FMO DATABASE

FMODB ID: R8G48

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

Total energy (hartree)

FMO2-HF: Electronic energy	-594850.598873
FMO2-HF: Nuclear repulsion	559699.685974
FMO2-HF: Total energy	-35150.912899
FMO2-MP2: Total energy	-35252.090239

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.
-16.323	-15.409	10.532	-6.136	-5.31	-0.026

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 : -0.004 / q_NPA : -0.009

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

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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	0.030	0.013	1.824	-15.432	-15.734	9.352	-5.316	-3.733	-0.031
4	A	20	PRO	0	-0.009	0.005	4.540	1.128	1.250	-0.001	-0.008	-0.113	0.000
5	A	21	GLY	0	0.025	0.008	6.386	-0.115	-0.115	0.000	0.000	0.000	0.000
6	A	22	LYS	1	0.906	0.958	9.780	0.798	0.798	0.000	0.000	0.000	0.000
7	A	23	VAL	0	0.016	0.020	12.544	-0.108	-0.108	0.000	0.000	0.000	0.000
8	A	24	THR	0	0.005	0.008	14.322	0.064	0.064	0.000	0.000	0.000	0.000
9	A	25	LEU	0	-0.004	0.019	15.589	-0.006	-0.006	0.000	0.000	0.000	0.000
10	A	26	GLN	0	0.002	-0.016	19.222	0.028	0.028	0.000	0.000	0.000	0.000
11	A	27	LYS	1	0.739	0.860	22.918	0.000	0.000	0.000	0.000	0.000	0.000
12	A	28	ASP	-1	-0.754	-0.883	24.706	0.056	0.056	0.000	0.000	0.000	0.000
13	A	29	ALA	0	-0.004	-0.010	26.460	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	30	GLN	0	-0.069	-0.030	27.585	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	31	ASN	0	-0.057	-0.029	27.682	0.001	0.001	0.000	0.000	0.000	0.000
16	A	32	LEU	0	-0.027	-0.014	23.864	0.014	0.014	0.000	0.000	0.000	0.000
17	A	33	ILE	0	0.046	0.014	17.887	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	34	GLY	0	0.056	0.026	19.772	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	35	ILE	0	-0.012	0.003	15.335	0.043	0.043	0.000	0.000	0.000	0.000
20	A	36	SER	0	0.000	0.012	18.118	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	37	ILE	0	0.018	0.005	17.501	0.058	0.058	0.000	0.000	0.000	0.000
22	A	38	GLY	0	-0.003	-0.012	17.802	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	39	GLY	0	0.030	0.018	18.506	0.006	0.006	0.000	0.000	0.000	0.000
24	A	40	GLY	0	-0.003	-0.007	19.289	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	41	ALA	0	-0.040	-0.005	21.277	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	42	GLN	0	0.056	0.029	23.134	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	43	TYR	0	-0.002	-0.016	24.025	0.016	0.016	0.000	0.000	0.000	0.000
28	A	44	CYS	0	0.011	0.022	17.528	0.032	0.032	0.000	0.000	0.000	0.000
29	A	45	PRO	0	-0.019	-0.025	20.391	0.012	0.012	0.000	0.000	0.000	0.000
30	A	46	CYS	0	-0.068	-0.017	15.143	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	47	LEU	0	0.010	0.001	16.416	0.018	0.018	0.000	0.000	0.000	0.000
32	A	48	TYR	0	0.036	0.004	11.830	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	49	ILE	0	0.013	0.017	11.680	-0.133	-0.133	0.000	0.000	0.000	0.000
34	A	50	VAL	0	-0.059	-0.025	13.671	0.151	0.151	0.000	0.000	0.000	0.000
35	A	51	GLN	0	0.013	0.003	16.140	0.061	0.061	0.000	0.000	0.000	0.000
36	A	52	VAL	0	0.015	0.011	13.223	-0.045	-0.045	0.000	0.000	0.000	0.000
37	A	53	PHE	0	-0.036	-0.026	16.489	0.016	0.016	0.000	0.000	0.000	0.000
38	A	54	ASP	-1	-0.837	-0.899	19.375	0.281	0.281	0.000	0.000	0.000	0.000
39	A	55	ASN	0	-0.086	-0.054	20.569	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	56	THR	0	0.019	0.001	19.823	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	57	PRO	0	0.023	0.005	19.832	0.000	0.000	0.000	0.000	0.000	0.000
42	A	58	ALA	0	-0.010	-0.011	15.649	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	59	ALA	0	-0.018	-0.002	15.131	0.011	0.011	0.000	0.000	0.000	0.000
44	A	60	LEU	0	-0.079	-0.039	15.845	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	61	ASP	-1	-0.849	-0.910	13.567	-0.319	-0.319	0.000	0.000	0.000	0.000
46	A	62	GLY	0	0.011	0.016	12.507	-0.098	-0.098	0.000	0.000	0.000	0.000
47	A	63	THR	0	-0.085	-0.041	8.881	-0.033	-0.033	0.000	0.000	0.000	0.000
48	A	64	VAL	0	-0.016	-0.018	8.530	0.222	0.222	0.000	0.000	0.000	0.000
49	A	65	ALA	0	-0.008	-0.007	8.085	0.005	0.005	0.000	0.000	0.000	0.000
50	A	66	ALA	0	-0.009	-0.006	10.168	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	67	GLY	0	-0.008	-0.006	9.978	0.333	0.333	0.000	0.000	0.000	0.000
52	A	68	ASP	-1	-0.785	-0.864	7.080	1.905	1.905	0.000	0.000	0.000	0.000
53	A	69	GLU	-1	-0.878	-0.935	9.116	0.137	0.137	0.000	0.000	0.000	0.000
54	A	70	ILE	0	-0.003	-0.004	10.788	-0.139	-0.139	0.000	0.000	0.000	0.000
55	A	71	THR	0	-0.010	-0.020	11.887	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	72	GLY	0	-0.027	-0.031	14.580	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	73	VAL	0	0.005	0.002	16.512	0.015	0.015	0.000	0.000	0.000	0.000
58	A	74	ASN	0	0.029	0.013	19.149	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	75	GLY	0	-0.004	0.000	19.164	0.002	0.002	0.000	0.000	0.000	0.000
60	A	76	ARG	1	0.919	0.977	20.296	0.053	0.053	0.000	0.000	0.000	0.000
61	A	77	SER	0	0.028	0.010	18.619	0.025	0.025	0.000	0.000	0.000	0.000
62	A	78	ILE	0	0.029	0.013	17.253	0.004	0.004	0.000	0.000	0.000	0.000
63	A	79	LYS	1	0.975	0.986	18.521	-0.075	-0.075	0.000	0.000	0.000	0.000
64	A	80	GLY	0	0.014	0.004	21.170	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	81	LYS	1	0.757	0.881	22.844	-0.064	-0.064	0.000	0.000	0.000	0.000
66	A	82	THR	0	0.020	-0.022	23.172	0.027	0.027	0.000	0.000	0.000	0.000
67	A	83	LYS	1	0.961	0.962	21.652	-0.309	-0.309	0.000	0.000	0.000	0.000
68	A	84	VAL	0	0.010	0.001	23.144	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	85	GLU	-1	-0.748	-0.832	25.831	0.068	0.068	0.000	0.000	0.000	0.000
70	A	86	VAL	0	0.011	0.005	19.490	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	87	ALA	0	0.010	0.013	22.839	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	88	LYS	1	0.882	0.934	23.706	-0.091	-0.091	0.000	0.000	0.000	0.000
73	A	89	MET	0	-0.004	-0.001	23.673	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	90	ILE	0	0.044	0.015	19.169	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	91	GLN	0	0.014	0.012	23.289	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	92	GLU	-1	-0.912	-0.945	26.163	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	93	VAL	0	0.008	0.023	24.441	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	94	LYS	1	0.890	0.938	26.928	0.018	0.018	0.000	0.000	0.000	0.000
79	A	95	GLY	0	0.014	0.016	27.576	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	96	GLU	-1	-0.859	-0.927	22.612	-0.164	-0.164	0.000	0.000	0.000	0.000
81	A	97	VAL	0	-0.030	-0.014	19.985	0.007	0.007	0.000	0.000	0.000	0.000
82	A	98	THR	0	-0.040	-0.027	16.573	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	99	ILE	0	0.005	0.005	13.461	0.033	0.033	0.000	0.000	0.000	0.000
84	A	100	HIS	0	-0.002	-0.007	12.813	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	101	TYR	0	0.042	0.013	6.718	0.116	0.116	0.000	0.000	0.000	0.000
86	A	102	ASN	0	-0.045	-0.046	7.072	-0.615	-0.615	0.000	0.000	0.000	0.000
87	A	103	LYS	1	0.792	0.882	2.488	-2.456	-1.511	1.181	-0.785	-1.342	0.005
88	A	104	LEU	0	0.013	0.012	4.323	-0.211	-0.062	0.000	-0.027	-0.122	0.000
89	A	105	GLN	0	0.017	0.011	5.096	1.112	1.112	0.000	0.000	0.000	0.000
90	A	106	TYR	0	0.006	0.010	5.566	-1.095	-1.095	0.000	0.000	0.000	0.000
91	A	107	TYR	0	-0.007	-0.021	8.421	0.100	0.100	0.000	0.000	0.000	0.000
92	A	108	LYS	1	0.958	0.983	11.192	-1.136	-1.136	0.000	0.000	0.000	0.000
93	A	109	VAL	0	0.020	0.016	13.365	-0.071	-0.071	0.000	0.000	0.000	0.000

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