FMO DATABASE

FMODB ID: YY852

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	OptHSide
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	-533476.879723
FMO2-HF: Nuclear repulsion	500279.212341
FMO2-HF: Total energy	-33197.667382
FMO2-MP2: Total energy	-33290.197162

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.
-3.38	0.188	0.272	-1.622	-2.219	0.008

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 : 0.028 / q_NPA : 0.006

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	-0.005	0.009	3.121	-2.430	1.106	0.273	-1.619	-2.191	0.008
4	C	90	THR	0	0.014	-0.016	5.403	-0.900	-0.868	-0.001	-0.003	-0.028	0.000
5	C	91	THR	0	-0.042	-0.017	9.126	-0.180	-0.180	0.000	0.000	0.000	0.000
6	C	92	ALA	0	-0.004	0.005	9.306	0.064	0.064	0.000	0.000	0.000	0.000
7	C	93	THR	0	-0.015	-0.003	11.312	-0.011	-0.011	0.000	0.000	0.000	0.000
8	C	94	PHE	0	-0.022	-0.010	10.796	-0.032	-0.032	0.000	0.000	0.000	0.000
9	C	95	SER	0	0.036	0.018	16.726	0.022	0.022	0.000	0.000	0.000	0.000
10	C	96	ILE	0	-0.026	-0.015	19.412	-0.026	-0.026	0.000	0.000	0.000	0.000
11	C	97	GLY	0	0.015	0.017	22.438	0.014	0.014	0.000	0.000	0.000	0.000
12	C	98	SER	0	-0.020	-0.018	25.449	-0.002	-0.002	0.000	0.000	0.000	0.000
13	C	99	THR	0	-0.025	-0.027	27.494	0.005	0.005	0.000	0.000	0.000	0.000
14	C	100	GLY	0	0.025	0.035	24.642	0.009	0.009	0.000	0.000	0.000	0.000
15	C	101	LEU	0	-0.035	-0.020	20.695	-0.006	-0.006	0.000	0.000	0.000	0.000
16	C	102	VAL	0	0.017	-0.001	16.335	0.003	0.003	0.000	0.000	0.000	0.000
17	C	103	VAL	0	-0.003	0.006	15.035	0.001	0.001	0.000	0.000	0.000	0.000
18	C	104	TYR	0	-0.050	-0.047	11.553	-0.010	-0.010	0.000	0.000	0.000	0.000
19	C	105	ASP	-1	-0.818	-0.926	12.102	0.381	0.381	0.000	0.000	0.000	0.000
20	C	106	TYR	0	-0.001	-0.024	8.244	-0.115	-0.115	0.000	0.000	0.000	0.000
21	C	107	GLN	0	-0.006	0.018	10.075	0.113	0.113	0.000	0.000	0.000	0.000
22	C	108	GLN	0	-0.016	-0.018	11.771	-0.083	-0.083	0.000	0.000	0.000	0.000
23	C	109	LEU	0	-0.014	-0.002	12.470	-0.059	-0.059	0.000	0.000	0.000	0.000
24	C	110	LEU	0	-0.033	-0.013	14.750	-0.049	-0.049	0.000	0.000	0.000	0.000
25	C	111	ILE	0	0.022	0.018	15.236	0.013	0.013	0.000	0.000	0.000	0.000
26	C	112	ALA	0	-0.014	0.010	17.389	-0.001	-0.001	0.000	0.000	0.000	0.000
27	C	113	TYR	0	0.022	-0.005	19.696	-0.010	-0.010	0.000	0.000	0.000	0.000
28	C	114	LYS	1	0.909	0.954	22.144	-0.014	-0.014	0.000	0.000	0.000	0.000
29	C	115	PRO	0	0.037	0.027	24.887	-0.004	-0.004	0.000	0.000	0.000	0.000
30	C	116	ALA	0	0.062	0.033	27.216	-0.004	-0.004	0.000	0.000	0.000	0.000
31	C	117	PRO	0	-0.019	-0.015	28.294	0.006	0.006	0.000	0.000	0.000	0.000
32	C	118	GLY	0	0.020	0.013	29.648	-0.002	-0.002	0.000	0.000	0.000	0.000
33	C	119	THR	0	0.006	0.002	29.974	-0.002	-0.002	0.000	0.000	0.000	0.000
34	C	120	CYS	0	-0.072	-0.032	29.642	0.006	0.006	0.000	0.000	0.000	0.000
35	C	121	CYS	0	-0.070	-0.048	22.760	-0.017	-0.017	0.000	0.000	0.000	0.000
36	C	122	TYR	0	0.048	0.025	24.826	0.002	0.002	0.000	0.000	0.000	0.000
37	C	123	ILE	0	-0.026	-0.011	21.153	0.001	0.001	0.000	0.000	0.000	0.000
38	C	124	MET	0	0.005	-0.001	20.193	-0.012	-0.012	0.000	0.000	0.000	0.000
39	C	125	LYS	1	0.860	0.926	18.309	-0.043	-0.043	0.000	0.000	0.000	0.000
40	C	126	ILE	0	-0.035	-0.019	13.494	-0.027	-0.027	0.000	0.000	0.000	0.000
41	C	127	ALA	0	0.030	0.017	17.018	0.035	0.035	0.000	0.000	0.000	0.000
42	C	128	PRO	0	0.001	-0.010	13.251	-0.030	-0.030	0.000	0.000	0.000	0.000
43	C	129	GLU	-1	-0.897	-0.952	13.420	-0.206	-0.206	0.000	0.000	0.000	0.000
44	C	130	SER	0	-0.061	-0.034	15.856	-0.046	-0.046	0.000	0.000	0.000	0.000
45	C	131	ILE	0	0.019	0.028	10.156	0.055	0.055	0.000	0.000	0.000	0.000
46	C	132	PRO	0	-0.042	-0.010	13.930	-0.072	-0.072	0.000	0.000	0.000	0.000
47	C	133	SER	0	0.085	0.037	13.834	0.011	0.011	0.000	0.000	0.000	0.000
48	C	134	LEU	0	0.110	0.044	14.718	0.052	0.052	0.000	0.000	0.000	0.000
49	C	135	GLU	-1	-0.857	-0.908	16.419	-0.222	-0.222	0.000	0.000	0.000	0.000
50	C	136	ALA	0	-0.057	-0.030	18.271	0.035	0.035	0.000	0.000	0.000	0.000
51	C	137	LEU	0	-0.016	-0.008	17.258	0.031	0.031	0.000	0.000	0.000	0.000
52	C	138	THR	0	0.029	0.005	19.892	0.032	0.032	0.000	0.000	0.000	0.000
53	C	139	ARG	1	0.898	0.935	21.240	0.259	0.259	0.000	0.000	0.000	0.000
54	C	140	LYS	1	0.919	0.967	20.330	0.188	0.188	0.000	0.000	0.000	0.000
55	C	141	VAL	0	0.015	0.013	22.931	0.012	0.012	0.000	0.000	0.000	0.000
56	C	142	HIS	0	-0.047	-0.023	25.480	0.002	0.002	0.000	0.000	0.000	0.000
57	C	143	ASN	0	-0.027	-0.003	27.884	0.008	0.008	0.000	0.000	0.000	0.000
58	C	144	PHE	0	-0.052	-0.029	24.660	0.005	0.005	0.000	0.000	0.000	0.000
59	C	145	GLN	0	0.023	0.014	29.743	0.004	0.004	0.000	0.000	0.000	0.000
60	C	146	MET	0	-0.072	-0.038	25.442	0.003	0.003	0.000	0.000	0.000	0.000
61	C	147	GLU	-1	-0.861	-0.942	29.360	-0.053	-0.053	0.000	0.000	0.000	0.000
62	C	149	SER	0	0.053	0.025	32.853	0.003	0.003	0.000	0.000	0.000	0.000
63	C	150	LEU	0	-0.053	-0.018	36.014	0.001	0.001	0.000	0.000	0.000	0.000
64	C	151	GLN	0	-0.012	-0.004	33.864	0.000	0.000	0.000	0.000	0.000	0.000
65	C	180	PHE	0	0.023	0.017	21.019	-0.006	-0.006	0.000	0.000	0.000	0.000
66	C	181	LEU	0	-0.021	-0.013	20.796	0.014	0.014	0.000	0.000	0.000	0.000
67	C	182	GLY	0	0.081	0.042	17.529	0.006	0.006	0.000	0.000	0.000	0.000
68	C	183	MET	0	0.036	0.017	17.977	-0.027	-0.027	0.000	0.000	0.000	0.000
69	C	184	ALA	0	0.033	0.019	15.902	-0.022	-0.022	0.000	0.000	0.000	0.000
70	C	185	VAL	0	0.044	0.013	17.208	-0.027	-0.027	0.000	0.000	0.000	0.000
71	C	186	SER	0	-0.016	-0.021	19.575	-0.025	-0.025	0.000	0.000	0.000	0.000
72	C	187	THR	0	-0.050	-0.025	20.894	-0.010	-0.010	0.000	0.000	0.000	0.000
73	C	188	LEU	0	-0.018	0.002	20.180	-0.011	-0.011	0.000	0.000	0.000	0.000
74	C	190	GLY	0	0.035	0.043	25.073	-0.004	-0.004	0.000	0.000	0.000	0.000
75	C	191	GLU	-1	-0.965	-0.986	27.386	0.035	0.035	0.000	0.000	0.000	0.000
76	C	192	VAL	0	-0.044	-0.008	28.066	-0.006	-0.006	0.000	0.000	0.000	0.000
77	C	193	PRO	0	-0.027	-0.010	29.677	0.004	0.004	0.000	0.000	0.000	0.000
78	C	194	LEU	0	0.002	0.002	25.727	-0.002	-0.002	0.000	0.000	0.000	0.000
79	C	195	TYR	0	0.007	0.011	27.736	-0.001	-0.001	0.000	0.000	0.000	0.000
80	C	196	TYR	0	0.033	0.009	23.855	-0.002	-0.002	0.000	0.000	0.000	0.000
81	C	197	ILE	0	-0.014	-0.003	24.507	-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)