FMO DATABASE

FMODB ID: 3QR1L

Calculation Name: 2YAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: A

ChEMBL ID:

UniProt ID: P11686

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge	DGL=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-474351.076877
FMO2-HF: Nuclear repulsion	443600.77315
FMO2-HF: Total energy	-30750.303726
FMO2-MP2: Total energy	-30835.368892

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:90:THR)

Summations of interaction energy for fragment #1(A:90:THR)

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.
-4.395	1.862	3.775	-4.169	-5.861	0.001

Interaction energy analysis for fragmet #1(A:90:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / q_NPA : 0.028

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	92	ALA	0	0.015	0.011	3.561	-1.116	2.104	0.015	-1.813	-1.422	0.004
4	A	93	THR	0	-0.006	0.002	5.807	-0.054	-0.054	0.000	0.000	0.000	0.000
5	A	94	PHE	0	-0.025	-0.011	8.097	0.001	0.001	0.000	0.000	0.000	0.000
6	A	95	SER	0	0.041	0.015	12.621	0.042	0.042	0.000	0.000	0.000	0.000
7	A	96	ILE	0	-0.032	-0.018	16.295	-0.035	-0.035	0.000	0.000	0.000	0.000
8	A	97	GLY	0	0.016	0.011	19.083	0.019	0.019	0.000	0.000	0.000	0.000
9	A	98	SER	0	-0.001	-0.007	22.000	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	99	THR	0	-0.045	-0.035	22.877	0.013	0.013	0.000	0.000	0.000	0.000
11	A	100	GLY	0	0.030	0.044	20.209	0.011	0.011	0.000	0.000	0.000	0.000
12	A	101	LEU	0	-0.032	-0.019	15.839	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	102	VAL	0	0.000	-0.008	11.333	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	103	VAL	0	0.004	0.004	8.632	0.054	0.054	0.000	0.000	0.000	0.000
15	A	104	TYR	0	-0.056	-0.044	6.701	0.018	0.018	0.000	0.000	0.000	0.000
16	A	105	ASP	-1	-0.802	-0.927	4.570	-2.809	-2.711	-0.001	-0.024	-0.073	0.000
17	A	106	TYR	0	0.004	-0.012	2.389	-0.837	1.001	0.953	-0.771	-2.020	0.003
18	A	107	GLN	0	-0.038	-0.004	1.867	-1.919	-1.027	2.769	-1.552	-2.108	-0.005
19	A	108	GLN	0	0.028	0.007	3.358	1.070	1.279	0.039	-0.009	-0.238	-0.001
20	A	109	LEU	0	-0.022	-0.006	6.094	0.448	0.448	0.000	0.000	0.000	0.000
21	A	110	LEU	0	-0.011	-0.002	7.929	0.408	0.408	0.000	0.000	0.000	0.000
22	A	111	ILE	0	0.005	0.008	9.013	-0.283	-0.283	0.000	0.000	0.000	0.000
23	A	112	ALA	0	0.000	0.003	11.673	0.110	0.110	0.000	0.000	0.000	0.000
24	A	113	TYR	0	0.012	-0.006	13.807	-0.019	-0.019	0.000	0.000	0.000	0.000
25	A	114	LYS	1	0.912	0.970	16.611	0.046	0.046	0.000	0.000	0.000	0.000
26	A	115	PRO	0	0.011	0.016	19.353	0.002	0.002	0.000	0.000	0.000	0.000
27	A	116	ALA	0	0.056	0.032	22.029	0.007	0.007	0.000	0.000	0.000	0.000
28	A	117	PRO	0	0.009	-0.001	22.963	0.001	0.001	0.000	0.000	0.000	0.000
29	A	118	GLY	0	0.021	0.012	23.880	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	119	THR	0	-0.015	-0.012	24.021	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	120	CYS	0	-0.088	-0.041	23.030	0.011	0.011	0.000	0.000	0.000	0.000
32	A	121	CYS	0	-0.066	-0.056	15.149	-0.042	-0.042	0.000	0.000	0.000	0.000
33	A	122	TYR	0	0.046	0.034	19.138	0.004	0.004	0.000	0.000	0.000	0.000
34	A	123	ILE	0	-0.024	-0.014	13.782	-0.046	-0.046	0.000	0.000	0.000	0.000
35	A	124	MET	0	-0.002	0.003	14.441	0.045	0.045	0.000	0.000	0.000	0.000
36	A	125	LYS	1	0.870	0.928	10.728	0.569	0.569	0.000	0.000	0.000	0.000
37	A	126	ILE	0	-0.027	-0.009	8.859	0.049	0.049	0.000	0.000	0.000	0.000
38	A	127	ALA	0	0.033	0.019	12.086	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	128	PRO	0	0.003	-0.014	9.677	-0.071	-0.071	0.000	0.000	0.000	0.000
40	A	129	DGL	-1	-0.948	-0.974	11.089	-0.464	-0.464	0.000	0.000	0.000	0.000
41	A	130	SER	0	-0.012	-0.009	13.628	0.059	0.059	0.000	0.000	0.000	0.000
42	A	131	ILE	0	-0.019	0.007	7.989	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	132	PRO	0	0.012	0.024	12.104	0.046	0.046	0.000	0.000	0.000	0.000
44	A	133	SER	0	0.070	0.029	12.461	-0.083	-0.083	0.000	0.000	0.000	0.000
45	A	134	LEU	0	0.088	0.036	12.814	0.035	0.035	0.000	0.000	0.000	0.000
46	A	135	GLU	-1	-0.798	-0.864	14.366	-0.251	-0.251	0.000	0.000	0.000	0.000
47	A	136	ALA	0	-0.019	-0.004	16.944	0.042	0.042	0.000	0.000	0.000	0.000
48	A	137	LEU	0	-0.029	-0.010	13.416	0.039	0.039	0.000	0.000	0.000	0.000
49	A	138	THR	0	0.023	-0.001	17.108	0.045	0.045	0.000	0.000	0.000	0.000
50	A	139	ARG	1	0.851	0.894	19.520	0.321	0.321	0.000	0.000	0.000	0.000
51	A	140	LYS	1	0.896	0.961	17.671	0.401	0.401	0.000	0.000	0.000	0.000
52	A	141	VAL	0	0.027	-0.005	18.841	0.023	0.023	0.000	0.000	0.000	0.000
53	A	142	HIS	0	-0.009	-0.004	21.779	0.029	0.029	0.000	0.000	0.000	0.000
54	A	143	ASN	0	0.000	0.002	24.930	0.018	0.018	0.000	0.000	0.000	0.000
55	A	144	PHE	0	-0.066	-0.037	24.303	0.009	0.009	0.000	0.000	0.000	0.000
56	A	145	GLN	0	-0.006	0.012	26.391	0.014	0.014	0.000	0.000	0.000	0.000
57	A	146	MET	0	-0.052	0.003	21.456	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	147	GLU	-1	-0.900	-0.981	23.666	-0.128	-0.128	0.000	0.000	0.000	0.000
59	A	149	DSN	0	-0.036	-0.004	26.730	0.016	0.016	0.000	0.000	0.000	0.000
60	A	181	LEU	0	-0.007	-0.010	11.224	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	182	GLY	0	0.057	0.035	7.954	0.132	0.132	0.000	0.000	0.000	0.000
62	A	183	MET	0	0.016	0.004	8.403	-0.071	-0.071	0.000	0.000	0.000	0.000
63	A	184	ALA	0	0.037	0.033	7.610	-0.088	-0.088	0.000	0.000	0.000	0.000
64	A	185	VAL	0	0.029	0.012	8.787	-0.100	-0.100	0.000	0.000	0.000	0.000
65	A	186	SER	0	-0.002	-0.017	11.206	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	187	THR	0	-0.042	-0.026	12.358	0.004	0.004	0.000	0.000	0.000	0.000
67	A	188	LEU	0	-0.028	0.001	13.467	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	190	GLY	0	0.049	0.039	17.109	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	191	GLU	-1	-0.963	-0.997	19.075	0.052	0.052	0.000	0.000	0.000	0.000
70	A	192	VAL	0	-0.056	-0.002	20.754	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	193	PRO	0	0.013	0.009	22.155	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	194	LEU	0	0.003	0.005	17.733	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	195	TYR	0	-0.006	-0.015	20.389	0.010	0.010	0.000	0.000	0.000	0.000
74	A	196	TYR	0	0.033	0.008	15.526	-0.023	-0.023	0.000	0.000	0.000	0.000
75	A	197	ILE	0	-0.017	-0.009	18.713	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:90:THR)