FMO DATABASE

FMODB ID: KGKG3

Calculation Name: 5V50-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: 5V50

Chain ID: A

ChEMBL ID:
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UniProt ID: H6U756

Base Structure: X-ray

Registration Date: 2023-09-22

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	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. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1193651.134029
FMO2-HF: Nuclear repulsion	1139816.099647
FMO2-HF: Total energy	-53835.034382
FMO2-MP2: Total energy	-53990.521605

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:31:GLN)

Summations of interaction energy for fragment #1(A:31: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.
-0.248	2.016	-0.04	-0.986	-1.238	-0.002

Interaction energy analysis for fragmet #1(A:31:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.048 / q_NPA : -0.034

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	33	ASP	-1	-0.800	-0.869	3.776	2.958	5.222	-0.040	-0.986	-1.238	-0.002
4	A	34	PRO	0	0.028	0.011	6.750	-0.982	-0.982	0.000	0.000	0.000	0.000
5	A	35	ASP	-1	-0.823	-0.902	9.752	0.979	0.979	0.000	0.000	0.000	0.000
6	A	36	SER	0	-0.042	-0.038	8.881	-0.471	-0.471	0.000	0.000	0.000	0.000
7	A	37	PHE	0	-0.047	-0.020	9.404	-0.328	-0.328	0.000	0.000	0.000	0.000
8	A	38	LYS	1	0.875	0.924	11.256	-1.293	-1.293	0.000	0.000	0.000	0.000
9	A	39	ASN	0	-0.029	-0.027	14.494	-0.222	-0.222	0.000	0.000	0.000	0.000
10	A	40	LYS	1	0.867	0.942	13.271	-0.166	-0.166	0.000	0.000	0.000	0.000
11	A	41	TRP	0	0.031	0.000	13.149	-0.115	-0.115	0.000	0.000	0.000	0.000
12	A	42	LEU	0	0.009	0.010	16.656	-0.051	-0.051	0.000	0.000	0.000	0.000
13	A	43	GLU	-1	-0.913	-0.944	18.269	0.180	0.180	0.000	0.000	0.000	0.000
14	A	44	LEU	0	-0.060	-0.030	16.549	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	45	HIS	0	0.013	0.007	19.646	-0.048	-0.048	0.000	0.000	0.000	0.000
16	A	46	ASN	0	0.066	0.021	22.702	-0.038	-0.038	0.000	0.000	0.000	0.000
17	A	47	ASN	0	0.000	0.018	22.244	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	48	GLU	-1	-0.806	-0.884	25.024	0.002	0.002	0.000	0.000	0.000	0.000
19	A	49	ARG	1	0.840	0.912	26.707	-0.145	-0.145	0.000	0.000	0.000	0.000
20	A	50	THR	0	-0.001	-0.010	27.695	0.000	0.000	0.000	0.000	0.000	0.000
21	A	51	THR	0	-0.066	-0.041	29.029	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	52	ARG	1	0.754	0.858	29.203	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	53	GLN	0	-0.073	-0.025	33.688	0.002	0.002	0.000	0.000	0.000	0.000
24	A	54	LEU	0	0.012	0.025	31.509	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	55	ASP	-1	-0.874	-0.929	31.661	0.163	0.163	0.000	0.000	0.000	0.000
26	A	56	SER	0	-0.083	-0.042	26.515	0.000	0.000	0.000	0.000	0.000	0.000
27	A	57	LEU	0	-0.025	-0.004	24.640	0.003	0.003	0.000	0.000	0.000	0.000
28	A	58	GLU	-1	-0.893	-0.948	24.281	0.339	0.339	0.000	0.000	0.000	0.000
29	A	59	TRP	0	0.003	-0.021	14.957	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	60	ASP	-1	-0.835	-0.924	20.760	0.380	0.380	0.000	0.000	0.000	0.000
31	A	61	GLY	0	-0.020	-0.019	17.890	0.006	0.006	0.000	0.000	0.000	0.000
32	A	62	ASP	-1	-0.876	-0.935	18.051	0.438	0.438	0.000	0.000	0.000	0.000
33	A	63	LEU	0	-0.034	-0.004	19.863	-0.024	-0.024	0.000	0.000	0.000	0.000
34	A	64	ALA	0	0.019	0.001	15.196	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	65	TRP	0	-0.022	0.010	15.067	-0.054	-0.054	0.000	0.000	0.000	0.000
36	A	66	LYS	1	0.816	0.901	16.265	-0.212	-0.212	0.000	0.000	0.000	0.000
37	A	67	ALA	0	-0.009	-0.004	16.191	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	68	GLN	0	0.007	0.005	9.360	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	69	GLN	0	-0.075	-0.020	14.116	-0.118	-0.118	0.000	0.000	0.000	0.000
40	A	70	VAL	0	0.009	0.001	16.580	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	71	ALA	0	-0.012	-0.007	13.565	-0.053	-0.053	0.000	0.000	0.000	0.000
42	A	72	THR	0	-0.057	-0.060	12.683	-0.087	-0.087	0.000	0.000	0.000	0.000
43	A	73	GLN	0	-0.039	-0.006	14.037	-0.069	-0.069	0.000	0.000	0.000	0.000
44	A	74	CYS	0	-0.054	-0.005	9.896	0.077	0.077	0.000	0.000	0.000	0.000
45	A	75	ASN	0	0.014	0.010	17.099	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	76	VAL	0	0.014	-0.009	19.531	0.020	0.020	0.000	0.000	0.000	0.000
47	A	77	ASP	-1	-0.925	-0.956	21.728	-0.163	-0.163	0.000	0.000	0.000	0.000
48	A	78	ASN	0	-0.097	-0.052	24.562	0.032	0.032	0.000	0.000	0.000	0.000
49	A	79	PRO	0	0.017	0.028	21.502	0.002	0.002	0.000	0.000	0.000	0.000
50	A	80	GLN	0	-0.018	-0.008	22.786	0.004	0.004	0.000	0.000	0.000	0.000
51	A	81	LEU	0	-0.017	-0.010	22.961	0.017	0.017	0.000	0.000	0.000	0.000
52	A	82	TRP	0	0.042	0.002	21.558	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	83	GLY	0	0.038	0.005	26.195	0.013	0.013	0.000	0.000	0.000	0.000
54	A	84	ASP	-1	-0.887	-0.936	28.645	0.108	0.108	0.000	0.000	0.000	0.000
55	A	85	ASN	0	0.013	0.020	26.247	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	86	GLY	0	0.032	0.014	25.942	0.005	0.005	0.000	0.000	0.000	0.000
57	A	87	ALA	0	0.038	0.012	25.455	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	88	SER	0	-0.074	-0.024	26.773	-0.022	-0.022	0.000	0.000	0.000	0.000
59	A	89	PHE	0	-0.003	-0.013	21.699	0.023	0.023	0.000	0.000	0.000	0.000
60	A	90	ASN	0	-0.042	-0.007	22.239	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	91	ILE	0	0.047	0.008	18.901	0.013	0.013	0.000	0.000	0.000	0.000
62	A	92	GLY	0	0.041	0.038	18.741	0.004	0.004	0.000	0.000	0.000	0.000
63	A	93	ARG	1	0.939	0.990	16.879	0.335	0.335	0.000	0.000	0.000	0.000
64	A	94	TYR	0	0.023	0.005	14.485	0.041	0.041	0.000	0.000	0.000	0.000
65	A	95	THR	0	0.009	-0.010	11.872	0.030	0.030	0.000	0.000	0.000	0.000
66	A	96	LYS	1	0.910	0.948	9.359	0.267	0.267	0.000	0.000	0.000	0.000
67	A	97	GLU	-1	-0.850	-0.911	14.626	-0.071	-0.071	0.000	0.000	0.000	0.000
68	A	98	GLN	0	0.015	0.022	16.158	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	99	ALA	0	0.009	0.015	17.189	0.027	0.027	0.000	0.000	0.000	0.000
70	A	100	PHE	0	0.042	0.014	18.695	0.034	0.034	0.000	0.000	0.000	0.000
71	A	101	ALA	0	-0.003	-0.007	20.530	0.020	0.020	0.000	0.000	0.000	0.000
72	A	102	GLU	-1	-0.970	-0.979	21.950	-0.213	-0.213	0.000	0.000	0.000	0.000
73	A	103	TRP	0	0.017	-0.006	18.950	0.032	0.032	0.000	0.000	0.000	0.000
74	A	104	THR	0	0.046	0.023	24.618	0.006	0.006	0.000	0.000	0.000	0.000
75	A	105	ALA	0	-0.031	-0.003	26.580	0.009	0.009	0.000	0.000	0.000	0.000
76	A	106	THR	0	-0.071	-0.038	28.274	0.005	0.005	0.000	0.000	0.000	0.000
77	A	107	SER	0	0.002	-0.017	30.669	0.007	0.007	0.000	0.000	0.000	0.000
78	A	108	GLY	0	-0.048	-0.022	32.488	0.006	0.006	0.000	0.000	0.000	0.000
79	A	109	SER	0	-0.044	-0.031	35.073	0.001	0.001	0.000	0.000	0.000	0.000
80	A	110	PHE	0	0.007	0.032	35.325	0.004	0.004	0.000	0.000	0.000	0.000
81	A	111	PRO	0	-0.069	-0.039	37.061	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.769	-0.882	36.926	-0.037	-0.037	0.000	0.000	0.000	0.000
83	A	113	ASP	-1	-0.818	-0.911	35.589	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	114	ARG	1	0.773	0.865	33.453	0.038	0.038	0.000	0.000	0.000	0.000
85	A	115	SER	0	0.027	0.021	31.940	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	116	ILE	0	-0.003	-0.004	29.931	0.008	0.008	0.000	0.000	0.000	0.000
87	A	117	PRO	0	0.007	0.004	26.408	0.014	0.014	0.000	0.000	0.000	0.000
88	A	118	TRP	0	-0.004	-0.001	27.467	0.015	0.015	0.000	0.000	0.000	0.000
89	A	119	GLN	0	-0.033	-0.037	28.974	0.022	0.022	0.000	0.000	0.000	0.000
90	A	120	ARG	1	0.843	0.945	25.918	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	121	ILE	0	-0.041	-0.011	24.385	0.018	0.018	0.000	0.000	0.000	0.000
92	A	122	VAL	0	-0.033	-0.021	27.139	0.019	0.019	0.000	0.000	0.000	0.000
93	A	123	ALA	0	0.001	0.023	30.415	0.001	0.001	0.000	0.000	0.000	0.000
94	A	124	ASN	0	-0.022	-0.032	31.909	0.019	0.019	0.000	0.000	0.000	0.000
95	A	125	SER	0	0.008	0.021	34.153	0.010	0.010	0.000	0.000	0.000	0.000
96	A	126	ALA	0	-0.055	-0.019	28.559	0.013	0.013	0.000	0.000	0.000	0.000
97	A	127	GLN	0	0.021	-0.007	29.194	0.015	0.015	0.000	0.000	0.000	0.000
98	A	128	LYS	1	0.863	0.929	24.513	-0.273	-0.273	0.000	0.000	0.000	0.000
99	A	129	VAL	0	0.011	0.006	20.424	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	130	GLY	0	-0.002	0.006	18.504	0.061	0.061	0.000	0.000	0.000	0.000
101	A	131	CYS	0	-0.064	-0.012	15.673	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	132	GLY	0	0.017	-0.005	12.451	0.141	0.141	0.000	0.000	0.000	0.000
103	A	133	GLU	-1	-0.867	-0.936	8.555	-0.812	-0.812	0.000	0.000	0.000	0.000
104	A	134	ALA	0	0.030	0.022	9.341	0.108	0.108	0.000	0.000	0.000	0.000
105	A	135	THR	0	-0.036	-0.009	7.101	0.011	0.011	0.000	0.000	0.000	0.000
106	A	137	VAL	0	0.025	-0.004	12.935	-0.111	-0.111	0.000	0.000	0.000	0.000
107	A	138	LEU	0	-0.016	0.005	15.101	0.106	0.106	0.000	0.000	0.000	0.000
108	A	139	GLU	-1	-0.925	-0.967	18.013	-0.578	-0.578	0.000	0.000	0.000	0.000
109	A	140	GLY	0	-0.046	-0.025	19.598	0.020	0.020	0.000	0.000	0.000	0.000
110	A	141	ASP	-1	-0.883	-0.938	18.228	-0.643	-0.643	0.000	0.000	0.000	0.000
111	A	142	MET	0	-0.105	-0.045	14.350	-0.116	-0.116	0.000	0.000	0.000	0.000
112	A	143	ALA	0	-0.012	-0.006	10.977	0.089	0.089	0.000	0.000	0.000	0.000
113	A	144	TYR	0	-0.040	-0.022	12.740	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	145	THR	0	0.012	0.000	9.573	-0.080	-0.080	0.000	0.000	0.000	0.000
115	A	146	VAL	0	-0.013	-0.006	11.993	0.113	0.113	0.000	0.000	0.000	0.000
116	A	147	ASN	0	-0.055	-0.046	13.333	0.030	0.030	0.000	0.000	0.000	0.000
117	A	148	VAL	0	0.035	0.013	15.227	0.005	0.005	0.000	0.000	0.000	0.000
118	A	150	TYR	0	0.006	-0.022	19.299	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	151	TYR	0	-0.035	-0.048	21.879	0.015	0.015	0.000	0.000	0.000	0.000
120	A	152	ASP	-1	-0.854	-0.926	25.076	0.176	0.176	0.000	0.000	0.000	0.000
121	A	153	PRO	0	0.060	0.035	27.607	0.011	0.011	0.000	0.000	0.000	0.000
122	A	154	PRO	0	-0.018	-0.018	29.565	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	155	LEU	0	-0.052	-0.012	30.541	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	156	SER	0	-0.003	-0.006	32.459	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	157	ASP	-1	-0.836	-0.891	36.188	0.044	0.044	0.000	0.000	0.000	0.000
126	A	158	TYR	0	-0.008	-0.021	38.818	0.004	0.004	0.000	0.000	0.000	0.000
127	A	159	TYR	0	-0.037	-0.021	40.031	0.000	0.000	0.000	0.000	0.000	0.000
128	A	160	THR	0	-0.025	-0.039	37.672	0.005	0.005	0.000	0.000	0.000	0.000
129	A	161	ASN	0	-0.011	-0.001	35.421	0.014	0.014	0.000	0.000	0.000	0.000
130	A	162	ALA	0	0.019	0.009	36.329	0.005	0.005	0.000	0.000	0.000	0.000
131	A	163	GLY	0	-0.030	0.002	38.690	0.001	0.001	0.000	0.000	0.000	0.000
132	A	164	ASP	-1	-0.923	-0.946	38.233	0.101	0.101	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:GLN)