FMO DATABASE

FMODB ID: QVG5Y

Calculation Name: 2GZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GZV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NRD5

Base Structure: X-ray

Registration Date: 2023-09-23

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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-594625.06305
FMO2-HF: Nuclear repulsion	559473.998878
FMO2-HF: Total energy	-35151.064171
FMO2-MP2: Total energy	-35252.250615

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:17:SER)

Summations of interaction energy for fragment #1(A:17:SER)

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.
-12.984	-9.156	4.791	-4.192	-4.426	-0.02

Interaction energy analysis for fragmet #1(A:17:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.006

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	19	VAL	0	0.020	0.003	2.055	-12.669	-10.352	3.958	-3.372	-2.903	-0.022
4	A	20	PRO	0	0.004	0.003	4.565	0.959	1.057	-0.001	-0.005	-0.092	0.000
5	A	21	GLY	0	0.014	0.002	6.357	-0.001	-0.001	0.000	0.000	0.000	0.000
6	A	22	LYS	1	0.905	0.958	9.810	0.811	0.811	0.000	0.000	0.000	0.000
7	A	23	VAL	0	0.024	0.026	12.530	-0.111	-0.111	0.000	0.000	0.000	0.000
8	A	24	THR	0	-0.001	0.003	14.431	0.045	0.045	0.000	0.000	0.000	0.000
9	A	25	LEU	0	-0.010	0.014	15.937	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	26	GLN	0	0.009	-0.001	19.642	0.029	0.029	0.000	0.000	0.000	0.000
11	A	27	LYS	1	0.755	0.872	22.930	0.027	0.027	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.751	-0.873	25.172	0.041	0.041	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.023	-0.018	26.830	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	30	GLN	0	-0.061	-0.031	27.571	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	31	ASN	0	-0.062	-0.029	28.003	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	32	LEU	0	-0.030	-0.018	23.873	0.007	0.007	0.000	0.000	0.000	0.000
17	A	33	ILE	0	0.048	0.013	18.041	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	34	GLY	0	0.068	0.022	19.854	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	35	ILE	0	-0.018	-0.001	15.437	0.040	0.040	0.000	0.000	0.000	0.000
20	A	36	SER	0	0.004	0.008	17.950	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	37	ILE	0	0.002	-0.001	17.406	0.047	0.047	0.000	0.000	0.000	0.000
22	A	38	GLY	0	0.020	0.005	17.562	-0.029	-0.029	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.029	0.024	18.039	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	40	GLY	0	-0.007	-0.007	18.735	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	41	ALA	0	-0.041	-0.006	21.460	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.020	0.010	23.194	-0.025	-0.025	0.000	0.000	0.000	0.000
27	A	43	TYR	0	0.040	0.009	23.567	0.017	0.017	0.000	0.000	0.000	0.000
28	A	44	CYS	0	-0.013	0.004	17.319	0.022	0.022	0.000	0.000	0.000	0.000
29	A	45	PRO	0	0.004	-0.006	19.803	0.016	0.016	0.000	0.000	0.000	0.000
30	A	46	CYS	0	-0.051	-0.017	14.913	-0.055	-0.055	0.000	0.000	0.000	0.000
31	A	47	LEU	0	0.016	0.000	16.147	0.028	0.028	0.000	0.000	0.000	0.000
32	A	48	TYR	0	0.045	-0.001	11.669	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	49	ILE	0	0.004	0.015	11.792	-0.094	-0.094	0.000	0.000	0.000	0.000
34	A	50	VAL	0	-0.049	-0.017	13.468	0.148	0.148	0.000	0.000	0.000	0.000
35	A	51	GLN	0	0.002	-0.002	15.987	0.066	0.066	0.000	0.000	0.000	0.000
36	A	52	VAL	0	0.008	0.004	13.430	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	53	PHE	0	-0.022	-0.012	16.582	0.029	0.029	0.000	0.000	0.000	0.000
38	A	54	ASP	-1	-0.838	-0.904	20.044	0.248	0.248	0.000	0.000	0.000	0.000
39	A	55	ASN	0	-0.064	-0.045	21.034	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	56	THR	0	-0.017	-0.004	20.438	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	57	PRO	0	0.032	-0.001	20.432	0.003	0.003	0.000	0.000	0.000	0.000
42	A	58	ALA	0	0.001	-0.004	15.830	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.036	-0.007	15.626	0.012	0.012	0.000	0.000	0.000	0.000
44	A	60	LEU	0	-0.061	-0.022	16.763	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.831	-0.897	14.073	-0.284	-0.284	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.007	0.011	13.140	-0.068	-0.068	0.000	0.000	0.000	0.000
47	A	63	THR	0	-0.094	-0.056	9.614	-0.024	-0.024	0.000	0.000	0.000	0.000
48	A	64	VAL	0	-0.019	-0.016	8.857	0.069	0.069	0.000	0.000	0.000	0.000
49	A	65	ALA	0	0.000	-0.005	8.184	0.033	0.033	0.000	0.000	0.000	0.000
50	A	66	ALA	0	-0.017	-0.011	10.301	-0.031	-0.031	0.000	0.000	0.000	0.000
51	A	67	GLY	0	-0.005	-0.001	9.447	0.307	0.307	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.806	-0.876	7.340	1.290	1.290	0.000	0.000	0.000	0.000
53	A	69	GLU	-1	-0.850	-0.913	8.882	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.015	-0.011	10.579	-0.161	-0.161	0.000	0.000	0.000	0.000
55	A	71	THR	0	0.004	-0.014	11.740	0.014	0.014	0.000	0.000	0.000	0.000
56	A	72	GLY	0	-0.018	-0.027	14.514	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	73	VAL	0	0.004	0.012	16.630	0.003	0.003	0.000	0.000	0.000	0.000
58	A	74	ASN	0	0.035	0.011	19.373	-0.006	-0.006	0.000	0.000	0.000	0.000
59	A	75	GLY	0	0.009	0.012	19.414	0.004	0.004	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.921	0.977	20.416	0.086	0.086	0.000	0.000	0.000	0.000
61	A	77	SER	0	0.023	0.006	17.916	0.018	0.018	0.000	0.000	0.000	0.000
62	A	78	ILE	0	0.003	-0.002	16.930	0.013	0.013	0.000	0.000	0.000	0.000
63	A	79	LYS	1	0.934	0.968	16.992	0.000	0.000	0.000	0.000	0.000	0.000
64	A	80	GLY	0	0.036	0.024	20.777	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.733	0.854	22.702	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	82	THR	0	0.027	-0.017	22.676	0.021	0.021	0.000	0.000	0.000	0.000
67	A	83	LYS	1	0.929	0.945	21.492	-0.263	-0.263	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.027	0.016	23.007	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	85	GLU	-1	-0.749	-0.829	25.593	0.029	0.029	0.000	0.000	0.000	0.000
70	A	86	VAL	0	0.015	0.008	19.311	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	87	ALA	0	0.022	0.015	22.703	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	88	LYS	1	0.881	0.939	23.540	-0.060	-0.060	0.000	0.000	0.000	0.000
73	A	89	MET	0	-0.009	-0.010	23.725	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	90	ILE	0	0.035	0.010	19.089	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	91	GLN	0	0.034	0.031	23.176	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	92	GLU	-1	-0.884	-0.919	26.305	-0.031	-0.031	0.000	0.000	0.000	0.000
77	A	93	VAL	0	0.009	0.012	24.671	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	94	LYS	1	0.840	0.912	26.764	0.037	0.037	0.000	0.000	0.000	0.000
79	A	95	GLY	0	0.025	0.021	27.970	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	96	GLU	-1	-0.876	-0.947	22.880	-0.176	-0.176	0.000	0.000	0.000	0.000
81	A	97	VAL	0	-0.021	-0.007	20.424	0.002	0.002	0.000	0.000	0.000	0.000
82	A	98	THR	0	-0.056	-0.034	16.866	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	99	ILE	0	0.007	-0.003	13.698	0.035	0.035	0.000	0.000	0.000	0.000
84	A	100	HIS	0	-0.003	-0.015	13.011	-0.057	-0.057	0.000	0.000	0.000	0.000
85	A	101	TYR	0	0.035	0.014	7.162	0.127	0.127	0.000	0.000	0.000	0.000
86	A	102	ASN	0	-0.042	-0.050	7.052	-0.738	-0.738	0.000	0.000	0.000	0.000
87	A	103	LYS	1	0.784	0.878	2.354	-1.344	-0.463	0.812	-0.617	-1.076	0.003
88	A	104	LEU	0	0.015	0.012	3.552	-0.135	0.306	0.023	-0.191	-0.273	-0.001
89	A	105	GLN	0	0.031	0.026	4.695	1.324	1.415	-0.001	-0.007	-0.082	0.000
90	A	106	TYR	0	-0.007	0.002	5.273	-1.191	-1.191	0.000	0.000	0.000	0.000
91	A	107	TYR	0	-0.009	-0.025	8.025	0.165	0.165	0.000	0.000	0.000	0.000
92	A	108	LYS	1	0.956	0.984	10.818	-1.097	-1.097	0.000	0.000	0.000	0.000
93	A	109	VAL	0	0.025	0.017	13.385	-0.084	-0.084	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:17:SER)