FMO DATABASE

FMODB ID: MVR8Z

Calculation Name: 5KXF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KXF

Chain ID: A

ChEMBL ID:

UniProt ID: Q8LPQ9

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1082409.65622
FMO2-HF: Nuclear repulsion	1032256.033003
FMO2-HF: Total energy	-50153.623217
FMO2-MP2: Total energy	-50296.332839

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:439:HIS)

Summations of interaction energy for fragment #1(A:439: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.
-1.945	-0.536	0.001	-0.625	-0.786	0.002

Interaction energy analysis for fragmet #1(A:439:HIS)

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 : -0.014

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	441	TRP	0	-0.035	-0.008	3.754	-1.630	-0.221	0.001	-0.625	-0.786	0.002
4	A	442	ARG	1	0.869	0.888	6.347	-0.014	-0.014	0.000	0.000	0.000	0.000
5	A	443	GLY	0	0.016	0.017	7.988	-0.077	-0.077	0.000	0.000	0.000	0.000
6	A	444	MET	0	-0.047	-0.008	11.308	0.114	0.114	0.000	0.000	0.000	0.000
7	A	445	ILE	0	0.007	0.011	15.088	-0.095	-0.095	0.000	0.000	0.000	0.000
8	A	446	ALA	0	0.021	0.003	17.800	0.048	0.048	0.000	0.000	0.000	0.000
9	A	447	LYS	1	0.875	0.942	21.225	-0.031	-0.031	0.000	0.000	0.000	0.000
10	A	448	GLY	0	0.009	0.008	24.836	0.017	0.017	0.000	0.000	0.000	0.000
11	A	449	GLY	0	-0.040	-0.019	23.638	0.007	0.007	0.000	0.000	0.000	0.000
12	A	450	THR	0	0.004	0.009	23.917	0.019	0.019	0.000	0.000	0.000	0.000
13	A	451	PRO	0	0.015	-0.009	20.764	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	452	VAL	0	-0.063	-0.016	20.800	0.004	0.004	0.000	0.000	0.000	0.000
15	A	453	CYS	0	-0.069	-0.046	17.069	0.010	0.010	0.000	0.000	0.000	0.000
16	A	454	CYS	0	0.007	0.019	13.728	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	455	ALA	0	0.002	-0.009	13.105	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	456	ARG	1	0.862	0.910	8.195	-1.054	-1.054	0.000	0.000	0.000	0.000
19	A	457	CYS	0	-0.048	-0.016	9.199	-0.161	-0.161	0.000	0.000	0.000	0.000
20	A	458	VAL	0	-0.002	0.005	9.328	0.127	0.127	0.000	0.000	0.000	0.000
21	A	459	PRO	0	0.031	0.003	9.217	0.000	0.000	0.000	0.000	0.000	0.000
22	A	460	MET	0	-0.034	-0.003	12.081	0.180	0.180	0.000	0.000	0.000	0.000
23	A	461	GLY	0	0.004	0.006	15.682	0.009	0.009	0.000	0.000	0.000	0.000
24	A	462	LYS	1	0.727	0.854	12.588	1.016	1.016	0.000	0.000	0.000	0.000
25	A	463	GLY	0	-0.033	-0.014	13.075	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	464	ILE	0	-0.079	-0.038	12.840	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	465	GLU	-1	-0.785	-0.871	9.805	-1.137	-1.137	0.000	0.000	0.000	0.000
28	A	466	THR	0	-0.023	-0.025	9.978	-0.392	-0.392	0.000	0.000	0.000	0.000
29	A	467	LYS	1	0.828	0.898	7.688	1.318	1.318	0.000	0.000	0.000	0.000
30	A	468	LEU	0	0.046	0.024	9.518	0.316	0.316	0.000	0.000	0.000	0.000
31	A	469	PRO	0	0.035	0.032	10.098	-0.099	-0.099	0.000	0.000	0.000	0.000
32	A	470	GLU	-1	-0.920	-0.964	11.238	-0.100	-0.100	0.000	0.000	0.000	0.000
33	A	471	VAL	0	-0.011	-0.016	12.451	0.109	0.109	0.000	0.000	0.000	0.000
34	A	472	VAL	0	0.019	0.018	14.085	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	473	ASN	0	0.020	-0.001	16.725	0.080	0.080	0.000	0.000	0.000	0.000
36	A	474	CYS	0	-0.036	0.011	20.372	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	475	SER	0	-0.079	-0.040	23.016	0.028	0.028	0.000	0.000	0.000	0.000
38	A	476	ALA	0	0.018	0.008	25.235	0.018	0.018	0.000	0.000	0.000	0.000
39	A	477	ARG	1	0.915	0.947	26.713	0.081	0.081	0.000	0.000	0.000	0.000
40	A	478	THR	0	0.013	0.011	27.257	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	479	ASP	-1	-0.816	-0.874	29.950	-0.117	-0.117	0.000	0.000	0.000	0.000
42	A	480	LEU	0	0.041	0.020	28.273	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	481	ASN	0	0.038	0.013	31.331	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	482	MET	0	-0.072	-0.031	32.153	0.003	0.003	0.000	0.000	0.000	0.000
45	A	483	LEU	0	-0.004	-0.005	25.266	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	484	ALA	0	0.043	0.018	28.996	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	485	LYS	1	0.906	0.957	31.243	0.148	0.148	0.000	0.000	0.000	0.000
48	A	486	HIS	0	0.019	0.008	27.717	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	487	TYR	0	0.005	-0.021	25.245	-0.021	-0.021	0.000	0.000	0.000	0.000
50	A	488	ALA	0	-0.025	-0.010	28.232	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	489	VAL	0	-0.024	-0.005	30.436	0.006	0.006	0.000	0.000	0.000	0.000
52	A	490	ALA	0	-0.050	-0.016	25.387	-0.013	-0.013	0.000	0.000	0.000	0.000
53	A	491	ILE	0	-0.024	-0.010	24.968	0.009	0.009	0.000	0.000	0.000	0.000
54	A	492	GLY	0	0.015	0.002	22.126	-0.033	-0.033	0.000	0.000	0.000	0.000
55	A	493	CYS	0	-0.027	-0.011	21.653	0.030	0.030	0.000	0.000	0.000	0.000
56	A	494	GLU	-1	-0.747	-0.858	15.314	-1.083	-1.083	0.000	0.000	0.000	0.000
57	A	495	ILE	0	-0.008	-0.024	17.121	0.027	0.027	0.000	0.000	0.000	0.000
58	A	496	VAL	0	-0.008	0.003	11.612	-0.071	-0.071	0.000	0.000	0.000	0.000
59	A	497	PHE	0	0.020	0.002	14.623	0.083	0.083	0.000	0.000	0.000	0.000
60	A	498	PHE	0	0.027	0.017	13.128	-0.054	-0.054	0.000	0.000	0.000	0.000
61	A	499	VAL	0	-0.013	0.004	12.878	0.033	0.033	0.000	0.000	0.000	0.000
62	A	500	PRO	0	0.029	0.020	14.219	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	501	ASP	-1	-0.839	-0.886	10.847	1.108	1.108	0.000	0.000	0.000	0.000
64	A	502	ARG	1	0.790	0.864	13.294	-0.510	-0.510	0.000	0.000	0.000	0.000
65	A	503	GLU	-1	-0.844	-0.916	16.137	0.495	0.495	0.000	0.000	0.000	0.000
66	A	504	GLU	-1	-0.784	-0.877	18.423	0.477	0.477	0.000	0.000	0.000	0.000
67	A	505	ASP	-1	-0.789	-0.880	16.250	0.353	0.353	0.000	0.000	0.000	0.000
68	A	506	PHE	0	-0.015	-0.015	19.500	-0.055	-0.055	0.000	0.000	0.000	0.000
69	A	507	ALA	0	0.028	0.025	21.195	-0.038	-0.038	0.000	0.000	0.000	0.000
70	A	508	SER	0	0.049	0.015	22.041	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	509	TYR	0	-0.011	-0.025	17.928	-0.033	-0.033	0.000	0.000	0.000	0.000
72	A	510	THR	0	-0.017	-0.020	21.671	-0.037	-0.037	0.000	0.000	0.000	0.000
73	A	511	GLU	-1	-0.867	-0.941	24.801	0.006	0.006	0.000	0.000	0.000	0.000
74	A	512	PHE	0	-0.008	-0.009	21.627	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	513	LEU	0	0.021	0.009	21.952	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	514	ARG	1	0.825	0.937	25.539	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	515	TYR	0	0.001	0.008	27.111	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	516	LEU	0	-0.056	-0.015	24.595	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	517	SER	0	0.050	-0.020	28.750	0.000	0.000	0.000	0.000	0.000	0.000
80	A	518	SER	0	-0.036	-0.024	30.409	0.001	0.001	0.000	0.000	0.000	0.000
81	A	519	LYS	1	0.795	0.876	32.824	0.047	0.047	0.000	0.000	0.000	0.000
82	A	520	ASP	-1	-0.849	-0.905	32.859	-0.081	-0.081	0.000	0.000	0.000	0.000
83	A	521	ARG	1	0.807	0.877	30.356	0.089	0.089	0.000	0.000	0.000	0.000
84	A	522	ALA	0	0.029	0.024	25.147	0.008	0.008	0.000	0.000	0.000	0.000
85	A	523	GLY	0	0.014	-0.022	24.346	0.010	0.010	0.000	0.000	0.000	0.000
86	A	524	VAL	0	-0.032	-0.012	23.537	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	525	ALA	0	0.048	0.026	19.167	0.031	0.031	0.000	0.000	0.000	0.000
88	A	526	LYS	1	0.867	0.929	18.982	0.381	0.381	0.000	0.000	0.000	0.000
89	A	527	LEU	0	0.037	0.030	13.257	0.035	0.035	0.000	0.000	0.000	0.000
90	A	528	ASP	-1	-0.815	-0.913	12.269	-0.887	-0.887	0.000	0.000	0.000	0.000
91	A	529	ASP	-1	-0.842	-0.877	15.106	-0.839	-0.839	0.000	0.000	0.000	0.000
92	A	530	GLY	0	0.009	0.007	17.175	0.066	0.066	0.000	0.000	0.000	0.000
93	A	531	THR	0	-0.035	-0.043	17.580	0.087	0.087	0.000	0.000	0.000	0.000
94	A	532	THR	0	-0.074	-0.049	18.914	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	533	LEU	0	0.003	0.025	15.736	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	534	PHE	0	0.002	-0.012	19.469	0.065	0.065	0.000	0.000	0.000	0.000
97	A	535	LEU	0	-0.016	0.000	18.584	-0.022	-0.022	0.000	0.000	0.000	0.000
98	A	536	VAL	0	0.040	0.009	21.705	0.040	0.040	0.000	0.000	0.000	0.000
99	A	537	PRO	0	0.022	0.025	23.188	0.005	0.005	0.000	0.000	0.000	0.000
100	A	538	PRO	0	-0.020	-0.010	24.509	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	539	SER	0	-0.026	-0.024	26.959	0.006	0.006	0.000	0.000	0.000	0.000
102	A	540	ASP	-1	-0.755	-0.871	29.457	-0.073	-0.073	0.000	0.000	0.000	0.000
103	A	541	PHE	0	0.034	0.017	26.420	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	542	LEU	0	-0.027	-0.005	24.355	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	543	THR	0	-0.015	-0.032	27.451	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	544	ASP	-1	-0.892	-0.932	29.908	-0.117	-0.117	0.000	0.000	0.000	0.000
107	A	545	VAL	0	-0.065	-0.028	29.725	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	546	LEU	0	-0.024	-0.018	23.602	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	547	GLN	0	-0.058	0.000	26.292	-0.020	-0.020	0.000	0.000	0.000	0.000
110	A	548	VAL	0	-0.006	-0.001	22.683	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	549	THR	0	-0.001	-0.009	23.528	0.016	0.016	0.000	0.000	0.000	0.000
112	A	550	ARG	1	0.886	0.954	24.001	0.049	0.049	0.000	0.000	0.000	0.000
113	A	551	GLN	0	0.017	0.003	19.552	0.065	0.065	0.000	0.000	0.000	0.000
114	A	552	GLU	-1	-0.782	-0.886	24.408	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	553	ARG	1	0.871	0.928	18.668	-0.069	-0.069	0.000	0.000	0.000	0.000
116	A	554	LEU	0	0.023	0.014	18.525	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	555	TYR	0	-0.017	-0.023	18.655	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	556	GLY	0	0.007	-0.005	16.468	0.017	0.017	0.000	0.000	0.000	0.000
119	A	557	VAL	0	-0.022	-0.016	16.993	-0.073	-0.073	0.000	0.000	0.000	0.000
120	A	558	VAL	0	0.041	0.016	16.272	0.026	0.026	0.000	0.000	0.000	0.000
121	A	559	LEU	0	-0.008	-0.003	19.415	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	560	LYS	1	0.907	0.957	21.008	0.533	0.533	0.000	0.000	0.000	0.000
123	A	561	LEU	0	0.041	0.018	22.870	0.024	0.024	0.000	0.000	0.000	0.000
124	A	562	PRO	0	0.036	0.015	26.037	-0.037	-0.037	0.000	0.000	0.000	0.000
125	A	563	PRO	0	-0.043	-0.005	27.044	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	564	PRO	0	0.018	-0.004	28.652	0.021	0.021	0.000	0.000	0.000	0.000
127	A	565	ALA	0	0.003	0.015	31.563	-0.016	-0.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:439:HIS)