FMO DATABASE

FMODB ID: QYLVY

Calculation Name: 4JPB-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JPB

Chain ID: B

ChEMBL ID:

UniProt ID: Q56310

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	84
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-361958.055063
FMO2-HF: Nuclear repulsion	329147.884486
FMO2-HF: Total energy	-32810.170577
FMO2-MP2: Total energy	-32905.960914

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:108:GLN)

Summations of interaction energy for fragment #1(B:108:GLN)

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.
-7.105	-4.329	0.334	-0.968	-2.142	0

Interaction energy analysis for fragmet #1(B:108:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.003

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	110	GLY	0	-0.002	-0.007	2.727	-2.424	-0.760	0.287	-0.720	-1.231	0.001
4	B	111	GLU	-1	-0.888	-0.955	3.138	-7.007	-6.171	0.048	-0.207	-0.677	-0.001
5	B	112	THR	0	0.032	0.022	4.324	1.669	1.945	-0.001	-0.041	-0.234	0.000
6	B	113	LEU	0	-0.016	-0.007	6.239	0.218	0.218	0.000	0.000	0.000	0.000
7	B	114	GLU	-1	-0.845	-0.917	7.749	-0.414	-0.414	0.000	0.000	0.000	0.000
8	B	115	ASN	0	0.011	0.010	7.641	0.002	0.002	0.000	0.000	0.000	0.000
9	B	116	ILE	0	-0.015	-0.017	10.142	0.099	0.099	0.000	0.000	0.000	0.000
10	B	117	ARG	1	0.929	0.974	12.127	0.224	0.224	0.000	0.000	0.000	0.000
11	B	118	SER	0	-0.050	-0.025	12.421	-0.008	-0.008	0.000	0.000	0.000	0.000
12	B	119	ILE	0	-0.001	0.001	12.950	0.015	0.015	0.000	0.000	0.000	0.000
13	B	120	GLU	-1	-0.887	-0.949	16.131	0.241	0.241	0.000	0.000	0.000	0.000
14	B	121	LYS	1	0.922	0.955	17.592	0.235	0.235	0.000	0.000	0.000	0.000
15	B	122	LEU	0	-0.035	-0.028	16.974	-0.008	-0.008	0.000	0.000	0.000	0.000
16	B	123	ILE	0	0.017	0.005	19.784	0.003	0.003	0.000	0.000	0.000	0.000
17	B	124	GLN	0	-0.008	-0.007	22.022	-0.006	-0.006	0.000	0.000	0.000	0.000
18	B	125	ASN	0	-0.038	-0.035	23.420	0.012	0.012	0.000	0.000	0.000	0.000
19	B	126	ILE	0	0.035	0.031	23.090	0.000	0.000	0.000	0.000	0.000	0.000
20	B	127	MET	0	-0.007	0.009	26.175	0.011	0.011	0.000	0.000	0.000	0.000
21	B	128	ARG	1	0.944	0.977	24.510	0.079	0.079	0.000	0.000	0.000	0.000
22	B	129	ILE	0	0.052	0.032	27.726	0.001	0.001	0.000	0.000	0.000	0.000
23	B	130	ALA	0	0.002	-0.016	30.545	0.003	0.003	0.000	0.000	0.000	0.000
24	B	131	ARG	1	0.949	0.967	32.402	0.009	0.009	0.000	0.000	0.000	0.000
25	B	132	GLU	-1	-0.971	-0.982	33.654	-0.053	-0.053	0.000	0.000	0.000	0.000
26	B	133	THR	0	-0.010	0.002	34.246	-0.001	-0.001	0.000	0.000	0.000	0.000
27	B	134	ASN	0	-0.005	0.001	36.658	0.004	0.004	0.000	0.000	0.000	0.000
28	B	135	ILE	0	-0.033	-0.015	38.649	0.002	0.002	0.000	0.000	0.000	0.000
29	B	136	LEU	0	0.028	0.029	38.432	0.000	0.000	0.000	0.000	0.000	0.000
30	B	137	ALA	0	0.015	-0.004	40.562	0.000	0.000	0.000	0.000	0.000	0.000
31	B	138	LEU	0	0.007	0.022	42.296	0.002	0.002	0.000	0.000	0.000	0.000
32	B	139	ASN	0	0.011	-0.007	44.369	0.001	0.001	0.000	0.000	0.000	0.000
33	B	140	ALA	0	0.017	0.024	44.469	0.000	0.000	0.000	0.000	0.000	0.000
34	B	141	THR	0	0.014	-0.012	46.116	0.000	0.000	0.000	0.000	0.000	0.000
35	B	142	ILE	0	-0.047	-0.012	48.529	0.000	0.000	0.000	0.000	0.000	0.000
36	B	143	GLU	-1	-0.957	-0.993	49.539	-0.018	-0.018	0.000	0.000	0.000	0.000
37	B	144	ALA	0	-0.010	-0.004	50.081	0.000	0.000	0.000	0.000	0.000	0.000
38	B	145	ALA	0	0.003	0.004	51.917	0.000	0.000	0.000	0.000	0.000	0.000
39	B	146	ARG	1	0.948	0.980	51.960	0.011	0.011	0.000	0.000	0.000	0.000
40	B	147	ALA	0	-0.008	-0.006	54.323	-0.001	-0.001	0.000	0.000	0.000	0.000
41	B	148	GLY	0	-0.009	-0.014	55.939	0.000	0.000	0.000	0.000	0.000	0.000
42	B	149	GLU	-1	-0.967	-0.977	57.781	0.003	0.003	0.000	0.000	0.000	0.000
43	B	150	ALA	0	-0.006	0.000	59.395	0.000	0.000	0.000	0.000	0.000	0.000
44	B	151	GLY	0	0.007	0.002	59.970	0.000	0.000	0.000	0.000	0.000	0.000
45	B	152	LYS	1	0.959	0.978	61.327	-0.003	-0.003	0.000	0.000	0.000	0.000
46	B	153	GLY	0	0.006	0.006	63.649	0.001	0.001	0.000	0.000	0.000	0.000
47	B	154	PHE	0	-0.007	-0.006	64.249	0.000	0.000	0.000	0.000	0.000	0.000
48	B	155	MET	0	0.007	-0.009	63.683	0.000	0.000	0.000	0.000	0.000	0.000
49	B	156	ILE	0	-0.023	-0.006	67.201	0.001	0.001	0.000	0.000	0.000	0.000
50	B	157	VAL	0	0.035	0.025	68.727	0.000	0.000	0.000	0.000	0.000	0.000
51	B	158	ALA	0	-0.022	-0.011	69.117	0.000	0.000	0.000	0.000	0.000	0.000
52	B	159	ASN	0	-0.017	-0.030	71.087	0.000	0.000	0.000	0.000	0.000	0.000
53	B	160	GLU	-1	-0.937	-0.969	73.223	-0.003	-0.003	0.000	0.000	0.000	0.000
54	B	161	VAL	0	0.006	0.016	73.972	0.000	0.000	0.000	0.000	0.000	0.000
55	B	162	GLN	0	-0.024	-0.007	75.166	-0.001	-0.001	0.000	0.000	0.000	0.000
56	B	163	ASN	0	-0.025	-0.033	77.104	0.000	0.000	0.000	0.000	0.000	0.000
57	B	164	LEU	0	0.071	0.051	79.246	0.000	0.000	0.000	0.000	0.000	0.000
58	B	165	SER	0	-0.023	0.002	79.294	0.000	0.000	0.000	0.000	0.000	0.000
59	B	166	ASN	0	-0.041	-0.036	80.282	0.000	0.000	0.000	0.000	0.000	0.000
60	B	167	GLU	-1	-0.911	-0.942	83.460	-0.003	-0.003	0.000	0.000	0.000	0.000
61	B	168	THR	0	-0.026	-0.028	84.433	0.000	0.000	0.000	0.000	0.000	0.000
62	B	169	ASN	0	-0.050	-0.014	85.672	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	170	GLU	-1	-0.877	-0.947	87.565	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	171	VAL	0	0.032	0.019	89.466	0.000	0.000	0.000	0.000	0.000	0.000
65	B	172	THR	0	-0.001	0.003	89.742	0.000	0.000	0.000	0.000	0.000	0.000
66	B	173	LYS	1	0.857	0.916	89.880	0.005	0.005	0.000	0.000	0.000	0.000
67	B	174	GLN	0	0.030	0.021	92.990	0.000	0.000	0.000	0.000	0.000	0.000
68	B	175	ILE	0	-0.023	0.001	94.045	0.000	0.000	0.000	0.000	0.000	0.000
69	B	176	VAL	0	-0.036	-0.015	96.361	0.000	0.000	0.000	0.000	0.000	0.000
70	B	177	GLU	-1	-0.957	-0.983	98.162	-0.003	-0.003	0.000	0.000	0.000	0.000
71	B	178	LYS	1	0.970	0.985	99.824	0.003	0.003	0.000	0.000	0.000	0.000
72	B	179	ALA	0	0.002	-0.008	100.893	0.000	0.000	0.000	0.000	0.000	0.000
73	B	180	ARG	1	0.917	0.971	99.897	0.006	0.006	0.000	0.000	0.000	0.000
74	B	181	GLU	-1	-0.877	-0.948	103.436	-0.003	-0.003	0.000	0.000	0.000	0.000
75	B	182	ILE	0	-0.027	-0.007	103.558	0.000	0.000	0.000	0.000	0.000	0.000
76	B	183	LEU	0	-0.010	0.007	106.961	0.000	0.000	0.000	0.000	0.000	0.000
77	B	184	GLU	-1	-0.809	-0.903	108.798	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	185	SER	0	-0.044	-0.032	109.669	0.000	0.000	0.000	0.000	0.000	0.000
79	B	186	SER	0	-0.063	-0.045	110.195	0.000	0.000	0.000	0.000	0.000	0.000
80	B	187	GLN	0	-0.038	-0.009	112.760	0.000	0.000	0.000	0.000	0.000	0.000
81	B	188	ARG	1	0.917	0.947	112.652	0.003	0.003	0.000	0.000	0.000	0.000
82	B	189	SER	0	-0.094	-0.036	116.147	0.000	0.000	0.000	0.000	0.000	0.000
83	B	190	LEU	0	-0.059	-0.035	117.542	0.000	0.000	0.000	0.000	0.000	0.000
84	B	191	GLU	-1	-1.009	-0.979	119.069	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:108:GLN)