884	-0.929	3.826	-2.928	-0.738	-0.033	-1.023	-1.133	-0.002
4	A	13	ILE	0	0.034	0.007	6.829	0.421	0.421	0.000	0.000	0.000	0.000
5	A	14	ASN	0	-0.084	-0.048	9.994	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	15	GLU	-1	-0.768	-0.836	7.040	-1.242	-1.242	0.000	0.000	0.000	0.000
7	A	16	THR	0	-0.019	-0.026	9.098	0.241	0.241	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.015	-0.013	6.474	-0.147	-0.147	0.000	0.000	0.000	0.000
9	A	18	VAL	0	0.030	0.031	9.025	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	19	ILE	0	0.005	-0.013	11.226	0.031	0.031	0.000	0.000	0.000	0.000
11	A	20	GLN	0	0.018	0.035	6.920	-0.194	-0.194	0.000	0.000	0.000	0.000
12	A	21	GLN	0	-0.025	-0.007	10.906	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	22	ARG	1	0.948	0.962	12.999	-0.167	-0.167	0.000	0.000	0.000	0.000
14	A	23	GLY	0	0.004	0.012	14.877	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	24	VAL	0	-0.022	-0.002	14.446	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	25	ARG	1	0.865	0.945	16.011	0.057	0.057	0.000	0.000	0.000	0.000
17	A	26	VAL	0	0.082	0.028	13.894	0.009	0.009	0.000	0.000	0.000	0.000
18	A	27	TYR	0	-0.055	-0.012	17.283	0.008	0.008	0.000	0.000	0.000	0.000
19	A	28	ASP	-1	-0.782	-0.873	20.075	-0.217	-0.217	0.000	0.000	0.000	0.000
20	A	29	GLY	0	0.029	0.013	21.730	0.004	0.004	0.000	0.000	0.000	0.000
21	A	30	GLU	-1	-0.897	-0.947	24.988	-0.082	-0.082	0.000	0.000	0.000	0.000
22	A	31	GLU	-1	-0.872	-0.934	22.997	-0.134	-0.134	0.000	0.000	0.000	0.000
23	A	32	LYS	1	0.973	1.001	25.892	0.081	0.081	0.000	0.000	0.000	0.000
24	A	33	ILE	0	-0.052	-0.059	24.268	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	34	LYS	1	0.799	0.896	20.768	0.170	0.170	0.000	0.000	0.000	0.000
26	A	35	PHE	0	-0.028	-0.001	19.233	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	36	ASP	-1	-0.829	-0.901	14.511	-0.237	-0.237	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.052	-0.032	15.991	0.011	0.011	0.000	0.000	0.000	0.000
29	A	38	GLY	0	0.038	0.003	12.339	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	39	THR	0	-0.127	-0.088	9.631	0.054	0.054	0.000	0.000	0.000	0.000
31	A	40	LEU	0	0.056	0.041	9.793	-0.065	-0.065	0.000	0.000	0.000	0.000
32	A	41	LEU	0	-0.061	-0.036	4.672	0.087	0.159	-0.001	-0.003	-0.067	0.000
33	A	42	LEU	0	0.014	0.016	8.390	-0.177	-0.177	0.000	0.000	0.000	0.000
34	A	43	SER	0	-0.047	-0.052	7.556	0.161	0.161	0.000	0.000	0.000	0.000
35	A	44	THR	0	0.056	0.023	9.682	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	45	HIS	0	-0.005	-0.010	10.461	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	46	ARG	1	0.867	0.912	2.656	2.306	3.130	0.114	-0.315	-0.623	0.001
38	A	47	LEU	0	-0.002	0.000	9.739	0.116	0.116	0.000	0.000	0.000	0.000
39	A	48	ILE	0	0.017	0.001	3.921	-0.340	-0.064	0.001	-0.044	-0.233	0.000
40	A	49	TRP	0	0.014	0.012	6.925	0.238	0.238	0.000	0.000	0.000	0.000
41	A	50	ARG	1	0.925	0.972	3.537	-0.833	-0.531	0.001	-0.054	-0.249	0.000
42	A	51	ASP	-1	-0.766	-0.906	6.790	-0.185	-0.185	0.000	0.000	0.000	0.000
43	A	52	GLN	0	-0.042	-0.027	9.789	0.035	0.035	0.000	0.000	0.000	0.000
44	A	53	LYS	1	0.895	0.947	12.394	0.222	0.222	0.000	0.000	0.000	0.000
45	A	54	ASN	0	0.035	-0.017	9.137	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	55	ASN	0	0.030	0.016	8.380	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	56	GLU	-1	-0.930	-0.953	8.675	-0.472	-0.472	0.000	0.000	0.000	0.000
48	A	57	CYS	0	-0.081	-0.045	5.244	0.002	0.002	0.000	0.000	0.000	0.000
49	A	58	CYS	0	-0.110	-0.024	2.463	-0.740	-0.451	1.478	-0.352	-1.416	0.001
50	A	59	MET	0	0.069	0.044	4.438	-0.337	-0.193	-0.001	-0.014	-0.128	0.000
51	A	60	ALA	0	-0.009	-0.004	6.730	-0.154	-0.154	0.000	0.000	0.000	0.000
52	A	61	ILE	0	-0.001	-0.014	5.711	-0.195	-0.195	0.000	0.000	0.000	0.000
53	A	62	PRO	0	-0.009	-0.002	9.043	0.028	0.028	0.000	0.000	0.000	0.000
54	A	63	LEU	0	-0.061	-0.015	12.041	-0.017	-0.017	0.000	0.000	0.000	0.000
55	A	64	SER	0	0.042	0.014	13.921	0.003	0.003	0.000	0.000	0.000	0.000
56	A	65	GLN	0	-0.022	-0.004	15.697	0.006	0.006	0.000	0.000	0.000	0.000
57	A	66	ILE	0	-0.037	0.015	15.839	0.014	0.014	0.000	0.000	0.000	0.000
58	A	67	VAL	0	-0.008	0.012	18.618	0.018	0.018	0.000	0.000	0.000	0.000
59	A	68	PHE	0	-0.005	-0.013	22.356	0.014	0.014	0.000	0.000	0.000	0.000
60	A	69	ILE	0	-0.016	-0.009	19.168	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	70	GLU	-1	-0.868	-0.938	22.522	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	71	GLU	-1	-0.922	-0.964	23.929	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	72	GLN	0	-0.002	0.001	26.210	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	73	ALA	0	-0.006	-0.004	27.786	0.003	0.003	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.908	0.965	23.044	0.069	0.069	0.000	0.000	0.000	0.000
66	A	82	ILE	0	-0.004	-0.006	19.013	0.006	0.006	0.000	0.000	0.000	0.000
67	A	83	VAL	0	0.004	0.006	20.762	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.029	-0.007	17.116	0.004	0.004	0.000	0.000	0.000	0.000
69	A	85	HIS	0	-0.014	0.000	20.269	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	86	LEU	0	0.001	-0.030	15.708	0.000	0.000	0.000	0.000	0.000	0.000
71	A	87	HIS	0	0.020	0.030	19.142	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	101	SER	0	-0.010	-0.015	30.232	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.966	0.978	24.509	0.174	0.174	0.000	0.000	0.000	0.000
74	A	103	ASN	0	-0.030	-0.014	21.875	0.010	0.010	0.000	0.000	0.000	0.000
75	A	104	SER	0	0.027	0.007	24.048	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	105	TYR	0	-0.045	-0.023	21.728	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	106	ILE	0	0.051	0.054	16.106	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	107	ARG	1	0.818	0.885	20.212	0.113	0.113	0.000	0.000	0.000	0.000
79	A	108	LEU	0	0.034	0.008	15.516	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	109	SER	0	-0.073	-0.047	19.157	0.021	0.021	0.000	0.000	0.000	0.000
81	A	110	PHE	0	0.033	0.016	16.249	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.896	0.958	20.592	0.012	0.012	0.000	0.000	0.000	0.000
83	A	112	GLU	-1	-0.916	-0.955	19.106	0.098	0.098	0.000	0.000	0.000	0.000
84	A	113	HIS	0	0.032	0.008	20.171	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.072	0.008	18.904	0.020	0.020	0.000	0.000	0.000	0.000
86	A	115	GLN	0	0.063	0.051	19.072	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	116	ILE	0	-0.029	-0.033	21.484	0.010	0.010	0.000	0.000	0.000	0.000
88	A	117	GLU	-1	-0.951	-0.968	19.504	0.124	0.124	0.000	0.000	0.000	0.000
89	A	118	PHE	0	0.025	-0.008	12.489	0.010	0.010	0.000	0.000	0.000	0.000
90	A	119	TYR	0	0.031	0.027	18.002	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	120	ARG	1	0.949	0.977	20.639	-0.062	-0.062	0.000	0.000	0.000	0.000
92	A	121	ARG	1	0.940	0.962	16.253	-0.108	-0.108	0.000	0.000	0.000	0.000
93	A	122	LEU	0	0.001	0.011	15.572	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	123	SER	0	-0.022	-0.014	17.332	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.924	-0.970	19.773	0.046	0.046	0.000	0.000	0.000	0.000
96	A	125	GLU	-1	-0.891	-0.935	14.255	0.052	0.052	0.000	0.000	0.000	0.000
97	A	126	MET	0	-0.062	-0.009	17.327	-0.019	-0.019	0.000	0.000	0.000	0.000
98	A	127	THR	0	-0.004	-0.069	18.156	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	128	GLN	0	-0.003	0.060	20.387	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.919	0.986	14.405	0.230	0.230	0.000	0.000	0.000	0.000
101	A	130	ARG	1	0.881	0.949	18.670	0.126	0.126	0.000	0.000	0.000	0.000

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