FMO DATABASE

FMODB ID: 98MK2

Calculation Name: 5D4Z-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D4Z

Chain ID: B

ChEMBL ID:

UniProt ID: T1S9Z0

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	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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-676554.074707
FMO2-HF: Nuclear repulsion	635693.587591
FMO2-HF: Total energy	-40860.487116
FMO2-MP2: Total energy	-40978.050612

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(B:92:VAL)

Summations of interaction energy for fragment #1(B:92:VAL)

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.
-20.168	-14.796	8.983	-4.98	-9.375	0.001

Interaction energy analysis for fragmet #1(B:92:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.001

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

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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	B	94	LYS	1	0.947	0.964	2.559	-17.297	-14.401	3.186	-2.284	-3.798	0.011
4	B	95	GLN	0	-0.010	0.005	2.007	-2.368	-1.431	5.362	-2.239	-4.059	-0.009
5	B	96	ALA	0	0.044	0.027	3.868	0.126	0.658	0.003	-0.208	-0.327	0.000
6	B	97	ALA	0	0.008	0.006	5.884	0.205	0.205	0.000	0.000	0.000	0.000
7	B	98	ALA	0	0.007	0.009	7.045	-0.050	-0.050	0.000	0.000	0.000	0.000
8	B	99	THR	0	-0.022	-0.012	7.211	0.083	0.083	0.000	0.000	0.000	0.000
9	B	100	LEU	0	0.020	0.011	9.563	0.064	0.064	0.000	0.000	0.000	0.000
10	B	101	ASN	0	-0.006	-0.017	11.266	0.011	0.011	0.000	0.000	0.000	0.000
11	B	102	ALA	0	-0.032	-0.018	12.459	0.013	0.013	0.000	0.000	0.000	0.000
12	B	103	TRP	0	-0.064	-0.045	12.391	-0.008	-0.008	0.000	0.000	0.000	0.000
13	B	104	MET	0	0.081	0.048	14.670	0.040	0.040	0.000	0.000	0.000	0.000
14	B	105	ARG	1	0.870	0.986	16.984	-0.028	-0.028	0.000	0.000	0.000	0.000
15	B	106	LYS	1	0.881	0.951	18.578	0.101	0.101	0.000	0.000	0.000	0.000
16	B	107	ASP	-1	-0.707	-0.858	19.901	-0.134	-0.134	0.000	0.000	0.000	0.000
17	B	108	THR	0	-0.038	-0.021	22.091	0.018	0.018	0.000	0.000	0.000	0.000
18	B	109	GLU	-1	-0.972	-0.974	20.093	-0.104	-0.104	0.000	0.000	0.000	0.000
19	B	110	MET	0	-0.018	-0.001	23.906	0.013	0.013	0.000	0.000	0.000	0.000
20	B	111	THR	0	0.025	-0.027	18.875	-0.002	-0.002	0.000	0.000	0.000	0.000
21	B	112	SER	0	-0.072	-0.069	20.508	0.011	0.011	0.000	0.000	0.000	0.000
22	B	113	GLU	-1	-0.794	-0.901	17.246	0.094	0.094	0.000	0.000	0.000	0.000
23	B	114	LYS	1	0.922	0.958	19.171	-0.053	-0.053	0.000	0.000	0.000	0.000
24	B	115	LYS	1	0.946	0.951	21.710	0.032	0.032	0.000	0.000	0.000	0.000
25	B	116	VAL	0	0.111	0.074	15.306	-0.010	-0.010	0.000	0.000	0.000	0.000
26	B	117	ALA	0	-0.027	-0.015	18.020	-0.024	-0.024	0.000	0.000	0.000	0.000
27	B	118	VAL	0	-0.082	-0.042	18.916	-0.010	-0.010	0.000	0.000	0.000	0.000
28	B	119	ALA	0	-0.013	0.000	19.643	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	120	ALA	0	-0.007	-0.001	16.096	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	121	GLY	0	-0.010	0.006	18.136	-0.013	-0.013	0.000	0.000	0.000	0.000
31	B	122	ILE	0	-0.051	-0.026	15.339	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.023	0.010	18.461	0.017	0.017	0.000	0.000	0.000	0.000
33	B	124	PRO	0	0.048	-0.017	18.196	0.001	0.001	0.000	0.000	0.000	0.000
34	B	125	ALA	0	-0.031	-0.013	19.076	0.013	0.013	0.000	0.000	0.000	0.000
35	B	126	THR	0	0.024	-0.003	14.470	0.038	0.038	0.000	0.000	0.000	0.000
36	B	127	VAL	0	0.029	0.032	13.552	0.012	0.012	0.000	0.000	0.000	0.000
37	B	128	ASN	0	-0.037	0.003	13.361	0.061	0.061	0.000	0.000	0.000	0.000
38	B	129	ARG	1	0.996	1.001	13.553	-0.052	-0.052	0.000	0.000	0.000	0.000
39	B	130	ILE	0	0.015	0.009	8.169	0.117	0.117	0.000	0.000	0.000	0.000
40	B	131	MET	0	-0.042	-0.016	9.608	0.108	0.108	0.000	0.000	0.000	0.000
41	B	132	LYS	1	0.884	0.952	11.092	-0.290	-0.290	0.000	0.000	0.000	0.000
42	B	133	ALA	0	-0.036	-0.020	6.962	0.201	0.201	0.000	0.000	0.000	0.000
43	B	134	GLU	-1	-0.953	-0.965	8.763	0.775	0.775	0.000	0.000	0.000	0.000
44	B	135	VAL	0	-0.048	-0.029	10.141	0.001	0.001	0.000	0.000	0.000	0.000
45	B	136	SER	0	-0.029	-0.017	4.911	-0.118	-0.118	0.000	0.000	0.000	0.000
46	B	137	THR	0	0.012	0.006	5.999	-0.030	-0.030	0.000	0.000	0.000	0.000
47	B	138	THR	0	0.038	0.020	6.712	-0.222	-0.222	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.107	0.029	6.969	-0.034	-0.034	0.000	0.000	0.000	0.000
49	B	140	GLY	0	0.011	0.021	8.793	0.039	0.039	0.000	0.000	0.000	0.000
50	B	141	VAL	0	0.012	0.001	10.817	0.018	0.018	0.000	0.000	0.000	0.000
51	B	142	LEU	0	-0.003	0.000	5.384	0.037	0.037	0.000	0.000	0.000	0.000
52	B	143	SER	0	-0.029	-0.016	9.348	0.064	0.064	0.000	0.000	0.000	0.000
53	B	144	SER	0	-0.011	-0.019	12.255	0.024	0.024	0.000	0.000	0.000	0.000
54	B	145	LEU	0	-0.032	-0.008	10.208	0.050	0.050	0.000	0.000	0.000	0.000
55	B	146	ALA	0	0.036	0.010	11.409	0.035	0.035	0.000	0.000	0.000	0.000
56	B	147	ARG	1	0.848	0.926	13.235	0.428	0.428	0.000	0.000	0.000	0.000
57	B	148	ALA	0	-0.033	0.000	16.489	0.031	0.031	0.000	0.000	0.000	0.000
58	B	149	PHE	0	0.017	0.009	15.009	0.018	0.018	0.000	0.000	0.000	0.000
59	B	150	GLY	0	-0.065	-0.021	17.926	0.013	0.013	0.000	0.000	0.000	0.000
60	B	151	HIS	1	0.782	0.882	14.012	0.352	0.352	0.000	0.000	0.000	0.000
61	B	152	GLU	-1	-0.783	-0.896	13.478	-0.392	-0.392	0.000	0.000	0.000	0.000
62	B	153	ALA	0	-0.008	-0.033	8.873	-0.051	-0.051	0.000	0.000	0.000	0.000
63	B	154	TYR	0	0.030	0.000	7.475	-0.191	-0.191	0.000	0.000	0.000	0.000
64	B	155	GLU	-1	-0.782	-0.881	7.699	-0.642	-0.642	0.000	0.000	0.000	0.000
65	B	156	MET	0	-0.040	-0.004	7.666	0.038	0.038	0.000	0.000	0.000	0.000
66	B	157	ILE	0	-0.082	-0.029	2.916	-1.022	-0.220	0.433	-0.234	-1.002	-0.001
67	B	158	ILE	0	0.010	0.020	4.561	-0.434	-0.229	-0.001	-0.015	-0.189	0.000
68	B	159	PRO	0	-0.021	-0.008	5.321	0.142	0.142	0.000	0.000	0.000	0.000
69	B	160	VAL	0	0.051	0.017	7.098	0.103	0.103	0.000	0.000	0.000	0.000
70	B	161	GLY	0	-0.026	-0.009	9.608	0.033	0.033	0.000	0.000	0.000	0.000
71	B	162	ALA	0	-0.020	-0.007	11.368	0.009	0.009	0.000	0.000	0.000	0.000
72	B	163	PRO	0	0.018	0.017	11.070	0.041	0.041	0.000	0.000	0.000	0.000
73	B	164	GLY	0	-0.013	-0.018	12.388	-0.071	-0.071	0.000	0.000	0.000	0.000
74	B	165	ILE	0	-0.043	-0.018	11.636	-0.014	-0.014	0.000	0.000	0.000	0.000
75	B	166	ILE	0	-0.022	-0.011	15.764	0.036	0.036	0.000	0.000	0.000	0.000
76	B	167	ASP	-1	-0.934	-0.962	19.092	-0.180	-0.180	0.000	0.000	0.000	0.000
77	B	168	TYR	0	-0.023	-0.024	20.568	0.005	0.005	0.000	0.000	0.000	0.000
78	B	169	ASP	-1	-0.837	-0.909	22.550	-0.166	-0.166	0.000	0.000	0.000	0.000
79	B	170	HIS	0	0.078	0.010	18.643	0.013	0.013	0.000	0.000	0.000	0.000
80	B	171	ARG	1	0.985	0.999	23.600	0.124	0.124	0.000	0.000	0.000	0.000
81	B	172	MET	0	-0.066	-0.027	26.764	0.010	0.010	0.000	0.000	0.000	0.000
82	B	173	TYR	0	0.034	0.011	24.090	0.010	0.010	0.000	0.000	0.000	0.000
83	B	174	ALA	0	-0.017	-0.026	25.158	0.002	0.002	0.000	0.000	0.000	0.000
84	B	175	ALA	0	-0.084	-0.035	26.915	0.005	0.005	0.000	0.000	0.000	0.000
85	B	176	LEU	0	-0.068	-0.014	29.252	0.008	0.008	0.000	0.000	0.000	0.000
86	B	177	PRO	0	0.027	0.019	31.113	-0.006	-0.006	0.000	0.000	0.000	0.000
87	B	178	GLN	0	0.064	0.015	30.808	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	179	GLU	-1	-0.925	-0.956	31.467	-0.100	-0.100	0.000	0.000	0.000	0.000
89	B	180	GLU	-1	-0.880	-0.975	32.457	-0.107	-0.107	0.000	0.000	0.000	0.000
90	B	181	LYS	1	0.824	0.942	26.773	0.147	0.147	0.000	0.000	0.000	0.000
91	B	182	ASN	0	0.072	0.024	28.446	-0.009	-0.009	0.000	0.000	0.000	0.000
92	B	183	LYS	1	0.985	1.006	30.060	0.103	0.103	0.000	0.000	0.000	0.000
93	B	184	ILE	0	0.036	0.021	25.316	0.002	0.002	0.000	0.000	0.000	0.000
94	B	185	THR	0	-0.019	0.003	25.409	-0.007	-0.007	0.000	0.000	0.000	0.000
95	B	186	SER	0	-0.016	-0.016	26.656	0.000	0.000	0.000	0.000	0.000	0.000
96	B	187	PHE	0	-0.050	-0.017	28.869	0.004	0.004	0.000	0.000	0.000	0.000
97	B	188	ILE	0	0.008	0.004	22.421	0.004	0.004	0.000	0.000	0.000	0.000
98	B	189	ASN	0	0.010	-0.020	24.006	-0.004	-0.004	0.000	0.000	0.000	0.000
99	B	190	PHE	0	-0.012	0.020	26.014	0.006	0.006	0.000	0.000	0.000	0.000
100	B	191	VAL	0	0.003	-0.004	25.543	0.007	0.007	0.000	0.000	0.000	0.000
101	B	192	PHE	0	-0.036	-0.024	20.261	0.001	0.001	0.000	0.000	0.000	0.000
102	B	193	GLU	-1	-0.928	-0.979	24.876	-0.131	-0.131	0.000	0.000	0.000	0.000
103	B	194	GLN	0	-0.036	0.009	27.346	0.008	0.008	0.000	0.000	0.000	0.000
104	B	195	ASN	0	-0.087	-0.042	25.387	0.009	0.009	0.000	0.000	0.000	0.000
105	B	196	LYS	1	0.925	0.976	25.462	0.095	0.095	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:92:VAL)