FMO DATABASE

FMODB ID: YZ542

Calculation Name: 3GEK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GEK

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CHK5

Base Structure: X-ray

Registration Date: 2023-09-20

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101914.474715
FMO2-HF: Nuclear repulsion	1050761.326074
FMO2-HF: Total energy	-51153.148641
FMO2-MP2: Total energy	-51301.507365

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(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-15.422	-14.055	15.636	-7.552	-9.45	-0.064

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.024

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	A	3	MET	0	0.036	0.008	3.293	-1.660	0.381	0.082	-1.013	-1.109	0.001
4	A	4	ILE	0	0.002	-0.007	6.088	0.351	0.351	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.809	-0.906	1.869	-12.315	-14.777	12.560	-5.316	-4.782	-0.061
6	A	6	GLN	0	-0.059	-0.044	2.735	-1.420	0.333	2.974	-1.340	-3.386	-0.004
7	A	7	LEU	0	-0.030	0.006	4.382	-0.599	-0.564	0.020	0.117	-0.173	0.000
8	A	8	ASN	0	-0.006	0.007	5.504	-0.287	-0.287	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.003	-0.002	6.279	0.147	0.147	0.000	0.000	0.000	0.000
10	A	10	THR	0	0.024	-0.003	8.838	-0.128	-0.128	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.884	-0.937	10.884	-0.286	-0.286	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.013	-0.007	13.491	0.050	0.050	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.021	-0.007	15.120	0.015	0.015	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.012	0.001	18.761	0.017	0.017	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.026	-0.014	21.580	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.016	0.004	25.139	0.005	0.005	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.846	-0.896	28.840	-0.103	-0.103	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.845	-0.940	31.153	-0.105	-0.105	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.026	-0.016	33.888	0.008	0.008	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.015	-0.003	33.545	0.005	0.005	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.891	-0.917	35.667	-0.079	-0.079	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.965	0.970	36.623	0.060	0.060	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.004	0.006	37.985	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.009	-0.002	38.304	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.042	-0.022	35.870	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.819	0.911	32.064	0.083	0.083	0.000	0.000	0.000	0.000
27	A	27	ILE	0	0.019	0.010	30.423	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.021	0.000	26.452	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.851	0.903	25.200	0.111	0.111	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.019	0.011	18.393	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.011	0.003	19.574	0.027	0.027	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.007	-0.001	14.221	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.896	0.944	13.683	0.289	0.289	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.012	0.025	10.488	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.013	-0.007	9.248	0.071	0.071	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.058	-0.025	9.660	0.054	0.054	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.010	-0.009	9.452	0.069	0.069	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.877	-0.957	11.683	0.480	0.480	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.001	0.012	7.160	0.026	0.026	0.000	0.000	0.000	0.000
40	A	40	HIS	0	-0.002	-0.016	8.632	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.046	0.018	12.890	-0.074	-0.074	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.015	-0.024	16.056	0.011	0.011	0.000	0.000	0.000	0.000
43	A	43	PRO	0	-0.004	-0.023	19.006	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.013	0.008	21.425	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.010	0.022	20.180	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.029	-0.016	20.448	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.019	-0.013	15.328	0.022	0.022	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.019	-0.012	15.995	-0.042	-0.042	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.051	0.022	17.458	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.023	0.001	16.554	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.030	0.017	13.275	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	52	SER	0	0.028	0.006	14.299	-0.043	-0.043	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.005	-0.012	16.990	-0.026	-0.026	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.013	0.017	12.296	-0.021	-0.021	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.028	0.007	13.097	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.024	0.004	14.395	-0.037	-0.037	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.925	-0.973	16.018	-0.119	-0.119	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.008	0.000	10.142	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.014	-0.033	14.174	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.011	0.019	16.121	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.004	0.005	16.756	0.012	0.012	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.034	-0.016	12.456	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.004	0.006	16.308	0.013	0.013	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.002	-0.036	19.912	0.015	0.015	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.046	0.021	16.103	0.043	0.043	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.018	0.003	19.244	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.056	-0.019	20.800	0.014	0.014	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.020	-0.011	23.478	0.012	0.012	0.000	0.000	0.000	0.000
69	A	69	SER	0	0.014	0.002	22.164	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.018	-0.004	22.159	0.012	0.012	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.085	-0.045	23.628	0.012	0.012	0.000	0.000	0.000	0.000
72	A	72	TYR	0	-0.040	-0.013	23.450	0.010	0.010	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.006	0.007	17.126	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.052	-0.022	19.465	0.018	0.018	0.000	0.000	0.000	0.000
75	A	75	PHE	0	-0.014	-0.003	17.851	-0.018	-0.018	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.072	0.051	18.705	0.009	0.009	0.000	0.000	0.000	0.000
77	A	77	GLN	0	-0.089	-0.047	20.283	0.016	0.016	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.016	-0.034	23.810	0.012	0.012	0.000	0.000	0.000	0.000
79	A	79	ILE	0	0.055	0.043	20.550	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	80	ASN	0	-0.040	-0.015	23.688	0.009	0.009	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.038	0.012	22.934	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	82	ASN	0	-0.023	0.001	25.072	0.012	0.012	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.036	-0.036	21.145	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.041	-0.022	25.955	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.020	-0.015	26.292	0.007	0.007	0.000	0.000	0.000	0.000
86	A	86	PRO	0	-0.011	0.007	24.449	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.851	0.918	18.299	0.018	0.018	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.884	0.935	20.733	-0.033	-0.033	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.043	-0.005	14.914	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.832	-0.908	16.024	0.061	0.061	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.025	0.015	16.019	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	92	PHE	0	-0.029	-0.023	14.250	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.015	0.023	15.104	0.016	0.016	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.023	-0.030	15.847	-0.052	-0.052	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.027	0.020	16.649	0.023	0.023	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.760	0.840	18.558	0.107	0.107	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.016	0.017	21.510	0.014	0.014	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.007	-0.007	23.269	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.032	-0.011	25.944	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.010	0.002	28.019	0.006	0.006	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.924	0.952	29.963	0.061	0.061	0.000	0.000	0.000	0.000
102	A	102	ASN	0	0.066	0.043	29.462	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.001	-0.001	30.324	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.905	0.944	30.448	0.067	0.067	0.000	0.000	0.000	0.000
105	A	105	ARG	1	1.019	0.995	29.352	0.043	0.043	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.040	0.030	27.370	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	HIS	0	0.029	0.058	24.760	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.027	-0.010	26.067	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	TRP	0	0.027	0.002	22.576	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.813	-0.900	25.770	-0.068	-0.068	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.005	-0.011	20.233	-0.009	-0.009	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.814	0.912	23.475	0.087	0.087	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.015	-0.001	18.226	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	114	THR	0	-0.003	0.010	20.623	0.018	0.018	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.721	-0.858	20.227	-0.057	-0.057	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.794	-0.890	19.181	-0.060	-0.060	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.090	-0.050	21.617	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.828	-0.877	23.850	-0.102	-0.102	0.000	0.000	0.000	0.000
119	A	119	THR	0	-0.024	-0.006	25.583	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.020	-0.009	24.739	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.004	0.012	20.981	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	SER	0	-0.017	-0.020	21.912	0.013	0.013	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.014	0.027	23.769	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.004	-0.018	20.468	0.008	0.008	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.044	-0.007	24.453	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	126	VAL	0	0.032	0.019	20.447	0.006	0.006	0.000	0.000	0.000	0.000
127	A	127	VAL	0	-0.067	-0.031	23.689	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.032	0.002	20.348	0.004	0.004	0.000	0.000	0.000	0.000
129	A	129	ALA	0	0.011	-0.005	23.143	0.007	0.007	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.058	-0.029	23.164	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.008	-0.008	22.753	0.012	0.012	0.000	0.000	0.000	0.000
132	A	132	PRO	0	0.030	0.023	24.371	-0.007	-0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)