FMO DATABASE

FMODB ID: G5LM1

Calculation Name: 2ZVN-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZVN

Chain ID: B

ChEMBL ID:

UniProt ID: O88522

Base Structure: X-ray

Registration Date: 2023-09-20

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-409629.490305
FMO2-HF: Nuclear repulsion	374613.328331
FMO2-HF: Total energy	-35016.161974
FMO2-MP2: Total energy	-35120.147237

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(B:252:SER)

Summations of interaction energy for fragment #1(B:252: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.
4.771	-30.703	7.452	40.826	-12.803	-0.045

Interaction energy analysis for fragmet #1(B:252:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.136 / q_NPA : -0.057

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	B	254	GLU	-1	-0.809	-1.080	1.734	11.390	-29.209	6.453	43.550	-9.403	-0.023
4	B	255	ASH	0	-0.013	0.087	2.422	-7.234	-2.624	0.999	-2.539	-3.070	-0.023
5	B	256	LEU	0	0.026	0.014	3.887	1.019	1.534	0.000	-0.185	-0.330	0.001
6	B	257	ARG	1	0.966	0.974	5.643	-0.435	-0.435	0.000	0.000	0.000	0.000
7	B	258	GLN	0	0.011	0.009	6.256	-0.044	-0.044	0.000	0.000	0.000	0.000
8	B	259	GLN	0	-0.004	0.004	6.591	0.020	0.020	0.000	0.000	0.000	0.000
9	B	260	LEU	0	-0.009	0.010	10.099	0.143	0.143	0.000	0.000	0.000	0.000
10	B	261	GLN	0	-0.004	-0.008	12.180	-0.011	-0.011	0.000	0.000	0.000	0.000
11	B	262	GLN	0	-0.029	-0.028	12.025	0.075	0.075	0.000	0.000	0.000	0.000
12	B	263	ALA	0	-0.025	-0.010	14.199	0.039	0.039	0.000	0.000	0.000	0.000
13	B	264	GLU	-1	-0.924	-0.967	15.925	0.046	0.046	0.000	0.000	0.000	0.000
14	B	265	GLU	-1	-0.895	-0.954	17.063	-0.371	-0.371	0.000	0.000	0.000	0.000
15	B	266	ALA	0	-0.041	-0.013	18.942	0.005	0.005	0.000	0.000	0.000	0.000
16	B	267	LEU	0	-0.037	-0.026	19.524	0.022	0.022	0.000	0.000	0.000	0.000
17	B	268	VAL	0	0.016	0.015	22.142	0.017	0.017	0.000	0.000	0.000	0.000
18	B	269	ALA	0	0.063	0.034	23.702	0.009	0.009	0.000	0.000	0.000	0.000
19	B	270	LYS	1	0.895	0.945	22.623	0.180	0.180	0.000	0.000	0.000	0.000
20	B	271	GLN	0	-0.005	-0.010	26.160	0.009	0.009	0.000	0.000	0.000	0.000
21	B	272	GLU	-1	-0.878	-0.926	28.061	-0.114	-0.114	0.000	0.000	0.000	0.000
22	B	273	LEU	0	-0.077	-0.042	28.886	0.006	0.006	0.000	0.000	0.000	0.000
23	B	274	ILE	0	-0.040	-0.014	28.542	0.007	0.007	0.000	0.000	0.000	0.000
24	B	275	ASP	-1	-0.854	-0.932	32.187	-0.045	-0.045	0.000	0.000	0.000	0.000
25	B	276	LYS	1	0.901	0.966	34.063	0.097	0.097	0.000	0.000	0.000	0.000
26	B	277	LEU	0	0.000	-0.009	33.523	0.005	0.005	0.000	0.000	0.000	0.000
27	B	278	LYS	1	0.869	0.943	33.981	0.033	0.033	0.000	0.000	0.000	0.000
28	B	279	GLU	-1	-0.911	-0.958	37.790	-0.047	-0.047	0.000	0.000	0.000	0.000
29	B	280	GLU	-1	-0.868	-0.945	39.690	-0.071	-0.071	0.000	0.000	0.000	0.000
30	B	281	ALA	0	-0.048	-0.022	40.397	0.003	0.003	0.000	0.000	0.000	0.000
31	B	282	GLU	-1	-0.937	-0.988	42.150	-0.016	-0.016	0.000	0.000	0.000	0.000
32	B	283	GLN	0	0.022	0.031	44.147	0.005	0.005	0.000	0.000	0.000	0.000
33	B	284	HIS	0	-0.003	-0.004	45.371	0.000	0.000	0.000	0.000	0.000	0.000
34	B	285	LYS	1	0.898	0.935	43.852	0.021	0.021	0.000	0.000	0.000	0.000
35	B	286	ILE	0	0.025	0.029	48.035	0.002	0.002	0.000	0.000	0.000	0.000
36	B	287	VAL	0	0.017	-0.001	50.074	0.001	0.001	0.000	0.000	0.000	0.000
37	B	288	MET	0	-0.047	-0.029	49.657	0.000	0.000	0.000	0.000	0.000	0.000
38	B	289	GLU	-1	-0.977	-0.961	52.069	-0.015	-0.015	0.000	0.000	0.000	0.000
39	B	290	THR	0	0.021	0.005	54.037	0.002	0.002	0.000	0.000	0.000	0.000
40	B	291	VAL	0	-0.014	-0.015	55.039	0.001	0.001	0.000	0.000	0.000	0.000
41	B	292	PRO	0	-0.051	-0.026	56.808	0.000	0.000	0.000	0.000	0.000	0.000
42	B	293	VAL	0	0.065	0.024	59.836	0.001	0.001	0.000	0.000	0.000	0.000
43	B	294	LEU	0	0.004	0.009	58.773	0.000	0.000	0.000	0.000	0.000	0.000
44	B	295	LYS	1	0.900	0.953	58.953	0.020	0.020	0.000	0.000	0.000	0.000
45	B	296	ALA	0	0.055	0.025	63.382	0.000	0.000	0.000	0.000	0.000	0.000
46	B	297	GLN	0	-0.008	0.009	65.067	0.000	0.000	0.000	0.000	0.000	0.000
47	B	298	ALA	0	-0.011	-0.005	65.693	0.000	0.000	0.000	0.000	0.000	0.000
48	B	299	ASP	-1	-0.977	-0.990	67.582	-0.014	-0.014	0.000	0.000	0.000	0.000
49	B	300	ILE	0	0.013	-0.006	69.483	0.000	0.000	0.000	0.000	0.000	0.000
50	B	301	TYR	0	0.006	0.016	68.819	0.000	0.000	0.000	0.000	0.000	0.000
51	B	302	LYS	1	0.942	0.980	71.735	0.017	0.017	0.000	0.000	0.000	0.000
52	B	303	ALA	0	0.021	0.010	73.719	0.000	0.000	0.000	0.000	0.000	0.000
53	B	304	ASP	-1	-0.840	-0.929	75.086	-0.013	-0.013	0.000	0.000	0.000	0.000
54	B	305	PHE	0	-0.078	-0.038	76.452	0.000	0.000	0.000	0.000	0.000	0.000
55	B	306	GLN	0	-0.068	-0.045	76.992	0.000	0.000	0.000	0.000	0.000	0.000
56	B	307	ALA	0	0.039	0.032	79.825	0.000	0.000	0.000	0.000	0.000	0.000
57	B	308	GLU	-1	-0.899	-0.954	81.080	-0.013	-0.013	0.000	0.000	0.000	0.000
58	B	309	ARG	1	0.849	0.926	81.750	0.016	0.016	0.000	0.000	0.000	0.000
59	B	310	HIS	0	0.010	-0.005	83.098	0.000	0.000	0.000	0.000	0.000	0.000
60	B	311	ALA	0	0.018	0.019	85.929	0.000	0.000	0.000	0.000	0.000	0.000
61	B	312	ARG	1	0.948	0.957	84.886	0.015	0.015	0.000	0.000	0.000	0.000
62	B	313	GLU	-1	-0.928	-0.961	87.056	-0.012	-0.012	0.000	0.000	0.000	0.000
63	B	314	LYS	1	0.880	0.938	89.728	0.009	0.009	0.000	0.000	0.000	0.000
64	B	315	LEU	0	0.013	0.007	90.876	0.000	0.000	0.000	0.000	0.000	0.000
65	B	316	VAL	0	-0.091	-0.038	90.846	0.000	0.000	0.000	0.000	0.000	0.000
66	B	317	GLU	-1	-0.819	-0.903	93.891	-0.009	-0.009	0.000	0.000	0.000	0.000
67	B	318	LYS	1	0.921	0.968	96.013	0.009	0.009	0.000	0.000	0.000	0.000
68	B	319	LYS	1	0.946	0.960	96.080	0.013	0.013	0.000	0.000	0.000	0.000
69	B	320	GLU	-1	-0.909	-0.963	97.627	-0.011	-0.011	0.000	0.000	0.000	0.000
70	B	321	TYR	0	0.014	0.026	99.894	0.000	0.000	0.000	0.000	0.000	0.000
71	B	322	LEU	0	-0.003	-0.031	100.947	0.000	0.000	0.000	0.000	0.000	0.000
72	B	323	GLN	0	-0.085	-0.016	101.789	0.000	0.000	0.000	0.000	0.000	0.000
73	B	324	GLU	-1	-0.864	-0.938	103.789	-0.010	-0.010	0.000	0.000	0.000	0.000
74	B	325	GLN	0	-0.056	-0.038	106.154	0.000	0.000	0.000	0.000	0.000	0.000
75	B	326	LEU	0	-0.024	-0.003	107.035	0.000	0.000	0.000	0.000	0.000	0.000
76	B	327	GLU	-1	-0.936	-0.972	105.621	-0.010	-0.010	0.000	0.000	0.000	0.000
77	B	328	GLN	0	-0.034	-0.021	109.880	0.000	0.000	0.000	0.000	0.000	0.000
78	B	329	LEU	0	0.055	0.021	112.000	0.000	0.000	0.000	0.000	0.000	0.000
79	B	330	GLN	0	-0.003	0.003	112.179	0.000	0.000	0.000	0.000	0.000	0.000
80	B	331	ARG	1	0.898	0.959	110.100	0.009	0.009	0.000	0.000	0.000	0.000
81	B	332	GLU	-1	-0.971	-0.999	116.031	-0.007	-0.007	0.000	0.000	0.000	0.000
82	B	333	PHE	0	-0.045	-0.013	117.251	0.000	0.000	0.000	0.000	0.000	0.000
83	B	334	ASN	0	-0.018	-0.013	115.970	0.000	0.000	0.000	0.000	0.000	0.000
84	B	335	LYS	1	0.882	0.960	119.885	0.007	0.007	0.000	0.000	0.000	0.000
85	B	336	LEU	0	0.013	0.017	122.539	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:252:SER)