FMO DATABASE

FMODB ID: QYGJY

Calculation Name: 3B4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q86U42

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-514420.288616
FMO2-HF: Nuclear repulsion	483377.446551
FMO2-HF: Total energy	-31042.842065
FMO2-MP2: Total energy	-31133.915317

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:169:ALA)

Summations of interaction energy for fragment #1(A:169:ALA)

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.
-9.199	-7.656	9.196	-4.904	-5.835	0.006

Interaction energy analysis for fragmet #1(A:169:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : 0.012

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	A	171	ALA	0	-0.034	-0.018	3.370	0.320	1.633	0.003	-0.560	-0.756	0.001
4	A	172	ARG	1	0.768	0.861	2.098	-12.814	-14.622	8.941	-3.399	-3.733	0.010
5	A	173	SER	0	0.004	-0.010	3.390	-0.635	0.052	0.007	-0.292	-0.402	0.000
6	A	174	ILE	0	-0.003	0.015	5.997	0.192	0.192	0.000	0.000	0.000	0.000
7	A	175	TYR	0	-0.013	-0.017	9.095	-0.136	-0.136	0.000	0.000	0.000	0.000
8	A	176	VAL	0	0.057	0.023	11.265	0.083	0.083	0.000	0.000	0.000	0.000
9	A	177	GLY	0	0.009	-0.004	14.361	-0.004	-0.004	0.000	0.000	0.000	0.000
10	A	178	ASN	0	-0.009	-0.018	17.154	0.026	0.026	0.000	0.000	0.000	0.000
11	A	179	VAL	0	0.042	0.038	16.337	0.023	0.023	0.000	0.000	0.000	0.000
12	A	180	ASP	-1	-0.829	-0.896	19.417	-0.154	-0.154	0.000	0.000	0.000	0.000
13	A	181	TYR	0	-0.007	-0.035	20.917	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	182	GLY	0	-0.026	-0.004	22.321	0.005	0.005	0.000	0.000	0.000	0.000
15	A	183	ALA	0	-0.061	-0.024	19.368	0.013	0.013	0.000	0.000	0.000	0.000
16	A	184	THR	0	-0.019	-0.035	19.435	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	185	ALA	0	-0.005	-0.029	14.824	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	186	GLU	-1	-0.927	-0.955	16.074	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	187	GLU	-1	-0.692	-0.808	18.595	-0.107	-0.107	0.000	0.000	0.000	0.000
20	A	188	LEU	0	-0.045	-0.031	14.476	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	189	GLU	-1	-0.860	-0.920	13.753	0.029	0.029	0.000	0.000	0.000	0.000
22	A	190	ALA	0	0.049	0.025	15.469	0.024	0.024	0.000	0.000	0.000	0.000
23	A	191	HIS	0	-0.090	-0.045	17.776	0.021	0.021	0.000	0.000	0.000	0.000
24	A	192	PHE	0	-0.005	-0.032	13.564	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	193	HIS	0	-0.027	-0.017	14.984	0.055	0.055	0.000	0.000	0.000	0.000
26	A	194	GLY	0	-0.011	-0.003	16.417	0.037	0.037	0.000	0.000	0.000	0.000
27	A	195	CYS	0	-0.084	-0.022	13.941	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	196	GLY	0	0.016	0.017	13.627	0.058	0.058	0.000	0.000	0.000	0.000
29	A	197	SER	0	0.012	0.007	11.097	-0.106	-0.106	0.000	0.000	0.000	0.000
30	A	198	VAL	0	0.020	0.014	9.715	0.109	0.109	0.000	0.000	0.000	0.000
31	A	199	ASN	0	-0.020	-0.002	5.221	0.022	0.022	0.000	0.000	0.000	0.000
32	A	200	ARG	1	0.920	0.954	5.873	0.561	0.561	0.000	0.000	0.000	0.000
33	A	201	VAL	0	0.058	0.049	8.406	-0.102	-0.102	0.000	0.000	0.000	0.000
34	A	202	THR	0	-0.074	-0.042	8.318	-0.049	-0.049	0.000	0.000	0.000	0.000
35	A	203	ILE	0	0.044	0.015	10.499	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	204	LEU	0	-0.025	-0.003	10.833	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	205	CYS	0	-0.013	-0.011	15.150	0.026	0.026	0.000	0.000	0.000	0.000
38	A	206	ASP	-1	-0.809	-0.889	18.960	-0.270	-0.270	0.000	0.000	0.000	0.000
39	A	207	LYS	1	0.786	0.885	21.509	0.160	0.160	0.000	0.000	0.000	0.000
40	A	208	PHE	0	0.059	0.015	21.018	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	209	SER	0	0.044	0.028	25.702	0.008	0.008	0.000	0.000	0.000	0.000
42	A	210	GLY	0	0.031	0.025	28.862	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	211	HIS	0	0.052	0.028	28.621	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	212	PRO	0	-0.005	0.013	23.331	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	213	LYS	1	0.833	0.900	20.225	0.258	0.258	0.000	0.000	0.000	0.000
46	A	214	GLY	0	0.063	0.021	18.382	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	215	PHE	0	-0.076	-0.031	11.996	0.018	0.018	0.000	0.000	0.000	0.000
48	A	216	ALA	0	0.053	0.034	12.608	0.007	0.007	0.000	0.000	0.000	0.000
49	A	217	TYR	0	-0.048	-0.036	7.157	-0.089	-0.089	0.000	0.000	0.000	0.000
50	A	218	ILE	0	0.031	0.028	8.984	0.052	0.052	0.000	0.000	0.000	0.000
51	A	219	GLU	-1	-0.853	-0.897	2.764	-0.703	0.547	0.246	-0.641	-0.855	-0.005
52	A	220	PHE	0	0.053	0.015	5.648	0.233	0.233	0.000	0.000	0.000	0.000
53	A	221	SER	0	-0.029	-0.024	5.726	0.647	0.647	0.000	0.000	0.000	0.000
54	A	222	ASP	-1	-0.851	-0.919	7.593	1.607	1.607	0.000	0.000	0.000	0.000
55	A	223	LYS	1	0.902	0.934	7.688	-0.909	-0.909	0.000	0.000	0.000	0.000
56	A	224	GLU	-1	-0.958	-0.975	9.137	0.224	0.224	0.000	0.000	0.000	0.000
57	A	225	SER	0	0.050	0.013	10.373	-0.076	-0.076	0.000	0.000	0.000	0.000
58	A	226	VAL	0	-0.013	0.011	8.041	-0.120	-0.120	0.000	0.000	0.000	0.000
59	A	227	ARG	1	0.909	0.958	10.907	-0.172	-0.172	0.000	0.000	0.000	0.000
60	A	228	THR	0	0.043	0.022	14.468	-0.044	-0.044	0.000	0.000	0.000	0.000
61	A	229	SER	0	0.002	-0.026	12.748	-0.060	-0.060	0.000	0.000	0.000	0.000
62	A	230	LEU	0	-0.022	-0.027	13.749	-0.042	-0.042	0.000	0.000	0.000	0.000
63	A	231	ALA	0	-0.029	-0.002	16.726	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	232	LEU	0	0.014	0.015	17.023	0.004	0.004	0.000	0.000	0.000	0.000
65	A	233	ASP	-1	-0.772	-0.849	18.829	-0.198	-0.198	0.000	0.000	0.000	0.000
66	A	234	GLU	-1	-0.962	-0.972	19.904	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	235	SER	0	-0.014	-0.014	20.519	0.012	0.012	0.000	0.000	0.000	0.000
68	A	236	LEU	0	-0.012	-0.014	22.959	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	237	PHE	0	0.044	0.018	19.460	0.003	0.003	0.000	0.000	0.000	0.000
70	A	238	ARG	1	0.755	0.835	21.687	0.122	0.122	0.000	0.000	0.000	0.000
71	A	239	GLY	0	0.000	0.009	25.038	0.000	0.000	0.000	0.000	0.000	0.000
72	A	240	ARG	1	0.817	0.909	23.025	0.151	0.151	0.000	0.000	0.000	0.000
73	A	241	GLN	0	-0.004	-0.001	24.143	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	242	ILE	0	-0.018	0.014	17.711	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	243	LYS	1	0.828	0.897	18.214	0.194	0.194	0.000	0.000	0.000	0.000
76	A	244	VAL	0	-0.012	-0.009	14.219	-0.058	-0.058	0.000	0.000	0.000	0.000
77	A	245	ILE	0	-0.021	-0.007	13.381	0.043	0.043	0.000	0.000	0.000	0.000
78	A	246	PRO	0	0.043	0.010	10.475	-0.084	-0.084	0.000	0.000	0.000	0.000
79	A	247	LYS	1	0.768	0.886	4.310	2.171	2.272	-0.001	-0.012	-0.089	0.000
80	A	248	ARG	1	0.910	0.976	8.743	0.502	0.502	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:169:ALA)