FMO DATABASE

FMODB ID: VRL31

Calculation Name: 2YAD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: C

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-536639.19842
FMO2-HF: Nuclear repulsion	503441.424641
FMO2-HF: Total energy	-33197.77378
FMO2-MP2: Total energy	-33290.355616

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(C:87:HIS)

Summations of interaction energy for fragment #1(C:87:HIS)

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.
-2.419	1.098	0.412	-1.634	-2.296	0.006

Interaction energy analysis for fragmet #1(C:87:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.014

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	C	89	VAL	0	-0.012	0.002	2.951	-1.736	1.739	0.413	-1.631	-2.258	0.006
4	C	90	THR	0	-0.006	-0.014	5.340	-0.534	-0.492	-0.001	-0.003	-0.038	0.000
5	C	91	THR	0	-0.010	-0.012	9.002	-0.198	-0.198	0.000	0.000	0.000	0.000
6	C	92	ALA	0	-0.017	0.000	9.309	0.036	0.036	0.000	0.000	0.000	0.000
7	C	93	THR	0	-0.005	0.002	11.257	0.003	0.003	0.000	0.000	0.000	0.000
8	C	94	PHE	0	-0.035	-0.015	10.959	-0.017	-0.017	0.000	0.000	0.000	0.000
9	C	95	SER	0	0.035	0.013	16.827	0.033	0.033	0.000	0.000	0.000	0.000
10	C	96	ILE	0	-0.023	-0.014	19.932	-0.032	-0.032	0.000	0.000	0.000	0.000
11	C	97	GLY	0	0.025	0.014	22.821	0.018	0.018	0.000	0.000	0.000	0.000
12	C	98	SER	0	-0.011	-0.013	25.641	-0.002	-0.002	0.000	0.000	0.000	0.000
13	C	99	THR	0	-0.053	-0.039	27.567	0.011	0.011	0.000	0.000	0.000	0.000
14	C	100	GLY	0	0.032	0.047	25.045	0.008	0.008	0.000	0.000	0.000	0.000
15	C	101	LEU	0	-0.033	-0.020	20.933	-0.010	-0.010	0.000	0.000	0.000	0.000
16	C	102	VAL	0	0.019	-0.005	16.500	-0.005	-0.005	0.000	0.000	0.000	0.000
17	C	103	VAL	0	-0.004	0.004	14.902	0.006	0.006	0.000	0.000	0.000	0.000
18	C	104	TYR	0	-0.058	-0.040	11.835	0.005	0.005	0.000	0.000	0.000	0.000
19	C	105	ASP	-1	-0.794	-0.925	12.540	-0.004	-0.004	0.000	0.000	0.000	0.000
20	C	106	TYR	0	0.005	-0.011	8.393	-0.117	-0.117	0.000	0.000	0.000	0.000
21	C	107	GLN	0	-0.008	0.017	10.552	0.050	0.050	0.000	0.000	0.000	0.000
22	C	108	GLN	0	-0.006	-0.017	12.379	-0.038	-0.038	0.000	0.000	0.000	0.000
23	C	109	LEU	0	-0.019	-0.002	12.603	-0.014	-0.014	0.000	0.000	0.000	0.000
24	C	110	LEU	0	-0.011	0.001	14.982	0.005	0.005	0.000	0.000	0.000	0.000
25	C	111	ILE	0	0.007	0.006	15.261	-0.033	-0.033	0.000	0.000	0.000	0.000
26	C	112	ALA	0	-0.005	0.009	17.436	0.022	0.022	0.000	0.000	0.000	0.000
27	C	113	TYR	0	-0.043	-0.045	19.660	-0.023	-0.023	0.000	0.000	0.000	0.000
28	C	114	LYS	1	0.905	0.961	22.413	0.077	0.077	0.000	0.000	0.000	0.000
29	C	115	PRO	0	0.040	0.029	25.192	0.000	0.000	0.000	0.000	0.000	0.000
30	C	116	ALA	0	0.045	0.032	27.552	0.002	0.002	0.000	0.000	0.000	0.000
31	C	117	PRO	0	0.011	0.000	28.204	0.002	0.002	0.000	0.000	0.000	0.000
32	C	118	GLY	0	0.005	0.005	29.582	-0.001	-0.001	0.000	0.000	0.000	0.000
33	C	119	THR	0	-0.005	-0.009	29.712	-0.003	-0.003	0.000	0.000	0.000	0.000
34	C	120	CYS	0	-0.054	-0.020	29.511	0.009	0.009	0.000	0.000	0.000	0.000
35	C	121	CYS	0	-0.075	-0.054	22.307	-0.015	-0.015	0.000	0.000	0.000	0.000
36	C	122	TYR	0	0.033	0.023	25.101	0.004	0.004	0.000	0.000	0.000	0.000
37	C	123	ILE	0	-0.034	-0.024	21.170	-0.014	-0.014	0.000	0.000	0.000	0.000
38	C	124	MET	0	0.011	0.009	20.302	-0.003	-0.003	0.000	0.000	0.000	0.000
39	C	125	LYS	1	0.856	0.917	18.248	0.227	0.227	0.000	0.000	0.000	0.000
40	C	126	ILE	0	-0.054	-0.028	13.775	-0.017	-0.017	0.000	0.000	0.000	0.000
41	C	127	ALA	0	0.046	0.029	17.190	0.025	0.025	0.000	0.000	0.000	0.000
42	C	128	PRO	0	0.001	-0.015	12.537	-0.060	-0.060	0.000	0.000	0.000	0.000
43	C	129	GLU	-1	-0.885	-0.945	12.790	-0.629	-0.629	0.000	0.000	0.000	0.000
44	C	130	SER	0	-0.057	-0.034	15.299	-0.001	-0.001	0.000	0.000	0.000	0.000
45	C	131	ILE	0	-0.001	0.012	10.111	0.084	0.084	0.000	0.000	0.000	0.000
46	C	132	PRO	0	-0.033	0.006	13.614	-0.071	-0.071	0.000	0.000	0.000	0.000
47	C	133	SER	0	0.081	0.038	13.922	-0.027	-0.027	0.000	0.000	0.000	0.000
48	C	134	LEU	0	0.092	0.038	14.841	0.070	0.070	0.000	0.000	0.000	0.000
49	C	135	GLU	-1	-0.802	-0.863	16.661	-0.324	-0.324	0.000	0.000	0.000	0.000
50	C	136	ALA	0	-0.030	-0.013	18.107	0.051	0.051	0.000	0.000	0.000	0.000
51	C	137	LEU	0	-0.033	-0.012	17.313	0.041	0.041	0.000	0.000	0.000	0.000
52	C	138	THR	0	0.018	0.000	20.013	0.048	0.048	0.000	0.000	0.000	0.000
53	C	139	ARG	1	0.845	0.888	21.413	0.396	0.396	0.000	0.000	0.000	0.000
54	C	140	LYS	1	0.914	0.965	19.982	0.416	0.416	0.000	0.000	0.000	0.000
55	C	141	VAL	0	0.025	0.009	23.009	0.019	0.019	0.000	0.000	0.000	0.000
56	C	142	HIS	0	-0.032	-0.025	25.587	0.012	0.012	0.000	0.000	0.000	0.000
57	C	143	ASN	0	-0.019	0.005	27.853	0.019	0.019	0.000	0.000	0.000	0.000
58	C	144	PHE	0	-0.069	-0.029	24.956	0.005	0.005	0.000	0.000	0.000	0.000
59	C	145	GLN	0	0.024	0.003	29.983	0.010	0.010	0.000	0.000	0.000	0.000
60	C	146	MET	0	-0.063	-0.020	25.243	0.002	0.002	0.000	0.000	0.000	0.000
61	C	147	GLU	-1	-0.801	-0.915	29.091	-0.143	-0.143	0.000	0.000	0.000	0.000
62	C	149	SER	0	0.039	0.024	32.825	0.007	0.007	0.000	0.000	0.000	0.000
63	C	150	LEU	0	-0.045	-0.014	35.855	0.005	0.005	0.000	0.000	0.000	0.000
64	C	151	GLN	0	-0.019	-0.010	33.667	-0.001	-0.001	0.000	0.000	0.000	0.000
65	C	180	PHE	0	0.027	0.019	20.757	0.000	0.000	0.000	0.000	0.000	0.000
66	C	181	LEU	0	-0.011	-0.006	20.758	-0.006	-0.006	0.000	0.000	0.000	0.000
67	C	182	GLY	0	0.070	0.037	17.094	0.020	0.020	0.000	0.000	0.000	0.000
68	C	183	MET	0	0.019	0.010	17.390	-0.015	-0.015	0.000	0.000	0.000	0.000
69	C	184	ALA	0	0.037	0.026	15.387	-0.009	-0.009	0.000	0.000	0.000	0.000
70	C	185	VAL	0	0.040	0.016	16.729	-0.019	-0.019	0.000	0.000	0.000	0.000
71	C	186	SER	0	-0.014	-0.017	19.083	-0.011	-0.011	0.000	0.000	0.000	0.000
72	C	187	THR	0	-0.049	-0.030	20.289	0.006	0.006	0.000	0.000	0.000	0.000
73	C	188	LEU	0	-0.020	0.005	20.156	-0.002	-0.002	0.000	0.000	0.000	0.000
74	C	190	GLY	0	0.047	0.037	24.647	0.000	0.000	0.000	0.000	0.000	0.000
75	C	191	GLU	-1	-0.973	-1.001	27.089	-0.017	-0.017	0.000	0.000	0.000	0.000
76	C	192	VAL	0	-0.042	0.001	28.089	-0.002	-0.002	0.000	0.000	0.000	0.000
77	C	193	PRO	0	-0.012	-0.004	29.804	-0.001	-0.001	0.000	0.000	0.000	0.000
78	C	194	LEU	0	0.002	0.005	25.765	-0.007	-0.007	0.000	0.000	0.000	0.000
79	C	195	TYR	0	0.010	0.002	27.554	0.004	0.004	0.000	0.000	0.000	0.000
80	C	196	TYR	0	0.027	0.012	23.747	-0.012	-0.012	0.000	0.000	0.000	0.000
81	C	197	ILE	0	-0.014	0.001	24.238	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:87:HIS)