FMO DATABASE

FMODB ID: Q16VY

Calculation Name: 1Y96-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y96

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WXD5

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-597204.751328
FMO2-HF: Nuclear repulsion	561448.690702
FMO2-HF: Total energy	-35756.060626
FMO2-MP2: Total energy	-35856.932095

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:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

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.
-2.92	2.589	2.76	-2.328	-5.942	-0.005

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.018

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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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	3	GLU	-1	-0.904	-0.971	3.459	-4.189	-2.246	0.011	-0.934	-1.020	-0.001
4	A	4	TRP	0	0.002	0.000	6.176	-0.155	-0.155	0.000	0.000	0.000	0.000
5	A	5	MET	0	-0.006	-0.019	2.280	-1.562	0.004	1.268	-0.645	-2.190	-0.005
6	A	6	LYS	1	0.886	0.952	2.240	2.879	4.670	1.474	-0.717	-2.548	0.001
7	A	7	LYS	1	0.941	1.002	3.818	1.393	1.602	0.007	-0.032	-0.184	0.000
8	A	8	GLY	0	0.034	0.034	7.377	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.030	-0.015	9.398	0.107	0.107	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.005	-0.009	11.810	0.065	0.065	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.898	-0.943	10.970	-1.046	-1.046	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.021	-0.015	6.768	0.140	0.140	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.021	-0.016	13.128	0.059	0.059	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.884	-0.932	16.499	-0.363	-0.363	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.052	-0.036	13.200	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.018	-0.003	17.958	0.038	0.038	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.046	-0.044	20.062	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.897	0.979	20.340	0.337	0.337	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.951	-0.978	21.723	-0.134	-0.134	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.001	-0.006	17.131	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.955	0.973	19.257	0.214	0.214	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.012	-0.012	13.677	-0.050	-0.050	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.021	0.021	15.011	0.048	0.048	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.015	-0.006	12.951	-0.073	-0.073	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.010	-0.019	11.622	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.979	-0.988	13.807	0.227	0.227	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.914	0.954	16.853	-0.081	-0.081	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.004	0.022	17.404	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.922	-0.967	17.659	-0.120	-0.120	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.007	-0.004	16.930	0.025	0.025	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.969	0.982	20.018	0.092	0.092	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.017	0.029	21.535	0.025	0.025	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.003	0.004	21.611	-0.029	-0.029	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.007	0.005	17.032	0.017	0.017	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.014	0.019	19.927	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.005	-0.014	16.763	-0.020	-0.020	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.007	-0.002	11.027	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.818	-0.886	12.670	0.060	0.060	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.022	-0.008	9.964	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.050	-0.007	8.695	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.065	-0.061	8.111	0.232	0.232	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.028	0.009	6.963	0.091	0.091	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.029	0.008	8.921	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.004	0.013	11.349	-0.047	-0.047	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.002	-0.001	14.011	0.052	0.052	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.026	-0.015	17.713	-0.030	-0.030	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.023	0.016	20.290	0.025	0.025	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.048	-0.050	23.910	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.006	-0.013	26.437	0.009	0.009	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.004	0.002	27.956	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.925	-0.973	31.431	-0.030	-0.030	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.894	-0.927	34.541	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.049	-0.018	35.393	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.087	-0.038	33.193	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.012	-0.022	28.491	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.005	0.007	26.070	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.015	-0.005	22.167	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.004	0.002	19.028	0.024	0.024	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.004	0.013	17.129	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.023	-0.007	12.797	0.033	0.033	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.014	-0.004	11.074	-0.036	-0.036	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.073	0.041	8.055	-0.050	-0.050	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.020	-0.036	6.020	-0.242	-0.242	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.070	-0.026	7.055	0.020	0.020	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.004	0.014	8.565	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.065	-0.030	8.399	-0.180	-0.180	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.009	-0.011	10.458	-0.160	-0.160	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.028	0.012	11.877	0.075	0.075	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.923	-0.955	14.400	-0.306	-0.306	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.017	-0.021	17.813	0.028	0.028	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.054	-0.013	20.400	0.008	0.008	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.002	-0.013	23.814	0.016	0.016	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.863	-0.934	24.022	-0.270	-0.270	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.021	0.017	26.173	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.915	-0.967	28.304	-0.112	-0.112	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.019	-0.025	30.909	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.983	0.986	32.962	0.079	0.079	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.005	0.009	28.719	0.007	0.007	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.944	0.982	26.076	0.173	0.173	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.888	-0.949	29.297	-0.096	-0.096	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.881	0.942	31.334	0.080	0.080	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.009	-0.007	25.172	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.027	-0.001	27.341	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.026	-0.008	28.655	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.050	-0.007	26.278	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.021	-0.003	24.293	-0.002	-0.002	0.000	0.000	0.000	0.000

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