FMO DATABASE

FMODB ID: ZV63N

Calculation Name: 3I3U-B-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3I3U

Chain ID: B

ChEMBL ID:
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UniProt ID: F9UPN6

Base Structure: X-ray

Registration Date: 2023-09-21

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-629060.885938
FMO2-HF: Nuclear repulsion	593102.459671
FMO2-HF: Total energy	-35958.426267
FMO2-MP2: Total energy	-36064.495537

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:2:ASN)

Summations of interaction energy for fragment #1(B:2:ASN)

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.
-37.439	-35.477	9.395	-5.525	-5.832	0.063

Interaction energy analysis for fragmet #1(B:2:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.001

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	B	4	LYS	1	0.959	0.984	3.091	2.981	5.166	0.029	-0.970	-1.244	0.002
4	B	5	LYS	1	0.925	0.968	1.803	-40.350	-40.835	9.367	-4.516	-4.366	0.061
5	B	6	ILE	0	0.058	0.035	4.232	0.369	0.631	-0.001	-0.039	-0.222	0.000
6	B	7	GLU	-1	-0.876	-0.921	6.343	-1.200	-1.200	0.000	0.000	0.000	0.000
7	B	8	LEU	0	-0.025	-0.014	8.023	0.535	0.535	0.000	0.000	0.000	0.000
8	B	9	LEU	0	-0.030	-0.036	7.304	0.225	0.225	0.000	0.000	0.000	0.000
9	B	10	THR	0	-0.003	-0.015	9.891	0.095	0.095	0.000	0.000	0.000	0.000
10	B	11	THR	0	0.017	0.009	12.094	0.120	0.120	0.000	0.000	0.000	0.000
11	B	12	TYR	0	-0.053	-0.025	13.256	0.125	0.125	0.000	0.000	0.000	0.000
12	B	13	LEU	0	0.010	-0.019	13.143	0.062	0.062	0.000	0.000	0.000	0.000
13	B	14	SER	0	-0.079	-0.009	16.119	0.000	0.000	0.000	0.000	0.000	0.000
14	B	15	LEU	0	0.030	0.021	18.028	0.009	0.009	0.000	0.000	0.000	0.000
15	B	16	TYR	0	-0.087	-0.061	18.845	0.071	0.071	0.000	0.000	0.000	0.000
16	B	17	ILE	0	0.003	0.012	21.704	-0.047	-0.047	0.000	0.000	0.000	0.000
17	B	18	ASP	-1	-0.822	-0.920	23.007	0.071	0.071	0.000	0.000	0.000	0.000
18	B	19	HIS	1	0.967	0.985	24.557	-0.095	-0.095	0.000	0.000	0.000	0.000
19	B	20	HIS	0	-0.025	-0.052	26.736	0.010	0.010	0.000	0.000	0.000	0.000
20	B	21	THR	0	-0.007	-0.001	26.173	-0.012	-0.012	0.000	0.000	0.000	0.000
21	B	22	VAL	0	0.014	-0.001	28.487	-0.009	-0.009	0.000	0.000	0.000	0.000
22	B	23	LEU	0	-0.002	0.017	30.622	0.002	0.002	0.000	0.000	0.000	0.000
23	B	24	ALA	0	0.006	0.005	32.019	0.002	0.002	0.000	0.000	0.000	0.000
24	B	25	ASP	-1	-0.853	-0.938	33.607	-0.087	-0.087	0.000	0.000	0.000	0.000
25	B	26	MET	0	-0.038	-0.010	33.530	0.009	0.009	0.000	0.000	0.000	0.000
26	B	27	GLN	0	-0.044	-0.023	36.101	0.013	0.013	0.000	0.000	0.000	0.000
27	B	28	ASN	0	-0.060	-0.032	36.161	0.000	0.000	0.000	0.000	0.000	0.000
28	B	29	ALA	0	0.009	0.015	37.034	-0.010	-0.010	0.000	0.000	0.000	0.000
29	B	30	THR	0	0.012	-0.004	39.057	0.013	0.013	0.000	0.000	0.000	0.000
30	B	31	GLY	0	-0.018	0.003	38.400	0.003	0.003	0.000	0.000	0.000	0.000
31	B	32	LYS	1	0.828	0.922	31.686	0.107	0.107	0.000	0.000	0.000	0.000
32	B	33	TYR	0	0.039	0.024	28.639	-0.006	-0.006	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.011	0.014	34.140	0.009	0.009	0.000	0.000	0.000	0.000
34	B	35	VAL	0	-0.012	-0.009	32.979	0.001	0.001	0.000	0.000	0.000	0.000
35	B	36	LEU	0	0.008	-0.001	33.258	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	37	ASP	-1	-0.788	-0.848	33.223	0.108	0.108	0.000	0.000	0.000	0.000
37	B	38	VAL	0	0.024	0.000	30.988	-0.005	-0.005	0.000	0.000	0.000	0.000
38	B	39	ARG	1	0.856	0.914	33.631	-0.110	-0.110	0.000	0.000	0.000	0.000
39	B	40	ASN	0	-0.026	-0.020	35.247	-0.001	-0.001	0.000	0.000	0.000	0.000
40	B	41	ALA	0	0.009	0.011	38.378	0.006	0.006	0.000	0.000	0.000	0.000
41	B	50	ILE	0	-0.001	-0.005	33.629	0.001	0.001	0.000	0.000	0.000	0.000
42	B	51	LYS	1	0.964	0.971	38.013	-0.028	-0.028	0.000	0.000	0.000	0.000
43	B	52	GLY	0	0.016	0.001	38.570	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	53	ALA	0	0.009	0.020	36.974	-0.006	-0.006	0.000	0.000	0.000	0.000
45	B	54	ILE	0	-0.004	-0.001	38.260	0.006	0.006	0.000	0.000	0.000	0.000
46	B	55	ALA	0	-0.017	0.004	38.484	0.001	0.001	0.000	0.000	0.000	0.000
47	B	56	MET	0	0.018	-0.004	36.418	-0.009	-0.009	0.000	0.000	0.000	0.000
48	B	57	PRO	0	-0.012	0.020	36.305	0.003	0.003	0.000	0.000	0.000	0.000
49	B	58	ALA	0	0.120	0.062	32.319	-0.011	-0.011	0.000	0.000	0.000	0.000
50	B	59	LYS	1	0.732	0.861	34.289	-0.081	-0.081	0.000	0.000	0.000	0.000
51	B	60	ASP	-1	-0.813	-0.910	36.687	0.055	0.055	0.000	0.000	0.000	0.000
52	B	61	LEU	0	-0.024	-0.011	32.395	-0.008	-0.008	0.000	0.000	0.000	0.000
53	B	62	ALA	0	0.019	0.015	35.564	-0.011	-0.011	0.000	0.000	0.000	0.000
54	B	63	THR	0	0.002	-0.011	36.844	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	64	ARG	1	0.755	0.856	39.633	-0.017	-0.017	0.000	0.000	0.000	0.000
56	B	65	ILE	0	0.018	0.008	33.888	-0.003	-0.003	0.000	0.000	0.000	0.000
57	B	66	GLY	0	-0.007	0.001	38.287	-0.010	-0.010	0.000	0.000	0.000	0.000
58	B	67	GLU	-1	-0.878	-0.899	41.165	-0.008	-0.008	0.000	0.000	0.000	0.000
59	B	68	LEU	0	-0.031	-0.006	35.667	0.004	0.004	0.000	0.000	0.000	0.000
60	B	69	ASP	-1	-0.799	-0.912	39.100	-0.098	-0.098	0.000	0.000	0.000	0.000
61	B	70	PRO	0	0.010	-0.001	35.578	0.000	0.000	0.000	0.000	0.000	0.000
62	B	71	ALA	0	-0.053	-0.015	35.066	-0.013	-0.013	0.000	0.000	0.000	0.000
63	B	72	LYS	1	0.790	0.904	35.727	0.084	0.084	0.000	0.000	0.000	0.000
64	B	73	THR	0	0.019	0.019	29.148	-0.004	-0.004	0.000	0.000	0.000	0.000
65	B	74	TYR	0	-0.009	-0.025	31.247	0.023	0.023	0.000	0.000	0.000	0.000
66	B	75	VAL	0	-0.020	-0.002	28.424	-0.007	-0.007	0.000	0.000	0.000	0.000
67	B	76	VAL	0	0.014	0.019	27.658	0.011	0.011	0.000	0.000	0.000	0.000
68	B	77	TYR	0	-0.035	-0.049	28.206	0.010	0.010	0.000	0.000	0.000	0.000
69	B	78	ASP	-1	-0.766	-0.860	28.508	0.198	0.198	0.000	0.000	0.000	0.000
70	B	79	TRP	0	-0.055	-0.033	30.372	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	80	THR	0	-0.017	-0.034	27.808	0.011	0.011	0.000	0.000	0.000	0.000
72	B	81	GLY	0	0.033	0.027	25.398	-0.005	-0.005	0.000	0.000	0.000	0.000
73	B	82	GLY	0	-0.013	-0.015	22.682	0.033	0.033	0.000	0.000	0.000	0.000
74	B	83	THR	0	-0.079	-0.054	23.631	0.032	0.032	0.000	0.000	0.000	0.000
75	B	84	THR	0	0.027	0.000	23.981	0.008	0.008	0.000	0.000	0.000	0.000
76	B	85	LEU	0	0.016	0.021	26.100	-0.029	-0.029	0.000	0.000	0.000	0.000
77	B	86	GLY	0	0.039	0.038	26.961	-0.025	-0.025	0.000	0.000	0.000	0.000
78	B	87	LYS	1	0.936	0.968	20.178	-0.298	-0.298	0.000	0.000	0.000	0.000
79	B	88	THR	0	-0.015	-0.010	24.956	-0.032	-0.032	0.000	0.000	0.000	0.000
80	B	89	ALA	0	0.033	0.002	27.696	-0.026	-0.026	0.000	0.000	0.000	0.000
81	B	90	LEU	0	0.003	0.004	23.015	-0.019	-0.019	0.000	0.000	0.000	0.000
82	B	91	LEU	0	-0.020	-0.015	23.997	-0.029	-0.029	0.000	0.000	0.000	0.000
83	B	92	VAL	0	-0.042	-0.009	26.453	-0.025	-0.025	0.000	0.000	0.000	0.000
84	B	93	LEU	0	0.016	0.001	29.220	-0.017	-0.017	0.000	0.000	0.000	0.000
85	B	94	LEU	0	0.017	0.009	23.455	-0.015	-0.015	0.000	0.000	0.000	0.000
86	B	95	SER	0	-0.078	-0.044	27.506	-0.028	-0.028	0.000	0.000	0.000	0.000
87	B	96	ALA	0	-0.081	-0.041	28.644	-0.011	-0.011	0.000	0.000	0.000	0.000
88	B	97	GLY	0	-0.005	0.009	29.986	-0.004	-0.004	0.000	0.000	0.000	0.000
89	B	98	PHE	0	-0.053	-0.020	30.927	-0.011	-0.011	0.000	0.000	0.000	0.000
90	B	99	GLU	-1	-0.828	-0.888	26.549	-0.262	-0.262	0.000	0.000	0.000	0.000
91	B	100	ALA	0	-0.034	-0.038	27.171	0.023	0.023	0.000	0.000	0.000	0.000
92	B	101	TYR	0	-0.052	-0.045	22.732	-0.015	-0.015	0.000	0.000	0.000	0.000
93	B	102	GLU	-1	-0.830	-0.902	23.460	0.201	0.201	0.000	0.000	0.000	0.000
94	B	103	LEU	0	-0.040	-0.033	24.597	-0.011	-0.011	0.000	0.000	0.000	0.000
95	B	104	ALA	0	-0.034	-0.004	22.820	0.033	0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ASN)