FMO DATABASE

FMODB ID: 1N4RZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-635397.29222
FMO2-HF: Nuclear repulsion	597128.020197
FMO2-HF: Total energy	-38269.272023
FMO2-MP2: Total energy	-38383.707864

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.
-0.616	2.762	0.168	-1.281	-2.265	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 : -0.022 / q_NPA : -0.030

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	-0.014	0.003	3.804	-4.378	-3.051	0.019	-0.572	-0.774	0.003
4	1	13	GLU	-1	-0.902	-0.966	6.261	1.982	1.982	0.000	0.000	0.000	0.000
5	1	14	PHE	0	-0.030	0.002	8.798	-0.318	-0.318	0.000	0.000	0.000	0.000
6	1	15	LYS	1	0.991	0.995	12.651	-0.123	-0.123	0.000	0.000	0.000	0.000
7	1	16	VAL	0	0.001	-0.015	16.240	-0.084	-0.084	0.000	0.000	0.000	0.000
8	1	17	SER	0	-0.007	-0.003	19.738	0.028	0.028	0.000	0.000	0.000	0.000
9	1	18	VAL	0	0.020	0.015	22.932	-0.030	-0.030	0.000	0.000	0.000	0.000
10	1	19	PRO	0	0.027	0.022	26.167	0.010	0.010	0.000	0.000	0.000	0.000
11	1	20	ALA	0	0.004	-0.021	29.562	0.002	0.002	0.000	0.000	0.000	0.000
12	1	21	ALA	0	-0.047	-0.016	32.292	-0.003	-0.003	0.000	0.000	0.000	0.000
13	1	22	GLU	-1	-0.929	-0.958	31.255	0.080	0.080	0.000	0.000	0.000	0.000
14	1	23	VAL	0	0.016	0.001	29.789	0.009	0.009	0.000	0.000	0.000	0.000
15	1	24	ASN	0	-0.008	0.002	32.535	-0.003	-0.003	0.000	0.000	0.000	0.000
16	1	25	ARG	1	0.985	0.973	36.122	-0.095	-0.095	0.000	0.000	0.000	0.000
17	1	26	ALA	0	0.002	0.011	32.067	-0.004	-0.004	0.000	0.000	0.000	0.000
18	1	27	TYR	0	0.040	0.021	29.833	0.004	0.004	0.000	0.000	0.000	0.000
19	1	28	ASP	-1	-0.904	-0.951	35.021	0.115	0.115	0.000	0.000	0.000	0.000
20	1	29	GLN	0	-0.025	-0.016	36.724	-0.007	-0.007	0.000	0.000	0.000	0.000
21	1	30	VAL	0	-0.007	0.005	32.716	-0.002	-0.002	0.000	0.000	0.000	0.000
22	1	31	TRP	0	0.009	0.013	35.963	-0.005	-0.005	0.000	0.000	0.000	0.000
23	1	32	ALA	0	0.026	-0.003	37.794	-0.003	-0.003	0.000	0.000	0.000	0.000
24	1	33	GLY	0	-0.025	0.006	39.070	-0.007	-0.007	0.000	0.000	0.000	0.000
25	1	34	LEU	0	0.074	0.029	33.898	-0.003	-0.003	0.000	0.000	0.000	0.000
26	1	35	ALA	0	-0.036	-0.010	38.568	-0.002	-0.002	0.000	0.000	0.000	0.000
27	1	36	ARG	1	0.792	0.886	41.667	-0.091	-0.091	0.000	0.000	0.000	0.000
28	1	37	ASP	-1	-0.869	-0.919	40.039	0.091	0.091	0.000	0.000	0.000	0.000
29	1	38	VAL	0	-0.058	-0.033	38.009	0.000	0.000	0.000	0.000	0.000	0.000
30	1	39	ARG	1	0.956	0.975	40.864	-0.102	-0.102	0.000	0.000	0.000	0.000
31	1	40	VAL	0	-0.001	-0.005	42.179	0.006	0.006	0.000	0.000	0.000	0.000
32	1	41	PRO	0	-0.002	-0.014	44.673	-0.005	-0.005	0.000	0.000	0.000	0.000
33	1	42	GLY	0	-0.053	-0.005	46.940	-0.003	-0.003	0.000	0.000	0.000	0.000
34	1	43	PHE	0	0.018	0.002	44.889	-0.005	-0.005	0.000	0.000	0.000	0.000
35	1	44	ARG	1	0.983	0.992	48.423	-0.063	-0.063	0.000	0.000	0.000	0.000
36	1	45	PRO	0	0.070	0.019	46.157	0.000	0.000	0.000	0.000	0.000	0.000
37	1	46	GLY	0	0.031	0.013	47.827	-0.004	-0.004	0.000	0.000	0.000	0.000
38	1	47	LYS	1	0.887	0.950	49.632	-0.067	-0.067	0.000	0.000	0.000	0.000
39	1	48	ALA	0	0.043	0.025	46.132	0.002	0.002	0.000	0.000	0.000	0.000
40	1	49	PRO	0	-0.046	-0.022	48.232	-0.001	-0.001	0.000	0.000	0.000	0.000
41	1	50	ARG	1	1.042	1.010	46.294	-0.088	-0.088	0.000	0.000	0.000	0.000
42	1	51	LYS	1	1.006	1.022	44.942	-0.101	-0.101	0.000	0.000	0.000	0.000
43	1	52	VAL	0	0.011	-0.006	45.496	-0.002	-0.002	0.000	0.000	0.000	0.000
44	1	53	ILE	0	0.042	0.013	40.972	0.003	0.003	0.000	0.000	0.000	0.000
45	1	54	GLU	-1	-0.873	-0.940	39.507	0.145	0.145	0.000	0.000	0.000	0.000
46	1	55	ASN	0	-0.027	-0.013	40.531	0.007	0.007	0.000	0.000	0.000	0.000
47	1	56	ARG	1	0.847	0.929	42.059	-0.119	-0.119	0.000	0.000	0.000	0.000
48	1	57	VAL	0	0.022	-0.005	37.034	0.004	0.004	0.000	0.000	0.000	0.000
49	1	58	GLY	0	0.021	0.022	36.414	0.009	0.009	0.000	0.000	0.000	0.000
50	1	59	LYS	1	0.897	0.958	35.612	-0.172	-0.172	0.000	0.000	0.000	0.000
51	1	60	GLY	0	0.141	0.068	31.689	0.010	0.010	0.000	0.000	0.000	0.000
52	1	61	TYR	0	-0.093	-0.058	31.051	0.014	0.014	0.000	0.000	0.000	0.000
53	1	62	VAL	0	0.002	-0.001	32.557	-0.015	-0.015	0.000	0.000	0.000	0.000
54	1	63	GLU	-1	-0.813	-0.920	29.167	0.244	0.244	0.000	0.000	0.000	0.000
55	1	64	SER	0	-0.050	-0.011	27.021	0.028	0.028	0.000	0.000	0.000	0.000
56	1	65	GLN	0	0.012	0.015	26.953	0.010	0.010	0.000	0.000	0.000	0.000
57	1	66	VAL	0	-0.025	-0.019	28.378	-0.004	-0.004	0.000	0.000	0.000	0.000
58	1	67	ARG	1	0.867	0.924	22.038	-0.417	-0.417	0.000	0.000	0.000	0.000
59	1	68	ASP	-1	-0.778	-0.880	22.858	0.417	0.417	0.000	0.000	0.000	0.000
60	1	69	ARG	1	0.923	0.980	24.527	-0.179	-0.179	0.000	0.000	0.000	0.000
61	1	70	LEU	0	-0.048	-0.031	25.486	-0.020	-0.020	0.000	0.000	0.000	0.000
62	1	71	LEU	0	0.036	0.018	19.524	-0.014	-0.014	0.000	0.000	0.000	0.000
63	1	72	GLU	-1	-0.883	-0.935	21.379	0.302	0.302	0.000	0.000	0.000	0.000
64	1	73	THR	0	-0.080	-0.051	22.977	-0.031	-0.031	0.000	0.000	0.000	0.000
65	1	74	HIS	0	0.005	-0.004	20.354	-0.011	-0.011	0.000	0.000	0.000	0.000
66	1	75	TYR	0	0.040	0.028	15.167	-0.018	-0.018	0.000	0.000	0.000	0.000
67	1	76	SER	0	-0.045	-0.024	19.626	-0.039	-0.039	0.000	0.000	0.000	0.000
68	1	77	GLN	0	-0.097	-0.065	22.766	-0.011	-0.011	0.000	0.000	0.000	0.000
69	1	78	GLY	0	0.056	0.041	19.519	-0.027	-0.027	0.000	0.000	0.000	0.000
70	1	79	LEU	0	-0.029	-0.014	17.041	-0.038	-0.038	0.000	0.000	0.000	0.000
71	1	80	ARG	1	0.865	0.936	20.672	-0.108	-0.108	0.000	0.000	0.000	0.000
72	1	81	GLU	-1	-0.907	-0.947	22.862	-0.005	-0.005	0.000	0.000	0.000	0.000
73	1	82	LEU	0	-0.052	-0.012	17.314	-0.029	-0.029	0.000	0.000	0.000	0.000
74	1	83	GLY	0	-0.006	0.010	20.988	-0.019	-0.019	0.000	0.000	0.000	0.000
75	1	84	LEU	0	-0.043	-0.037	14.610	-0.026	-0.026	0.000	0.000	0.000	0.000
76	1	85	ASN	0	-0.034	-0.017	16.224	0.023	0.023	0.000	0.000	0.000	0.000
77	1	86	LEU	0	0.033	0.013	10.594	-0.066	-0.066	0.000	0.000	0.000	0.000
78	1	87	VAL	0	-0.021	-0.009	7.139	-0.047	-0.047	0.000	0.000	0.000	0.000
79	1	88	ASP	-1	-0.931	-0.950	9.254	1.452	1.452	0.000	0.000	0.000	0.000
80	1	89	ALA	0	-0.003	-0.004	8.942	0.449	0.449	0.000	0.000	0.000	0.000
81	1	90	THR	0	-0.017	-0.017	11.128	-0.032	-0.032	0.000	0.000	0.000	0.000
82	1	91	VAL	0	-0.013	-0.012	12.694	0.019	0.019	0.000	0.000	0.000	0.000
83	1	92	ASP	-1	-0.816	-0.892	14.254	1.324	1.324	0.000	0.000	0.000	0.000
84	1	93	PRO	0	-0.090	-0.038	17.401	-0.072	-0.072	0.000	0.000	0.000	0.000
85	1	94	GLN	0	0.029	0.011	21.186	0.058	0.058	0.000	0.000	0.000	0.000
86	1	95	ASP	-1	-0.954	-0.965	22.694	0.342	0.342	0.000	0.000	0.000	0.000
87	1	96	VAL	0	-0.005	-0.005	26.256	-0.011	-0.011	0.000	0.000	0.000	0.000
88	1	97	GLN	0	0.023	0.014	28.904	-0.014	-0.014	0.000	0.000	0.000	0.000
89	1	98	SER	0	-0.030	-0.029	31.593	-0.007	-0.007	0.000	0.000	0.000	0.000
90	1	99	GLY	0	-0.008	-0.004	33.926	-0.009	-0.009	0.000	0.000	0.000	0.000
91	1	100	GLN	0	-0.040	-0.026	30.561	-0.002	-0.002	0.000	0.000	0.000	0.000
92	1	101	ALA	0	-0.001	0.001	27.900	0.004	0.004	0.000	0.000	0.000	0.000
93	1	102	PHE	0	-0.019	-0.003	25.035	0.002	0.002	0.000	0.000	0.000	0.000
94	1	103	GLU	-1	-0.948	-0.965	21.732	0.316	0.316	0.000	0.000	0.000	0.000
95	1	104	PHE	0	-0.021	-0.029	18.181	0.013	0.013	0.000	0.000	0.000	0.000
96	1	105	THR	0	0.013	0.001	15.023	-0.067	-0.067	0.000	0.000	0.000	0.000
97	1	106	VAL	0	0.005	0.021	12.963	0.060	0.060	0.000	0.000	0.000	0.000
98	1	107	LYS	1	0.846	0.909	8.508	-1.944	-1.944	0.000	0.000	0.000	0.000
99	1	108	GLY	0	0.023	0.007	7.226	-0.377	-0.377	0.000	0.000	0.000	0.000
100	1	109	GLU	-1	-0.968	-0.973	3.173	1.349	3.400	0.149	-0.709	-1.491	-0.001

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