FMO DATABASE

FMODB ID: 2N72R

Calculation Name: 1YD8-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YD8

Chain ID: G

ChEMBL ID:

UniProt ID: Q9NZ52

Base Structure: X-ray

Registration Date: 2023-09-20

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	93
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-650727.257232
FMO2-HF: Nuclear repulsion	612766.027031
FMO2-HF: Total energy	-37961.230201
FMO2-MP2: Total energy	-38071.333842

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(G:-1:GLY)

Summations of interaction energy for fragment #1(G:-1:GLY)

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.
-8.006	-7.856	5.889	-2.815	-3.226	0.014

Interaction energy analysis for fragmet #1(G:-1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.005

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	G	209	GLN	0	0.068	0.020	3.797	0.182	1.190	-0.009	-0.431	-0.569	0.001
4	G	210	LYS	1	0.927	0.957	1.944	-4.671	-5.864	5.896	-2.378	-2.325	0.013
5	G	211	VAL	0	0.079	0.045	3.569	-1.709	-1.427	0.003	-0.002	-0.284	0.000
6	G	212	THR	0	0.054	0.028	4.862	0.023	0.076	-0.001	-0.004	-0.048	0.000
7	G	213	LYS	1	0.946	0.969	6.984	-1.298	-1.298	0.000	0.000	0.000	0.000
8	G	214	ARG	1	0.981	1.007	7.088	-0.217	-0.217	0.000	0.000	0.000	0.000
9	G	215	LEU	0	0.090	0.052	8.619	-0.002	-0.002	0.000	0.000	0.000	0.000
10	G	216	HIS	0	-0.036	-0.034	10.629	0.034	0.034	0.000	0.000	0.000	0.000
11	G	217	THR	0	-0.060	-0.032	11.849	-0.003	-0.003	0.000	0.000	0.000	0.000
12	G	218	LEU	0	0.019	-0.003	12.049	-0.018	-0.018	0.000	0.000	0.000	0.000
13	G	219	GLU	-1	-0.898	-0.941	14.949	-0.040	-0.040	0.000	0.000	0.000	0.000
14	G	220	GLU	-1	-0.836	-0.882	16.673	0.177	0.177	0.000	0.000	0.000	0.000
15	G	221	VAL	0	-0.057	-0.033	17.651	-0.005	-0.005	0.000	0.000	0.000	0.000
16	G	222	ASN	0	0.023	0.000	19.188	-0.007	-0.007	0.000	0.000	0.000	0.000
17	G	223	ASN	0	0.000	-0.015	20.051	-0.005	-0.005	0.000	0.000	0.000	0.000
18	G	224	ASN	0	0.048	0.037	22.599	0.003	0.003	0.000	0.000	0.000	0.000
19	G	225	VAL	0	0.007	0.006	23.542	-0.005	-0.005	0.000	0.000	0.000	0.000
20	G	226	ARG	1	0.893	0.955	23.349	0.018	0.018	0.000	0.000	0.000	0.000
21	G	227	LEU	0	0.062	0.026	26.858	-0.001	-0.001	0.000	0.000	0.000	0.000
22	G	228	LEU	0	0.014	0.001	28.552	0.000	0.000	0.000	0.000	0.000	0.000
23	G	229	SER	0	-0.050	-0.041	29.332	-0.003	-0.003	0.000	0.000	0.000	0.000
24	G	230	GLU	-1	-0.941	-0.961	31.152	0.009	0.009	0.000	0.000	0.000	0.000
25	G	231	MET	0	0.007	-0.006	33.054	0.000	0.000	0.000	0.000	0.000	0.000
26	G	232	LEU	0	-0.040	-0.021	33.129	0.000	0.000	0.000	0.000	0.000	0.000
27	G	233	LEU	0	-0.010	0.002	35.026	-0.002	-0.002	0.000	0.000	0.000	0.000
28	G	234	HIS	0	-0.114	-0.046	36.340	-0.003	-0.003	0.000	0.000	0.000	0.000
29	G	235	TYR	0	-0.016	-0.011	39.114	0.003	0.003	0.000	0.000	0.000	0.000
30	G	236	SER	0	-0.028	-0.022	40.752	-0.002	-0.002	0.000	0.000	0.000	0.000
31	G	237	GLN	0	0.011	0.004	44.363	0.003	0.003	0.000	0.000	0.000	0.000
32	G	238	GLU	-1	-0.904	-0.922	46.517	0.012	0.012	0.000	0.000	0.000	0.000
33	G	239	ASP	-1	-0.985	-0.996	46.238	0.012	0.012	0.000	0.000	0.000	0.000
34	G	240	SER	0	0.072	0.023	41.701	0.001	0.001	0.000	0.000	0.000	0.000
35	G	241	SER	0	-0.070	-0.068	42.297	0.001	0.001	0.000	0.000	0.000	0.000
36	G	242	ASP	-1	-0.907	-0.970	42.792	0.029	0.029	0.000	0.000	0.000	0.000
37	G	243	GLY	0	0.001	-0.019	40.016	0.002	0.002	0.000	0.000	0.000	0.000
38	G	244	ASP	-1	-0.837	-0.877	38.212	0.028	0.028	0.000	0.000	0.000	0.000
39	G	245	ARG	1	0.882	0.924	37.317	-0.021	-0.021	0.000	0.000	0.000	0.000
40	G	246	GLU	-1	-1.009	-0.991	36.909	0.052	0.052	0.000	0.000	0.000	0.000
41	G	247	LEU	0	0.130	0.075	31.939	0.003	0.003	0.000	0.000	0.000	0.000
42	G	248	MET	0	-0.018	0.020	33.162	0.003	0.003	0.000	0.000	0.000	0.000
43	G	249	LYS	1	0.906	0.948	32.683	-0.030	-0.030	0.000	0.000	0.000	0.000
44	G	250	GLU	-1	-0.922	-0.952	31.009	0.076	0.076	0.000	0.000	0.000	0.000
45	G	251	LEU	0	-0.052	-0.041	27.400	0.007	0.007	0.000	0.000	0.000	0.000
46	G	252	PHE	0	-0.042	-0.023	28.278	0.003	0.003	0.000	0.000	0.000	0.000
47	G	253	ASP	-1	-0.883	-0.927	29.067	0.081	0.081	0.000	0.000	0.000	0.000
48	G	254	GLN	0	-0.045	-0.038	24.190	0.007	0.007	0.000	0.000	0.000	0.000
49	G	255	CYS	0	-0.047	-0.029	24.412	0.007	0.007	0.000	0.000	0.000	0.000
50	G	256	GLU	-1	-0.746	-0.884	24.644	0.047	0.047	0.000	0.000	0.000	0.000
51	G	257	ASN	0	-0.031	-0.008	23.963	0.001	0.001	0.000	0.000	0.000	0.000
52	G	258	LYS	1	0.832	0.920	18.840	-0.115	-0.115	0.000	0.000	0.000	0.000
53	G	259	ARG	1	0.805	0.912	19.959	-0.043	-0.043	0.000	0.000	0.000	0.000
54	G	260	ARG	1	0.912	0.941	21.378	-0.099	-0.099	0.000	0.000	0.000	0.000
55	G	261	THR	0	-0.047	-0.029	16.211	0.003	0.003	0.000	0.000	0.000	0.000
56	G	262	LEU	0	-0.034	-0.018	15.542	0.016	0.016	0.000	0.000	0.000	0.000
57	G	263	PHE	0	0.027	0.003	17.369	-0.016	-0.016	0.000	0.000	0.000	0.000
58	G	264	LYS	1	0.949	0.998	16.356	-0.242	-0.242	0.000	0.000	0.000	0.000
59	G	265	LEU	0	-0.013	-0.013	11.800	0.024	0.024	0.000	0.000	0.000	0.000
60	G	266	ALA	0	0.005	0.029	13.484	-0.025	-0.025	0.000	0.000	0.000	0.000
61	G	267	SER	0	-0.108	-0.070	15.741	-0.012	-0.012	0.000	0.000	0.000	0.000
62	G	268	GLU	-1	-0.983	-0.989	12.679	0.305	0.305	0.000	0.000	0.000	0.000
63	G	269	THR	0	-0.038	-0.043	11.059	-0.008	-0.008	0.000	0.000	0.000	0.000
64	G	270	GLU	-1	-0.958	-0.966	11.560	-0.018	-0.018	0.000	0.000	0.000	0.000
65	G	271	ASP	-1	-0.962	-0.991	13.752	-0.148	-0.148	0.000	0.000	0.000	0.000
66	G	272	ASN	0	-0.041	-0.011	8.862	-0.082	-0.082	0.000	0.000	0.000	0.000
67	G	273	ASP	-1	-0.847	-0.925	13.291	-0.264	-0.264	0.000	0.000	0.000	0.000
68	G	274	ASN	0	-0.048	-0.047	11.848	-0.078	-0.078	0.000	0.000	0.000	0.000
69	G	275	SER	0	0.053	0.052	10.005	0.062	0.062	0.000	0.000	0.000	0.000
70	G	276	LEU	0	0.024	0.028	11.715	0.065	0.065	0.000	0.000	0.000	0.000
71	G	277	GLY	0	0.040	0.029	15.109	0.031	0.031	0.000	0.000	0.000	0.000
72	G	278	ASP	-1	-0.913	-0.979	12.691	-0.262	-0.262	0.000	0.000	0.000	0.000
73	G	279	ILE	0	-0.078	-0.039	11.905	0.042	0.042	0.000	0.000	0.000	0.000
74	G	280	LEU	0	-0.002	-0.026	15.774	0.026	0.026	0.000	0.000	0.000	0.000
75	G	281	GLN	0	0.002	0.020	18.691	0.015	0.015	0.000	0.000	0.000	0.000
76	G	282	ALA	0	0.036	0.023	17.950	0.013	0.013	0.000	0.000	0.000	0.000
77	G	283	SER	0	-0.045	-0.030	19.573	0.012	0.012	0.000	0.000	0.000	0.000
78	G	284	ASP	-1	-0.814	-0.888	21.436	-0.020	-0.020	0.000	0.000	0.000	0.000
79	G	285	ASN	0	-0.003	-0.009	22.650	0.001	0.001	0.000	0.000	0.000	0.000
80	G	286	LEU	0	0.010	0.007	21.235	0.005	0.005	0.000	0.000	0.000	0.000
81	G	287	SER	0	-0.024	-0.017	24.909	0.006	0.006	0.000	0.000	0.000	0.000
82	G	288	ARG	1	0.817	0.892	27.372	0.025	0.025	0.000	0.000	0.000	0.000
83	G	289	VAL	0	0.029	0.004	27.936	0.000	0.000	0.000	0.000	0.000	0.000
84	G	290	ILE	0	-0.032	0.008	26.808	0.002	0.002	0.000	0.000	0.000	0.000
85	G	291	ASN	0	-0.023	-0.030	30.622	0.005	0.005	0.000	0.000	0.000	0.000
86	G	292	SER	0	-0.030	-0.001	32.698	0.000	0.000	0.000	0.000	0.000	0.000
87	G	293	TYR	0	0.063	0.013	33.146	0.000	0.000	0.000	0.000	0.000	0.000
88	G	294	LYS	1	0.867	0.952	32.634	-0.032	-0.032	0.000	0.000	0.000	0.000
89	G	295	THR	0	-0.003	-0.003	36.837	-0.001	-0.001	0.000	0.000	0.000	0.000
90	G	296	ILE	0	0.017	0.008	36.498	0.000	0.000	0.000	0.000	0.000	0.000
91	G	297	ILE	0	-0.042	-0.016	37.573	0.001	0.001	0.000	0.000	0.000	0.000
92	G	298	GLU	-1	-0.978	-0.986	40.348	0.020	0.020	0.000	0.000	0.000	0.000
93	G	299	GLY	0	-0.113	-0.044	42.533	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(G:-1:GLY)