FMO DATABASE

FMODB ID: VQRM1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-636569.119673
FMO2-HF: Nuclear repulsion	598301.320276
FMO2-HF: Total energy	-38267.799396
FMO2-MP2: Total energy	-38382.503672

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.
0.299	4.318	0.788	-1.643	-3.163	0.008

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 : -0.014 / q_NPA : -0.029

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	-0.011	0.010	3.804	-4.486	-3.030	0.007	-0.680	-0.782	0.002
4	1	13	GLU	-1	-0.914	-0.976	6.261	1.603	1.603	0.000	0.000	0.000	0.000
5	1	14	PHE	0	-0.026	0.000	8.397	-0.363	-0.363	0.000	0.000	0.000	0.000
6	1	15	LYS	1	1.005	1.018	12.679	0.061	0.061	0.000	0.000	0.000	0.000
7	1	16	VAL	0	-0.022	-0.034	16.209	-0.071	-0.071	0.000	0.000	0.000	0.000
8	1	17	SER	0	0.001	-0.006	19.770	0.014	0.014	0.000	0.000	0.000	0.000
9	1	18	VAL	0	0.024	0.018	22.904	-0.023	-0.023	0.000	0.000	0.000	0.000
10	1	19	PRO	0	0.020	0.021	26.200	0.005	0.005	0.000	0.000	0.000	0.000
11	1	20	ALA	0	0.012	-0.020	29.533	0.009	0.009	0.000	0.000	0.000	0.000
12	1	21	ALA	0	-0.039	-0.016	32.261	0.001	0.001	0.000	0.000	0.000	0.000
13	1	22	GLU	-1	-0.927	-0.959	31.224	0.073	0.073	0.000	0.000	0.000	0.000
14	1	23	VAL	0	0.007	0.002	29.953	0.013	0.013	0.000	0.000	0.000	0.000
15	1	24	ASN	0	-0.039	-0.027	32.558	-0.002	-0.002	0.000	0.000	0.000	0.000
16	1	25	ARG	1	1.025	0.999	36.031	-0.086	-0.086	0.000	0.000	0.000	0.000
17	1	26	ALA	0	-0.002	0.007	31.931	0.001	0.001	0.000	0.000	0.000	0.000
18	1	27	TYR	0	0.047	0.032	29.982	0.014	0.014	0.000	0.000	0.000	0.000
19	1	28	ASP	-1	-0.917	-0.949	34.799	0.121	0.121	0.000	0.000	0.000	0.000
20	1	29	GLN	0	-0.035	-0.022	36.431	-0.002	-0.002	0.000	0.000	0.000	0.000
21	1	30	VAL	0	-0.002	0.006	32.505	0.002	0.002	0.000	0.000	0.000	0.000
22	1	31	TRP	0	0.008	0.017	35.671	-0.002	-0.002	0.000	0.000	0.000	0.000
23	1	32	ALA	0	0.020	-0.007	37.517	-0.002	-0.002	0.000	0.000	0.000	0.000
24	1	33	GLY	0	0.023	0.025	38.748	-0.006	-0.006	0.000	0.000	0.000	0.000
25	1	34	LEU	0	0.075	0.029	33.781	-0.003	-0.003	0.000	0.000	0.000	0.000
26	1	35	ALA	0	-0.037	-0.010	38.225	-0.001	-0.001	0.000	0.000	0.000	0.000
27	1	36	ARG	1	0.751	0.868	41.338	-0.120	-0.120	0.000	0.000	0.000	0.000
28	1	37	ASP	-1	-0.869	-0.916	39.576	0.144	0.144	0.000	0.000	0.000	0.000
29	1	38	VAL	0	-0.053	-0.026	37.635	0.001	0.001	0.000	0.000	0.000	0.000
30	1	39	ARG	1	0.956	0.972	40.490	-0.150	-0.150	0.000	0.000	0.000	0.000
31	1	40	VAL	0	0.005	-0.002	41.860	0.005	0.005	0.000	0.000	0.000	0.000
32	1	41	PRO	0	0.001	-0.014	44.204	-0.006	-0.006	0.000	0.000	0.000	0.000
33	1	42	GLY	0	-0.058	-0.009	46.614	-0.005	-0.005	0.000	0.000	0.000	0.000
34	1	43	PHE	0	0.004	0.004	44.514	-0.008	-0.008	0.000	0.000	0.000	0.000
35	1	44	ARG	1	0.987	0.992	48.078	-0.085	-0.085	0.000	0.000	0.000	0.000
36	1	45	PRO	0	0.077	0.020	45.887	-0.002	-0.002	0.000	0.000	0.000	0.000
37	1	46	GLY	0	0.038	0.020	47.460	-0.004	-0.004	0.000	0.000	0.000	0.000
38	1	47	LYS	1	0.875	0.947	49.281	-0.086	-0.086	0.000	0.000	0.000	0.000
39	1	48	ALA	0	0.053	0.019	45.883	0.003	0.003	0.000	0.000	0.000	0.000
40	1	49	PRO	0	-0.049	-0.021	47.851	-0.003	-0.003	0.000	0.000	0.000	0.000
41	1	50	ARG	1	1.048	1.011	46.097	-0.091	-0.091	0.000	0.000	0.000	0.000
42	1	51	LYS	1	0.998	1.018	44.721	-0.095	-0.095	0.000	0.000	0.000	0.000
43	1	52	VAL	0	0.005	-0.010	45.233	-0.003	-0.003	0.000	0.000	0.000	0.000
44	1	53	ILE	0	0.045	0.012	40.578	0.004	0.004	0.000	0.000	0.000	0.000
45	1	54	GLU	-1	-0.881	-0.942	39.368	0.150	0.150	0.000	0.000	0.000	0.000
46	1	55	ASN	0	-0.015	-0.008	40.329	0.008	0.008	0.000	0.000	0.000	0.000
47	1	56	ARG	1	0.840	0.931	41.724	-0.138	-0.138	0.000	0.000	0.000	0.000
48	1	57	VAL	0	0.022	-0.002	36.648	0.004	0.004	0.000	0.000	0.000	0.000
49	1	58	GLY	0	0.026	0.023	36.160	0.011	0.011	0.000	0.000	0.000	0.000
50	1	59	LYS	1	0.924	0.968	35.350	-0.192	-0.192	0.000	0.000	0.000	0.000
51	1	60	GLY	0	0.121	0.055	31.473	0.006	0.006	0.000	0.000	0.000	0.000
52	1	61	TYR	0	-0.107	-0.060	30.792	0.015	0.015	0.000	0.000	0.000	0.000
53	1	62	VAL	0	0.007	0.005	32.350	-0.010	-0.010	0.000	0.000	0.000	0.000
54	1	63	GLU	-1	-0.804	-0.940	29.138	0.250	0.250	0.000	0.000	0.000	0.000
55	1	64	SER	0	-0.078	-0.021	26.768	0.028	0.028	0.000	0.000	0.000	0.000
56	1	65	GLN	0	0.032	0.027	26.668	0.018	0.018	0.000	0.000	0.000	0.000
57	1	66	VAL	0	-0.024	-0.013	28.052	0.006	0.006	0.000	0.000	0.000	0.000
58	1	67	ARG	1	0.990	1.001	21.911	-0.465	-0.465	0.000	0.000	0.000	0.000
59	1	68	ASP	-1	-0.873	-0.948	22.844	0.503	0.503	0.000	0.000	0.000	0.000
60	1	69	ARG	1	0.896	0.972	24.158	-0.238	-0.238	0.000	0.000	0.000	0.000
61	1	70	LEU	0	-0.029	-0.029	25.191	-0.012	-0.012	0.000	0.000	0.000	0.000
62	1	71	LEU	0	0.049	0.007	19.393	-0.012	-0.012	0.000	0.000	0.000	0.000
63	1	72	GLU	-1	-0.876	-0.923	21.109	0.578	0.578	0.000	0.000	0.000	0.000
64	1	73	THR	0	-0.100	-0.028	22.567	-0.019	-0.019	0.000	0.000	0.000	0.000
65	1	74	HIS	0	0.002	0.003	20.292	-0.003	-0.003	0.000	0.000	0.000	0.000
66	1	75	TYR	0	0.051	0.036	14.050	-0.027	-0.027	0.000	0.000	0.000	0.000
67	1	76	SER	0	-0.050	-0.059	19.642	-0.017	-0.017	0.000	0.000	0.000	0.000
68	1	77	GLN	0	-0.060	-0.063	22.785	-0.025	-0.025	0.000	0.000	0.000	0.000
69	1	78	GLY	0	0.083	0.055	19.558	-0.031	-0.031	0.000	0.000	0.000	0.000
70	1	79	LEU	0	-0.021	-0.010	17.036	-0.019	-0.019	0.000	0.000	0.000	0.000
71	1	80	ARG	1	0.843	0.936	20.713	-0.292	-0.292	0.000	0.000	0.000	0.000
72	1	81	GLU	-1	-0.967	-0.975	22.837	0.123	0.123	0.000	0.000	0.000	0.000
73	1	82	LEU	0	-0.060	-0.015	17.605	-0.033	-0.033	0.000	0.000	0.000	0.000
74	1	83	GLY	0	-0.004	0.011	21.053	-0.020	-0.020	0.000	0.000	0.000	0.000
75	1	84	LEU	0	-0.042	-0.037	14.582	-0.017	-0.017	0.000	0.000	0.000	0.000
76	1	85	ASN	0	-0.029	-0.019	16.242	0.005	0.005	0.000	0.000	0.000	0.000
77	1	86	LEU	0	0.038	0.018	10.557	-0.011	-0.011	0.000	0.000	0.000	0.000
78	1	87	VAL	0	-0.026	-0.005	7.136	-0.070	-0.070	0.000	0.000	0.000	0.000
79	1	88	ASP	-1	-0.921	-0.953	8.793	2.465	2.465	0.000	0.000	0.000	0.000
80	1	89	ALA	0	-0.014	-0.005	8.477	0.609	0.609	0.000	0.000	0.000	0.000
81	1	90	THR	0	-0.035	-0.027	10.724	-0.059	-0.059	0.000	0.000	0.000	0.000
82	1	91	VAL	0	-0.001	-0.014	12.395	-0.049	-0.049	0.000	0.000	0.000	0.000
83	1	92	ASP	-1	-0.901	-0.946	14.259	1.172	1.172	0.000	0.000	0.000	0.000
84	1	93	PRO	0	-0.130	-0.061	17.254	-0.082	-0.082	0.000	0.000	0.000	0.000
85	1	94	GLN	0	0.079	0.061	21.086	0.031	0.031	0.000	0.000	0.000	0.000
86	1	95	ASP	-1	-0.989	-1.005	22.629	0.255	0.255	0.000	0.000	0.000	0.000
87	1	96	VAL	0	-0.008	-0.001	26.217	-0.009	-0.009	0.000	0.000	0.000	0.000
88	1	97	GLN	0	-0.003	-0.017	28.832	0.000	0.000	0.000	0.000	0.000	0.000
89	1	98	SER	0	-0.050	-0.037	31.560	-0.001	-0.001	0.000	0.000	0.000	0.000
90	1	99	GLY	0	0.003	-0.001	33.874	-0.003	-0.003	0.000	0.000	0.000	0.000
91	1	100	GLN	0	-0.008	0.006	30.450	-0.002	-0.002	0.000	0.000	0.000	0.000
92	1	101	ALA	0	-0.003	-0.005	27.815	0.009	0.009	0.000	0.000	0.000	0.000
93	1	102	PHE	0	-0.003	0.002	24.438	-0.003	-0.003	0.000	0.000	0.000	0.000
94	1	103	GLU	-1	-0.966	-0.962	21.654	0.192	0.192	0.000	0.000	0.000	0.000
95	1	104	PHE	0	-0.005	-0.026	17.187	0.014	0.014	0.000	0.000	0.000	0.000
96	1	105	THR	0	0.019	0.003	15.018	-0.083	-0.083	0.000	0.000	0.000	0.000
97	1	106	VAL	0	0.013	0.024	12.352	0.067	0.067	0.000	0.000	0.000	0.000
98	1	107	LYS	1	0.936	0.981	7.828	-2.469	-2.469	0.000	0.000	0.000	0.000
99	1	108	GLY	0	0.011	-0.006	6.946	-0.328	-0.328	0.000	0.000	0.000	0.000
100	1	109	GLU	-1	-0.953	-0.963	2.671	2.150	4.713	0.781	-0.963	-2.381	0.006

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