FMO DATABASE

FMODB ID: 49YJN

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	OptAll
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	-362241.676419
FMO2-HF: Nuclear repulsion	329430.282878
FMO2-HF: Total energy	-32811.393542
FMO2-MP2: Total energy	-32907.004104

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.
-36.013	-32.453	9.859	-6.074	-7.345	-0.056

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 : 0.018 / q_NPA : -0.013

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	0.019	0.008	3.200	-4.164	-2.386	0.026	-0.801	-1.003	0.001
4	B	111	GLU	-1	-0.843	-0.909	1.831	-35.208	-35.331	9.185	-4.376	-4.686	-0.057
5	B	112	THR	0	-0.006	-0.006	2.481	-2.233	-0.504	0.649	-0.873	-1.505	0.000
6	B	113	LEU	0	0.009	-0.004	4.606	0.875	1.051	-0.001	-0.024	-0.151	0.000
7	B	114	GLU	-1	-0.806	-0.856	7.625	-1.094	-1.094	0.000	0.000	0.000	0.000
8	B	115	ASN	0	-0.019	-0.009	5.037	1.894	1.894	0.000	0.000	0.000	0.000
9	B	116	ILE	0	-0.005	0.001	8.421	0.552	0.552	0.000	0.000	0.000	0.000
10	B	117	ARG	1	0.867	0.898	10.515	1.231	1.231	0.000	0.000	0.000	0.000
11	B	118	SER	0	-0.058	-0.034	11.468	0.261	0.261	0.000	0.000	0.000	0.000
12	B	119	ILE	0	-0.005	-0.005	10.763	0.199	0.199	0.000	0.000	0.000	0.000
13	B	120	GLU	-1	-0.916	-0.958	14.257	-0.382	-0.382	0.000	0.000	0.000	0.000
14	B	121	LYS	1	0.930	0.957	16.427	1.022	1.022	0.000	0.000	0.000	0.000
15	B	122	LEU	0	-0.007	-0.004	15.297	0.096	0.096	0.000	0.000	0.000	0.000
16	B	123	ILE	0	0.030	0.011	18.441	0.085	0.085	0.000	0.000	0.000	0.000
17	B	124	GLN	0	0.019	-0.001	20.394	0.091	0.091	0.000	0.000	0.000	0.000
18	B	125	ASN	0	-0.024	-0.006	21.822	0.083	0.083	0.000	0.000	0.000	0.000
19	B	126	ILE	0	0.017	0.012	20.990	0.044	0.044	0.000	0.000	0.000	0.000
20	B	127	MET	0	-0.003	0.001	23.584	0.056	0.056	0.000	0.000	0.000	0.000
21	B	128	ARG	1	0.882	0.949	24.025	0.514	0.514	0.000	0.000	0.000	0.000
22	B	129	ILE	0	0.086	0.044	25.793	0.025	0.025	0.000	0.000	0.000	0.000
23	B	130	ALA	0	0.010	0.019	28.635	0.027	0.027	0.000	0.000	0.000	0.000
24	B	131	ARG	1	0.952	0.978	30.384	0.277	0.277	0.000	0.000	0.000	0.000
25	B	132	GLU	-1	-0.966	-0.993	31.638	-0.307	-0.307	0.000	0.000	0.000	0.000
26	B	133	THR	0	-0.014	-0.017	32.132	0.012	0.012	0.000	0.000	0.000	0.000
27	B	134	ASN	0	-0.018	-0.007	34.589	0.020	0.020	0.000	0.000	0.000	0.000
28	B	135	ILE	0	-0.031	-0.013	36.468	0.015	0.015	0.000	0.000	0.000	0.000
29	B	136	LEU	0	0.034	0.022	37.138	0.012	0.012	0.000	0.000	0.000	0.000
30	B	137	ALA	0	0.025	0.012	38.613	0.010	0.010	0.000	0.000	0.000	0.000
31	B	138	LEU	0	0.004	0.015	40.402	0.013	0.013	0.000	0.000	0.000	0.000
32	B	139	ASN	0	-0.031	-0.026	42.382	0.002	0.002	0.000	0.000	0.000	0.000
33	B	140	ALA	0	0.036	0.014	42.891	0.008	0.008	0.000	0.000	0.000	0.000
34	B	141	THR	0	-0.020	-0.015	44.058	0.008	0.008	0.000	0.000	0.000	0.000
35	B	142	ILE	0	-0.033	-0.016	46.492	0.008	0.008	0.000	0.000	0.000	0.000
36	B	143	GLU	-1	-0.836	-0.879	47.574	-0.142	-0.142	0.000	0.000	0.000	0.000
37	B	144	ALA	0	0.012	0.004	48.316	0.005	0.005	0.000	0.000	0.000	0.000
38	B	145	ALA	0	-0.008	0.003	50.181	0.006	0.006	0.000	0.000	0.000	0.000
39	B	146	ARG	1	0.824	0.868	49.827	0.140	0.140	0.000	0.000	0.000	0.000
40	B	147	ALA	0	0.007	0.009	52.697	0.004	0.004	0.000	0.000	0.000	0.000
41	B	148	GLY	0	0.010	0.007	54.295	0.003	0.003	0.000	0.000	0.000	0.000
42	B	149	GLU	-1	-0.862	-0.918	56.056	-0.086	-0.086	0.000	0.000	0.000	0.000
43	B	150	ALA	0	-0.006	0.002	57.738	0.004	0.004	0.000	0.000	0.000	0.000
44	B	151	GLY	0	0.012	0.009	58.418	0.003	0.003	0.000	0.000	0.000	0.000
45	B	152	LYS	1	0.857	0.905	59.881	0.091	0.091	0.000	0.000	0.000	0.000
46	B	153	GLY	0	0.006	0.000	62.011	0.004	0.004	0.000	0.000	0.000	0.000
47	B	154	PHE	0	-0.010	-0.008	62.765	0.003	0.003	0.000	0.000	0.000	0.000
48	B	155	MET	0	-0.016	-0.017	62.302	0.001	0.001	0.000	0.000	0.000	0.000
49	B	156	ILE	0	-0.002	0.010	65.582	0.003	0.003	0.000	0.000	0.000	0.000
50	B	157	VAL	0	0.044	0.022	67.524	0.002	0.002	0.000	0.000	0.000	0.000
51	B	158	ALA	0	0.001	0.005	67.910	0.002	0.002	0.000	0.000	0.000	0.000
52	B	159	ASN	0	-0.021	-0.017	69.858	0.003	0.003	0.000	0.000	0.000	0.000
53	B	160	GLU	-1	-0.947	-0.963	71.832	-0.063	-0.063	0.000	0.000	0.000	0.000
54	B	161	VAL	0	0.024	0.009	72.690	0.002	0.002	0.000	0.000	0.000	0.000
55	B	162	GLN	0	-0.020	0.000	73.640	0.000	0.000	0.000	0.000	0.000	0.000
56	B	163	ASN	0	-0.012	-0.006	75.029	0.002	0.002	0.000	0.000	0.000	0.000
57	B	164	LEU	0	0.071	0.034	77.135	0.002	0.002	0.000	0.000	0.000	0.000
58	B	165	SER	0	-0.043	-0.016	77.705	0.001	0.001	0.000	0.000	0.000	0.000
59	B	166	ASN	0	-0.083	-0.054	78.939	0.002	0.002	0.000	0.000	0.000	0.000
60	B	167	GLU	-1	-0.918	-0.950	82.137	-0.052	-0.052	0.000	0.000	0.000	0.000
61	B	168	THR	0	-0.001	-0.015	82.760	0.002	0.002	0.000	0.000	0.000	0.000
62	B	169	ASN	0	-0.026	-0.003	84.509	0.001	0.001	0.000	0.000	0.000	0.000
63	B	170	GLU	-1	-0.809	-0.885	86.267	-0.048	-0.048	0.000	0.000	0.000	0.000
64	B	171	VAL	0	0.009	0.014	88.032	0.002	0.002	0.000	0.000	0.000	0.000
65	B	172	THR	0	-0.023	-0.025	88.207	0.001	0.001	0.000	0.000	0.000	0.000
66	B	173	LYS	1	0.806	0.873	89.248	0.050	0.050	0.000	0.000	0.000	0.000
67	B	174	GLN	0	0.020	0.006	90.892	0.002	0.002	0.000	0.000	0.000	0.000
68	B	175	ILE	0	-0.017	0.000	92.043	0.001	0.001	0.000	0.000	0.000	0.000
69	B	176	VAL	0	-0.036	-0.024	94.286	0.001	0.001	0.000	0.000	0.000	0.000
70	B	177	GLU	-1	-1.007	-0.995	96.743	-0.040	-0.040	0.000	0.000	0.000	0.000
71	B	178	LYS	1	0.863	0.900	97.852	0.039	0.039	0.000	0.000	0.000	0.000
72	B	179	ALA	0	-0.001	0.002	99.413	0.001	0.001	0.000	0.000	0.000	0.000
73	B	180	ARG	1	0.938	0.973	98.031	0.042	0.042	0.000	0.000	0.000	0.000
74	B	181	GLU	-1	-0.760	-0.861	101.519	-0.037	-0.037	0.000	0.000	0.000	0.000
75	B	182	ILE	0	0.008	0.023	102.011	0.001	0.001	0.000	0.000	0.000	0.000
76	B	183	LEU	0	-0.005	0.020	105.586	0.001	0.001	0.000	0.000	0.000	0.000
77	B	184	GLU	-1	-0.800	-0.888	107.487	-0.032	-0.032	0.000	0.000	0.000	0.000
78	B	185	SER	0	-0.052	-0.048	108.136	0.001	0.001	0.000	0.000	0.000	0.000
79	B	186	SER	0	-0.048	-0.038	108.923	0.001	0.001	0.000	0.000	0.000	0.000
80	B	187	GLN	0	-0.036	-0.011	111.153	0.000	0.000	0.000	0.000	0.000	0.000
81	B	188	ARG	1	0.877	0.922	112.042	0.032	0.032	0.000	0.000	0.000	0.000
82	B	189	SER	0	-0.110	-0.056	114.439	0.001	0.001	0.000	0.000	0.000	0.000
83	B	190	LEU	0	-0.041	-0.022	115.935	0.001	0.001	0.000	0.000	0.000	0.000
84	B	191	GLU	-1	-1.010	-0.990	117.403	-0.028	-0.028	0.000	0.000	0.000	0.000

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