FMO DATABASE

FMODB ID: 82MYY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-500009.562953
FMO2-HF: Nuclear repulsion	468459.879458
FMO2-HF: Total energy	-31549.683495
FMO2-MP2: Total energy	-31637.27444

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.
-7.371	-0.495	3.377	-3.766	-6.486	-0.018

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 : 0.000 / q_NPA : -0.012

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	B	91	THR	0	-0.009	-0.011	2.307	-1.921	0.087	1.074	-1.144	-1.938	0.001
4	B	92	ALA	0	0.011	0.010	4.843	0.314	0.356	-0.001	-0.009	-0.031	0.000
5	B	93	THR	0	-0.006	-0.003	8.562	-0.078	-0.078	0.000	0.000	0.000	0.000
6	B	94	PHE	0	-0.035	-0.012	11.271	0.063	0.063	0.000	0.000	0.000	0.000
7	B	95	SER	0	0.036	0.011	14.857	-0.020	-0.020	0.000	0.000	0.000	0.000
8	B	96	ILE	0	-0.023	-0.016	17.886	0.016	0.016	0.000	0.000	0.000	0.000
9	B	97	GLY	0	0.016	0.013	20.803	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	98	SER	0	-0.018	-0.020	24.028	-0.003	-0.003	0.000	0.000	0.000	0.000
11	B	99	THR	0	-0.030	-0.028	23.598	0.005	0.005	0.000	0.000	0.000	0.000
12	B	100	GLY	0	0.025	0.043	20.660	-0.015	-0.015	0.000	0.000	0.000	0.000
13	B	101	LEU	0	-0.032	-0.018	15.826	-0.001	-0.001	0.000	0.000	0.000	0.000
14	B	102	VAL	0	0.009	-0.006	12.457	0.003	0.003	0.000	0.000	0.000	0.000
15	B	103	VAL	0	-0.003	0.004	7.514	-0.025	-0.025	0.000	0.000	0.000	0.000
16	B	104	TYR	0	-0.050	-0.040	8.468	0.066	0.066	0.000	0.000	0.000	0.000
17	B	105	ASP	-1	-0.797	-0.919	3.253	-4.187	-2.460	0.227	-0.898	-1.056	-0.007
18	B	106	TYR	0	0.012	-0.010	5.045	0.243	0.243	0.000	0.000	0.000	0.000
19	B	107	GLN	0	-0.030	-0.007	2.291	-3.302	-0.833	2.073	-1.622	-2.920	-0.012
20	B	108	GLN	0	-0.016	-0.022	3.868	-0.090	0.139	0.000	-0.029	-0.200	0.000
21	B	109	LEU	0	-0.018	-0.005	5.868	0.110	0.110	0.000	0.000	0.000	0.000
22	B	110	LEU	0	-0.018	-0.002	7.700	0.078	0.078	0.000	0.000	0.000	0.000
23	B	111	ILE	0	0.014	0.008	8.767	-0.071	-0.071	0.000	0.000	0.000	0.000
24	B	112	ALA	0	-0.006	0.004	11.034	0.033	0.033	0.000	0.000	0.000	0.000
25	B	113	TYR	0	0.029	-0.003	12.581	-0.011	-0.011	0.000	0.000	0.000	0.000
26	B	114	LYS	1	0.892	0.955	15.867	0.341	0.341	0.000	0.000	0.000	0.000
27	B	115	PRO	0	0.033	0.019	18.088	0.000	0.000	0.000	0.000	0.000	0.000
28	B	116	ALA	0	0.053	0.037	21.678	0.014	0.014	0.000	0.000	0.000	0.000
29	B	117	PRO	0	-0.001	-0.004	21.039	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	118	GLY	0	0.025	0.020	21.786	0.014	0.014	0.000	0.000	0.000	0.000
31	B	119	THR	0	-0.018	-0.019	22.105	0.010	0.010	0.000	0.000	0.000	0.000
32	B	120	CYS	0	-0.094	-0.056	20.514	0.006	0.006	0.000	0.000	0.000	0.000
33	B	121	CYS	0	-0.055	-0.047	12.412	0.046	0.046	0.000	0.000	0.000	0.000
34	B	122	TYR	0	0.040	0.033	17.164	0.005	0.005	0.000	0.000	0.000	0.000
35	B	123	ILE	0	-0.019	-0.011	12.025	-0.039	-0.039	0.000	0.000	0.000	0.000
36	B	124	MET	0	0.005	0.018	13.436	0.069	0.069	0.000	0.000	0.000	0.000
37	B	125	LYS	1	0.861	0.930	10.233	0.204	0.204	0.000	0.000	0.000	0.000
38	B	126	ILE	0	-0.022	-0.012	10.406	0.019	0.019	0.000	0.000	0.000	0.000
39	B	127	ALA	0	0.025	0.014	13.381	0.003	0.003	0.000	0.000	0.000	0.000
40	B	128	PRO	0	-0.015	-0.008	12.696	-0.018	-0.018	0.000	0.000	0.000	0.000
41	B	129	GLU	-1	-0.885	-0.949	13.899	0.170	0.170	0.000	0.000	0.000	0.000
42	B	130	SER	0	-0.058	-0.034	16.108	-0.003	-0.003	0.000	0.000	0.000	0.000
43	B	131	ILE	0	-0.002	0.010	10.975	-0.044	-0.044	0.000	0.000	0.000	0.000
44	B	132	PRO	0	0.000	0.023	13.890	0.016	0.016	0.000	0.000	0.000	0.000
45	B	133	SER	0	0.078	0.032	15.294	-0.028	-0.028	0.000	0.000	0.000	0.000
46	B	134	LEU	0	0.087	0.037	15.672	-0.008	-0.008	0.000	0.000	0.000	0.000
47	B	135	GLU	-1	-0.786	-0.842	17.683	-0.087	-0.087	0.000	0.000	0.000	0.000
48	B	136	ALA	0	0.000	-0.001	19.535	0.000	0.000	0.000	0.000	0.000	0.000
49	B	137	LEU	0	-0.010	0.000	14.745	0.001	0.001	0.000	0.000	0.000	0.000
50	B	138	THR	0	0.014	-0.008	18.758	-0.006	-0.006	0.000	0.000	0.000	0.000
51	B	139	ARG	1	0.773	0.847	21.498	0.091	0.091	0.000	0.000	0.000	0.000
52	B	140	LYS	1	0.888	0.949	17.619	0.172	0.172	0.000	0.000	0.000	0.000
53	B	141	VAL	0	0.019	-0.010	19.644	0.001	0.001	0.000	0.000	0.000	0.000
54	B	142	HIS	0	0.017	0.008	22.206	0.005	0.005	0.000	0.000	0.000	0.000
55	B	143	ASN	0	-0.032	-0.021	25.478	0.004	0.004	0.000	0.000	0.000	0.000
56	B	144	PHE	0	-0.039	-0.030	22.601	0.005	0.005	0.000	0.000	0.000	0.000
57	B	145	GLN	0	-0.018	0.008	25.242	-0.003	-0.003	0.000	0.000	0.000	0.000
58	B	146	MET	0	-0.035	0.014	19.466	-0.012	-0.012	0.000	0.000	0.000	0.000
59	B	147	GLU	-1	-0.878	-0.957	23.348	-0.151	-0.151	0.000	0.000	0.000	0.000
60	B	149	SER	0	-0.016	0.011	24.810	0.001	0.001	0.000	0.000	0.000	0.000
61	B	180	PHE	0	0.008	-0.006	10.155	0.009	0.009	0.000	0.000	0.000	0.000
62	B	181	LEU	0	0.017	0.019	7.805	-0.079	-0.079	0.000	0.000	0.000	0.000
63	B	182	GLY	0	0.082	0.040	3.885	-0.144	-0.044	0.000	-0.023	-0.077	0.000
64	B	183	MET	0	0.003	-0.007	3.628	0.117	0.418	0.004	-0.041	-0.264	0.000
65	B	184	ALA	0	0.038	0.034	5.301	0.289	0.289	0.000	0.000	0.000	0.000
66	B	185	VAL	0	0.041	0.018	6.552	0.216	0.216	0.000	0.000	0.000	0.000
67	B	186	SER	0	-0.005	-0.015	8.188	0.200	0.200	0.000	0.000	0.000	0.000
68	B	187	THR	0	-0.042	-0.024	9.664	0.124	0.124	0.000	0.000	0.000	0.000
69	B	188	LEU	0	-0.022	0.002	11.081	0.083	0.083	0.000	0.000	0.000	0.000
70	B	190	GLY	0	0.055	0.043	14.268	0.031	0.031	0.000	0.000	0.000	0.000
71	B	191	GLU	-1	-0.964	-1.000	15.953	-0.231	-0.231	0.000	0.000	0.000	0.000
72	B	192	VAL	0	-0.058	-0.004	17.768	0.025	0.025	0.000	0.000	0.000	0.000
73	B	193	PRO	0	0.007	0.014	18.788	-0.018	-0.018	0.000	0.000	0.000	0.000
74	B	194	LEU	0	-0.003	-0.007	14.430	-0.016	-0.016	0.000	0.000	0.000	0.000
75	B	195	TYR	0	-0.019	-0.016	18.085	0.021	0.021	0.000	0.000	0.000	0.000
76	B	196	TYR	0	0.016	0.003	13.167	-0.007	-0.007	0.000	0.000	0.000	0.000
77	B	197	ILE	0	-0.030	-0.015	17.861	0.021	0.021	0.000	0.000	0.000	0.000

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