FMO DATABASE

FMODB ID: 76M5K

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:

Apendix: None

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-677074.239534
FMO2-HF: Nuclear repulsion	636212.517216
FMO2-HF: Total energy	-40861.722318
FMO2-MP2: Total energy	-40979.10436

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.
-13.976	-6.509	2.915	-3.556	-6.825	0.003

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 : 0.021 / 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	B	94	LYS	1	0.892	0.926	2.467	-4.956	-1.649	1.188	-1.707	-2.788	0.009
4	B	95	GLN	0	0.012	0.014	2.700	-6.042	-3.338	0.552	-1.194	-2.063	-0.005
5	B	96	ALA	0	0.065	0.042	3.965	-1.089	-0.553	0.000	-0.257	-0.279	0.001
6	B	97	ALA	0	-0.025	-0.010	5.998	0.000	0.000	0.000	0.000	0.000	0.000
7	B	98	ALA	0	0.002	-0.003	7.633	-0.241	-0.241	0.000	0.000	0.000	0.000
8	B	99	THR	0	0.003	-0.003	7.431	-0.213	-0.213	0.000	0.000	0.000	0.000
9	B	100	LEU	0	-0.007	-0.002	9.746	-0.099	-0.099	0.000	0.000	0.000	0.000
10	B	101	ASN	0	-0.010	-0.012	11.749	-0.126	-0.126	0.000	0.000	0.000	0.000
11	B	102	ALA	0	-0.013	-0.007	12.827	-0.061	-0.061	0.000	0.000	0.000	0.000
12	B	103	TRP	0	-0.026	-0.022	11.905	-0.059	-0.059	0.000	0.000	0.000	0.000
13	B	104	MET	0	0.045	0.035	14.930	-0.025	-0.025	0.000	0.000	0.000	0.000
14	B	105	ARG	1	0.846	0.947	17.253	-0.241	-0.241	0.000	0.000	0.000	0.000
15	B	106	LYS	1	0.912	0.959	19.116	-0.139	-0.139	0.000	0.000	0.000	0.000
16	B	107	ASP	-1	-0.791	-0.890	20.295	0.030	0.030	0.000	0.000	0.000	0.000
17	B	108	THR	0	-0.045	-0.029	22.126	0.008	0.008	0.000	0.000	0.000	0.000
18	B	109	GLU	-1	-0.822	-0.907	20.929	0.042	0.042	0.000	0.000	0.000	0.000
19	B	110	MET	0	-0.003	0.018	23.397	0.004	0.004	0.000	0.000	0.000	0.000
20	B	111	THR	0	0.025	-0.020	19.303	0.006	0.006	0.000	0.000	0.000	0.000
21	B	112	SER	0	-0.035	-0.022	20.321	-0.011	-0.011	0.000	0.000	0.000	0.000
22	B	113	GLU	-1	-0.740	-0.860	17.496	0.117	0.117	0.000	0.000	0.000	0.000
23	B	114	LYS	1	0.819	0.899	18.723	-0.086	-0.086	0.000	0.000	0.000	0.000
24	B	115	LYS	1	0.801	0.893	21.583	-0.068	-0.068	0.000	0.000	0.000	0.000
25	B	116	VAL	0	0.116	0.056	15.253	-0.016	-0.016	0.000	0.000	0.000	0.000
26	B	117	ALA	0	-0.069	-0.031	17.618	-0.026	-0.026	0.000	0.000	0.000	0.000
27	B	118	VAL	0	-0.022	-0.013	18.577	-0.019	-0.019	0.000	0.000	0.000	0.000
28	B	119	ALA	0	-0.002	0.003	19.458	-0.010	-0.010	0.000	0.000	0.000	0.000
29	B	120	ALA	0	-0.022	-0.004	15.500	-0.016	-0.016	0.000	0.000	0.000	0.000
30	B	121	GLY	0	0.018	0.018	17.509	-0.024	-0.024	0.000	0.000	0.000	0.000
31	B	122	ILE	0	-0.056	-0.030	14.819	-0.015	-0.015	0.000	0.000	0.000	0.000
32	B	123	GLY	0	0.072	0.034	18.088	0.022	0.022	0.000	0.000	0.000	0.000
33	B	124	PRO	0	0.068	0.004	18.066	0.001	0.001	0.000	0.000	0.000	0.000
34	B	125	ALA	0	-0.033	-0.004	19.109	0.022	0.022	0.000	0.000	0.000	0.000
35	B	126	THR	0	-0.028	-0.031	13.646	0.011	0.011	0.000	0.000	0.000	0.000
36	B	127	VAL	0	0.043	0.024	13.406	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	128	ASN	0	-0.041	-0.025	13.434	0.033	0.033	0.000	0.000	0.000	0.000
38	B	129	ARG	1	0.954	0.997	13.276	0.072	0.072	0.000	0.000	0.000	0.000
39	B	130	ILE	0	0.008	0.006	7.847	0.060	0.060	0.000	0.000	0.000	0.000
40	B	131	MET	0	-0.023	-0.012	9.367	0.125	0.125	0.000	0.000	0.000	0.000
41	B	132	LYS	1	0.794	0.878	11.521	-0.118	-0.118	0.000	0.000	0.000	0.000
42	B	133	ALA	0	-0.031	-0.015	6.057	0.162	0.162	0.000	0.000	0.000	0.000
43	B	134	GLU	-1	-0.839	-0.900	7.740	0.166	0.166	0.000	0.000	0.000	0.000
44	B	135	VAL	0	-0.040	-0.027	9.575	-0.084	-0.084	0.000	0.000	0.000	0.000
45	B	136	SER	0	-0.026	-0.040	4.649	-0.107	-0.075	-0.001	-0.003	-0.028	0.000
46	B	137	THR	0	-0.020	-0.005	5.505	0.147	0.147	0.000	0.000	0.000	0.000
47	B	138	THR	0	0.033	0.019	6.290	-0.194	-0.194	0.000	0.000	0.000	0.000
48	B	139	ILE	0	0.088	0.021	6.386	0.026	0.026	0.000	0.000	0.000	0.000
49	B	140	GLY	0	0.009	0.018	8.402	0.072	0.072	0.000	0.000	0.000	0.000
50	B	141	VAL	0	0.011	0.000	10.537	0.050	0.050	0.000	0.000	0.000	0.000
51	B	142	LEU	0	0.013	0.006	4.903	0.056	0.056	0.000	0.000	0.000	0.000
52	B	143	SER	0	0.011	0.009	8.976	0.081	0.081	0.000	0.000	0.000	0.000
53	B	144	SER	0	-0.013	0.000	11.837	0.037	0.037	0.000	0.000	0.000	0.000
54	B	145	LEU	0	-0.034	-0.023	9.946	0.043	0.043	0.000	0.000	0.000	0.000
55	B	146	ALA	0	0.030	0.009	10.899	0.050	0.050	0.000	0.000	0.000	0.000
56	B	147	ARG	1	0.810	0.880	12.783	0.286	0.286	0.000	0.000	0.000	0.000
57	B	148	ALA	0	-0.030	-0.004	15.993	0.023	0.023	0.000	0.000	0.000	0.000
58	B	149	PHE	0	-0.011	-0.004	14.764	0.030	0.030	0.000	0.000	0.000	0.000
59	B	150	GLY	0	-0.021	-0.005	17.571	0.013	0.013	0.000	0.000	0.000	0.000
60	B	151	HIS	1	0.789	0.880	13.387	0.058	0.058	0.000	0.000	0.000	0.000
61	B	152	GLU	-1	-0.778	-0.878	12.815	-0.289	-0.289	0.000	0.000	0.000	0.000
62	B	153	ALA	0	-0.026	-0.027	8.830	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	154	TYR	0	0.026	0.001	7.101	-0.110	-0.110	0.000	0.000	0.000	0.000
64	B	155	GLU	-1	-0.777	-0.872	7.296	-0.180	-0.180	0.000	0.000	0.000	0.000
65	B	156	MET	0	-0.067	-0.017	7.174	0.095	0.095	0.000	0.000	0.000	0.000
66	B	157	ILE	0	-0.069	-0.035	2.505	-0.857	-0.145	1.177	-0.386	-1.501	-0.002
67	B	158	ILE	0	0.023	0.035	4.396	-0.450	-0.274	-0.001	-0.009	-0.166	0.000
68	B	159	PRO	0	-0.032	-0.013	5.558	0.382	0.382	0.000	0.000	0.000	0.000
69	B	160	VAL	0	0.027	-0.001	7.230	-0.120	-0.120	0.000	0.000	0.000	0.000
70	B	161	GLY	0	0.005	-0.002	9.887	-0.049	-0.049	0.000	0.000	0.000	0.000
71	B	162	ALA	0	-0.026	-0.002	11.440	-0.056	-0.056	0.000	0.000	0.000	0.000
72	B	163	PRO	0	0.004	0.004	10.797	-0.041	-0.041	0.000	0.000	0.000	0.000
73	B	164	GLY	0	0.013	-0.002	12.229	-0.053	-0.053	0.000	0.000	0.000	0.000
74	B	165	ILE	0	-0.055	-0.015	11.278	-0.035	-0.035	0.000	0.000	0.000	0.000
75	B	166	ILE	0	-0.013	-0.013	15.744	0.026	0.026	0.000	0.000	0.000	0.000
76	B	167	ASP	-1	-0.919	-0.954	19.144	0.013	0.013	0.000	0.000	0.000	0.000
77	B	168	TYR	0	-0.020	-0.018	19.845	-0.010	-0.010	0.000	0.000	0.000	0.000
78	B	169	ASP	-1	-0.821	-0.911	22.411	-0.031	-0.031	0.000	0.000	0.000	0.000
79	B	170	HIS	0	0.052	0.003	17.910	-0.015	-0.015	0.000	0.000	0.000	0.000
80	B	171	ARG	1	0.952	0.979	23.091	0.021	0.021	0.000	0.000	0.000	0.000
81	B	172	MET	0	-0.064	-0.024	26.258	-0.002	-0.002	0.000	0.000	0.000	0.000
82	B	173	TYR	0	0.017	0.008	23.113	0.001	0.001	0.000	0.000	0.000	0.000
83	B	174	ALA	0	-0.027	-0.027	24.864	-0.003	-0.003	0.000	0.000	0.000	0.000
84	B	175	ALA	0	-0.029	-0.008	26.681	-0.001	-0.001	0.000	0.000	0.000	0.000
85	B	176	LEU	0	-0.024	0.011	29.880	0.003	0.003	0.000	0.000	0.000	0.000
86	B	177	PRO	0	0.041	0.021	30.878	-0.007	-0.007	0.000	0.000	0.000	0.000
87	B	178	GLN	0	0.059	0.019	30.436	0.002	0.002	0.000	0.000	0.000	0.000
88	B	179	GLU	-1	-0.899	-0.946	31.028	-0.052	-0.052	0.000	0.000	0.000	0.000
89	B	180	GLU	-1	-0.830	-0.922	31.639	-0.041	-0.041	0.000	0.000	0.000	0.000
90	B	181	LYS	1	0.824	0.927	26.265	0.071	0.071	0.000	0.000	0.000	0.000
91	B	182	ASN	0	0.052	0.021	28.004	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	183	LYS	1	0.854	0.932	30.058	0.043	0.043	0.000	0.000	0.000	0.000
93	B	184	ILE	0	0.027	0.017	25.485	0.001	0.001	0.000	0.000	0.000	0.000
94	B	185	THR	0	0.015	0.002	24.876	-0.001	-0.001	0.000	0.000	0.000	0.000
95	B	186	SER	0	-0.018	-0.014	26.568	-0.003	-0.003	0.000	0.000	0.000	0.000
96	B	187	PHE	0	-0.013	-0.001	27.832	0.001	0.001	0.000	0.000	0.000	0.000
97	B	188	ILE	0	0.010	0.008	22.341	0.003	0.003	0.000	0.000	0.000	0.000
98	B	189	ASN	0	-0.012	-0.026	23.869	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	190	PHE	0	-0.021	0.006	25.840	0.001	0.001	0.000	0.000	0.000	0.000
100	B	191	VAL	0	0.004	-0.002	25.097	0.003	0.003	0.000	0.000	0.000	0.000
101	B	192	PHE	0	-0.035	-0.017	19.959	0.003	0.003	0.000	0.000	0.000	0.000
102	B	193	GLU	-1	-0.763	-0.869	24.565	-0.088	-0.088	0.000	0.000	0.000	0.000
103	B	194	GLN	0	-0.094	-0.032	27.216	0.005	0.005	0.000	0.000	0.000	0.000
104	B	195	ASN	0	-0.064	-0.033	25.484	0.013	0.013	0.000	0.000	0.000	0.000
105	B	196	LYS	1	0.774	0.878	24.922	0.081	0.081	0.000	0.000	0.000	0.000

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