FMO DATABASE

FMODB ID: 4999N

Calculation Name: 4E5X-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E5X

Chain ID: G

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-764261.959749
FMO2-HF: Nuclear repulsion	721592.898484
FMO2-HF: Total energy	-42669.061265
FMO2-MP2: Total energy	-42789.24156

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(G:2:LYS)

Summations of interaction energy for fragment #1(G:2:LYS)

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.
11.397	13.154	-0.013	-0.847	-0.897	0.002

Interaction energy analysis for fragmet #1(G:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.017 / q_NPA : 0.997

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	G	4	VAL	0	0.037	0.003	3.633	-1.586	0.086	-0.012	-0.838	-0.822	0.002
4	G	5	GLU	-1	-0.951	-0.959	6.389	-19.307	-19.307	0.000	0.000	0.000	0.000
5	G	6	PHE	0	-0.081	-0.054	9.389	0.770	0.770	0.000	0.000	0.000	0.000
6	G	7	LYS	1	0.978	0.999	11.819	17.337	17.337	0.000	0.000	0.000	0.000
7	G	8	GLU	-1	-0.873	-0.906	14.793	-12.811	-12.811	0.000	0.000	0.000	0.000
8	G	9	PRO	0	-0.033	-0.010	18.207	0.123	0.123	0.000	0.000	0.000	0.000
9	G	10	ALA	0	0.056	0.039	19.874	0.439	0.439	0.000	0.000	0.000	0.000
10	G	11	CYS	0	-0.054	-0.038	22.967	0.032	0.032	0.000	0.000	0.000	0.000
11	G	12	ASN	0	0.016	0.003	25.962	0.244	0.244	0.000	0.000	0.000	0.000
12	G	13	VAL	0	-0.002	0.008	29.658	-0.077	-0.077	0.000	0.000	0.000	0.000
13	G	14	THR	0	-0.081	-0.035	32.481	0.229	0.229	0.000	0.000	0.000	0.000
14	G	15	PHE	0	0.079	0.008	35.583	-0.087	-0.087	0.000	0.000	0.000	0.000
15	G	16	LYS	1	0.958	0.990	39.026	7.226	7.226	0.000	0.000	0.000	0.000
16	G	17	SER	0	0.033	0.025	41.748	-0.014	-0.014	0.000	0.000	0.000	0.000
17	G	18	GLU	-1	-0.957	-0.992	43.578	-7.009	-7.009	0.000	0.000	0.000	0.000
18	G	19	ALA	0	0.010	0.007	46.127	-0.012	-0.012	0.000	0.000	0.000	0.000
19	G	20	ASN	0	-0.006	0.014	49.140	0.059	0.059	0.000	0.000	0.000	0.000
20	G	21	GLU	-1	-0.796	-0.893	44.839	-6.654	-6.654	0.000	0.000	0.000	0.000
21	G	22	CYS	0	-0.053	-0.019	41.212	0.011	0.011	0.000	0.000	0.000	0.000
22	G	23	THR	0	-0.037	-0.014	39.677	-0.210	-0.210	0.000	0.000	0.000	0.000
23	G	24	THR	0	-0.013	-0.017	35.755	-0.042	-0.042	0.000	0.000	0.000	0.000
24	G	25	LEU	0	-0.013	-0.024	32.002	-0.126	-0.126	0.000	0.000	0.000	0.000
25	G	26	ILE	0	0.024	0.026	27.844	-0.014	-0.014	0.000	0.000	0.000	0.000
26	G	27	LYS	1	0.963	0.978	27.334	9.206	9.206	0.000	0.000	0.000	0.000
27	G	29	THR	0	-0.041	-0.012	21.621	-0.062	-0.062	0.000	0.000	0.000	0.000
28	G	30	THR	0	0.027	-0.005	16.124	-0.356	-0.356	0.000	0.000	0.000	0.000
29	G	31	GLU	-1	-0.861	-0.918	14.222	-14.963	-14.963	0.000	0.000	0.000	0.000
30	G	32	HIS	0	-0.040	-0.014	10.750	-0.314	-0.314	0.000	0.000	0.000	0.000
31	G	33	GLU	-1	-0.895	-0.940	11.304	-21.025	-21.025	0.000	0.000	0.000	0.000
32	G	34	LYS	1	0.922	0.957	13.567	18.930	18.930	0.000	0.000	0.000	0.000
33	G	35	LEU	0	0.024	0.011	15.956	-0.794	-0.794	0.000	0.000	0.000	0.000
34	G	36	ILE	0	-0.090	-0.045	18.562	0.393	0.393	0.000	0.000	0.000	0.000
35	G	37	ILE	0	0.013	0.014	21.152	-0.209	-0.209	0.000	0.000	0.000	0.000
36	G	38	ARG	1	0.931	0.963	20.349	13.437	13.437	0.000	0.000	0.000	0.000
37	G	39	HIS	0	0.029	-0.013	26.227	0.202	0.202	0.000	0.000	0.000	0.000
38	G	40	LYS	1	0.857	0.952	29.822	8.319	8.319	0.000	0.000	0.000	0.000
39	G	41	ASP	-1	-0.878	-0.937	30.949	-9.112	-9.112	0.000	0.000	0.000	0.000
40	G	42	LYS	1	0.881	0.951	30.696	8.606	8.606	0.000	0.000	0.000	0.000
41	G	43	ILE	0	0.010	-0.020	24.516	-0.423	-0.423	0.000	0.000	0.000	0.000
42	G	44	GLY	0	0.014	0.015	25.644	0.291	0.291	0.000	0.000	0.000	0.000
43	G	45	LYS	1	0.903	0.960	19.518	13.636	13.636	0.000	0.000	0.000	0.000
44	G	46	TYR	0	0.018	0.011	22.275	-0.231	-0.231	0.000	0.000	0.000	0.000
45	G	47	ALA	0	0.034	-0.010	25.290	0.092	0.092	0.000	0.000	0.000	0.000
46	G	48	VAL	0	-0.025	0.008	27.925	-0.052	-0.052	0.000	0.000	0.000	0.000
47	G	49	TYR	0	0.037	0.019	30.464	0.037	0.037	0.000	0.000	0.000	0.000
48	G	50	ALA	0	-0.014	-0.025	34.263	-0.062	-0.062	0.000	0.000	0.000	0.000
49	G	51	ILE	0	0.068	0.056	36.904	0.021	0.021	0.000	0.000	0.000	0.000
50	G	52	TRP	0	-0.078	-0.043	37.224	0.034	0.034	0.000	0.000	0.000	0.000
51	G	53	GLN	0	-0.008	-0.011	40.322	0.152	0.152	0.000	0.000	0.000	0.000
52	G	54	PRO	0	0.001	-0.026	42.340	-0.112	-0.112	0.000	0.000	0.000	0.000
53	G	55	GLY	0	-0.035	-0.007	42.764	0.097	0.097	0.000	0.000	0.000	0.000
54	G	56	ASP	-1	-0.774	-0.868	38.348	-7.787	-7.787	0.000	0.000	0.000	0.000
55	G	57	THR	0	-0.056	-0.078	33.076	0.029	0.029	0.000	0.000	0.000	0.000
56	G	58	ASN	0	-0.013	-0.020	34.773	0.119	0.119	0.000	0.000	0.000	0.000
57	G	59	ASP	-1	-0.895	-0.911	29.615	-9.949	-9.949	0.000	0.000	0.000	0.000
58	G	60	TYR	0	0.031	0.028	26.317	0.221	0.221	0.000	0.000	0.000	0.000
59	G	61	ASN	0	-0.027	-0.005	22.961	-0.553	-0.553	0.000	0.000	0.000	0.000
60	G	62	VAL	0	0.055	0.016	20.317	0.123	0.123	0.000	0.000	0.000	0.000
61	G	63	THR	0	-0.045	0.000	15.935	-0.422	-0.422	0.000	0.000	0.000	0.000
62	G	64	VAL	0	0.041	0.037	14.188	0.350	0.350	0.000	0.000	0.000	0.000
63	G	65	PHE	0	-0.035	-0.047	12.341	-0.611	-0.611	0.000	0.000	0.000	0.000
64	G	66	GLN	0	0.089	0.019	7.302	2.342	2.342	0.000	0.000	0.000	0.000
65	G	67	GLY	0	0.006	0.027	6.740	-3.008	-3.008	0.000	0.000	0.000	0.000
66	G	68	GLU	-1	-0.898	-0.954	6.273	-28.242	-28.242	0.000	0.000	0.000	0.000
67	G	69	ASN	0	-0.110	-0.033	4.055	1.250	1.335	-0.001	-0.009	-0.075	0.000
68	G	70	ARG	1	0.973	0.955	8.230	21.577	21.577	0.000	0.000	0.000	0.000
69	G	71	LYS	1	0.938	0.986	11.758	16.684	16.684	0.000	0.000	0.000	0.000
70	G	72	THR	0	-0.041	-0.033	14.331	0.218	0.218	0.000	0.000	0.000	0.000
71	G	73	PHE	0	-0.003	0.010	16.434	-0.176	-0.176	0.000	0.000	0.000	0.000
72	G	74	MET	0	0.003	-0.012	20.752	0.099	0.099	0.000	0.000	0.000	0.000
73	G	75	TYR	0	-0.041	-0.049	22.631	-0.073	-0.073	0.000	0.000	0.000	0.000
74	G	76	LYS	1	0.933	0.958	27.452	9.342	9.342	0.000	0.000	0.000	0.000
75	G	77	PHE	0	0.041	0.012	31.223	-0.108	-0.108	0.000	0.000	0.000	0.000
76	G	78	PRO	0	0.054	0.036	33.724	0.063	0.063	0.000	0.000	0.000	0.000
77	G	79	PHE	0	0.028	0.003	32.917	0.112	0.112	0.000	0.000	0.000	0.000
78	G	80	TYR	0	0.008	0.006	38.417	0.134	0.134	0.000	0.000	0.000	0.000
79	G	81	GLU	-1	-0.911	-0.954	40.675	-7.258	-7.258	0.000	0.000	0.000	0.000
80	G	82	MET	0	0.021	0.022	37.860	0.143	0.143	0.000	0.000	0.000	0.000
81	G	84	ASP	-1	-0.828	-0.898	43.032	-6.207	-6.207	0.000	0.000	0.000	0.000
82	G	85	ILE	0	-0.024	-0.010	42.809	0.154	0.154	0.000	0.000	0.000	0.000
83	G	86	THR	0	-0.056	-0.044	42.509	0.076	0.076	0.000	0.000	0.000	0.000
84	G	87	MET	0	-0.076	-0.013	44.995	0.048	0.048	0.000	0.000	0.000	0.000
85	G	88	TYR	0	0.015	0.017	47.869	0.133	0.133	0.000	0.000	0.000	0.000
86	G	89	MET	0	0.014	-0.005	50.496	0.118	0.118	0.000	0.000	0.000	0.000
87	G	90	SER	0	0.031	-0.016	50.676	0.076	0.076	0.000	0.000	0.000	0.000
88	G	91	LYS	1	0.836	0.915	50.011	6.201	6.201	0.000	0.000	0.000	0.000
89	G	92	GLN	0	-0.045	-0.006	53.414	0.117	0.117	0.000	0.000	0.000	0.000
90	G	93	TYR	0	-0.041	-0.020	56.010	0.092	0.092	0.000	0.000	0.000	0.000
91	G	94	LYS	1	0.880	0.938	56.077	5.287	5.287	0.000	0.000	0.000	0.000
92	G	95	LEU	0	-0.005	0.002	53.690	0.002	0.002	0.000	0.000	0.000	0.000
93	G	96	TRP	0	0.023	0.031	44.925	-0.099	-0.099	0.000	0.000	0.000	0.000
94	G	97	PRO	0	-0.037	-0.041	48.773	0.072	0.072	0.000	0.000	0.000	0.000
95	G	98	PRO	0	0.043	0.027	47.033	0.125	0.125	0.000	0.000	0.000	0.000
96	G	99	GLN	0	-0.033	-0.019	50.319	-0.004	-0.004	0.000	0.000	0.000	0.000
97	G	100	LYS	1	0.995	1.006	47.994	6.328	6.328	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:2:LYS)