FMO DATABASE

FMODB ID: ZYK9N

Calculation Name: 3GKU-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: C

ChEMBL ID:

UniProt ID: D0VX24

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	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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1093636.176204
FMO2-HF: Nuclear repulsion	1039020.020835
FMO2-HF: Total energy	-54616.155369
FMO2-MP2: Total energy	-54773.395557

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(C:1:MET)

Summations of interaction energy for fragment #1(C: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.
-28.046	-31.826	17.557	-5.692	-8.085	0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.010

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	C	3	MET	0	-0.100	-0.068	3.141	1.236	3.349	0.102	-1.126	-1.089	-0.002
4	C	4	VAL	0	0.044	0.038	5.848	-0.518	-0.518	0.000	0.000	0.000	0.000
5	C	5	THR	0	0.001	-0.023	8.942	0.159	0.159	0.000	0.000	0.000	0.000
6	C	6	VAL	0	0.013	0.024	12.333	-0.105	-0.105	0.000	0.000	0.000	0.000
7	C	7	THR	0	-0.041	-0.048	14.788	0.008	0.008	0.000	0.000	0.000	0.000
8	C	8	ALA	0	-0.010	-0.019	18.374	-0.028	-0.028	0.000	0.000	0.000	0.000
9	C	9	LYS	1	0.953	0.996	21.566	-0.209	-0.209	0.000	0.000	0.000	0.000
10	C	10	THR	0	0.007	-0.003	23.933	-0.003	-0.003	0.000	0.000	0.000	0.000
11	C	11	VAL	0	0.076	0.027	18.738	0.021	0.021	0.000	0.000	0.000	0.000
12	C	12	GLU	-1	-0.872	-0.967	19.544	0.435	0.435	0.000	0.000	0.000	0.000
13	C	13	GLU	-1	-0.866	-0.942	20.801	0.290	0.290	0.000	0.000	0.000	0.000
14	C	14	ALA	0	-0.020	-0.010	17.329	0.002	0.002	0.000	0.000	0.000	0.000
15	C	15	VAL	0	0.015	0.023	15.918	0.080	0.080	0.000	0.000	0.000	0.000
16	C	16	THR	0	0.018	0.002	16.403	0.030	0.030	0.000	0.000	0.000	0.000
17	C	17	LYS	1	0.876	0.953	17.668	-0.435	-0.435	0.000	0.000	0.000	0.000
18	C	18	ALA	0	0.025	0.012	12.841	0.009	0.009	0.000	0.000	0.000	0.000
19	C	19	LEU	0	-0.079	-0.034	13.732	0.000	0.000	0.000	0.000	0.000	0.000
20	C	20	ILE	0	-0.062	-0.019	14.641	-0.023	-0.023	0.000	0.000	0.000	0.000
21	C	21	GLU	-1	-0.912	-0.951	12.569	0.477	0.477	0.000	0.000	0.000	0.000
22	C	22	LEU	0	-0.056	-0.049	8.612	0.015	0.015	0.000	0.000	0.000	0.000
23	C	23	GLN	0	0.060	0.061	12.560	0.019	0.019	0.000	0.000	0.000	0.000
24	C	24	THR	0	-0.107	-0.073	10.804	-0.016	-0.016	0.000	0.000	0.000	0.000
25	C	25	THR	0	0.011	-0.021	12.678	-0.001	-0.001	0.000	0.000	0.000	0.000
26	C	26	SER	0	0.015	0.013	12.915	0.060	0.060	0.000	0.000	0.000	0.000
27	C	27	ASP	-1	-0.774	-0.863	13.487	0.261	0.261	0.000	0.000	0.000	0.000
28	C	28	LYS	1	0.871	0.924	9.674	-0.070	-0.070	0.000	0.000	0.000	0.000
29	C	29	LEU	0	0.002	0.022	8.479	0.201	0.201	0.000	0.000	0.000	0.000
30	C	30	THR	0	-0.025	-0.021	6.887	-0.184	-0.184	0.000	0.000	0.000	0.000
31	C	31	TYR	0	-0.027	-0.026	8.967	0.273	0.273	0.000	0.000	0.000	0.000
32	C	32	GLU	-1	-0.886	-0.931	9.908	1.751	1.751	0.000	0.000	0.000	0.000
33	C	33	ILE	0	0.008	-0.007	12.528	-0.093	-0.093	0.000	0.000	0.000	0.000
34	C	34	VAL	0	0.003	-0.001	15.912	-0.016	-0.016	0.000	0.000	0.000	0.000
35	C	35	GLU	-1	-0.934	-0.957	18.437	0.356	0.356	0.000	0.000	0.000	0.000
36	C	47	LYS	1	0.949	0.961	27.941	-0.208	-0.208	0.000	0.000	0.000	0.000
37	C	48	PRO	0	-0.087	-0.043	24.082	0.001	0.001	0.000	0.000	0.000	0.000
38	C	49	ALA	0	0.162	0.082	21.909	0.003	0.003	0.000	0.000	0.000	0.000
39	C	50	ILE	0	-0.072	-0.017	16.679	-0.015	-0.015	0.000	0.000	0.000	0.000
40	C	51	ILE	0	0.010	0.024	13.667	0.030	0.030	0.000	0.000	0.000	0.000
41	C	52	ARG	1	0.873	0.944	8.114	-1.529	-1.529	0.000	0.000	0.000	0.000
42	C	53	ALA	0	0.032	0.013	9.810	0.196	0.196	0.000	0.000	0.000	0.000
43	C	54	LYS	1	0.939	0.959	2.331	-19.536	-26.572	15.565	-3.815	-4.715	0.039
44	C	55	ARG	1	0.918	0.954	5.808	-0.533	-0.533	0.000	0.000	0.000	0.000
45	C	56	LYS	1	0.885	0.947	4.231	0.309	0.526	0.000	-0.019	-0.198	0.000
46	C	57	GLU	-1	-0.901	-0.957	2.415	-5.756	-5.059	1.884	-0.719	-1.862	-0.007
47	C	58	THR	0	-0.092	-0.024	3.824	1.042	1.148	0.007	-0.012	-0.101	0.000
48	C	59	LEU	0	0.038	-0.003	7.102	-0.345	-0.345	0.000	0.000	0.000	0.000
49	C	60	GLN	0	-0.006	-0.023	8.961	-0.132	-0.132	0.000	0.000	0.000	0.000
50	C	61	ASP	-1	-0.741	-0.888	4.731	-3.426	-3.303	-0.001	-0.001	-0.120	0.000
51	C	62	LYS	1	0.878	0.981	6.277	1.088	1.088	0.000	0.000	0.000	0.000
52	C	63	ALA	0	0.011	-0.010	7.798	0.084	0.084	0.000	0.000	0.000	0.000
53	C	64	ILE	0	-0.014	0.000	8.337	0.195	0.195	0.000	0.000	0.000	0.000
54	C	65	GLU	-1	-0.882	-0.923	5.481	-3.064	-3.064	0.000	0.000	0.000	0.000
55	C	66	PHE	0	-0.025	-0.037	8.147	0.442	0.442	0.000	0.000	0.000	0.000
56	C	67	LEU	0	-0.027	-0.026	11.083	0.200	0.200	0.000	0.000	0.000	0.000
57	C	68	GLU	-1	-0.903	-0.956	8.134	-1.092	-1.092	0.000	0.000	0.000	0.000
58	C	69	GLN	0	-0.005	0.000	10.231	0.311	0.311	0.000	0.000	0.000	0.000
59	C	70	VAL	0	-0.064	-0.028	12.340	0.144	0.144	0.000	0.000	0.000	0.000
60	C	71	PHE	0	-0.009	-0.041	15.222	0.083	0.083	0.000	0.000	0.000	0.000
61	C	72	ASP	-1	-0.899	-0.930	13.626	-0.433	-0.433	0.000	0.000	0.000	0.000
62	C	73	ALA	0	-0.009	0.006	15.660	0.069	0.069	0.000	0.000	0.000	0.000
63	C	74	MET	0	-0.132	-0.061	17.805	0.042	0.042	0.000	0.000	0.000	0.000
64	C	75	ASN	0	-0.073	-0.031	19.210	0.027	0.027	0.000	0.000	0.000	0.000
65	C	76	MET	0	-0.038	-0.025	19.005	0.033	0.033	0.000	0.000	0.000	0.000
66	C	77	ALA	0	0.038	0.030	16.936	-0.047	-0.047	0.000	0.000	0.000	0.000
67	C	78	VAL	0	-0.025	-0.009	16.071	0.031	0.031	0.000	0.000	0.000	0.000
68	C	79	ASP	-1	-0.884	-0.946	15.008	-0.396	-0.396	0.000	0.000	0.000	0.000
69	C	80	ILE	0	0.009	-0.001	12.604	0.032	0.032	0.000	0.000	0.000	0.000
70	C	81	SER	0	0.001	0.002	13.723	0.000	0.000	0.000	0.000	0.000	0.000
71	C	82	VAL	0	-0.007	0.008	12.358	0.058	0.058	0.000	0.000	0.000	0.000
72	C	83	GLU	-1	-0.959	-0.966	15.730	-0.335	-0.335	0.000	0.000	0.000	0.000
73	C	84	TYR	0	-0.032	-0.043	14.264	-0.010	-0.010	0.000	0.000	0.000	0.000
74	C	85	ASN	0	0.114	0.107	16.791	0.029	0.029	0.000	0.000	0.000	0.000
75	C	86	GLU	-1	-0.916	-0.965	15.354	-0.293	-0.293	0.000	0.000	0.000	0.000
76	C	87	THR	0	-0.099	-0.079	18.766	0.027	0.027	0.000	0.000	0.000	0.000
77	C	88	GLU	-1	-0.975	-1.015	22.114	-0.150	-0.150	0.000	0.000	0.000	0.000
78	C	89	LYS	1	0.833	0.949	19.538	0.175	0.175	0.000	0.000	0.000	0.000
79	C	90	GLU	-1	-0.960	-0.984	19.975	-0.253	-0.253	0.000	0.000	0.000	0.000
80	C	91	MET	0	-0.044	-0.012	12.626	-0.048	-0.048	0.000	0.000	0.000	0.000
81	C	92	ASN	0	-0.009	-0.011	18.047	0.013	0.013	0.000	0.000	0.000	0.000
82	C	93	VAL	0	0.035	0.014	15.785	-0.018	-0.018	0.000	0.000	0.000	0.000
83	C	94	ASN	0	-0.047	-0.044	17.880	0.045	0.045	0.000	0.000	0.000	0.000
84	C	95	LEU	0	-0.001	-0.007	17.503	-0.046	-0.046	0.000	0.000	0.000	0.000
85	C	96	LYS	1	0.903	0.929	17.489	0.419	0.419	0.000	0.000	0.000	0.000
86	C	97	GLY	0	0.006	-0.075	20.512	-0.007	-0.007	0.000	0.000	0.000	0.000
87	C	98	ASP	-1	-0.913	-0.919	21.562	-0.214	-0.214	0.000	0.000	0.000	0.000
88	C	99	ASP	-1	-0.840	-0.929	23.507	-0.181	-0.181	0.000	0.000	0.000	0.000
89	C	100	MET	0	-0.050	0.036	21.502	-0.002	-0.002	0.000	0.000	0.000	0.000
90	C	101	GLY	0	-0.021	-0.030	25.432	-0.003	-0.003	0.000	0.000	0.000	0.000
91	C	102	ILE	0	0.002	0.003	25.417	0.005	0.005	0.000	0.000	0.000	0.000
92	C	103	LEU	0	0.047	0.000	20.783	0.002	0.002	0.000	0.000	0.000	0.000
93	C	104	ILE	0	-0.037	0.024	24.930	-0.002	-0.002	0.000	0.000	0.000	0.000
94	C	105	GLY	0	0.012	0.011	28.137	-0.001	-0.001	0.000	0.000	0.000	0.000
95	C	106	LYS	1	0.928	0.936	29.548	0.154	0.154	0.000	0.000	0.000	0.000
96	C	107	ARG	1	0.915	0.945	32.298	0.151	0.151	0.000	0.000	0.000	0.000
97	C	108	GLY	0	0.110	0.080	29.419	0.004	0.004	0.000	0.000	0.000	0.000
98	C	109	GLN	0	-0.108	-0.062	28.039	-0.002	-0.002	0.000	0.000	0.000	0.000
99	C	110	THR	0	0.028	0.019	25.599	-0.006	-0.006	0.000	0.000	0.000	0.000
100	C	111	LEU	0	0.110	0.073	23.140	-0.023	-0.023	0.000	0.000	0.000	0.000
101	C	112	ASP	-1	-0.860	-0.932	23.405	-0.259	-0.259	0.000	0.000	0.000	0.000
102	C	113	SER	0	-0.062	-0.026	24.041	-0.013	-0.013	0.000	0.000	0.000	0.000
103	C	114	LEU	0	0.071	0.024	18.910	-0.014	-0.014	0.000	0.000	0.000	0.000
104	C	115	GLN	0	-0.020	-0.016	19.638	-0.031	-0.031	0.000	0.000	0.000	0.000
105	C	116	TYR	0	-0.036	-0.024	19.758	-0.017	-0.017	0.000	0.000	0.000	0.000
106	C	117	LEU	0	-0.006	0.000	18.178	-0.003	-0.003	0.000	0.000	0.000	0.000
107	C	118	VAL	0	0.068	0.025	13.923	-0.033	-0.033	0.000	0.000	0.000	0.000
108	C	119	SER	0	-0.043	-0.033	15.309	-0.048	-0.048	0.000	0.000	0.000	0.000
109	C	120	LEU	0	-0.024	-0.010	16.755	-0.005	-0.005	0.000	0.000	0.000	0.000
110	C	121	VAL	0	-0.051	-0.016	11.924	0.037	0.037	0.000	0.000	0.000	0.000
111	C	122	VAL	0	0.037	0.017	11.757	0.006	0.006	0.000	0.000	0.000	0.000
112	C	123	ASN	0	0.014	-0.028	13.246	0.055	0.055	0.000	0.000	0.000	0.000
113	C	124	LYS	1	0.888	0.977	12.657	0.518	0.518	0.000	0.000	0.000	0.000
114	C	125	SER	0	-0.087	-0.050	10.909	0.029	0.029	0.000	0.000	0.000	0.000
115	C	126	SER	0	-0.021	-0.002	12.706	-0.006	-0.006	0.000	0.000	0.000	0.000
116	C	127	SER	0	-0.048	-0.014	15.162	0.027	0.027	0.000	0.000	0.000	0.000
117	C	128	ASP	-1	-0.859	-0.920	18.155	-0.130	-0.130	0.000	0.000	0.000	0.000
118	C	129	TYR	0	0.000	-0.011	18.774	-0.032	-0.032	0.000	0.000	0.000	0.000
119	C	130	ILE	0	-0.010	-0.002	16.202	0.007	0.007	0.000	0.000	0.000	0.000
120	C	131	ARG	1	0.942	0.970	19.526	0.223	0.223	0.000	0.000	0.000	0.000
121	C	132	VAL	0	0.032	0.043	16.407	-0.021	-0.021	0.000	0.000	0.000	0.000
122	C	133	LYS	1	0.939	0.997	19.651	0.314	0.314	0.000	0.000	0.000	0.000
123	C	134	LEU	0	-0.013	-0.007	18.526	-0.033	-0.033	0.000	0.000	0.000	0.000
124	C	135	ASP	-1	-0.876	-0.964	21.240	-0.220	-0.220	0.000	0.000	0.000	0.000
125	C	136	THR	0	0.040	0.039	22.083	-0.013	-0.013	0.000	0.000	0.000	0.000
126	C	137	GLU	-1	-0.744	-0.877	24.701	-0.196	-0.196	0.000	0.000	0.000	0.000
127	C	138	ASN	0	-0.107	-0.042	27.808	0.011	0.011	0.000	0.000	0.000	0.000
128	C	139	TYR	0	0.062	0.028	27.483	0.016	0.016	0.000	0.000	0.000	0.000
129	C	140	ARG	1	0.812	0.897	28.789	0.182	0.182	0.000	0.000	0.000	0.000
130	C	141	GLU	-1	-0.768	-0.871	30.444	-0.130	-0.130	0.000	0.000	0.000	0.000
131	C	142	ARG	1	0.768	0.891	27.840	0.218	0.218	0.000	0.000	0.000	0.000
132	C	143	ARG	1	0.875	0.939	29.698	0.180	0.180	0.000	0.000	0.000	0.000
133	C	144	LYS	1	0.825	0.901	34.990	0.131	0.131	0.000	0.000	0.000	0.000
134	C	145	GLU	-1	-0.955	-0.959	37.560	-0.116	-0.116	0.000	0.000	0.000	0.000

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