FMO DATABASE

FMODB ID: Z651N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-512790.994924
FMO2-HF: Nuclear repulsion	481748.63723
FMO2-HF: Total energy	-31042.357694
FMO2-MP2: Total energy	-31133.401668

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.
-7.592	-1.279	2.281	-3.549	-5.044	-0.009

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 : 0.032 / q_NPA : 0.005

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	-0.039	-0.022	3.044	-1.650	0.588	0.043	-1.059	-1.222	0.004
4	A	172	ARG	1	0.806	0.890	2.750	-3.103	-1.233	2.045	-1.405	-2.510	-0.005
5	A	173	SER	0	0.003	-0.004	3.885	-0.824	-0.271	0.000	-0.250	-0.302	0.000
6	A	174	ILE	0	-0.004	0.021	6.153	0.419	0.419	0.000	0.000	0.000	0.000
7	A	175	TYR	0	-0.036	-0.030	9.853	-0.178	-0.178	0.000	0.000	0.000	0.000
8	A	176	VAL	0	0.063	0.030	12.111	0.092	0.092	0.000	0.000	0.000	0.000
9	A	177	GLY	0	-0.022	-0.031	14.958	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	178	ASN	0	-0.025	-0.026	18.033	0.016	0.016	0.000	0.000	0.000	0.000
11	A	179	VAL	0	0.044	0.037	16.652	0.015	0.015	0.000	0.000	0.000	0.000
12	A	180	ASP	-1	-0.840	-0.916	19.891	-0.188	-0.188	0.000	0.000	0.000	0.000
13	A	181	TYR	0	-0.059	-0.074	21.336	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	182	GLY	0	-0.034	-0.016	23.126	0.001	0.001	0.000	0.000	0.000	0.000
15	A	183	ALA	0	-0.040	-0.001	19.486	0.008	0.008	0.000	0.000	0.000	0.000
16	A	184	THR	0	0.008	0.007	19.234	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	185	ALA	0	0.010	-0.021	14.463	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	186	GLU	-1	-0.946	-0.964	16.037	-0.181	-0.181	0.000	0.000	0.000	0.000
19	A	187	GLU	-1	-0.733	-0.874	18.429	-0.176	-0.176	0.000	0.000	0.000	0.000
20	A	188	LEU	0	-0.039	-0.027	14.605	0.004	0.004	0.000	0.000	0.000	0.000
21	A	189	GLU	-1	-0.876	-0.927	14.150	-0.179	-0.179	0.000	0.000	0.000	0.000
22	A	190	ALA	0	0.060	0.028	15.564	0.033	0.033	0.000	0.000	0.000	0.000
23	A	191	HIS	0	-0.100	-0.053	18.111	0.024	0.024	0.000	0.000	0.000	0.000
24	A	192	PHE	0	-0.024	-0.044	13.988	0.013	0.013	0.000	0.000	0.000	0.000
25	A	193	HIS	0	-0.042	-0.016	15.291	0.058	0.058	0.000	0.000	0.000	0.000
26	A	194	GLY	0	-0.007	-0.006	16.688	0.028	0.028	0.000	0.000	0.000	0.000
27	A	195	CYS	0	-0.109	-0.043	14.045	0.027	0.027	0.000	0.000	0.000	0.000
28	A	196	GLY	0	0.030	0.016	12.895	0.071	0.071	0.000	0.000	0.000	0.000
29	A	197	SER	0	0.006	0.009	11.279	-0.078	-0.078	0.000	0.000	0.000	0.000
30	A	198	VAL	0	0.014	0.011	9.711	0.016	0.016	0.000	0.000	0.000	0.000
31	A	199	ASN	0	-0.021	-0.013	6.245	0.313	0.313	0.000	0.000	0.000	0.000
32	A	200	ARG	1	0.940	0.961	6.095	1.214	1.214	0.000	0.000	0.000	0.000
33	A	201	VAL	0	0.046	0.039	8.108	-0.097	-0.097	0.000	0.000	0.000	0.000
34	A	202	THR	0	-0.076	-0.036	8.318	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	203	ILE	0	0.054	0.024	10.756	0.003	0.003	0.000	0.000	0.000	0.000
36	A	204	LEU	0	-0.044	-0.024	11.613	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	205	CYS	0	-0.029	-0.006	15.799	0.034	0.034	0.000	0.000	0.000	0.000
38	A	206	ASP	-1	-0.890	-0.950	19.647	-0.290	-0.290	0.000	0.000	0.000	0.000
39	A	207	LYS	1	0.775	0.885	22.232	0.172	0.172	0.000	0.000	0.000	0.000
40	A	208	PHE	0	0.044	0.005	21.916	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	209	SER	0	0.042	0.028	26.275	0.007	0.007	0.000	0.000	0.000	0.000
42	A	210	GLY	0	0.016	0.012	29.354	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	211	HIS	0	0.041	0.039	29.308	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	212	PRO	0	0.032	0.030	24.200	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	213	LYS	1	0.966	0.972	22.474	0.210	0.210	0.000	0.000	0.000	0.000
46	A	214	GLY	0	0.072	0.035	19.188	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	215	PHE	0	-0.061	-0.020	12.870	0.034	0.034	0.000	0.000	0.000	0.000
48	A	216	ALA	0	0.066	0.036	12.934	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	217	TYR	0	-0.059	-0.039	7.588	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	218	ILE	0	0.033	0.025	9.065	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	219	GLU	-1	-0.890	-0.933	3.187	-4.774	-3.122	0.193	-0.835	-1.010	-0.008
52	A	220	PHE	0	0.046	0.017	5.974	0.252	0.252	0.000	0.000	0.000	0.000
53	A	221	SER	0	0.017	0.000	5.353	0.051	0.051	0.000	0.000	0.000	0.000
54	A	222	ASP	-1	-0.875	-0.922	6.982	1.044	1.044	0.000	0.000	0.000	0.000
55	A	223	LYS	1	0.913	0.931	6.971	-2.087	-2.087	0.000	0.000	0.000	0.000
56	A	224	GLU	-1	-0.959	-0.982	7.931	0.293	0.293	0.000	0.000	0.000	0.000
57	A	225	SER	0	0.051	0.031	9.862	-0.128	-0.128	0.000	0.000	0.000	0.000
58	A	226	VAL	0	-0.009	0.012	7.620	-0.117	-0.117	0.000	0.000	0.000	0.000
59	A	227	ARG	1	0.926	0.960	10.597	-0.507	-0.507	0.000	0.000	0.000	0.000
60	A	228	THR	0	0.052	0.029	13.999	-0.040	-0.040	0.000	0.000	0.000	0.000
61	A	229	SER	0	0.003	-0.018	12.813	-0.065	-0.065	0.000	0.000	0.000	0.000
62	A	230	LEU	0	-0.025	-0.027	13.737	-0.035	-0.035	0.000	0.000	0.000	0.000
63	A	231	ALA	0	-0.010	0.011	16.556	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	232	LEU	0	-0.007	-0.001	17.180	-0.007	-0.007	0.000	0.000	0.000	0.000
65	A	233	ASP	-1	-0.845	-0.911	18.871	-0.114	-0.114	0.000	0.000	0.000	0.000
66	A	234	GLU	-1	-0.960	-0.971	20.085	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	235	SER	0	-0.054	-0.030	20.831	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	236	LEU	0	-0.023	-0.021	23.505	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	237	PHE	0	0.033	0.013	19.682	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	238	ARG	1	0.798	0.877	21.948	0.173	0.173	0.000	0.000	0.000	0.000
71	A	239	GLY	0	-0.013	0.000	25.253	0.001	0.001	0.000	0.000	0.000	0.000
72	A	240	ARG	1	0.855	0.931	24.113	0.156	0.156	0.000	0.000	0.000	0.000
73	A	241	GLN	0	0.041	0.028	24.560	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	242	ILE	0	-0.021	0.007	18.031	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	243	LYS	1	0.954	0.996	18.334	0.162	0.162	0.000	0.000	0.000	0.000
76	A	244	VAL	0	-0.006	0.000	14.314	-0.059	-0.059	0.000	0.000	0.000	0.000
77	A	245	ILE	0	-0.042	-0.019	13.823	0.051	0.051	0.000	0.000	0.000	0.000
78	A	246	PRO	0	0.034	0.012	10.687	-0.096	-0.096	0.000	0.000	0.000	0.000
79	A	247	LYS	1	0.865	0.953	5.330	2.232	2.232	0.000	0.000	0.000	0.000
80	A	248	ARG	1	0.923	0.980	9.433	0.416	0.416	0.000	0.000	0.000	0.000

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