FMO DATABASE

FMODB ID: QY1VY

Calculation Name: 2Y3W-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y3W

Chain ID: C

ChEMBL ID:

UniProt ID: Q7ZVT3

Base Structure: X-ray

Registration Date: 2023-06-21

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	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-928691.564068
FMO2-HF: Nuclear repulsion	883838.591048
FMO2-HF: Total energy	-44852.97302
FMO2-MP2: Total energy	-44985.604758

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:2:THR)

Summations of interaction energy for fragment #1(C:2:THR)

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.
-20.182	-26.006	24.059	-10.188	-8.044	-0.06

Interaction energy analysis for fragmet #1(C:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.056

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	C	4	LEU	0	-0.041	-0.018	3.883	-1.253	0.459	-0.013	-0.875	-0.823	0.003
4	C	5	LEU	0	0.004	0.002	6.182	0.925	0.925	0.000	0.000	0.000	0.000
5	C	6	PHE	0	0.013	-0.005	9.070	0.450	0.450	0.000	0.000	0.000	0.000
6	C	7	ASN	0	-0.008	-0.005	9.389	0.035	0.035	0.000	0.000	0.000	0.000
7	C	8	LYS	1	0.835	0.912	11.927	0.743	0.743	0.000	0.000	0.000	0.000
8	C	9	ARG	1	0.853	0.911	15.713	0.431	0.431	0.000	0.000	0.000	0.000
9	C	10	LEU	0	0.003	0.003	18.308	0.008	0.008	0.000	0.000	0.000	0.000
10	C	11	GLN	0	-0.004	-0.004	21.103	0.025	0.025	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.027	0.012	21.076	-0.010	-0.010	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.015	-0.016	24.409	0.018	0.018	0.000	0.000	0.000	0.000
13	C	14	VAL	0	-0.022	-0.022	24.546	0.018	0.018	0.000	0.000	0.000	0.000
14	C	22	ARG	1	0.996	0.995	30.668	0.151	0.151	0.000	0.000	0.000	0.000
15	C	23	ARG	1	0.898	0.948	28.361	0.175	0.175	0.000	0.000	0.000	0.000
16	C	24	SER	0	0.000	0.002	25.358	0.019	0.019	0.000	0.000	0.000	0.000
17	C	25	VAL	0	-0.027	-0.011	22.270	-0.011	-0.011	0.000	0.000	0.000	0.000
18	C	26	ILE	0	0.016	0.022	19.009	0.009	0.009	0.000	0.000	0.000	0.000
19	C	27	ARG	1	0.813	0.884	13.095	0.737	0.737	0.000	0.000	0.000	0.000
20	C	28	VAL	0	-0.004	-0.003	13.783	0.022	0.022	0.000	0.000	0.000	0.000
21	C	29	SER	0	-0.043	-0.047	7.806	-0.006	-0.006	0.000	0.000	0.000	0.000
22	C	30	ILE	0	0.002	-0.005	9.072	0.229	0.229	0.000	0.000	0.000	0.000
23	C	31	GLU	-1	-0.882	-0.921	3.812	-3.958	-3.694	0.001	-0.048	-0.216	0.000
24	C	32	LEU	0	0.039	0.023	3.668	0.736	2.040	0.001	-0.631	-0.674	-0.001
25	C	33	GLN	0	0.052	0.046	1.810	-19.005	-28.109	24.070	-8.634	-6.331	-0.062
26	C	44	LEU	0	-0.003	0.010	6.899	0.013	0.013	0.000	0.000	0.000	0.000
27	C	45	VAL	0	-0.066	-0.041	5.982	0.458	0.458	0.000	0.000	0.000	0.000
28	C	46	VAL	0	0.016	0.015	8.056	-0.379	-0.379	0.000	0.000	0.000	0.000
29	C	47	ARG	1	0.914	0.941	8.429	1.101	1.101	0.000	0.000	0.000	0.000
30	C	48	LEU	0	0.009	-0.002	11.500	-0.083	-0.083	0.000	0.000	0.000	0.000
31	C	49	THR	0	0.026	0.011	13.767	0.003	0.003	0.000	0.000	0.000	0.000
32	C	50	ASP	-1	-0.754	-0.842	16.179	-0.334	-0.334	0.000	0.000	0.000	0.000
33	C	51	ASP	-1	-0.832	-0.892	17.579	-0.571	-0.571	0.000	0.000	0.000	0.000
34	C	52	THR	0	-0.139	-0.091	19.661	0.026	0.026	0.000	0.000	0.000	0.000
35	C	53	ASP	-1	-0.824	-0.922	21.637	-0.168	-0.168	0.000	0.000	0.000	0.000
36	C	54	LEU	0	-0.048	-0.012	17.928	-0.031	-0.031	0.000	0.000	0.000	0.000
37	C	55	TYR	0	-0.026	-0.026	18.680	0.001	0.001	0.000	0.000	0.000	0.000
38	C	56	PHE	0	-0.022	0.001	19.283	0.009	0.009	0.000	0.000	0.000	0.000
39	C	57	LEU	0	0.021	0.004	13.032	-0.056	-0.056	0.000	0.000	0.000	0.000
40	C	58	TYR	0	-0.053	-0.029	15.993	0.060	0.060	0.000	0.000	0.000	0.000
41	C	59	ASN	0	-0.069	-0.029	12.204	-0.064	-0.064	0.000	0.000	0.000	0.000
42	C	60	LEU	0	0.046	0.016	12.402	0.091	0.091	0.000	0.000	0.000	0.000
43	C	61	ILE	0	0.004	0.016	9.293	-0.156	-0.156	0.000	0.000	0.000	0.000
44	C	62	ILE	0	-0.011	-0.009	10.537	0.055	0.055	0.000	0.000	0.000	0.000
45	C	63	SER	0	-0.004	-0.018	10.695	0.000	0.000	0.000	0.000	0.000	0.000
46	C	64	GLU	-1	-0.834	-0.902	11.848	0.212	0.212	0.000	0.000	0.000	0.000
47	C	65	GLU	-1	-0.909	-0.953	14.107	0.184	0.184	0.000	0.000	0.000	0.000
48	C	66	ASP	-1	-0.831	-0.921	14.721	0.087	0.087	0.000	0.000	0.000	0.000
49	C	67	PHE	0	-0.050	-0.015	14.811	-0.058	-0.058	0.000	0.000	0.000	0.000
50	C	68	GLN	0	-0.010	-0.026	16.780	-0.050	-0.050	0.000	0.000	0.000	0.000
51	C	69	SER	0	0.009	0.008	19.867	-0.012	-0.012	0.000	0.000	0.000	0.000
52	C	70	LEU	0	-0.076	-0.022	17.255	-0.013	-0.013	0.000	0.000	0.000	0.000
53	C	71	LYS	1	0.789	0.879	20.375	0.013	0.013	0.000	0.000	0.000	0.000
54	C	72	VAL	0	-0.031	-0.011	22.045	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	73	GLN	0	-0.103	-0.064	22.250	-0.007	-0.007	0.000	0.000	0.000	0.000
56	C	74	GLN	0	-0.056	-0.043	22.039	0.002	0.002	0.000	0.000	0.000	0.000
57	C	75	GLY	0	0.027	0.025	25.463	-0.013	-0.013	0.000	0.000	0.000	0.000
58	C	76	LEU	0	-0.012	-0.003	19.890	0.004	0.004	0.000	0.000	0.000	0.000
59	C	77	LEU	0	-0.010	0.008	23.184	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	78	ILE	0	-0.029	-0.008	18.471	0.019	0.019	0.000	0.000	0.000	0.000
61	C	79	ASP	-1	-0.761	-0.890	17.426	0.044	0.044	0.000	0.000	0.000	0.000
62	C	80	PHE	0	0.042	0.034	9.367	-0.082	-0.082	0.000	0.000	0.000	0.000
63	C	81	THR	0	-0.006	-0.015	12.778	-0.095	-0.095	0.000	0.000	0.000	0.000
64	C	82	SER	0	-0.004	-0.015	13.842	-0.060	-0.060	0.000	0.000	0.000	0.000
65	C	83	PHE	0	0.001	0.004	13.621	-0.046	-0.046	0.000	0.000	0.000	0.000
66	C	84	PRO	0	0.035	0.022	10.971	-0.038	-0.038	0.000	0.000	0.000	0.000
67	C	85	GLN	0	-0.019	-0.013	13.279	-0.094	-0.094	0.000	0.000	0.000	0.000
68	C	86	LYS	1	0.842	0.906	15.700	0.299	0.299	0.000	0.000	0.000	0.000
69	C	87	PHE	0	0.029	-0.005	13.804	0.017	0.017	0.000	0.000	0.000	0.000
70	C	88	ILE	0	0.032	0.012	11.952	0.010	0.010	0.000	0.000	0.000	0.000
71	C	89	ASP	-1	-0.790	-0.870	16.390	-0.362	-0.362	0.000	0.000	0.000	0.000
72	C	90	LEU	0	-0.006	0.002	19.959	0.029	0.029	0.000	0.000	0.000	0.000
73	C	91	LEU	0	-0.001	0.013	15.627	0.029	0.029	0.000	0.000	0.000	0.000
74	C	92	GLU	-1	-0.788	-0.881	18.672	-0.560	-0.560	0.000	0.000	0.000	0.000
75	C	93	GLN	0	-0.033	-0.013	21.135	0.027	0.027	0.000	0.000	0.000	0.000
76	C	94	CYS	0	-0.056	-0.017	22.597	0.029	0.029	0.000	0.000	0.000	0.000
77	C	95	ILE	0	-0.025	-0.015	19.208	0.018	0.018	0.000	0.000	0.000	0.000
78	C	96	CYS	0	-0.083	-0.050	23.696	0.019	0.019	0.000	0.000	0.000	0.000
79	C	97	GLU	-1	-0.800	-0.890	26.637	-0.180	-0.180	0.000	0.000	0.000	0.000
80	C	98	GLN	0	-0.027	-0.010	24.066	0.002	0.002	0.000	0.000	0.000	0.000
81	C	99	ASP	-1	-0.935	-0.952	28.405	-0.242	-0.242	0.000	0.000	0.000	0.000
82	C	100	LYS	1	0.779	0.869	31.422	0.198	0.198	0.000	0.000	0.000	0.000
83	C	101	GLU	-1	-0.836	-0.911	33.725	-0.163	-0.163	0.000	0.000	0.000	0.000
84	C	102	ASN	0	-0.053	-0.035	35.718	0.012	0.012	0.000	0.000	0.000	0.000
85	C	103	PRO	0	-0.029	0.006	30.141	0.002	0.002	0.000	0.000	0.000	0.000
86	C	104	ARG	1	0.897	0.961	31.223	0.184	0.184	0.000	0.000	0.000	0.000
87	C	105	PHE	0	0.014	0.012	25.654	-0.001	-0.001	0.000	0.000	0.000	0.000
88	C	106	LEU	0	-0.006	-0.006	26.611	-0.008	-0.008	0.000	0.000	0.000	0.000
89	C	107	LEU	0	0.039	0.016	19.875	-0.002	-0.002	0.000	0.000	0.000	0.000
90	C	108	GLN	0	-0.016	-0.001	24.159	0.016	0.016	0.000	0.000	0.000	0.000
91	C	109	LEU	0	0.029	0.020	21.120	-0.019	-0.019	0.000	0.000	0.000	0.000
92	C	110	SER	0	0.012	0.023	24.362	0.019	0.019	0.000	0.000	0.000	0.000
93	C	111	SER	0	0.017	0.009	25.544	0.004	0.004	0.000	0.000	0.000	0.000
94	C	119	SER	0	0.056	0.023	24.863	0.008	0.008	0.000	0.000	0.000	0.000
95	C	120	PRO	0	-0.030	-0.026	22.102	-0.018	-0.018	0.000	0.000	0.000	0.000
96	C	121	SER	0	-0.017	0.016	21.780	0.010	0.010	0.000	0.000	0.000	0.000
97	C	122	ASN	0	-0.065	-0.037	21.657	-0.003	-0.003	0.000	0.000	0.000	0.000
98	C	123	LEU	0	0.014	0.013	17.453	0.003	0.003	0.000	0.000	0.000	0.000
99	C	124	ASN	0	-0.003	-0.007	21.245	-0.002	-0.002	0.000	0.000	0.000	0.000
100	C	125	ILE	0	0.020	0.010	19.706	-0.012	-0.012	0.000	0.000	0.000	0.000
101	C	126	VAL	0	-0.041	-0.027	23.952	0.022	0.022	0.000	0.000	0.000	0.000
102	C	127	GLU	-1	-0.885	-0.942	27.739	-0.187	-0.187	0.000	0.000	0.000	0.000
103	C	128	THR	0	-0.095	-0.062	30.095	0.019	0.019	0.000	0.000	0.000	0.000
104	C	137	LEU	0	0.054	0.029	18.834	0.000	0.000	0.000	0.000	0.000	0.000
105	C	138	SER	0	-0.070	-0.057	21.933	0.003	0.003	0.000	0.000	0.000	0.000
106	C	139	LEU	0	0.028	0.024	15.659	0.006	0.006	0.000	0.000	0.000	0.000
107	C	140	LYS	1	0.981	0.989	19.364	0.078	0.078	0.000	0.000	0.000	0.000
108	C	141	LEU	0	0.002	0.018	15.484	0.014	0.014	0.000	0.000	0.000	0.000
109	C	142	LEU	0	0.038	0.008	16.758	0.038	0.038	0.000	0.000	0.000	0.000
110	C	143	PRO	0	0.018	0.024	17.521	-0.041	-0.041	0.000	0.000	0.000	0.000
111	C	144	GLY	0	-0.063	-0.043	16.540	0.058	0.058	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:THR)