FMO DATABASE

FMODB ID: GNLG1

Calculation Name: 2YAD-C-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-539967.097639
FMO2-HF: Nuclear repulsion	506447.531221
FMO2-HF: Total energy	-33519.566418
FMO2-MP2: Total energy	-33613.049028

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:86:ACE )

Summations of interaction energy for fragment #1(C:86:ACE )

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.
1.118	1.931	-0.006	-0.36	-0.448	-0.001

Interaction energy analysis for fragmet #1(C:86:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.008

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	88	LEU	0	-0.002	0.014	3.819	1.051	1.864	-0.006	-0.360	-0.448	-0.001
4	C	89	VAL	0	0.002	0.012	6.848	0.087	0.087	0.000	0.000	0.000	0.000
5	C	90	THR	0	0.019	-0.002	10.498	0.103	0.103	0.000	0.000	0.000	0.000
6	C	91	THR	0	-0.037	-0.013	13.756	0.030	0.030	0.000	0.000	0.000	0.000
7	C	92	ALA	0	0.008	0.007	16.061	-0.034	-0.034	0.000	0.000	0.000	0.000
8	C	93	THR	0	-0.018	-0.002	18.415	0.025	0.025	0.000	0.000	0.000	0.000
9	C	94	PHE	0	-0.017	-0.010	18.996	-0.007	-0.007	0.000	0.000	0.000	0.000
10	C	95	SER	0	0.026	0.013	24.530	0.008	0.008	0.000	0.000	0.000	0.000
11	C	96	ILE	0	-0.020	-0.012	27.890	-0.005	-0.005	0.000	0.000	0.000	0.000
12	C	97	GLY	0	0.016	0.019	30.600	0.006	0.006	0.000	0.000	0.000	0.000
13	C	98	SER	0	-0.028	-0.023	33.440	-0.003	-0.003	0.000	0.000	0.000	0.000
14	C	99	THR	0	-0.022	-0.021	34.890	0.001	0.001	0.000	0.000	0.000	0.000
15	C	100	GLY	0	0.032	0.040	32.553	0.000	0.000	0.000	0.000	0.000	0.000
16	C	101	LEU	0	-0.033	-0.024	27.278	-0.006	-0.006	0.000	0.000	0.000	0.000
17	C	102	VAL	0	0.012	0.000	24.320	0.005	0.005	0.000	0.000	0.000	0.000
18	C	103	VAL	0	-0.005	0.006	21.359	-0.010	-0.010	0.000	0.000	0.000	0.000
19	C	104	TYR	0	-0.042	-0.046	19.207	0.013	0.013	0.000	0.000	0.000	0.000
20	C	105	ASP	-1	-0.844	-0.947	18.523	-0.214	-0.214	0.000	0.000	0.000	0.000
21	C	106	TYR	0	-0.004	-0.021	14.586	0.008	0.008	0.000	0.000	0.000	0.000
22	C	107	GLN	0	-0.033	-0.005	13.498	-0.040	-0.040	0.000	0.000	0.000	0.000
23	C	108	GLN	0	-0.048	-0.033	16.113	0.025	0.025	0.000	0.000	0.000	0.000
24	C	109	LEU	0	-0.037	-0.001	17.611	0.016	0.016	0.000	0.000	0.000	0.000
25	C	110	LEU	0	-0.001	-0.006	20.261	0.024	0.024	0.000	0.000	0.000	0.000
26	C	111	ILE	0	-0.001	0.003	22.087	-0.018	-0.018	0.000	0.000	0.000	0.000
27	C	112	ALA	0	-0.013	0.011	24.565	0.014	0.014	0.000	0.000	0.000	0.000
28	C	113	TYR	0	0.012	-0.011	26.974	-0.008	-0.008	0.000	0.000	0.000	0.000
29	C	114	LYS	1	0.931	0.962	29.624	0.081	0.081	0.000	0.000	0.000	0.000
30	C	115	PRO	0	0.032	0.028	32.161	-0.003	-0.003	0.000	0.000	0.000	0.000
31	C	116	ALA	0	0.066	0.030	34.906	0.000	0.000	0.000	0.000	0.000	0.000
32	C	117	PRO	0	-0.037	-0.025	35.086	0.000	0.000	0.000	0.000	0.000	0.000
33	C	118	GLY	0	0.024	0.014	36.300	0.003	0.003	0.000	0.000	0.000	0.000
34	C	119	THR	0	0.006	0.003	37.031	0.001	0.001	0.000	0.000	0.000	0.000
35	C	148	CYS	0	-0.065	-0.033	36.348	0.003	0.003	0.000	0.000	0.000	0.000
36	C	189	CYS	0	-0.068	-0.053	28.536	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	122	TYR	0	0.052	0.032	32.088	0.005	0.005	0.000	0.000	0.000	0.000
38	C	123	ILE	0	-0.037	-0.021	27.296	-0.009	-0.009	0.000	0.000	0.000	0.000
39	C	124	MET	0	0.011	0.011	27.457	0.005	0.005	0.000	0.000	0.000	0.000
40	C	125	LYS	1	0.940	0.976	24.944	0.091	0.091	0.000	0.000	0.000	0.000
41	C	126	ILE	0	-0.040	-0.025	20.382	0.001	0.001	0.000	0.000	0.000	0.000
42	C	127	ALA	0	0.025	0.017	22.680	-0.001	-0.001	0.000	0.000	0.000	0.000
43	C	128	PRO	0	-0.002	-0.012	17.780	-0.015	-0.015	0.000	0.000	0.000	0.000
44	C	129	GLU	-1	-0.891	-0.951	19.060	-0.157	-0.157	0.000	0.000	0.000	0.000
45	C	130	SER	0	-0.064	-0.029	21.390	0.004	0.004	0.000	0.000	0.000	0.000
46	C	131	ILE	0	0.026	0.025	17.235	0.009	0.009	0.000	0.000	0.000	0.000
47	C	132	PRO	0	-0.047	-0.014	21.300	-0.001	-0.001	0.000	0.000	0.000	0.000
48	C	133	SER	0	0.079	0.039	22.189	-0.009	-0.009	0.000	0.000	0.000	0.000
49	C	134	LEU	0	0.110	0.048	23.192	0.012	0.012	0.000	0.000	0.000	0.000
50	C	135	GLU	-1	-0.913	-0.951	24.900	-0.112	-0.112	0.000	0.000	0.000	0.000
51	C	136	ALA	0	-0.081	-0.044	26.520	0.012	0.012	0.000	0.000	0.000	0.000
52	C	137	LEU	0	-0.009	-0.007	25.496	0.011	0.011	0.000	0.000	0.000	0.000
53	C	138	THR	0	0.031	0.008	28.200	0.010	0.010	0.000	0.000	0.000	0.000
54	C	139	ARG	1	0.963	0.982	29.677	0.115	0.115	0.000	0.000	0.000	0.000
55	C	140	LYS	1	0.918	0.965	28.134	0.122	0.122	0.000	0.000	0.000	0.000
56	C	141	VAL	0	0.026	0.019	31.106	0.006	0.006	0.000	0.000	0.000	0.000
57	C	142	HIS	0	-0.053	-0.025	33.698	0.003	0.003	0.000	0.000	0.000	0.000
58	C	143	ASN	0	-0.027	-0.008	36.182	0.006	0.006	0.000	0.000	0.000	0.000
59	C	144	PHE	0	-0.042	-0.020	32.662	0.004	0.004	0.000	0.000	0.000	0.000
60	C	145	GLN	0	0.011	0.008	37.764	0.002	0.002	0.000	0.000	0.000	0.000
61	C	146	MET	0	-0.064	-0.034	32.977	-0.001	-0.001	0.000	0.000	0.000	0.000
62	C	147	GLU	-1	-0.870	-0.946	37.165	-0.067	-0.067	0.000	0.000	0.000	0.000
63	C	149	SER	0	0.041	0.020	40.220	0.002	0.002	0.000	0.000	0.000	0.000
64	C	150	LEU	0	-0.050	-0.018	43.185	0.003	0.003	0.000	0.000	0.000	0.000
65	C	151	GLN	0	-0.041	-0.042	40.562	0.000	0.000	0.000	0.000	0.000	0.000
66	C	152	NME	0	0.026	0.029	43.510	-0.001	-0.001	0.000	0.000	0.000	0.000
67	C	179	ACE	0	0.006	-0.007	27.242	0.000	0.000	0.000	0.000	0.000	0.000
68	C	180	PHE	0	-0.028	-0.017	23.291	0.004	0.004	0.000	0.000	0.000	0.000
69	C	181	LEU	0	0.040	0.034	24.975	-0.007	-0.007	0.000	0.000	0.000	0.000
70	C	182	GLY	0	0.083	0.043	21.613	0.005	0.005	0.000	0.000	0.000	0.000
71	C	183	MET	0	0.031	0.020	21.114	0.005	0.005	0.000	0.000	0.000	0.000
72	C	184	ALA	0	0.037	0.021	20.721	0.007	0.007	0.000	0.000	0.000	0.000
73	C	185	VAL	0	0.046	0.015	22.654	0.005	0.005	0.000	0.000	0.000	0.000
74	C	186	SER	0	-0.019	-0.029	25.021	0.010	0.010	0.000	0.000	0.000	0.000
75	C	187	THR	0	-0.050	-0.023	25.285	0.008	0.008	0.000	0.000	0.000	0.000
76	C	188	LEU	0	-0.040	-0.010	26.750	0.005	0.005	0.000	0.000	0.000	0.000
77	C	190	GLY	0	0.038	0.046	30.623	0.005	0.005	0.000	0.000	0.000	0.000
78	C	191	GLU	-1	-0.965	-0.990	32.313	-0.047	-0.047	0.000	0.000	0.000	0.000
79	C	192	VAL	0	-0.057	-0.007	33.976	0.002	0.002	0.000	0.000	0.000	0.000
80	C	193	PRO	0	-0.038	-0.016	35.382	-0.001	-0.001	0.000	0.000	0.000	0.000
81	C	194	LEU	0	-0.002	-0.002	31.355	-0.005	-0.005	0.000	0.000	0.000	0.000
82	C	195	TYR	0	0.002	0.011	34.288	0.005	0.005	0.000	0.000	0.000	0.000
83	C	196	TYR	0	-0.009	-0.013	29.249	-0.008	-0.008	0.000	0.000	0.000	0.000
84	C	197	ILE	-1	-0.914	-0.954	31.042	-0.079	-0.079	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:86:ACE )