FMO DATABASE

FMODB ID: YZ5R2

Calculation Name: 3ADL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ADL

Chain ID: A

ChEMBL ID:

UniProt ID: Q15633

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptHSide
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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-461916.757082
FMO2-HF: Nuclear repulsion	432095.976877
FMO2-HF: Total energy	-29820.780204
FMO2-MP2: Total energy	-29907.384878

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:152:GLY)

Summations of interaction energy for fragment #1(A:152:GLY)

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.
1.456	3.775	0.156	-1.186	-1.289	-0.005

Interaction energy analysis for fragmet #1(A:152:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.004

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	154	VAL	0	0.000	0.018	3.786	0.972	2.498	-0.021	-0.788	-0.718	0.000
4	A	155	PRO	0	0.029	0.008	6.752	-0.251	-0.251	0.000	0.000	0.000	0.000
5	A	156	ARG	1	0.978	0.979	10.213	0.194	0.194	0.000	0.000	0.000	0.000
6	A	157	GLY	0	-0.040	-0.018	12.223	0.075	0.075	0.000	0.000	0.000	0.000
7	A	158	SER	0	-0.003	-0.004	11.220	0.030	0.030	0.000	0.000	0.000	0.000
8	A	159	HIS	0	0.010	-0.005	12.419	-0.106	-0.106	0.000	0.000	0.000	0.000
9	A	160	GLU	-1	-0.805	-0.897	8.256	0.178	0.178	0.000	0.000	0.000	0.000
10	A	161	VAL	0	-0.031	-0.035	11.554	0.047	0.047	0.000	0.000	0.000	0.000
11	A	162	GLY	0	0.021	0.015	13.512	0.029	0.029	0.000	0.000	0.000	0.000
12	A	163	ALA	0	0.088	0.048	14.413	0.019	0.019	0.000	0.000	0.000	0.000
13	A	164	LEU	0	-0.019	-0.004	13.015	0.023	0.023	0.000	0.000	0.000	0.000
14	A	165	GLN	0	-0.043	-0.019	15.750	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	166	GLU	-1	-0.916	-0.969	18.632	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	167	LEU	0	-0.014	0.000	17.155	0.006	0.006	0.000	0.000	0.000	0.000
17	A	168	VAL	0	-0.041	-0.043	18.289	0.004	0.004	0.000	0.000	0.000	0.000
18	A	169	VAL	0	0.028	0.021	21.058	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	170	GLN	0	-0.010	-0.001	23.553	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	171	LYS	1	0.857	0.946	21.056	-0.144	-0.144	0.000	0.000	0.000	0.000
21	A	172	GLY	0	0.018	0.029	24.966	0.001	0.001	0.000	0.000	0.000	0.000
22	A	173	TRP	0	-0.038	-0.029	19.273	0.008	0.008	0.000	0.000	0.000	0.000
23	A	174	ARG	1	0.971	0.974	24.438	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	175	LEU	0	0.014	0.001	21.045	0.011	0.011	0.000	0.000	0.000	0.000
25	A	176	PRO	0	0.000	-0.002	16.496	0.001	0.001	0.000	0.000	0.000	0.000
26	A	177	GLU	-1	-0.879	-0.911	18.313	-0.026	-0.026	0.000	0.000	0.000	0.000
27	A	178	TYR	0	-0.005	-0.033	11.905	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	179	THR	0	0.040	0.017	15.499	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	180	VAL	0	-0.033	-0.035	14.457	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	181	THR	0	0.017	0.023	14.249	0.015	0.015	0.000	0.000	0.000	0.000
31	A	182	GLN	0	0.001	0.000	13.343	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	183	GLU	-1	-0.797	-0.896	14.003	-0.288	-0.288	0.000	0.000	0.000	0.000
33	A	184	SER	0	-0.005	0.013	13.580	0.043	0.043	0.000	0.000	0.000	0.000
34	A	185	GLY	0	0.065	0.027	15.998	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	186	PRO	0	0.022	-0.002	17.307	0.004	0.004	0.000	0.000	0.000	0.000
36	A	187	ALA	0	0.019	0.004	18.249	-0.027	-0.027	0.000	0.000	0.000	0.000
37	A	188	HIS	0	0.034	0.016	19.334	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	189	ARG	1	0.882	0.934	15.018	0.217	0.217	0.000	0.000	0.000	0.000
39	A	190	LYS	1	0.917	0.969	15.007	0.233	0.233	0.000	0.000	0.000	0.000
40	A	191	GLU	-1	-0.901	-0.940	9.038	-0.812	-0.812	0.000	0.000	0.000	0.000
41	A	192	PHE	0	-0.079	-0.048	10.602	0.118	0.118	0.000	0.000	0.000	0.000
42	A	193	THR	0	0.041	0.007	9.425	-0.157	-0.157	0.000	0.000	0.000	0.000
43	A	194	MET	0	-0.092	-0.028	9.676	0.070	0.070	0.000	0.000	0.000	0.000
44	A	195	THR	0	0.030	-0.003	10.572	0.048	0.048	0.000	0.000	0.000	0.000
45	A	196	CYS	0	-0.050	-0.022	12.107	-0.031	-0.031	0.000	0.000	0.000	0.000
46	A	197	ARG	1	0.927	0.952	13.826	0.044	0.044	0.000	0.000	0.000	0.000
47	A	198	VAL	0	0.037	0.007	17.005	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	199	GLU	-1	-0.761	-0.825	19.108	0.160	0.160	0.000	0.000	0.000	0.000
49	A	200	ARG	1	0.836	0.878	21.243	-0.165	-0.165	0.000	0.000	0.000	0.000
50	A	201	PHE	0	-0.031	-0.016	16.391	0.020	0.020	0.000	0.000	0.000	0.000
51	A	202	ILE	0	0.030	0.000	15.143	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	203	GLU	-1	-0.774	-0.861	10.582	0.593	0.593	0.000	0.000	0.000	0.000
53	A	204	ILE	0	-0.014	-0.005	8.599	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	205	GLY	0	0.027	0.006	6.009	0.261	0.261	0.000	0.000	0.000	0.000
55	A	206	SER	0	0.011	0.004	5.112	-0.034	-0.034	0.000	0.000	0.000	0.000
56	A	207	GLY	0	0.002	-0.006	4.904	-0.897	-0.873	-0.001	-0.002	-0.020	0.000
57	A	208	THR	0	0.115	0.071	7.110	0.219	0.219	0.000	0.000	0.000	0.000
58	A	209	SER	0	-0.018	-0.013	9.720	0.167	0.167	0.000	0.000	0.000	0.000
59	A	210	LYS	1	0.944	0.973	10.085	0.139	0.139	0.000	0.000	0.000	0.000
60	A	211	LYS	1	0.968	0.987	11.146	0.538	0.538	0.000	0.000	0.000	0.000
61	A	212	LEU	0	-0.022	-0.012	6.859	0.077	0.077	0.000	0.000	0.000	0.000
62	A	213	ALA	0	0.035	0.034	6.462	-0.244	-0.244	0.000	0.000	0.000	0.000
63	A	214	LYS	1	0.926	0.966	7.541	0.310	0.310	0.000	0.000	0.000	0.000
64	A	215	ARG	1	0.953	0.980	7.273	1.161	1.161	0.000	0.000	0.000	0.000
65	A	216	ASN	0	0.002	-0.005	3.096	-0.591	0.130	0.179	-0.395	-0.505	-0.005
66	A	217	ALA	0	0.013	0.009	5.055	0.660	0.708	-0.001	-0.001	-0.046	0.000
67	A	218	ALA	0	-0.048	-0.026	8.189	0.155	0.155	0.000	0.000	0.000	0.000
68	A	219	ALA	0	0.067	0.043	5.974	0.069	0.069	0.000	0.000	0.000	0.000
69	A	220	LYS	1	0.881	0.932	6.373	-0.632	-0.632	0.000	0.000	0.000	0.000
70	A	221	MET	0	-0.025	0.004	8.376	-0.071	-0.071	0.000	0.000	0.000	0.000
71	A	222	LEU	0	-0.013	-0.001	11.164	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	223	LEU	0	0.000	0.005	8.057	-0.018	-0.018	0.000	0.000	0.000	0.000
73	A	224	ARG	1	0.841	0.933	12.102	-0.524	-0.524	0.000	0.000	0.000	0.000
74	A	225	VAL	0	-0.037	-0.033	14.198	-0.052	-0.052	0.000	0.000	0.000	0.000
75	A	226	HIS	0	-0.016	-0.008	14.795	-0.045	-0.045	0.000	0.000	0.000	0.000
76	A	227	THR	0	-0.113	-0.049	14.735	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:152:GLY)