FMO DATABASE

FMODB ID: ZV56N

Calculation Name: 1YN3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YN3

Chain ID: A

ChEMBL ID:

UniProt ID: Q99QS1

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	98
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-702218.62675
FMO2-HF: Nuclear repulsion	665074.294445
FMO2-HF: Total energy	-37144.332305
FMO2-MP2: Total energy	-37255.598458

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(A:157:GLY)

Summations of interaction energy for fragment #1(A:157: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.
-4.336	-0.432	4.871	-4.178	-4.595	-0.025

Interaction energy analysis for fragmet #1(A:157:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.004

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

Sort

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	A	159	THR	0	-0.009	-0.003	3.785	-0.530	0.728	-0.016	-0.638	-0.604	0.002
4	A	160	VAL	0	-0.019	0.004	6.287	0.043	0.043	0.000	0.000	0.000	0.000
5	A	161	PRO	0	0.041	0.032	9.225	0.081	0.081	0.000	0.000	0.000	0.000
6	A	162	TYR	0	-0.045	-0.059	11.925	-0.024	-0.024	0.000	0.000	0.000	0.000
7	A	163	THR	0	0.022	0.003	14.855	0.025	0.025	0.000	0.000	0.000	0.000
8	A	164	ILE	0	0.022	0.016	17.549	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	165	THR	0	-0.067	-0.034	20.505	0.013	0.013	0.000	0.000	0.000	0.000
10	A	166	VAL	0	0.035	0.014	24.197	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	167	ASN	0	0.017	-0.003	26.890	0.006	0.006	0.000	0.000	0.000	0.000
12	A	168	GLY	0	0.017	0.025	29.977	0.003	0.003	0.000	0.000	0.000	0.000
13	A	169	THR	0	-0.038	-0.025	26.451	0.005	0.005	0.000	0.000	0.000	0.000
14	A	170	SER	0	0.001	0.015	28.834	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	171	GLN	0	0.053	0.041	24.924	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	172	ASN	0	0.030	0.021	22.787	0.002	0.002	0.000	0.000	0.000	0.000
17	A	173	ILE	0	-0.037	-0.004	17.507	0.008	0.008	0.000	0.000	0.000	0.000
18	A	174	LEU	0	0.008	-0.005	16.726	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	175	SER	0	0.014	0.017	13.423	0.037	0.037	0.000	0.000	0.000	0.000
20	A	176	ASN	0	0.030	-0.011	8.793	-0.121	-0.121	0.000	0.000	0.000	0.000
21	A	177	LEU	0	0.005	0.022	8.605	0.044	0.044	0.000	0.000	0.000	0.000
22	A	178	THR	0	-0.001	0.002	2.524	-0.381	0.002	0.396	-0.259	-0.520	-0.001
23	A	179	PHE	0	0.007	-0.007	3.625	0.262	0.517	0.001	-0.069	-0.186	0.000
24	A	180	ASN	0	0.033	0.021	2.485	-4.361	-2.892	2.784	-2.256	-1.997	-0.022
25	A	181	LYS	1	0.974	0.982	2.329	-0.554	-0.130	1.687	-0.931	-1.179	-0.004
26	A	182	ASN	0	-0.022	-0.008	3.740	0.129	0.244	0.019	-0.025	-0.109	0.000
27	A	183	GLN	0	0.077	0.055	7.029	0.018	0.018	0.000	0.000	0.000	0.000
28	A	184	ASN	0	-0.012	-0.010	8.416	-0.094	-0.094	0.000	0.000	0.000	0.000
29	A	185	ILE	0	0.002	0.002	9.903	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	186	SER	0	0.035	0.007	12.766	0.019	0.019	0.000	0.000	0.000	0.000
31	A	187	TYR	0	0.003	-0.026	15.431	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	188	LYS	1	0.895	0.966	17.824	0.121	0.121	0.000	0.000	0.000	0.000
33	A	189	ASP	-1	-0.813	-0.911	13.064	-0.237	-0.237	0.000	0.000	0.000	0.000
34	A	190	LEU	0	-0.067	-0.040	12.264	-0.029	-0.029	0.000	0.000	0.000	0.000
35	A	191	GLU	-1	-0.799	-0.875	14.220	-0.130	-0.130	0.000	0.000	0.000	0.000
36	A	192	GLY	0	0.044	0.029	15.758	0.014	0.014	0.000	0.000	0.000	0.000
37	A	193	LYS	1	0.855	0.933	7.520	0.696	0.696	0.000	0.000	0.000	0.000
38	A	194	VAL	0	-0.002	-0.007	13.081	0.017	0.017	0.000	0.000	0.000	0.000
39	A	195	LYS	1	0.865	0.905	15.591	0.128	0.128	0.000	0.000	0.000	0.000
40	A	196	SER	0	-0.018	0.019	14.301	0.016	0.016	0.000	0.000	0.000	0.000
41	A	197	VAL	0	0.001	-0.005	12.856	0.018	0.018	0.000	0.000	0.000	0.000
42	A	198	LEU	0	-0.026	-0.016	15.875	0.020	0.020	0.000	0.000	0.000	0.000
43	A	199	GLU	-1	-0.900	-0.940	19.382	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	200	SER	0	0.005	-0.007	16.706	0.006	0.006	0.000	0.000	0.000	0.000
45	A	201	ASN	0	-0.056	-0.023	16.008	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	202	ARG	1	0.849	0.888	19.610	0.049	0.049	0.000	0.000	0.000	0.000
47	A	203	GLY	0	0.044	0.053	22.431	0.003	0.003	0.000	0.000	0.000	0.000
48	A	204	ILE	0	-0.052	-0.018	23.081	0.001	0.001	0.000	0.000	0.000	0.000
49	A	205	THR	0	0.033	0.003	22.919	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	206	ASP	-1	-0.829	-0.928	23.039	-0.095	-0.095	0.000	0.000	0.000	0.000
51	A	207	VAL	0	-0.020	-0.013	25.572	0.000	0.000	0.000	0.000	0.000	0.000
52	A	208	ASP	-1	-0.767	-0.875	27.027	-0.046	-0.046	0.000	0.000	0.000	0.000
53	A	209	LEU	0	-0.016	-0.008	22.608	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	210	ARG	1	0.908	0.962	27.212	0.056	0.056	0.000	0.000	0.000	0.000
55	A	211	LEU	0	-0.030	-0.008	30.245	0.002	0.002	0.000	0.000	0.000	0.000
56	A	212	SER	0	-0.006	-0.025	29.228	0.001	0.001	0.000	0.000	0.000	0.000
57	A	213	LYS	1	0.956	0.978	31.312	0.041	0.041	0.000	0.000	0.000	0.000
58	A	214	GLN	0	-0.112	-0.066	28.560	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	215	ALA	0	0.095	0.061	25.077	0.000	0.000	0.000	0.000	0.000	0.000
60	A	216	LYS	1	0.941	0.976	23.799	0.102	0.102	0.000	0.000	0.000	0.000
61	A	217	TYR	0	0.049	0.017	17.043	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	218	THR	0	-0.060	-0.023	20.010	0.011	0.011	0.000	0.000	0.000	0.000
63	A	219	VAL	0	0.023	0.019	14.960	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	220	ASN	0	-0.057	-0.037	16.803	0.040	0.040	0.000	0.000	0.000	0.000
65	A	221	PHE	0	0.044	0.012	14.900	-0.046	-0.046	0.000	0.000	0.000	0.000
66	A	222	LYS	1	0.884	0.929	10.073	0.598	0.598	0.000	0.000	0.000	0.000
67	A	223	ASN	0	0.015	0.031	16.367	0.014	0.014	0.000	0.000	0.000	0.000
68	A	224	GLY	0	0.012	0.013	19.506	0.019	0.019	0.000	0.000	0.000	0.000
69	A	225	THR	0	-0.041	-0.015	20.123	0.008	0.008	0.000	0.000	0.000	0.000
70	A	226	LYS	1	1.001	0.984	20.187	0.100	0.100	0.000	0.000	0.000	0.000
71	A	227	LYS	1	0.948	0.985	20.014	0.144	0.144	0.000	0.000	0.000	0.000
72	A	228	VAL	0	-0.023	-0.009	20.992	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	229	ILE	0	-0.036	-0.015	20.005	0.007	0.007	0.000	0.000	0.000	0.000
74	A	230	ASP	-1	-0.855	-0.929	23.036	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	231	LEU	0	-0.018	-0.044	19.971	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.822	0.915	23.991	0.064	0.064	0.000	0.000	0.000	0.000
77	A	233	SER	0	-0.040	-0.012	26.530	0.007	0.007	0.000	0.000	0.000	0.000
78	A	234	GLY	0	0.053	0.035	25.487	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	235	ILE	0	-0.057	-0.025	26.979	0.001	0.001	0.000	0.000	0.000	0.000
80	A	236	TYR	0	-0.053	-0.067	21.513	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	237	THR	0	-0.130	-0.129	21.609	0.002	0.002	0.000	0.000	0.000	0.000
82	A	238	ALA	0	0.124	0.116	21.490	-0.014	-0.014	0.000	0.000	0.000	0.000
83	A	239	ASN	0	0.019	-0.016	19.226	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	240	LEU	0	-0.120	-0.001	15.551	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	241	ILE	0	0.134	0.053	13.103	0.020	0.020	0.000	0.000	0.000	0.000
86	A	242	ASN	0	0.077	0.037	9.849	-0.097	-0.097	0.000	0.000	0.000	0.000
87	A	243	SER	0	0.006	-0.017	5.793	0.045	0.045	0.000	0.000	0.000	0.000
88	A	244	SER	0	-0.005	-0.009	7.364	-0.231	-0.231	0.000	0.000	0.000	0.000
89	A	245	ASP	-1	-0.870	-0.934	8.711	-0.279	-0.279	0.000	0.000	0.000	0.000
90	A	246	ILE	0	-0.054	-0.023	10.168	0.082	0.082	0.000	0.000	0.000	0.000
91	A	247	LYS	1	0.919	0.957	11.264	0.122	0.122	0.000	0.000	0.000	0.000
92	A	248	SER	0	-0.014	-0.015	13.351	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	249	ILE	0	0.014	0.014	12.392	0.005	0.005	0.000	0.000	0.000	0.000
94	A	250	ASN	0	-0.046	-0.005	15.814	0.014	0.014	0.000	0.000	0.000	0.000
95	A	251	ILE	0	0.061	0.030	16.065	0.000	0.000	0.000	0.000	0.000	0.000
96	A	252	ASN	0	-0.063	-0.045	20.241	0.001	0.001	0.000	0.000	0.000	0.000
97	A	253	ILE	0	0.039	0.030	23.343	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	254	ASP	-1	-0.806	-0.868	26.319	-0.052	-0.052	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:157:GLY)