FMO DATABASE

FMODB ID: M3Y5Z

Calculation Name: 2YAD-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: F

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

Total energy (hartree)

FMO2-HF: Electronic energy	-474604.922878
FMO2-HF: Nuclear repulsion	443851.578609
FMO2-HF: Total energy	-30753.344269
FMO2-MP2: Total energy	-30838.46219

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(F:89:VAL)

Summations of interaction energy for fragment #1(F:89: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.
-3.124	-0.153	2.324	-1.602	-3.69	-0.005

Interaction energy analysis for fragmet #1(F:89:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.018

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	F	91	THR	0	-0.026	-0.012	3.480	-2.135	-0.332	0.021	-0.857	-0.966	-0.001
4	F	92	ALA	0	0.021	0.008	5.065	0.346	0.431	-0.001	-0.002	-0.081	0.000
5	F	93	THR	0	-0.016	-0.003	6.988	-0.109	-0.109	0.000	0.000	0.000	0.000
6	F	94	PHE	0	0.000	0.001	8.565	0.044	0.044	0.000	0.000	0.000	0.000
7	F	95	SER	0	0.033	0.017	13.362	-0.009	-0.009	0.000	0.000	0.000	0.000
8	F	96	ILE	0	-0.037	-0.024	16.454	-0.008	-0.008	0.000	0.000	0.000	0.000
9	F	97	GLY	0	0.013	0.017	19.149	0.003	0.003	0.000	0.000	0.000	0.000
10	F	98	SER	0	-0.009	-0.013	22.780	0.005	0.005	0.000	0.000	0.000	0.000
11	F	99	THR	0	-0.029	-0.027	23.469	0.009	0.009	0.000	0.000	0.000	0.000
12	F	100	GLY	0	0.019	0.032	20.537	-0.001	-0.001	0.000	0.000	0.000	0.000
13	F	101	LEU	0	-0.025	-0.018	16.340	0.013	0.013	0.000	0.000	0.000	0.000
14	F	102	VAL	0	-0.016	-0.009	11.868	-0.022	-0.022	0.000	0.000	0.000	0.000
15	F	103	VAL	0	0.015	0.011	9.348	0.039	0.039	0.000	0.000	0.000	0.000
16	F	104	TYR	0	-0.046	-0.032	6.574	-0.010	-0.010	0.000	0.000	0.000	0.000
17	F	105	ASP	-1	-0.838	-0.939	6.115	-1.128	-1.128	0.000	0.000	0.000	0.000
18	F	106	TYR	0	0.018	-0.014	2.326	-0.990	-0.256	2.306	-0.708	-2.331	-0.004
19	F	107	GLN	0	-0.023	0.005	4.560	-0.190	0.053	-0.001	-0.032	-0.210	0.000
20	F	108	GLN	0	-0.044	-0.029	5.352	0.335	0.441	-0.001	-0.003	-0.102	0.000
21	F	109	LEU	0	-0.032	0.006	7.518	0.211	0.211	0.000	0.000	0.000	0.000
22	F	110	LEU	0	-0.020	-0.025	8.963	0.216	0.216	0.000	0.000	0.000	0.000
23	F	111	ILE	0	-0.008	-0.005	9.435	-0.064	-0.064	0.000	0.000	0.000	0.000
24	F	112	ALA	0	-0.008	0.005	11.719	0.036	0.036	0.000	0.000	0.000	0.000
25	F	113	TYR	0	0.008	-0.005	14.100	0.014	0.014	0.000	0.000	0.000	0.000
26	F	114	LYS	1	0.950	0.981	16.713	0.060	0.060	0.000	0.000	0.000	0.000
27	F	115	PRO	0	0.016	0.019	19.524	0.011	0.011	0.000	0.000	0.000	0.000
28	F	116	ALA	0	0.060	0.031	22.289	0.011	0.011	0.000	0.000	0.000	0.000
29	F	117	PRO	0	-0.011	-0.008	24.084	-0.006	-0.006	0.000	0.000	0.000	0.000
30	F	118	GLY	0	0.019	0.013	24.991	0.000	0.000	0.000	0.000	0.000	0.000
31	F	119	THR	0	-0.006	-0.005	24.614	-0.005	-0.005	0.000	0.000	0.000	0.000
32	F	148	CYS	0	-0.076	-0.024	23.902	0.005	0.005	0.000	0.000	0.000	0.000
33	F	121	CYS	0	-0.064	-0.057	17.169	0.004	0.004	0.000	0.000	0.000	0.000
34	F	122	TYR	0	0.039	0.028	19.123	-0.001	-0.001	0.000	0.000	0.000	0.000
35	F	123	ILE	0	-0.022	-0.019	15.195	-0.023	-0.023	0.000	0.000	0.000	0.000
36	F	124	MET	0	-0.001	0.012	15.112	0.018	0.018	0.000	0.000	0.000	0.000
37	F	125	LYS	1	0.965	0.989	13.786	0.394	0.394	0.000	0.000	0.000	0.000
38	F	126	ILE	0	-0.040	-0.015	8.225	0.054	0.054	0.000	0.000	0.000	0.000
39	F	127	ALA	0	0.043	0.020	11.733	-0.059	-0.059	0.000	0.000	0.000	0.000
40	F	128	PRO	0	0.020	-0.007	9.199	-0.017	-0.017	0.000	0.000	0.000	0.000
41	F	129	GLU	-1	-0.894	-0.942	10.185	-0.619	-0.619	0.000	0.000	0.000	0.000
42	F	130	SER	0	-0.077	-0.042	12.132	0.096	0.096	0.000	0.000	0.000	0.000
43	F	131	ILE	0	0.008	0.018	6.369	0.008	0.008	0.000	0.000	0.000	0.000
44	F	132	PRO	0	-0.038	-0.002	10.314	0.049	0.049	0.000	0.000	0.000	0.000
45	F	133	SER	0	0.083	0.026	11.110	-0.018	-0.018	0.000	0.000	0.000	0.000
46	F	134	LEU	0	0.096	0.043	12.538	-0.001	-0.001	0.000	0.000	0.000	0.000
47	F	135	GLU	-1	-0.832	-0.904	13.767	-0.079	-0.079	0.000	0.000	0.000	0.000
48	F	136	ALA	0	-0.003	0.004	15.420	0.013	0.013	0.000	0.000	0.000	0.000
49	F	137	LEU	0	-0.004	0.005	13.163	0.007	0.007	0.000	0.000	0.000	0.000
50	F	138	THR	0	0.022	-0.002	16.332	0.016	0.016	0.000	0.000	0.000	0.000
51	F	139	ARG	1	0.810	0.890	19.141	0.123	0.123	0.000	0.000	0.000	0.000
52	F	140	LYS	1	0.903	0.954	17.479	0.260	0.260	0.000	0.000	0.000	0.000
53	F	141	VAL	0	0.029	-0.007	18.776	0.002	0.002	0.000	0.000	0.000	0.000
54	F	142	HIS	0	0.029	0.027	21.377	0.007	0.007	0.000	0.000	0.000	0.000
55	F	143	ASN	0	-0.044	-0.035	23.457	0.012	0.012	0.000	0.000	0.000	0.000
56	F	144	PHE	0	-0.069	-0.042	22.161	-0.004	-0.004	0.000	0.000	0.000	0.000
57	F	145	GLN	0	-0.015	0.019	25.109	0.000	0.000	0.000	0.000	0.000	0.000
58	F	146	MET	0	-0.093	-0.025	19.505	-0.006	-0.006	0.000	0.000	0.000	0.000
59	F	147	GLU	-1	-0.876	-0.963	23.937	-0.079	-0.079	0.000	0.000	0.000	0.000
60	F	181	LEU	0	0.030	-0.002	14.765	0.009	0.009	0.000	0.000	0.000	0.000
61	F	182	GLY	0	0.076	0.049	11.914	-0.077	-0.077	0.000	0.000	0.000	0.000
62	F	183	MET	0	0.004	-0.004	12.628	0.038	0.038	0.000	0.000	0.000	0.000
63	F	184	ALA	0	0.040	0.030	10.264	0.030	0.030	0.000	0.000	0.000	0.000
64	F	185	VAL	0	0.052	0.017	11.114	0.023	0.023	0.000	0.000	0.000	0.000
65	F	186	SER	0	-0.017	-0.027	13.652	0.024	0.024	0.000	0.000	0.000	0.000
66	F	187	THR	0	-0.042	-0.018	15.544	0.026	0.026	0.000	0.000	0.000	0.000
67	F	188	LEU	0	-0.040	-0.016	14.704	0.011	0.011	0.000	0.000	0.000	0.000
68	F	190	GLY	0	0.040	0.046	19.221	-0.002	-0.002	0.000	0.000	0.000	0.000
69	F	191	GLU	-1	-0.973	-0.996	21.674	-0.014	-0.014	0.000	0.000	0.000	0.000
70	F	192	VAL	0	-0.039	0.002	22.302	0.005	0.005	0.000	0.000	0.000	0.000
71	F	193	PRO	0	-0.019	-0.001	23.919	-0.009	-0.009	0.000	0.000	0.000	0.000
72	F	194	LEU	0	-0.007	-0.012	19.505	-0.009	-0.009	0.000	0.000	0.000	0.000
73	F	195	TYR	0	0.016	0.006	21.887	0.006	0.006	0.000	0.000	0.000	0.000
74	F	196	TYR	0	0.010	0.008	18.339	-0.025	-0.025	0.000	0.000	0.000	0.000
75	F	197	ILE	0	-0.009	-0.006	19.498	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:89:VAL)