FMO DATABASE

FMODB ID: 8582Y

Calculation Name: 3K8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DW05

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1285749.285599
FMO2-HF: Nuclear repulsion	1232138.430335
FMO2-HF: Total energy	-53610.855264
FMO2-MP2: Total energy	-53769.308754

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:5:HIS)

Summations of interaction energy for fragment #1(A:5:HIS)

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.
-3.456	-1.881	-0.012	-0.692	-0.872	0.001

Interaction energy analysis for fragmet #1(A:5:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / 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	A	7	LYS	1	0.843	0.922	3.841	-2.077	-0.502	-0.012	-0.692	-0.872	0.001
4	A	8	LEU	0	0.016	0.031	5.889	-0.299	-0.299	0.000	0.000	0.000	0.000
5	A	9	VAL	0	-0.048	-0.024	9.042	0.074	0.074	0.000	0.000	0.000	0.000
6	A	10	PRO	0	-0.005	0.005	11.839	-0.089	-0.089	0.000	0.000	0.000	0.000
7	A	11	GLN	0	-0.037	-0.038	14.588	-0.042	-0.042	0.000	0.000	0.000	0.000
8	A	12	ILE	0	-0.003	-0.009	18.392	0.016	0.016	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.753	-0.849	21.047	0.250	0.250	0.000	0.000	0.000	0.000
10	A	14	THR	0	0.018	-0.001	23.086	0.019	0.019	0.000	0.000	0.000	0.000
11	A	15	ARG	1	0.861	0.926	24.638	-0.244	-0.244	0.000	0.000	0.000	0.000
12	A	16	ASP	-1	-0.764	-0.866	20.945	0.343	0.343	0.000	0.000	0.000	0.000
13	A	17	CYS	0	-0.024	0.027	19.805	0.035	0.035	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.085	0.029	19.011	0.030	0.030	0.000	0.000	0.000	0.000
15	A	19	PRO	0	-0.028	-0.014	19.112	0.026	0.026	0.000	0.000	0.000	0.000
16	A	20	ALA	0	0.018	0.021	16.022	0.028	0.028	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.025	0.032	14.535	0.080	0.080	0.000	0.000	0.000	0.000
18	A	22	LEU	0	0.008	0.010	14.463	0.023	0.023	0.000	0.000	0.000	0.000
19	A	23	ALA	0	0.013	0.001	15.034	0.012	0.012	0.000	0.000	0.000	0.000
20	A	24	SER	0	-0.065	-0.040	10.641	0.108	0.108	0.000	0.000	0.000	0.000
21	A	25	VAL	0	0.037	0.017	10.419	0.054	0.054	0.000	0.000	0.000	0.000
22	A	26	ALA	0	-0.012	0.004	12.195	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.917	0.952	8.944	-1.038	-1.038	0.000	0.000	0.000	0.000
24	A	28	HIS	0	-0.044	-0.024	6.266	0.162	0.162	0.000	0.000	0.000	0.000
25	A	29	TYR	0	0.015	-0.016	8.877	0.083	0.083	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.022	0.030	11.331	-0.027	-0.027	0.000	0.000	0.000	0.000
27	A	31	SER	0	0.007	0.007	12.152	0.003	0.003	0.000	0.000	0.000	0.000
28	A	32	ASN	0	-0.026	-0.011	11.956	0.100	0.100	0.000	0.000	0.000	0.000
29	A	33	TYR	0	0.053	0.029	15.167	-0.045	-0.045	0.000	0.000	0.000	0.000
30	A	34	SER	0	0.015	0.002	16.846	0.041	0.041	0.000	0.000	0.000	0.000
31	A	35	ILE	0	0.044	0.018	16.617	-0.033	-0.033	0.000	0.000	0.000	0.000
32	A	36	ALA	0	0.007	-0.003	19.843	-0.028	-0.028	0.000	0.000	0.000	0.000
33	A	37	TYR	0	0.037	0.027	21.966	-0.027	-0.027	0.000	0.000	0.000	0.000
34	A	38	LEU	0	0.038	0.011	18.252	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	39	ARG	1	0.769	0.858	22.556	-0.321	-0.321	0.000	0.000	0.000	0.000
36	A	40	GLU	-1	-0.908	-0.937	24.832	0.193	0.193	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.001	-0.003	24.088	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	42	SER	0	-0.067	-0.031	24.064	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	43	LYS	1	0.859	0.915	26.213	-0.177	-0.177	0.000	0.000	0.000	0.000
40	A	44	THR	0	-0.033	0.003	25.048	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	45	ASN	0	0.056	0.025	27.785	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.956	0.967	29.427	-0.160	-0.160	0.000	0.000	0.000	0.000
43	A	47	GLN	0	-0.040	-0.028	30.675	0.005	0.005	0.000	0.000	0.000	0.000
44	A	48	GLY	0	0.013	0.024	26.743	0.004	0.004	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.016	-0.021	23.752	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	50	THR	0	0.017	0.009	26.100	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.088	0.035	24.379	0.011	0.011	0.000	0.000	0.000	0.000
48	A	52	LEU	0	0.018	0.015	25.143	0.006	0.006	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.062	0.036	26.903	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.009	-0.010	20.343	0.011	0.011	0.000	0.000	0.000	0.000
51	A	55	VAL	0	-0.006	-0.002	22.669	0.011	0.011	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.814	-0.892	24.261	0.174	0.174	0.000	0.000	0.000	0.000
53	A	57	ALA	0	0.002	-0.006	23.172	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	58	ALA	0	0.023	0.000	20.469	0.005	0.005	0.000	0.000	0.000	0.000
55	A	59	LYS	1	0.863	0.932	21.925	-0.162	-0.162	0.000	0.000	0.000	0.000
56	A	60	LYS	1	0.813	0.892	24.689	-0.207	-0.207	0.000	0.000	0.000	0.000
57	A	61	LEU	0	-0.070	-0.020	19.191	0.006	0.006	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.030	0.030	21.118	0.018	0.018	0.000	0.000	0.000	0.000
59	A	63	PHE	0	-0.042	-0.025	15.809	0.014	0.014	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.856	-0.908	21.240	0.115	0.115	0.000	0.000	0.000	0.000
61	A	65	THR	0	-0.043	-0.030	20.591	0.012	0.012	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.937	0.968	18.472	-0.134	-0.134	0.000	0.000	0.000	0.000
63	A	67	SER	0	0.002	-0.007	21.987	0.021	0.021	0.000	0.000	0.000	0.000
64	A	68	ILE	0	0.006	0.009	21.530	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	69	LYS	1	0.828	0.897	24.632	-0.091	-0.091	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.003	0.003	22.766	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.766	-0.858	24.615	0.002	0.002	0.000	0.000	0.000	0.000
68	A	72	MET	0	-0.022	-0.018	19.153	0.010	0.010	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.026	-0.029	20.902	-0.016	-0.016	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.017	0.001	18.418	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	75	PHE	0	-0.049	-0.053	15.253	0.001	0.001	0.000	0.000	0.000	0.000
72	A	76	ASP	-1	-0.838	-0.897	16.940	-0.196	-0.196	0.000	0.000	0.000	0.000
73	A	77	TYR	0	-0.083	-0.052	19.160	-0.010	-0.010	0.000	0.000	0.000	0.000
74	A	78	ASN	0	0.000	-0.021	16.993	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.856	-0.888	15.868	-0.162	-0.162	0.000	0.000	0.000	0.000
76	A	80	LEU	0	-0.075	-0.024	14.478	0.048	0.048	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.017	-0.018	13.578	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	82	TYR	0	0.009	0.034	9.557	0.052	0.052	0.000	0.000	0.000	0.000
79	A	83	PRO	0	-0.029	-0.018	8.407	0.007	0.007	0.000	0.000	0.000	0.000
80	A	84	PHE	0	-0.015	-0.011	10.459	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	85	ILE	0	-0.008	-0.005	13.694	0.055	0.055	0.000	0.000	0.000	0.000
82	A	86	VAL	0	0.000	0.007	16.266	-0.050	-0.050	0.000	0.000	0.000	0.000
83	A	87	HIS	0	-0.020	0.000	18.677	0.025	0.025	0.000	0.000	0.000	0.000
84	A	88	VAL	0	0.004	-0.003	19.395	-0.021	-0.021	0.000	0.000	0.000	0.000
85	A	89	ILE	0	0.005	0.004	22.382	0.013	0.013	0.000	0.000	0.000	0.000
86	A	90	LYS	1	0.819	0.907	19.635	-0.312	-0.312	0.000	0.000	0.000	0.000
87	A	91	GLY	0	0.017	0.005	24.577	0.005	0.005	0.000	0.000	0.000	0.000
88	A	92	LYS	1	0.952	0.952	28.267	-0.133	-0.133	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.816	0.914	22.083	-0.317	-0.317	0.000	0.000	0.000	0.000
90	A	94	LEU	0	0.040	0.012	26.089	0.007	0.007	0.000	0.000	0.000	0.000
91	A	95	GLN	0	0.007	0.020	25.821	0.002	0.002	0.000	0.000	0.000	0.000
92	A	96	HIS	0	-0.011	-0.025	18.757	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	97	TYR	0	-0.029	-0.041	18.893	-0.032	-0.032	0.000	0.000	0.000	0.000
94	A	98	TYR	0	-0.031	-0.031	14.377	0.052	0.052	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.010	0.009	10.410	-0.054	-0.054	0.000	0.000	0.000	0.000
96	A	100	VAL	0	0.001	-0.004	11.300	0.044	0.044	0.000	0.000	0.000	0.000
97	A	101	TYR	0	-0.001	-0.056	6.135	0.061	0.061	0.000	0.000	0.000	0.000
98	A	102	GLY	0	0.037	0.017	7.714	-0.145	-0.145	0.000	0.000	0.000	0.000
99	A	103	SER	0	-0.022	-0.003	9.537	0.099	0.099	0.000	0.000	0.000	0.000
100	A	104	GLN	0	0.033	0.019	9.368	-0.316	-0.316	0.000	0.000	0.000	0.000
101	A	105	ASN	0	0.004	0.002	12.169	0.015	0.015	0.000	0.000	0.000	0.000
102	A	106	ASN	0	0.068	0.037	15.685	0.043	0.043	0.000	0.000	0.000	0.000
103	A	107	GLN	0	-0.015	-0.005	13.105	0.000	0.000	0.000	0.000	0.000	0.000
104	A	108	LEU	0	0.036	0.028	12.717	-0.084	-0.084	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.031	-0.011	6.089	0.068	0.068	0.000	0.000	0.000	0.000
106	A	110	ILE	0	0.001	-0.005	9.529	0.002	0.002	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.022	-0.001	9.956	0.262	0.262	0.000	0.000	0.000	0.000
108	A	112	ASP	-1	-0.754	-0.873	11.210	0.351	0.351	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.017	-0.018	14.362	0.102	0.102	0.000	0.000	0.000	0.000
110	A	114	ASP	-1	-0.745	-0.835	15.954	0.427	0.427	0.000	0.000	0.000	0.000
111	A	115	PRO	0	-0.011	-0.009	15.861	0.078	0.078	0.000	0.000	0.000	0.000
112	A	116	SER	0	-0.071	-0.057	16.575	0.032	0.032	0.000	0.000	0.000	0.000
113	A	117	VAL	0	-0.049	-0.014	14.951	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	118	LYS	1	0.925	0.962	11.145	-0.860	-0.860	0.000	0.000	0.000	0.000
115	A	119	VAL	0	0.006	0.005	6.148	-0.159	-0.159	0.000	0.000	0.000	0.000
116	A	120	THR	0	-0.002	0.005	9.599	-0.035	-0.035	0.000	0.000	0.000	0.000
117	A	121	ARG	1	0.872	0.932	7.523	0.579	0.579	0.000	0.000	0.000	0.000
118	A	122	MET	0	-0.018	0.014	12.250	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	123	SER	0	0.009	0.000	15.504	-0.040	-0.040	0.000	0.000	0.000	0.000
120	A	124	LYS	1	0.893	0.917	17.659	0.183	0.183	0.000	0.000	0.000	0.000
121	A	125	GLU	-1	-0.826	-0.904	19.357	0.003	0.003	0.000	0.000	0.000	0.000
122	A	126	ARG	1	0.910	0.964	19.707	-0.104	-0.104	0.000	0.000	0.000	0.000
123	A	127	PHE	0	0.048	-0.003	17.743	0.027	0.027	0.000	0.000	0.000	0.000
124	A	128	GLN	0	-0.019	-0.026	19.849	0.013	0.013	0.000	0.000	0.000	0.000
125	A	129	SER	0	-0.058	-0.023	23.025	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	130	GLU	-1	-0.814	-0.878	20.478	0.247	0.247	0.000	0.000	0.000	0.000
127	A	131	TRP	0	-0.021	-0.007	20.896	0.010	0.010	0.000	0.000	0.000	0.000
128	A	132	THR	0	-0.003	-0.018	22.706	-0.020	-0.020	0.000	0.000	0.000	0.000
129	A	133	GLY	0	0.085	0.044	23.846	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	134	LEU	0	-0.081	-0.026	23.279	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	135	ALA	0	0.029	0.020	19.249	0.019	0.019	0.000	0.000	0.000	0.000
132	A	136	ILE	0	-0.007	-0.011	19.192	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	137	PHE	0	0.008	0.007	16.096	0.034	0.034	0.000	0.000	0.000	0.000
134	A	138	LEU	0	0.002	-0.018	16.049	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	139	ALA	0	0.038	0.030	15.870	0.016	0.016	0.000	0.000	0.000	0.000
136	A	140	PRO	0	0.014	0.013	15.773	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	141	GLN	0	-0.015	0.003	18.783	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:HIS)