FMO DATABASE

FMODB ID: G5N11

Calculation Name: 2D3O-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3O

Chain ID: 1

ChEMBL ID:

UniProt ID: Q9RXK0

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	OptAll
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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-639233.329791
FMO2-HF: Nuclear repulsion	600963.136473
FMO2-HF: Total energy	-38270.193318
FMO2-MP2: Total energy	-38384.63247

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(1:10:ASN)

Summations of interaction energy for fragment #1(1:10: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.
-2.397	1.4	0.638	-1.604	-2.833	-0.002

Interaction energy analysis for fragmet #1(1:10:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.035

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	1	12	VAL	0	-0.027	-0.004	3.794	-4.411	-3.109	0.028	-0.614	-0.717	0.003
4	1	13	GLU	-1	-0.909	-0.963	6.443	2.005	2.005	0.000	0.000	0.000	0.000
5	1	14	PHE	0	-0.030	-0.007	8.993	-0.305	-0.305	0.000	0.000	0.000	0.000
6	1	15	LYS	1	0.901	0.935	13.272	-0.209	-0.209	0.000	0.000	0.000	0.000
7	1	16	VAL	0	-0.003	-0.006	16.955	-0.079	-0.079	0.000	0.000	0.000	0.000
8	1	17	SER	0	0.014	0.007	20.414	0.031	0.031	0.000	0.000	0.000	0.000
9	1	18	VAL	0	-0.005	0.007	23.350	-0.032	-0.032	0.000	0.000	0.000	0.000
10	1	19	PRO	0	0.008	0.008	26.393	0.012	0.012	0.000	0.000	0.000	0.000
11	1	20	ALA	0	0.033	-0.016	29.741	-0.005	-0.005	0.000	0.000	0.000	0.000
12	1	21	ALA	0	-0.053	-0.007	32.507	-0.002	-0.002	0.000	0.000	0.000	0.000
13	1	22	GLU	-1	-0.864	-0.945	31.888	0.071	0.071	0.000	0.000	0.000	0.000
14	1	23	VAL	0	-0.027	-0.003	29.884	0.000	0.000	0.000	0.000	0.000	0.000
15	1	24	ASN	0	-0.029	-0.014	32.525	-0.004	-0.004	0.000	0.000	0.000	0.000
16	1	25	ARG	1	0.964	0.971	36.129	-0.090	-0.090	0.000	0.000	0.000	0.000
17	1	26	ALA	0	0.015	0.018	31.998	-0.006	-0.006	0.000	0.000	0.000	0.000
18	1	27	TYR	0	-0.008	0.000	29.712	0.001	0.001	0.000	0.000	0.000	0.000
19	1	28	ASP	-1	-0.886	-0.940	35.256	0.096	0.096	0.000	0.000	0.000	0.000
20	1	29	GLN	0	-0.012	-0.016	37.213	-0.006	-0.006	0.000	0.000	0.000	0.000
21	1	30	VAL	0	0.011	0.014	33.156	-0.004	-0.004	0.000	0.000	0.000	0.000
22	1	31	TRP	0	-0.020	-0.004	36.437	-0.004	-0.004	0.000	0.000	0.000	0.000
23	1	32	ALA	0	0.019	0.004	38.163	-0.003	-0.003	0.000	0.000	0.000	0.000
24	1	33	GLY	0	-0.010	0.015	39.338	-0.007	-0.007	0.000	0.000	0.000	0.000
25	1	34	LEU	0	0.099	0.034	34.461	-0.003	-0.003	0.000	0.000	0.000	0.000
26	1	35	ALA	0	-0.066	-0.022	39.089	-0.002	-0.002	0.000	0.000	0.000	0.000
27	1	36	ARG	1	0.798	0.876	42.312	-0.066	-0.066	0.000	0.000	0.000	0.000
28	1	37	ASP	-1	-0.878	-0.914	40.208	0.058	0.058	0.000	0.000	0.000	0.000
29	1	38	VAL	0	-0.047	-0.031	38.488	0.000	0.000	0.000	0.000	0.000	0.000
30	1	39	ARG	1	0.961	0.976	41.395	-0.069	-0.069	0.000	0.000	0.000	0.000
31	1	40	VAL	0	0.017	0.007	42.282	0.004	0.004	0.000	0.000	0.000	0.000
32	1	41	PRO	0	0.002	-0.013	44.656	-0.004	-0.004	0.000	0.000	0.000	0.000
33	1	42	GLY	0	-0.056	-0.010	47.440	-0.002	-0.002	0.000	0.000	0.000	0.000
34	1	43	PHE	0	-0.020	-0.022	44.941	-0.002	-0.002	0.000	0.000	0.000	0.000
35	1	44	ARG	1	0.968	0.998	48.709	-0.046	-0.046	0.000	0.000	0.000	0.000
36	1	45	PRO	0	0.056	0.026	46.240	0.001	0.001	0.000	0.000	0.000	0.000
37	1	46	GLY	0	0.053	0.015	48.067	-0.005	-0.005	0.000	0.000	0.000	0.000
38	1	47	LYS	1	0.883	0.939	49.990	-0.052	-0.052	0.000	0.000	0.000	0.000
39	1	48	ALA	0	0.081	0.047	46.276	0.002	0.002	0.000	0.000	0.000	0.000
40	1	49	PRO	0	-0.024	-0.014	48.364	0.000	0.000	0.000	0.000	0.000	0.000
41	1	50	ARG	1	0.972	0.990	46.490	-0.078	-0.078	0.000	0.000	0.000	0.000
42	1	51	LYS	1	1.037	1.024	45.604	-0.099	-0.099	0.000	0.000	0.000	0.000
43	1	52	VAL	0	-0.060	-0.030	45.579	-0.003	-0.003	0.000	0.000	0.000	0.000
44	1	53	ILE	0	0.028	0.018	40.889	0.002	0.002	0.000	0.000	0.000	0.000
45	1	54	GLU	-1	-0.782	-0.905	40.205	0.120	0.120	0.000	0.000	0.000	0.000
46	1	55	ASN	0	-0.008	-0.013	40.746	0.010	0.010	0.000	0.000	0.000	0.000
47	1	56	ARG	1	0.891	0.958	42.178	-0.101	-0.101	0.000	0.000	0.000	0.000
48	1	57	VAL	0	0.041	0.006	37.362	0.004	0.004	0.000	0.000	0.000	0.000
49	1	58	GLY	0	-0.002	0.013	36.504	0.008	0.008	0.000	0.000	0.000	0.000
50	1	59	LYS	1	0.807	0.887	35.688	-0.149	-0.149	0.000	0.000	0.000	0.000
51	1	60	GLY	0	0.113	0.070	31.341	0.011	0.011	0.000	0.000	0.000	0.000
52	1	61	TYR	0	-0.070	-0.043	31.120	0.007	0.007	0.000	0.000	0.000	0.000
53	1	62	VAL	0	-0.049	-0.014	32.950	-0.016	-0.016	0.000	0.000	0.000	0.000
54	1	63	GLU	-1	-0.735	-0.874	29.484	0.230	0.230	0.000	0.000	0.000	0.000
55	1	64	SER	0	-0.009	-0.014	27.217	0.016	0.016	0.000	0.000	0.000	0.000
56	1	65	GLN	0	-0.007	0.008	27.371	0.001	0.001	0.000	0.000	0.000	0.000
57	1	66	VAL	0	-0.061	-0.028	29.249	-0.013	-0.013	0.000	0.000	0.000	0.000
58	1	67	ARG	1	0.855	0.903	22.511	-0.362	-0.362	0.000	0.000	0.000	0.000
59	1	68	ASP	-1	-0.770	-0.870	23.068	0.345	0.345	0.000	0.000	0.000	0.000
60	1	69	ARG	1	0.952	0.989	24.433	-0.136	-0.136	0.000	0.000	0.000	0.000
61	1	70	LEU	0	-0.057	-0.018	25.510	-0.024	-0.024	0.000	0.000	0.000	0.000
62	1	71	LEU	0	0.038	0.020	19.616	-0.018	-0.018	0.000	0.000	0.000	0.000
63	1	72	GLU	-1	-0.829	-0.887	21.088	0.120	0.120	0.000	0.000	0.000	0.000
64	1	73	THR	0	-0.080	-0.058	22.799	-0.035	-0.035	0.000	0.000	0.000	0.000
65	1	74	HIS	0	-0.004	-0.004	20.371	-0.014	-0.014	0.000	0.000	0.000	0.000
66	1	75	TYR	0	0.016	0.019	15.606	-0.048	-0.048	0.000	0.000	0.000	0.000
67	1	76	SER	0	-0.041	-0.057	19.674	-0.052	-0.052	0.000	0.000	0.000	0.000
68	1	77	GLN	0	-0.131	-0.075	22.968	-0.005	-0.005	0.000	0.000	0.000	0.000
69	1	78	GLY	0	0.052	0.031	19.428	-0.025	-0.025	0.000	0.000	0.000	0.000
70	1	79	LEU	0	0.000	-0.007	17.056	-0.042	-0.042	0.000	0.000	0.000	0.000
71	1	80	ARG	1	0.846	0.927	20.487	-0.013	-0.013	0.000	0.000	0.000	0.000
72	1	81	GLU	-1	-0.892	-0.935	22.976	-0.084	-0.084	0.000	0.000	0.000	0.000
73	1	82	LEU	0	-0.042	-0.016	17.418	-0.025	-0.025	0.000	0.000	0.000	0.000
74	1	83	GLY	0	-0.024	0.003	20.654	-0.030	-0.030	0.000	0.000	0.000	0.000
75	1	84	LEU	0	-0.050	-0.027	14.416	-0.020	-0.020	0.000	0.000	0.000	0.000
76	1	85	ASN	0	-0.027	-0.019	15.874	0.043	0.043	0.000	0.000	0.000	0.000
77	1	86	LEU	0	0.014	0.005	10.898	-0.107	-0.107	0.000	0.000	0.000	0.000
78	1	87	VAL	0	-0.021	-0.005	7.011	-0.015	-0.015	0.000	0.000	0.000	0.000
79	1	88	ASP	-1	-0.863	-0.927	9.335	1.258	1.258	0.000	0.000	0.000	0.000
80	1	89	ALA	0	0.008	-0.004	9.532	0.163	0.163	0.000	0.000	0.000	0.000
81	1	90	THR	0	-0.013	-0.014	11.244	-0.159	-0.159	0.000	0.000	0.000	0.000
82	1	91	VAL	0	-0.001	0.000	12.973	0.102	0.102	0.000	0.000	0.000	0.000
83	1	92	ASP	-1	-0.803	-0.881	14.628	1.261	1.261	0.000	0.000	0.000	0.000
84	1	93	PRO	0	-0.079	-0.040	17.573	-0.079	-0.079	0.000	0.000	0.000	0.000
85	1	94	GLN	0	-0.008	-0.003	21.154	0.041	0.041	0.000	0.000	0.000	0.000
86	1	95	ASP	-1	-0.904	-0.937	22.569	0.331	0.331	0.000	0.000	0.000	0.000
87	1	96	VAL	0	-0.014	-0.012	26.269	-0.012	-0.012	0.000	0.000	0.000	0.000
88	1	97	GLN	0	0.019	0.007	28.959	-0.035	-0.035	0.000	0.000	0.000	0.000
89	1	98	SER	0	-0.030	-0.034	31.469	-0.010	-0.010	0.000	0.000	0.000	0.000
90	1	99	GLY	0	-0.030	0.000	34.056	-0.012	-0.012	0.000	0.000	0.000	0.000
91	1	100	GLN	0	-0.017	-0.017	31.043	-0.019	-0.019	0.000	0.000	0.000	0.000
92	1	101	ALA	0	-0.002	-0.001	28.297	-0.003	-0.003	0.000	0.000	0.000	0.000
93	1	102	PHE	0	-0.035	-0.025	25.271	0.003	0.003	0.000	0.000	0.000	0.000
94	1	103	GLU	-1	-0.853	-0.904	21.874	0.316	0.316	0.000	0.000	0.000	0.000
95	1	104	PHE	0	-0.021	-0.023	18.507	0.005	0.005	0.000	0.000	0.000	0.000
96	1	105	THR	0	0.033	0.017	15.019	-0.077	-0.077	0.000	0.000	0.000	0.000
97	1	106	VAL	0	0.000	0.000	12.942	-0.003	-0.003	0.000	0.000	0.000	0.000
98	1	107	LYS	1	0.771	0.875	8.805	-1.690	-1.690	0.000	0.000	0.000	0.000
99	1	108	GLY	0	0.060	0.033	7.457	-0.258	-0.258	0.000	0.000	0.000	0.000
100	1	109	GLU	-1	-0.984	-0.986	2.702	0.214	2.709	0.610	-0.990	-2.116	-0.005

Top

Graph

Manual

About

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