FMO DATABASE

FMODB ID: 14K1Z

Calculation Name: 2YAD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: B

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:

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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496352.197953
FMO2-HF: Nuclear repulsion	464802.757661
FMO2-HF: Total energy	-31549.440292
FMO2-MP2: Total energy	-31636.962454

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(B:89:VAL)

Summations of interaction energy for fragment #1(B: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.
-4.566	-0.24	3.736	-2.658	-5.402	-0.014

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / 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	B	91	THR	0	-0.023	-0.016	2.342	-1.193	0.599	0.842	-0.858	-1.776	0.001
4	B	92	ALA	0	0.025	0.011	4.775	0.152	0.174	-0.001	-0.008	-0.013	0.000
5	B	93	THR	0	-0.020	-0.002	8.546	-0.007	-0.007	0.000	0.000	0.000	0.000
6	B	94	PHE	0	-0.022	-0.006	11.261	0.052	0.052	0.000	0.000	0.000	0.000
7	B	95	SER	0	0.040	0.015	14.917	-0.018	-0.018	0.000	0.000	0.000	0.000
8	B	96	ILE	0	-0.034	-0.024	17.943	0.016	0.016	0.000	0.000	0.000	0.000
9	B	97	GLY	0	0.006	0.012	20.635	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	98	SER	0	-0.016	-0.016	24.340	-0.001	-0.001	0.000	0.000	0.000	0.000
11	B	99	THR	0	-0.033	-0.044	23.342	0.001	0.001	0.000	0.000	0.000	0.000
12	B	100	GLY	0	0.017	0.036	20.493	-0.016	-0.016	0.000	0.000	0.000	0.000
13	B	101	LEU	0	-0.025	-0.015	15.506	-0.006	-0.006	0.000	0.000	0.000	0.000
14	B	102	VAL	0	-0.008	-0.011	12.774	0.009	0.009	0.000	0.000	0.000	0.000
15	B	103	VAL	0	0.011	0.011	7.585	-0.034	-0.034	0.000	0.000	0.000	0.000
16	B	104	TYR	0	-0.048	-0.042	8.781	0.060	0.060	0.000	0.000	0.000	0.000
17	B	105	ASP	-1	-0.826	-0.941	3.561	-2.417	-1.691	0.035	-0.317	-0.444	-0.002
18	B	106	TYR	0	0.011	-0.021	5.333	0.192	0.192	0.000	0.000	0.000	0.000
19	B	107	GLN	0	-0.022	0.007	2.377	-2.765	-1.392	2.861	-1.425	-2.809	-0.013
20	B	108	GLN	0	-0.010	-0.006	4.344	0.093	0.252	-0.001	-0.022	-0.136	0.000
21	B	109	LEU	0	-0.013	0.006	6.101	0.059	0.059	0.000	0.000	0.000	0.000
22	B	110	LEU	0	-0.048	-0.023	8.169	0.049	0.049	0.000	0.000	0.000	0.000
23	B	111	ILE	0	0.011	0.005	9.014	-0.071	-0.071	0.000	0.000	0.000	0.000
24	B	112	ALA	0	-0.003	0.013	11.255	0.037	0.037	0.000	0.000	0.000	0.000
25	B	113	TYR	0	0.014	-0.005	12.705	-0.019	-0.019	0.000	0.000	0.000	0.000
26	B	114	LYS	1	0.976	0.995	15.948	0.319	0.319	0.000	0.000	0.000	0.000
27	B	115	PRO	0	0.030	0.026	18.278	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	116	ALA	0	0.075	0.047	21.757	0.008	0.008	0.000	0.000	0.000	0.000
29	B	117	PRO	0	-0.019	0.001	21.599	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	118	GLY	0	0.034	0.020	22.311	0.014	0.014	0.000	0.000	0.000	0.000
31	B	119	THR	0	-0.016	-0.026	22.675	0.009	0.009	0.000	0.000	0.000	0.000
32	B	120	CYS	0	-0.094	-0.054	20.805	0.002	0.002	0.000	0.000	0.000	0.000
33	B	121	CYS	0	-0.084	-0.065	13.119	0.036	0.036	0.000	0.000	0.000	0.000
34	B	122	TYR	0	0.033	0.039	17.403	0.017	0.017	0.000	0.000	0.000	0.000
35	B	123	ILE	0	-0.007	-0.008	12.292	-0.036	-0.036	0.000	0.000	0.000	0.000
36	B	124	MET	0	-0.003	0.001	14.082	0.055	0.055	0.000	0.000	0.000	0.000
37	B	125	LYS	1	0.910	0.968	10.460	0.134	0.134	0.000	0.000	0.000	0.000
38	B	126	ILE	0	-0.050	-0.032	10.300	0.009	0.009	0.000	0.000	0.000	0.000
39	B	127	ALA	0	0.024	0.010	13.419	0.016	0.016	0.000	0.000	0.000	0.000
40	B	128	PRO	0	-0.009	-0.017	12.782	-0.016	-0.016	0.000	0.000	0.000	0.000
41	B	129	GLU	-1	-0.881	-0.934	13.783	0.252	0.252	0.000	0.000	0.000	0.000
42	B	130	SER	0	-0.064	-0.031	16.461	-0.007	-0.007	0.000	0.000	0.000	0.000
43	B	131	ILE	0	0.012	0.008	11.047	-0.040	-0.040	0.000	0.000	0.000	0.000
44	B	132	PRO	0	-0.026	0.003	14.312	0.009	0.009	0.000	0.000	0.000	0.000
45	B	133	SER	0	0.077	0.031	15.701	-0.029	-0.029	0.000	0.000	0.000	0.000
46	B	134	LEU	0	0.115	0.048	15.954	-0.007	-0.007	0.000	0.000	0.000	0.000
47	B	135	GLU	-1	-0.898	-0.947	17.982	-0.080	-0.080	0.000	0.000	0.000	0.000
48	B	136	ALA	0	-0.014	-0.009	19.702	0.001	0.001	0.000	0.000	0.000	0.000
49	B	137	LEU	0	-0.007	0.000	15.102	0.003	0.003	0.000	0.000	0.000	0.000
50	B	138	THR	0	0.013	-0.005	19.144	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	139	ARG	1	0.880	0.945	21.819	0.077	0.077	0.000	0.000	0.000	0.000
52	B	140	LYS	1	0.935	0.985	18.786	0.106	0.106	0.000	0.000	0.000	0.000
53	B	141	VAL	0	0.036	0.006	19.930	0.002	0.002	0.000	0.000	0.000	0.000
54	B	142	HIS	0	0.019	0.023	22.610	0.003	0.003	0.000	0.000	0.000	0.000
55	B	143	ASN	0	-0.057	-0.050	25.823	0.004	0.004	0.000	0.000	0.000	0.000
56	B	144	PHE	0	-0.042	-0.035	23.693	0.006	0.006	0.000	0.000	0.000	0.000
57	B	145	GLN	0	-0.021	0.015	25.818	0.000	0.000	0.000	0.000	0.000	0.000
58	B	146	MET	0	-0.067	-0.016	20.004	-0.010	-0.010	0.000	0.000	0.000	0.000
59	B	147	GLU	-1	-0.870	-0.956	23.634	-0.135	-0.135	0.000	0.000	0.000	0.000
60	B	149	SER	0	-0.015	0.013	25.386	0.004	0.004	0.000	0.000	0.000	0.000
61	B	180	PHE	0	0.000	-0.012	10.380	0.013	0.013	0.000	0.000	0.000	0.000
62	B	181	LEU	0	0.024	0.017	8.125	-0.046	-0.046	0.000	0.000	0.000	0.000
63	B	182	GLY	0	0.084	0.043	4.496	-0.123	-0.072	-0.001	-0.008	-0.041	0.000
64	B	183	MET	0	0.027	0.020	3.880	0.175	0.378	0.001	-0.020	-0.183	0.000
65	B	184	ALA	0	0.034	0.026	5.823	0.225	0.225	0.000	0.000	0.000	0.000
66	B	185	VAL	0	0.035	0.014	7.184	0.173	0.173	0.000	0.000	0.000	0.000
67	B	186	SER	0	0.004	-0.025	8.910	0.156	0.156	0.000	0.000	0.000	0.000
68	B	187	THR	0	-0.055	-0.034	10.254	0.095	0.095	0.000	0.000	0.000	0.000
69	B	188	LEU	0	-0.039	-0.010	11.733	0.072	0.072	0.000	0.000	0.000	0.000
70	B	190	GLY	0	0.044	0.045	14.935	0.031	0.031	0.000	0.000	0.000	0.000
71	B	191	GLU	-1	-0.967	-0.995	16.403	-0.237	-0.237	0.000	0.000	0.000	0.000
72	B	192	VAL	0	-0.054	-0.003	18.251	0.025	0.025	0.000	0.000	0.000	0.000
73	B	193	PRO	0	-0.017	0.001	19.272	-0.014	-0.014	0.000	0.000	0.000	0.000
74	B	194	LEU	0	-0.006	-0.010	14.788	-0.014	-0.014	0.000	0.000	0.000	0.000
75	B	195	TYR	0	0.011	-0.005	18.541	0.019	0.019	0.000	0.000	0.000	0.000
76	B	196	TYR	0	0.018	0.006	14.267	-0.010	-0.010	0.000	0.000	0.000	0.000
77	B	197	ILE	0	-0.029	-0.014	18.490	0.017	0.017	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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