FMO DATABASE

FMODB ID: ZV59N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-594461.766091
FMO2-HF: Nuclear repulsion	559311.096465
FMO2-HF: Total energy	-35150.669626
FMO2-MP2: Total energy	-35251.858361

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.
-14.238	-15.383	11.421	-5.488	-4.786	-0.032

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 : -0.032 / q_NPA : -0.040

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	0.036	0.019	1.804	-14.249	-16.689	10.183	-4.605	-3.137	-0.038
4	A	20	PRO	0	-0.012	0.005	4.516	1.230	1.357	-0.001	-0.009	-0.116	0.000
5	A	21	GLY	0	0.013	0.000	6.385	-0.073	-0.073	0.000	0.000	0.000	0.000
6	A	22	LYS	1	0.906	0.955	9.783	0.696	0.696	0.000	0.000	0.000	0.000
7	A	23	VAL	0	0.032	0.029	12.558	-0.079	-0.079	0.000	0.000	0.000	0.000
8	A	24	THR	0	-0.023	-0.023	14.341	0.033	0.033	0.000	0.000	0.000	0.000
9	A	25	LEU	0	-0.015	0.001	15.591	0.009	0.009	0.000	0.000	0.000	0.000
10	A	26	GLN	0	0.025	-0.010	19.252	0.007	0.007	0.000	0.000	0.000	0.000
11	A	27	LYS	1	0.755	0.876	22.948	-0.036	-0.036	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.769	-0.897	24.742	0.134	0.134	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.011	-0.013	26.498	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	30	GLN	0	-0.061	-0.025	27.973	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	31	ASN	0	-0.075	-0.045	27.761	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	32	LEU	0	-0.028	-0.009	23.873	0.006	0.006	0.000	0.000	0.000	0.000
17	A	33	ILE	0	0.049	0.015	17.841	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	34	GLY	0	0.054	0.028	19.815	0.013	0.013	0.000	0.000	0.000	0.000
19	A	35	ILE	0	-0.008	0.006	15.348	0.051	0.051	0.000	0.000	0.000	0.000
20	A	36	SER	0	0.003	0.010	18.148	-0.038	-0.038	0.000	0.000	0.000	0.000
21	A	37	ILE	0	0.026	0.015	17.546	0.052	0.052	0.000	0.000	0.000	0.000
22	A	38	GLY	0	-0.007	-0.021	17.843	-0.031	-0.031	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.030	0.017	18.540	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	40	GLY	0	-0.003	-0.006	19.325	-0.023	-0.023	0.000	0.000	0.000	0.000
25	A	41	ALA	0	-0.039	-0.003	21.318	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.042	0.022	23.165	-0.019	-0.019	0.000	0.000	0.000	0.000
27	A	43	TYR	0	0.009	-0.010	23.863	0.006	0.006	0.000	0.000	0.000	0.000
28	A	44	CYS	0	0.005	0.019	17.547	0.024	0.024	0.000	0.000	0.000	0.000
29	A	45	PRO	0	-0.026	-0.026	20.155	0.011	0.011	0.000	0.000	0.000	0.000
30	A	46	CYS	0	-0.051	-0.016	15.484	-0.023	-0.023	0.000	0.000	0.000	0.000
31	A	47	LEU	0	0.014	0.006	16.445	0.026	0.026	0.000	0.000	0.000	0.000
32	A	48	TYR	0	0.033	0.006	11.672	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	49	ILE	0	0.007	0.012	11.635	-0.109	-0.109	0.000	0.000	0.000	0.000
34	A	50	VAL	0	-0.063	-0.020	13.717	0.123	0.123	0.000	0.000	0.000	0.000
35	A	51	GLN	0	0.009	-0.002	16.189	0.047	0.047	0.000	0.000	0.000	0.000
36	A	52	VAL	0	0.016	0.011	13.247	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	53	PHE	0	-0.040	-0.026	16.480	0.020	0.020	0.000	0.000	0.000	0.000
38	A	54	ASP	-1	-0.832	-0.902	19.322	0.438	0.438	0.000	0.000	0.000	0.000
39	A	55	ASN	0	-0.085	-0.052	20.561	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	56	THR	0	0.020	0.003	19.808	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	57	PRO	0	0.018	0.004	19.821	0.022	0.022	0.000	0.000	0.000	0.000
42	A	58	ALA	0	-0.005	-0.008	15.628	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.022	-0.004	15.117	0.047	0.047	0.000	0.000	0.000	0.000
44	A	60	LEU	0	-0.082	-0.040	15.839	0.025	0.025	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.839	-0.898	13.705	0.015	0.015	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.006	0.019	12.500	-0.043	-0.043	0.000	0.000	0.000	0.000
47	A	63	THR	0	-0.075	-0.054	8.988	0.123	0.123	0.000	0.000	0.000	0.000
48	A	64	VAL	0	-0.006	-0.016	8.569	0.244	0.244	0.000	0.000	0.000	0.000
49	A	65	ALA	0	0.006	0.002	8.169	0.045	0.045	0.000	0.000	0.000	0.000
50	A	66	ALA	0	-0.008	-0.006	10.215	-0.076	-0.076	0.000	0.000	0.000	0.000
51	A	67	GLY	0	-0.016	-0.010	10.027	0.295	0.295	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.783	-0.872	7.006	2.031	2.031	0.000	0.000	0.000	0.000
53	A	69	GLU	-1	-0.920	-0.963	9.156	-0.109	-0.109	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.005	-0.006	10.823	-0.113	-0.113	0.000	0.000	0.000	0.000
55	A	71	THR	0	-0.004	-0.017	11.999	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	72	GLY	0	-0.024	-0.030	14.603	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	73	VAL	0	0.001	0.002	16.538	0.022	0.022	0.000	0.000	0.000	0.000
58	A	74	ASN	0	0.024	0.005	19.173	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	75	GLY	0	-0.009	-0.006	19.178	0.001	0.001	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.925	0.976	20.306	0.063	0.063	0.000	0.000	0.000	0.000
61	A	77	SER	0	0.024	0.012	18.923	0.022	0.022	0.000	0.000	0.000	0.000
62	A	78	ILE	0	0.034	0.016	17.164	0.012	0.012	0.000	0.000	0.000	0.000
63	A	79	LYS	1	0.994	0.999	19.083	0.074	0.074	0.000	0.000	0.000	0.000
64	A	80	GLY	0	-0.007	-0.017	21.189	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.842	0.943	22.864	0.013	0.013	0.000	0.000	0.000	0.000
66	A	82	THR	0	0.033	0.005	23.203	0.020	0.020	0.000	0.000	0.000	0.000
67	A	83	LYS	1	0.966	0.962	21.686	-0.226	-0.226	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.000	-0.002	23.185	0.004	0.004	0.000	0.000	0.000	0.000
69	A	85	GLU	-1	-0.849	-0.916	25.853	0.031	0.031	0.000	0.000	0.000	0.000
70	A	86	VAL	0	0.010	0.000	19.562	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	87	ALA	0	0.013	0.015	22.880	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	88	LYS	1	0.888	0.946	23.748	-0.079	-0.079	0.000	0.000	0.000	0.000
73	A	89	MET	0	-0.001	0.000	23.469	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	90	ILE	0	0.036	0.013	19.165	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	91	GLN	0	-0.007	-0.002	23.326	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	92	GLU	-1	-0.983	-0.990	26.203	0.003	0.003	0.000	0.000	0.000	0.000
77	A	93	VAL	0	0.018	0.032	24.228	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	94	LYS	1	0.968	0.977	26.962	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	95	GLY	0	0.006	0.013	27.605	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	96	GLU	-1	-0.856	-0.919	22.621	-0.064	-0.064	0.000	0.000	0.000	0.000
81	A	97	VAL	0	-0.036	-0.015	19.917	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	98	THR	0	0.007	0.024	16.681	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	99	ILE	0	0.004	0.009	13.469	0.009	0.009	0.000	0.000	0.000	0.000
84	A	100	HIS	0	0.001	0.001	12.838	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	101	TYR	0	0.037	0.014	6.545	0.297	0.297	0.000	0.000	0.000	0.000
86	A	102	ASN	0	0.004	-0.015	6.894	-0.692	-0.692	0.000	0.000	0.000	0.000
87	A	103	LYS	1	0.783	0.878	2.450	-2.944	-1.918	1.239	-0.847	-1.418	0.006
88	A	104	LEU	0	0.002	0.008	4.339	-0.420	-0.278	0.000	-0.027	-0.115	0.000
89	A	105	GLN	0	-0.006	-0.003	5.107	0.981	0.981	0.000	0.000	0.000	0.000
90	A	106	TYR	0	0.002	0.007	5.666	-0.732	-0.732	0.000	0.000	0.000	0.000
91	A	107	TYR	0	0.023	0.001	8.437	-0.019	-0.019	0.000	0.000	0.000	0.000
92	A	108	LYS	1	0.957	0.982	11.209	-0.929	-0.929	0.000	0.000	0.000	0.000
93	A	109	VAL	0	0.020	0.015	13.386	-0.055	-0.055	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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