FMO DATABASE

FMODB ID: Z672N

Calculation Name: 4XVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XVV

Chain ID: A

ChEMBL ID:

UniProt ID: A6TE95

Base Structure: X-ray

Registration Date: 2023-06-22

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-489891.393181
FMO2-HF: Nuclear repulsion	458102.109115
FMO2-HF: Total energy	-31789.284066
FMO2-MP2: Total energy	-31877.110084

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-10.918	-5.274	1.093	-3.364	-3.371	-0.019

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.034

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	27	GLU	-1	-0.895	-0.946	3.311	-2.592	-0.181	0.014	-1.251	-1.174	0.006
4	A	28	GLU	-1	-0.907	-0.953	2.519	-11.099	-7.986	1.080	-2.104	-2.088	-0.025
5	A	29	THR	0	-0.106	-0.041	5.240	1.333	1.453	-0.001	-0.009	-0.109	0.000
6	A	30	THR	0	-0.082	-0.041	7.841	0.858	0.858	0.000	0.000	0.000	0.000
7	A	31	PRO	0	0.052	-0.001	9.537	-0.139	-0.139	0.000	0.000	0.000	0.000
8	A	32	GLN	0	0.029	0.028	9.393	0.238	0.238	0.000	0.000	0.000	0.000
9	A	33	ASN	0	-0.040	-0.048	7.810	0.478	0.478	0.000	0.000	0.000	0.000
10	A	34	MET	0	0.022	0.048	11.346	0.059	0.059	0.000	0.000	0.000	0.000
11	A	35	THR	0	-0.008	-0.008	13.672	0.108	0.108	0.000	0.000	0.000	0.000
12	A	36	CYS	0	-0.039	-0.028	17.060	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	37	GLN	0	-0.046	-0.025	20.420	0.028	0.028	0.000	0.000	0.000	0.000
14	A	38	GLU	-1	-0.834	-0.920	14.910	-0.785	-0.785	0.000	0.000	0.000	0.000
15	A	39	PHE	0	-0.009	-0.020	18.880	-0.001	-0.001	0.000	0.000	0.000	0.000
16	A	40	MET	0	-0.091	-0.045	19.976	0.028	0.028	0.000	0.000	0.000	0.000
17	A	41	ASP	-1	-0.858	-0.912	21.582	-0.326	-0.326	0.000	0.000	0.000	0.000
18	A	42	MET	0	-0.077	-0.008	18.459	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	43	ASN	0	-0.007	-0.013	21.153	0.064	0.064	0.000	0.000	0.000	0.000
20	A	44	PRO	0	0.105	0.018	22.574	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	45	LYS	1	0.913	0.954	23.896	0.288	0.288	0.000	0.000	0.000	0.000
22	A	46	SER	0	0.005	0.012	18.785	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	47	MET	0	-0.032	0.002	20.178	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	48	THR	0	0.085	0.026	21.934	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	49	PRO	0	-0.005	-0.005	19.052	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	50	VAL	0	0.020	0.017	16.193	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	51	ALA	0	0.049	0.008	18.257	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	52	PHE	0	0.014	0.005	19.265	0.016	0.016	0.000	0.000	0.000	0.000
29	A	53	TRP	0	0.006	0.011	11.593	0.023	0.023	0.000	0.000	0.000	0.000
30	A	54	VAL	0	0.009	0.003	17.075	0.018	0.018	0.000	0.000	0.000	0.000
31	A	55	VAL	0	-0.044	-0.010	18.351	0.036	0.036	0.000	0.000	0.000	0.000
32	A	56	ASN	0	-0.003	-0.010	19.724	0.061	0.061	0.000	0.000	0.000	0.000
33	A	57	ARG	1	0.862	0.956	12.116	0.566	0.566	0.000	0.000	0.000	0.000
34	A	58	ASN	0	-0.092	-0.049	15.446	0.016	0.016	0.000	0.000	0.000	0.000
35	A	59	THR	0	-0.042	-0.024	17.423	0.038	0.038	0.000	0.000	0.000	0.000
36	A	60	ASP	-1	-0.847	-0.927	20.923	-0.094	-0.094	0.000	0.000	0.000	0.000
37	A	61	PHE	0	-0.017	-0.030	18.642	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	62	SER	0	-0.045	-0.014	23.889	0.003	0.003	0.000	0.000	0.000	0.000
39	A	63	GLY	0	-0.016	-0.002	26.494	0.008	0.008	0.000	0.000	0.000	0.000
40	A	64	GLY	0	-0.039	-0.016	28.012	0.003	0.003	0.000	0.000	0.000	0.000
41	A	65	ASP	-1	-0.956	-0.950	26.515	-0.137	-0.137	0.000	0.000	0.000	0.000
42	A	66	TYR	0	-0.025	-0.012	23.880	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	67	VAL	0	-0.026	0.004	24.717	0.010	0.010	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.791	-0.901	25.228	-0.214	-0.214	0.000	0.000	0.000	0.000
45	A	69	TRP	0	0.004	-0.025	20.646	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	70	HIS	0	0.041	0.024	26.954	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.903	-0.933	28.984	-0.175	-0.175	0.000	0.000	0.000	0.000
48	A	72	VAL	0	-0.029	-0.026	23.407	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.962	-0.985	26.686	-0.243	-0.243	0.000	0.000	0.000	0.000
50	A	74	THR	0	-0.076	-0.061	28.201	0.006	0.006	0.000	0.000	0.000	0.000
51	A	75	VAL	0	-0.013	0.008	30.102	0.010	0.010	0.000	0.000	0.000	0.000
52	A	76	SER	0	-0.013	-0.017	25.135	0.006	0.006	0.000	0.000	0.000	0.000
53	A	77	VAL	0	0.017	0.021	24.470	-0.014	-0.014	0.000	0.000	0.000	0.000
54	A	78	PRO	0	0.008	0.001	26.440	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	79	LYS	1	0.860	0.956	27.741	0.194	0.194	0.000	0.000	0.000	0.000
56	A	80	MET	0	0.022	0.010	19.830	0.002	0.002	0.000	0.000	0.000	0.000
57	A	81	LEU	0	0.021	0.015	25.092	-0.005	-0.005	0.000	0.000	0.000	0.000
58	A	82	GLN	0	-0.039	-0.003	26.800	0.016	0.016	0.000	0.000	0.000	0.000
59	A	83	GLU	-1	-0.940	-0.983	25.466	-0.192	-0.192	0.000	0.000	0.000	0.000
60	A	85	HIS	0	-0.006	-0.033	24.803	0.006	0.006	0.000	0.000	0.000	0.000
61	A	86	LYS	1	0.850	0.946	28.059	0.182	0.182	0.000	0.000	0.000	0.000
62	A	87	ASN	0	-0.008	-0.012	23.679	0.010	0.010	0.000	0.000	0.000	0.000
63	A	88	PRO	0	0.077	0.038	23.286	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	89	ALA	0	-0.003	-0.001	20.616	-0.038	-0.038	0.000	0.000	0.000	0.000
65	A	90	ALA	0	-0.045	-0.006	19.357	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	91	LYS	1	0.996	0.999	13.522	0.402	0.402	0.000	0.000	0.000	0.000
67	A	92	LEU	0	0.037	-0.002	15.507	0.058	0.058	0.000	0.000	0.000	0.000
68	A	93	GLY	0	-0.044	-0.012	14.077	0.033	0.033	0.000	0.000	0.000	0.000
69	A	94	ASP	-1	-0.954	-0.967	14.967	-0.276	-0.276	0.000	0.000	0.000	0.000
70	A	95	LEU	0	-0.049	-0.033	18.247	0.053	0.053	0.000	0.000	0.000	0.000
71	A	96	SER	0	-0.009	-0.036	18.568	0.017	0.017	0.000	0.000	0.000	0.000
72	A	97	ALA	0	-0.010	-0.009	20.785	0.020	0.020	0.000	0.000	0.000	0.000
73	A	98	VAL	0	-0.006	-0.002	23.791	0.017	0.017	0.000	0.000	0.000	0.000
74	A	99	ILE	0	-0.004	-0.001	22.979	0.014	0.014	0.000	0.000	0.000	0.000
75	A	100	LYS	1	0.994	1.001	22.218	0.219	0.219	0.000	0.000	0.000	0.000
76	A	101	LYS	1	0.933	0.989	26.214	0.141	0.141	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)