FMO DATABASE

FMODB ID: QVGYY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-702461.441577
FMO2-HF: Nuclear repulsion	665315.523885
FMO2-HF: Total energy	-37145.917692
FMO2-MP2: Total energy	-37257.004799

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.
-3.259	-2.558	9.938	-5.34	-5.301	-0.038

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 : 0.053 / q_NPA : 0.028

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	-0.014	-0.008	3.786	-1.006	0.653	-0.005	-0.970	-0.684	0.003
4	A	160	VAL	0	-0.013	0.011	6.529	0.262	0.262	0.000	0.000	0.000	0.000
5	A	161	PRO	0	0.046	0.036	9.668	0.095	0.095	0.000	0.000	0.000	0.000
6	A	162	TYR	0	-0.050	-0.065	12.305	0.047	0.047	0.000	0.000	0.000	0.000
7	A	163	THR	0	0.033	0.011	15.064	0.015	0.015	0.000	0.000	0.000	0.000
8	A	164	ILE	0	0.006	0.005	17.975	0.005	0.005	0.000	0.000	0.000	0.000
9	A	165	THR	0	-0.063	-0.019	20.934	0.007	0.007	0.000	0.000	0.000	0.000
10	A	166	VAL	0	0.020	-0.003	24.605	0.006	0.006	0.000	0.000	0.000	0.000
11	A	167	ASN	0	-0.007	-0.002	27.478	0.009	0.009	0.000	0.000	0.000	0.000
12	A	168	GLY	0	0.041	0.027	30.735	0.005	0.005	0.000	0.000	0.000	0.000
13	A	169	THR	0	-0.039	-0.029	27.259	0.007	0.007	0.000	0.000	0.000	0.000
14	A	170	SER	0	0.010	0.015	28.968	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	171	GLN	0	0.033	0.033	25.444	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	172	ASN	0	0.030	0.014	23.658	0.010	0.010	0.000	0.000	0.000	0.000
17	A	173	ILE	0	-0.026	-0.006	18.080	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	174	LEU	0	0.001	-0.011	17.207	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	175	SER	0	0.010	0.016	14.146	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	176	ASN	0	0.009	-0.011	9.527	-0.143	-0.143	0.000	0.000	0.000	0.000
21	A	177	LEU	0	0.022	0.019	9.051	0.058	0.058	0.000	0.000	0.000	0.000
22	A	178	THR	0	0.016	0.014	3.010	-0.525	-0.171	0.114	-0.138	-0.331	0.000
23	A	179	PHE	0	0.004	-0.005	3.545	0.971	1.452	0.000	-0.219	-0.263	0.000
24	A	180	ASN	0	0.047	0.025	1.923	-5.415	-7.971	8.364	-3.154	-2.654	-0.037
25	A	181	LYS	1	0.946	0.987	2.268	0.070	0.688	1.456	-0.855	-1.219	-0.004
26	A	182	ASN	0	-0.005	0.004	3.812	0.623	0.768	0.009	-0.004	-0.150	0.000
27	A	183	GLN	0	0.068	0.061	7.223	0.301	0.301	0.000	0.000	0.000	0.000
28	A	184	ASN	0	0.006	0.002	8.624	-0.261	-0.261	0.000	0.000	0.000	0.000
29	A	185	ILE	0	-0.001	0.000	9.695	0.085	0.085	0.000	0.000	0.000	0.000
30	A	186	SER	0	0.022	-0.016	12.918	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	187	TYR	0	0.022	-0.022	15.215	-0.038	-0.038	0.000	0.000	0.000	0.000
32	A	188	LYS	1	0.873	0.938	17.503	0.007	0.007	0.000	0.000	0.000	0.000
33	A	189	ASP	-1	-0.790	-0.859	12.728	0.081	0.081	0.000	0.000	0.000	0.000
34	A	190	LEU	0	-0.056	-0.027	11.834	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	191	GLU	-1	-0.813	-0.897	14.012	-0.086	-0.086	0.000	0.000	0.000	0.000
36	A	192	GLY	0	0.046	0.030	15.853	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	193	LYS	1	0.855	0.920	7.464	0.506	0.506	0.000	0.000	0.000	0.000
38	A	194	VAL	0	0.005	-0.006	13.270	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	195	LYS	1	0.810	0.883	15.905	0.069	0.069	0.000	0.000	0.000	0.000
40	A	196	SER	0	0.009	0.028	14.533	0.004	0.004	0.000	0.000	0.000	0.000
41	A	197	VAL	0	-0.022	0.005	13.376	0.003	0.003	0.000	0.000	0.000	0.000
42	A	198	LEU	0	-0.035	-0.019	16.314	0.002	0.002	0.000	0.000	0.000	0.000
43	A	199	GLU	-1	-0.869	-0.933	19.972	-0.027	-0.027	0.000	0.000	0.000	0.000
44	A	200	SER	0	-0.029	-0.034	17.059	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	201	ASN	0	-0.004	0.005	16.129	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	202	ARG	1	0.823	0.873	20.080	0.171	0.171	0.000	0.000	0.000	0.000
47	A	203	GLY	0	0.049	0.053	23.117	0.007	0.007	0.000	0.000	0.000	0.000
48	A	204	ILE	0	-0.073	-0.026	23.773	0.008	0.008	0.000	0.000	0.000	0.000
49	A	205	THR	0	0.070	0.013	23.482	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	206	ASP	-1	-0.820	-0.916	24.151	-0.052	-0.052	0.000	0.000	0.000	0.000
51	A	207	VAL	0	-0.005	-0.006	25.560	0.000	0.000	0.000	0.000	0.000	0.000
52	A	208	ASP	-1	-0.797	-0.870	27.448	-0.061	-0.061	0.000	0.000	0.000	0.000
53	A	209	LEU	0	-0.031	-0.023	22.629	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	210	ARG	1	0.867	0.928	27.235	0.025	0.025	0.000	0.000	0.000	0.000
55	A	211	LEU	0	-0.008	-0.001	30.173	0.001	0.001	0.000	0.000	0.000	0.000
56	A	212	SER	0	-0.065	-0.022	29.421	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	213	LYS	1	0.946	0.966	31.617	0.086	0.086	0.000	0.000	0.000	0.000
58	A	214	GLN	0	-0.035	-0.034	28.589	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	215	ALA	0	0.075	0.051	25.547	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	216	LYS	1	0.900	0.954	23.955	0.181	0.181	0.000	0.000	0.000	0.000
61	A	217	TYR	0	0.024	0.006	16.608	-0.027	-0.027	0.000	0.000	0.000	0.000
62	A	218	THR	0	-0.022	-0.001	20.026	0.032	0.032	0.000	0.000	0.000	0.000
63	A	219	VAL	0	0.016	0.010	14.828	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	220	ASN	0	-0.023	-0.017	16.945	0.087	0.087	0.000	0.000	0.000	0.000
65	A	221	PHE	0	0.057	0.016	14.760	-0.085	-0.085	0.000	0.000	0.000	0.000
66	A	222	LYS	1	0.836	0.894	10.432	1.208	1.208	0.000	0.000	0.000	0.000
67	A	223	ASN	0	0.047	0.049	16.916	0.004	0.004	0.000	0.000	0.000	0.000
68	A	224	GLY	0	-0.006	0.008	19.983	0.031	0.031	0.000	0.000	0.000	0.000
69	A	225	THR	0	-0.051	-0.033	20.602	0.020	0.020	0.000	0.000	0.000	0.000
70	A	226	LYS	1	0.986	0.978	20.188	0.199	0.199	0.000	0.000	0.000	0.000
71	A	227	LYS	1	0.903	0.964	20.074	0.182	0.182	0.000	0.000	0.000	0.000
72	A	228	VAL	0	0.015	0.009	20.992	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	229	ILE	0	-0.034	-0.012	19.999	0.021	0.021	0.000	0.000	0.000	0.000
74	A	230	ASP	-1	-0.840	-0.920	23.015	-0.110	-0.110	0.000	0.000	0.000	0.000
75	A	231	LEU	0	-0.013	-0.033	20.118	0.005	0.005	0.000	0.000	0.000	0.000
76	A	232	LYS	1	0.830	0.917	23.974	0.085	0.085	0.000	0.000	0.000	0.000
77	A	233	SER	0	-0.044	-0.008	25.574	0.014	0.014	0.000	0.000	0.000	0.000
78	A	234	GLY	0	0.040	0.026	25.532	0.000	0.000	0.000	0.000	0.000	0.000
79	A	235	ILE	0	-0.039	-0.012	27.124	0.009	0.009	0.000	0.000	0.000	0.000
80	A	236	TYR	0	0.036	0.009	22.118	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	237	THR	0	-0.008	0.010	22.294	0.002	0.002	0.000	0.000	0.000	0.000
82	A	238	ALA	0	0.053	0.028	22.074	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	239	ASN	0	-0.069	-0.057	19.040	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	240	LEU	0	0.019	0.012	16.208	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	241	ILE	0	0.002	0.004	13.418	-0.012	-0.012	0.000	0.000	0.000	0.000
86	A	242	ASN	0	0.083	0.030	10.037	-0.131	-0.131	0.000	0.000	0.000	0.000
87	A	243	SER	0	-0.023	-0.043	6.202	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	244	SER	0	-0.013	-0.014	8.316	-0.378	-0.378	0.000	0.000	0.000	0.000
89	A	245	ASP	-1	-0.853	-0.912	9.205	-0.464	-0.464	0.000	0.000	0.000	0.000
90	A	246	ILE	0	-0.047	-0.012	10.029	0.059	0.059	0.000	0.000	0.000	0.000
91	A	247	LYS	1	0.898	0.946	11.620	0.265	0.265	0.000	0.000	0.000	0.000
92	A	248	SER	0	0.012	-0.001	13.890	-0.049	-0.049	0.000	0.000	0.000	0.000
93	A	249	ILE	0	0.000	0.008	12.304	0.054	0.054	0.000	0.000	0.000	0.000
94	A	250	ASN	0	-0.040	-0.026	15.972	0.001	0.001	0.000	0.000	0.000	0.000
95	A	251	ILE	0	0.055	0.026	16.414	0.029	0.029	0.000	0.000	0.000	0.000
96	A	252	ASN	0	-0.046	-0.022	20.588	0.005	0.005	0.000	0.000	0.000	0.000
97	A	253	ILE	0	0.067	0.050	23.191	0.010	0.010	0.000	0.000	0.000	0.000
98	A	254	ASP	-1	-0.830	-0.900	26.597	-0.090	-0.090	0.000	0.000	0.000	0.000

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