FMO DATABASE

FMODB ID: YZZY2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-766473.384278
FMO2-HF: Nuclear repulsion	723803.465906
FMO2-HF: Total energy	-42669.918371
FMO2-MP2: Total energy	-42790.181967

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.
12.484	14.42	-0.017	-1.043	-0.876	0

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 : 1.008

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].
3	G	4	VAL	0	0.051	0.023	3.770	-0.781	1.128	-0.016	-1.034	-0.859
4	G	5	GLU	-1	-0.830	-0.879	6.446	-17.075	-17.075	0.000	0.000	0.000
5	G	6	PHE	0	-0.051	-0.033	9.478	0.620	0.620	0.000	0.000	0.000
6	G	7	LYS	1	0.825	0.902	11.790	17.799	17.799	0.000	0.000	0.000
7	G	8	GLU	-1	-0.815	-0.892	15.034	-12.917	-12.917	0.000	0.000	0.000
8	G	9	PRO	0	-0.027	-0.008	18.402	0.072	0.072	0.000	0.000	0.000
9	G	10	ALA	0	0.053	0.027	19.849	0.520	0.520	0.000	0.000	0.000
10	G	11	CYS	0	-0.069	-0.026	22.655	0.057	0.057	0.000	0.000	0.000
11	G	12	ASN	0	0.015	0.000	25.571	0.283	0.283	0.000	0.000	0.000
12	G	13	VAL	0	-0.011	0.005	29.375	-0.150	-0.150	0.000	0.000	0.000
13	G	14	THR	0	-0.062	-0.027	32.237	0.233	0.233	0.000	0.000	0.000
14	G	15	PHE	0	0.069	0.006	35.339	-0.074	-0.074	0.000	0.000	0.000
15	G	16	LYS	1	0.831	0.905	38.828	7.183	7.183	0.000	0.000	0.000
16	G	17	SER	0	0.048	0.039	41.755	-0.031	-0.031	0.000	0.000	0.000
17	G	18	GLU	-1	-0.808	-0.902	42.337	-7.023	-7.023	0.000	0.000	0.000
18	G	19	ALA	0	0.003	-0.003	45.778	0.001	0.001	0.000	0.000	0.000
19	G	20	ASN	0	0.005	0.021	48.577	0.146	0.146	0.000	0.000	0.000
20	G	21	GLU	-1	-0.724	-0.868	44.785	-6.662	-6.662	0.000	0.000	0.000
21	G	22	CYS	0	-0.041	0.008	40.966	-0.013	-0.013	0.000	0.000	0.000
22	G	23	THR	0	-0.067	-0.038	39.618	-0.187	-0.187	0.000	0.000	0.000
23	G	24	THR	0	-0.018	-0.024	35.969	-0.050	-0.050	0.000	0.000	0.000
24	G	25	LEU	0	-0.023	-0.020	31.599	-0.113	-0.113	0.000	0.000	0.000
25	G	26	ILE	0	0.054	0.045	27.803	-0.015	-0.015	0.000	0.000	0.000
26	G	27	LYS	1	0.946	0.961	27.214	9.211	9.211	0.000	0.000	0.000
27	G	29	THR	0	-0.045	-0.021	21.422	-0.061	-0.061	0.000	0.000	0.000
28	G	30	THR	0	-0.016	-0.040	16.059	-0.339	-0.339	0.000	0.000	0.000
29	G	31	GLU	-1	-0.800	-0.885	13.660	-14.864	-14.864	0.000	0.000	0.000
30	G	32	HIS	0	-0.038	-0.022	10.234	-0.279	-0.279	0.000	0.000	0.000
31	G	33	GLU	-1	-0.819	-0.889	11.138	-20.311	-20.311	0.000	0.000	0.000
32	G	34	LYS	1	0.814	0.898	13.088	20.859	20.859	0.000	0.000	0.000
33	G	35	LEU	0	0.002	0.001	15.486	-0.653	-0.653	0.000	0.000	0.000
34	G	36	ILE	0	-0.047	-0.025	18.188	0.349	0.349	0.000	0.000	0.000
35	G	37	ILE	0	0.026	0.029	20.989	-0.190	-0.190	0.000	0.000	0.000
36	G	38	ARG	1	0.861	0.907	19.825	13.423	13.423	0.000	0.000	0.000
37	G	39	HIS	0	0.017	-0.018	26.588	0.177	0.177	0.000	0.000	0.000
38	G	40	LYS	1	0.822	0.933	30.172	8.173	8.173	0.000	0.000	0.000
39	G	41	ASP	-1	-0.800	-0.877	31.420	-8.923	-8.923	0.000	0.000	0.000
40	G	42	LYS	1	0.810	0.904	31.050	8.437	8.437	0.000	0.000	0.000
41	G	43	ILE	0	0.019	-0.010	24.832	-0.322	-0.322	0.000	0.000	0.000
42	G	44	GLY	0	0.022	0.014	25.731	0.306	0.306	0.000	0.000	0.000
43	G	45	LYS	1	0.884	0.942	19.884	13.099	13.099	0.000	0.000	0.000
44	G	46	TYR	0	0.038	0.020	21.849	-0.488	-0.488	0.000	0.000	0.000
45	G	47	ALA	0	0.021	-0.006	24.780	0.129	0.129	0.000	0.000	0.000
46	G	48	VAL	0	-0.011	0.003	27.753	-0.145	-0.145	0.000	0.000	0.000
47	G	49	TYR	0	-0.005	0.006	30.362	0.069	0.069	0.000	0.000	0.000
48	G	50	ALA	0	-0.001	-0.009	34.205	-0.039	-0.039	0.000	0.000	0.000
49	G	51	ILE	0	0.047	0.045	36.888	0.029	0.029	0.000	0.000	0.000
50	G	52	TRP	0	-0.060	-0.043	37.224	-0.054	-0.054	0.000	0.000	0.000
51	G	53	GLN	0	0.015	-0.007	40.532	0.142	0.142	0.000	0.000	0.000
52	G	54	PRO	0	0.003	-0.019	42.734	-0.123	-0.123	0.000	0.000	0.000
53	G	55	GLY	0	-0.015	0.000	42.815	0.195	0.195	0.000	0.000	0.000
54	G	56	ASP	-1	-0.770	-0.864	38.486	-7.817	-7.817	0.000	0.000	0.000
55	G	57	THR	0	-0.028	-0.037	33.733	0.096	0.096	0.000	0.000	0.000
56	G	58	ASN	0	-0.006	-0.012	35.385	0.131	0.131	0.000	0.000	0.000
57	G	59	ASP	-1	-0.900	-0.929	29.947	-9.820	-9.820	0.000	0.000	0.000
58	G	60	TYR	0	0.033	0.032	25.924	0.250	0.250	0.000	0.000	0.000
59	G	61	ASN	0	-0.010	0.003	23.632	-0.577	-0.577	0.000	0.000	0.000
60	G	62	VAL	0	0.054	0.018	19.847	0.158	0.158	0.000	0.000	0.000
61	G	63	THR	0	-0.055	-0.023	16.126	-0.045	-0.045	0.000	0.000	0.000
62	G	64	VAL	0	0.070	0.045	13.910	0.254	0.254	0.000	0.000	0.000
63	G	65	PHE	0	-0.027	-0.044	12.075	-0.633	-0.633	0.000	0.000	0.000
64	G	66	GLN	0	0.068	0.023	7.072	1.968	1.968	0.000	0.000	0.000
65	G	67	GLY	0	0.026	0.028	7.221	-3.602	-3.602	0.000	0.000	0.000
66	G	68	GLU	-1	-0.898	-0.960	6.633	-30.442	-30.442	0.000	0.000	0.000
67	G	69	ASN	0	-0.079	-0.038	4.426	0.249	0.276	-0.001	-0.009	-0.017
68	G	70	ARG	1	0.946	0.967	8.169	22.533	22.533	0.000	0.000	0.000
69	G	71	LYS	1	0.863	0.951	11.864	14.981	14.981	0.000	0.000	0.000
70	G	72	THR	0	0.002	0.010	14.612	0.277	0.277	0.000	0.000	0.000
71	G	73	PHE	0	0.032	0.034	16.285	-0.372	-0.372	0.000	0.000	0.000
72	G	74	MET	0	0.007	-0.004	21.001	-0.019	-0.019	0.000	0.000	0.000
73	G	75	TYR	0	-0.029	-0.038	22.270	0.036	0.036	0.000	0.000	0.000
74	G	76	LYS	1	0.929	0.947	27.715	9.433	9.433	0.000	0.000	0.000
75	G	77	PHE	0	0.038	0.016	31.520	-0.103	-0.103	0.000	0.000	0.000
76	G	78	PRO	0	0.080	0.056	33.735	0.041	0.041	0.000	0.000	0.000
77	G	79	PHE	0	-0.008	-0.018	32.545	0.111	0.111	0.000	0.000	0.000
78	G	80	TYR	0	-0.026	-0.027	38.133	0.124	0.124	0.000	0.000	0.000
79	G	81	GLU	-1	-0.903	-0.952	40.906	-7.136	-7.136	0.000	0.000	0.000
80	G	82	MET	0	0.022	0.018	37.684	0.144	0.144	0.000	0.000	0.000
81	G	84	ASP	-1	-0.815	-0.872	42.887	-6.120	-6.120	0.000	0.000	0.000
82	G	85	ILE	0	0.019	0.005	42.808	0.161	0.161	0.000	0.000	0.000
83	G	86	THR	0	-0.061	-0.047	42.388	0.089	0.089	0.000	0.000	0.000
84	G	87	MET	0	-0.046	0.003	44.912	0.045	0.045	0.000	0.000	0.000
85	G	88	TYR	0	-0.002	-0.004	47.716	0.132	0.132	0.000	0.000	0.000
86	G	89	MET	0	0.002	-0.005	50.404	0.113	0.113	0.000	0.000	0.000
87	G	90	SER	0	0.016	-0.015	50.685	0.081	0.081	0.000	0.000	0.000
88	G	91	LYS	1	0.810	0.903	49.630	6.196	6.196	0.000	0.000	0.000
89	G	92	GLN	0	-0.030	0.007	53.378	0.127	0.127	0.000	0.000	0.000
90	G	93	TYR	0	-0.021	-0.023	55.746	0.090	0.090	0.000	0.000	0.000
91	G	94	LYS	1	0.853	0.932	55.913	5.301	5.301	0.000	0.000	0.000
92	G	95	LEU	0	0.001	0.010	53.720	-0.018	-0.018	0.000	0.000	0.000
93	G	96	TRP	0	-0.003	0.001	44.626	-0.099	-0.099	0.000	0.000	0.000
94	G	97	PRO	0	-0.011	-0.021	48.901	0.075	0.075	0.000	0.000	0.000
95	G	98	PRO	0	0.001	0.010	47.084	0.123	0.123	0.000	0.000	0.000
96	G	99	GLN	0	0.010	0.005	50.397	-0.052	-0.052	0.000	0.000	0.000
97	G	100	LYS	1	0.881	0.941	47.398	6.390	6.390	0.000	0.000	0.000

Top

Graph

Manual

About

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