FMO DATABASE

FMODB ID: GNJG1

Calculation Name: 3K9I-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3K9I

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9KFK0

Base Structure: X-ray

Registration Date: 2023-06-19

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-815728.939959
FMO2-HF: Nuclear repulsion	772663.022672
FMO2-HF: Total energy	-43065.917286
FMO2-MP2: Total energy	-43193.434342

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:54:ALA)

Summations of interaction energy for fragment #1(A:54:ALA)

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.
-0.209	2.673	4.588	-3.141	-4.327	0.005

Interaction energy analysis for fragmet #1(A:54:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.039

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	56	ALA	0	0.025	0.005	2.290	-0.889	1.574	2.495	-2.467	-2.491	0.009
4	A	57	VAL	0	0.024	0.022	3.734	0.322	0.517	0.006	0.022	-0.223	0.000
5	A	58	PRO	0	0.050	0.018	6.403	0.328	0.328	0.000	0.000	0.000	0.000
6	A	59	TYR	0	-0.083	-0.022	6.530	0.169	0.169	0.000	0.000	0.000	0.000
7	A	60	TYR	0	0.082	0.020	4.918	0.190	0.190	0.000	0.000	0.000	0.000
8	A	61	GLU	-1	-0.913	-0.958	9.155	-0.698	-0.698	0.000	0.000	0.000	0.000
9	A	62	LYS	1	0.921	0.955	11.706	0.555	0.555	0.000	0.000	0.000	0.000
10	A	63	ALA	0	-0.014	0.003	11.903	0.039	0.039	0.000	0.000	0.000	0.000
11	A	64	ILE	0	0.001	-0.003	12.225	0.032	0.032	0.000	0.000	0.000	0.000
12	A	65	ALA	0	-0.045	-0.007	15.183	0.020	0.020	0.000	0.000	0.000	0.000
13	A	66	SER	0	-0.029	-0.038	17.368	0.001	0.001	0.000	0.000	0.000	0.000
14	A	67	GLY	0	-0.045	0.001	19.240	0.008	0.008	0.000	0.000	0.000	0.000
15	A	68	LEU	0	0.012	-0.011	15.273	0.010	0.010	0.000	0.000	0.000	0.000
16	A	69	GLN	0	-0.005	0.004	19.873	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	70	GLY	0	0.011	0.004	19.859	0.006	0.006	0.000	0.000	0.000	0.000
18	A	71	LYS	1	0.913	0.975	16.968	-0.178	-0.178	0.000	0.000	0.000	0.000
19	A	72	ASP	-1	-0.835	-0.932	16.885	0.053	0.053	0.000	0.000	0.000	0.000
20	A	73	LEU	0	0.024	0.018	15.361	0.008	0.008	0.000	0.000	0.000	0.000
21	A	74	ALA	0	0.008	0.011	15.197	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	75	GLU	-1	-0.865	-0.955	12.940	0.213	0.213	0.000	0.000	0.000	0.000
23	A	76	CYS	0	-0.047	-0.008	10.746	0.048	0.048	0.000	0.000	0.000	0.000
24	A	77	TYR	0	0.001	-0.011	10.549	-0.049	-0.049	0.000	0.000	0.000	0.000
25	A	78	LEU	0	-0.011	-0.007	10.623	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	79	GLY	0	0.023	0.004	8.171	0.039	0.039	0.000	0.000	0.000	0.000
27	A	80	LEU	0	-0.019	-0.009	6.596	0.057	0.057	0.000	0.000	0.000	0.000
28	A	81	GLY	0	0.045	0.010	7.131	-0.142	-0.142	0.000	0.000	0.000	0.000
29	A	82	SER	0	0.012	0.000	7.182	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	83	THR	0	-0.030	-0.011	2.081	0.311	-0.017	2.053	-0.538	-1.186	-0.004
31	A	84	PHE	0	0.039	0.001	4.313	-0.611	-0.584	-0.001	-0.002	-0.023	0.000
32	A	85	ARG	1	0.930	0.971	7.064	-0.416	-0.416	0.000	0.000	0.000	0.000
33	A	86	THR	0	-0.078	-0.050	5.172	0.024	0.024	0.000	0.000	0.000	0.000
34	A	87	LEU	0	-0.048	-0.020	3.101	-0.408	0.117	0.035	-0.156	-0.404	0.000
35	A	88	GLY	0	0.011	0.017	5.731	0.026	0.026	0.000	0.000	0.000	0.000
36	A	89	GLU	-1	-0.860	-0.915	8.917	-0.670	-0.670	0.000	0.000	0.000	0.000
37	A	90	TYR	0	0.036	0.006	10.664	0.012	0.012	0.000	0.000	0.000	0.000
38	A	91	ARG	1	1.023	1.004	13.185	0.193	0.193	0.000	0.000	0.000	0.000
39	A	92	LYS	1	0.838	0.923	11.099	0.789	0.789	0.000	0.000	0.000	0.000
40	A	93	ALA	0	0.001	-0.004	10.289	0.022	0.022	0.000	0.000	0.000	0.000
41	A	94	GLU	-1	-0.789	-0.849	11.629	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	95	ALA	0	-0.012	0.002	15.287	0.024	0.024	0.000	0.000	0.000	0.000
43	A	96	VAL	0	-0.009	-0.012	11.020	0.028	0.028	0.000	0.000	0.000	0.000
44	A	97	LEU	0	-0.006	0.007	11.838	0.034	0.034	0.000	0.000	0.000	0.000
45	A	98	ALA	0	0.034	0.028	14.891	0.024	0.024	0.000	0.000	0.000	0.000
46	A	99	ASN	0	-0.020	-0.002	17.085	0.019	0.019	0.000	0.000	0.000	0.000
47	A	100	GLY	0	0.049	0.026	16.783	0.007	0.007	0.000	0.000	0.000	0.000
48	A	101	VAL	0	-0.011	-0.009	17.696	0.012	0.012	0.000	0.000	0.000	0.000
49	A	102	LYS	1	0.889	0.938	20.224	0.078	0.078	0.000	0.000	0.000	0.000
50	A	103	GLN	0	-0.013	-0.002	20.409	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	104	PHE	0	-0.026	-0.005	18.834	0.006	0.006	0.000	0.000	0.000	0.000
52	A	105	PRO	0	0.039	0.026	21.876	0.013	0.013	0.000	0.000	0.000	0.000
53	A	106	ASN	0	-0.018	-0.012	24.192	0.004	0.004	0.000	0.000	0.000	0.000
54	A	107	HIS	0	0.019	0.012	16.574	0.008	0.008	0.000	0.000	0.000	0.000
55	A	108	GLN	0	0.090	0.037	20.046	0.002	0.002	0.000	0.000	0.000	0.000
56	A	109	ALA	0	0.031	0.027	16.089	0.005	0.005	0.000	0.000	0.000	0.000
57	A	110	LEU	0	0.004	0.005	14.400	0.015	0.015	0.000	0.000	0.000	0.000
58	A	111	ARG	1	0.825	0.900	16.591	-0.081	-0.081	0.000	0.000	0.000	0.000
59	A	112	VAL	0	0.037	0.023	16.789	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	113	PHE	0	0.003	-0.020	10.533	0.010	0.010	0.000	0.000	0.000	0.000
61	A	114	TYR	0	-0.034	-0.041	14.504	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	115	ALA	0	0.053	0.028	16.458	-0.017	-0.017	0.000	0.000	0.000	0.000
63	A	116	MET	0	-0.052	-0.020	13.576	0.013	0.013	0.000	0.000	0.000	0.000
64	A	117	VAL	0	-0.032	-0.020	12.562	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	118	LEU	0	-0.012	0.008	15.116	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	119	TYR	0	0.001	-0.003	16.841	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	120	ASN	0	-0.055	-0.024	13.800	0.021	0.021	0.000	0.000	0.000	0.000
68	A	121	LEU	0	-0.068	-0.041	16.666	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	122	GLY	0	0.009	0.018	18.786	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	123	ARG	1	0.747	0.853	20.638	0.038	0.038	0.000	0.000	0.000	0.000
71	A	124	TYR	0	0.011	-0.010	21.198	0.006	0.006	0.000	0.000	0.000	0.000
72	A	125	GLU	-1	-0.868	-0.916	24.329	0.029	0.029	0.000	0.000	0.000	0.000
73	A	126	GLN	0	0.086	0.038	23.739	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	127	GLY	0	0.008	-0.005	21.896	0.005	0.005	0.000	0.000	0.000	0.000
75	A	128	VAL	0	0.017	-0.011	22.542	0.014	0.014	0.000	0.000	0.000	0.000
76	A	129	GLU	-1	-0.804	-0.880	25.168	0.035	0.035	0.000	0.000	0.000	0.000
77	A	130	LEU	0	-0.043	-0.022	20.815	0.003	0.003	0.000	0.000	0.000	0.000
78	A	131	LEU	0	-0.002	-0.014	19.925	0.010	0.010	0.000	0.000	0.000	0.000
79	A	132	LEU	0	0.010	0.010	23.873	0.006	0.006	0.000	0.000	0.000	0.000
80	A	133	LYS	1	0.829	0.913	26.916	-0.040	-0.040	0.000	0.000	0.000	0.000
81	A	134	ILE	0	0.001	0.004	21.256	0.002	0.002	0.000	0.000	0.000	0.000
82	A	135	ILE	0	-0.005	0.016	25.260	0.003	0.003	0.000	0.000	0.000	0.000
83	A	136	ALA	0	0.018	0.015	27.358	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	137	GLU	-1	-0.900	-0.958	27.835	0.058	0.058	0.000	0.000	0.000	0.000
85	A	138	THR	0	-0.112	-0.078	25.384	0.002	0.002	0.000	0.000	0.000	0.000
86	A	139	SER	0	0.019	0.031	28.070	0.010	0.010	0.000	0.000	0.000	0.000
87	A	140	ASP	-1	-0.904	-0.948	28.669	0.114	0.114	0.000	0.000	0.000	0.000
88	A	141	ASP	-1	-0.845	-0.898	31.020	0.089	0.089	0.000	0.000	0.000	0.000
89	A	142	GLU	-1	-0.889	-0.943	32.976	0.069	0.069	0.000	0.000	0.000	0.000
90	A	143	THR	0	-0.077	-0.059	34.780	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	144	ILE	0	-0.006	-0.020	29.966	-0.005	-0.005	0.000	0.000	0.000	0.000
92	A	145	GLN	0	-0.055	-0.044	33.165	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	146	SER	0	-0.027	-0.003	35.856	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	147	TYR	0	-0.054	-0.026	36.338	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	148	LYS	1	0.922	0.976	32.777	-0.068	-0.068	0.000	0.000	0.000	0.000
96	A	149	GLN	0	0.008	-0.011	35.385	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	150	ALA	0	0.030	0.019	37.503	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	151	ILE	0	-0.012	0.000	31.208	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	152	LEU	0	-0.015	-0.026	31.590	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	153	PHE	0	-0.064	-0.015	33.858	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	154	TYR	0	0.028	-0.009	34.939	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	155	ALA	0	-0.041	-0.018	30.086	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	156	ASP	-1	-0.868	-0.916	30.722	0.027	0.027	0.000	0.000	0.000	0.000
104	A	157	LYS	1	0.822	0.897	32.543	-0.031	-0.031	0.000	0.000	0.000	0.000
105	A	158	LEU	0	-0.034	-0.008	29.627	0.001	0.001	0.000	0.000	0.000	0.000
106	A	159	ASP	-1	-0.892	-0.937	33.169	0.027	0.027	0.000	0.000	0.000	0.000
107	A	160	GLU	-1	-1.003	-0.984	35.473	0.013	0.013	0.000	0.000	0.000	0.000
108	A	161	THR	0	-0.041	-0.032	38.857	0.003	0.003	0.000	0.000	0.000	0.000
109	A	162	TRP	0	0.012	0.003	41.806	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	163	LYS	1	0.925	0.973	45.410	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:54:ALA)