FMO DATABASE

FMODB ID: R9588

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

Total energy (hartree)

FMO2-HF: Electronic energy	-927179.560684
FMO2-HF: Nuclear repulsion	882327.007768
FMO2-HF: Total energy	-44852.552916
FMO2-MP2: Total energy	-44985.163545

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.
-13.847	-19.504	22.136	-9.948	-6.532	-0.063

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 : -0.073 / q_NPA : -0.038

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	-0.043	-0.021	3.811	-0.930	0.935	-0.021	-0.912	-0.932	0.002
4	C	5	LEU	0	-0.006	-0.004	5.871	0.801	0.801	0.000	0.000	0.000	0.000
5	C	6	PHE	0	-0.001	-0.014	8.803	0.425	0.425	0.000	0.000	0.000	0.000
6	C	7	ASN	0	0.015	0.009	9.848	0.007	0.007	0.000	0.000	0.000	0.000
7	C	8	LYS	1	0.844	0.914	12.075	0.682	0.682	0.000	0.000	0.000	0.000
8	C	9	ARG	1	0.878	0.947	15.830	0.384	0.384	0.000	0.000	0.000	0.000
9	C	10	LEU	0	0.004	0.007	17.976	0.005	0.005	0.000	0.000	0.000	0.000
10	C	11	GLN	0	0.001	-0.005	21.042	0.018	0.018	0.000	0.000	0.000	0.000
11	C	12	VAL	0	0.038	0.016	21.093	-0.010	-0.010	0.000	0.000	0.000	0.000
12	C	13	LEU	0	-0.028	-0.008	24.428	0.016	0.016	0.000	0.000	0.000	0.000
13	C	14	VAL	0	0.025	0.008	24.873	0.006	0.006	0.000	0.000	0.000	0.000
14	C	22	ARG	1	0.996	0.995	30.851	0.132	0.132	0.000	0.000	0.000	0.000
15	C	23	ARG	1	0.903	0.948	28.250	0.162	0.162	0.000	0.000	0.000	0.000
16	C	24	SER	0	0.011	0.016	25.059	0.012	0.012	0.000	0.000	0.000	0.000
17	C	25	VAL	0	-0.013	-0.010	21.945	-0.012	-0.012	0.000	0.000	0.000	0.000
18	C	26	ILE	0	0.035	0.029	18.985	0.004	0.004	0.000	0.000	0.000	0.000
19	C	27	ARG	1	0.793	0.862	13.376	0.635	0.635	0.000	0.000	0.000	0.000
20	C	28	VAL	0	0.005	0.003	13.809	-0.001	-0.001	0.000	0.000	0.000	0.000
21	C	29	SER	0	-0.006	-0.019	8.142	-0.033	-0.033	0.000	0.000	0.000	0.000
22	C	30	ILE	0	-0.002	0.000	8.846	0.136	0.136	0.000	0.000	0.000	0.000
23	C	31	GLU	-1	-0.928	-0.956	3.524	-4.631	-4.093	0.005	-0.197	-0.347	-0.001
24	C	32	LEU	0	0.032	0.019	3.613	0.685	1.758	0.000	-0.518	-0.555	-0.001
25	C	33	GLN	0	0.074	0.039	1.706	-11.664	-20.797	22.152	-8.321	-4.698	-0.063
26	C	44	LEU	0	-0.003	0.010	6.778	-0.037	-0.037	0.000	0.000	0.000	0.000
27	C	45	VAL	0	-0.058	-0.042	6.340	0.402	0.402	0.000	0.000	0.000	0.000
28	C	46	VAL	0	0.009	0.016	8.192	-0.321	-0.321	0.000	0.000	0.000	0.000
29	C	47	ARG	1	0.920	0.951	9.105	0.898	0.898	0.000	0.000	0.000	0.000
30	C	48	LEU	0	0.006	0.002	11.810	-0.056	-0.056	0.000	0.000	0.000	0.000
31	C	49	THR	0	0.010	-0.003	13.838	0.007	0.007	0.000	0.000	0.000	0.000
32	C	50	ASP	-1	-0.755	-0.863	16.266	-0.288	-0.288	0.000	0.000	0.000	0.000
33	C	51	ASP	-1	-0.845	-0.898	17.676	-0.465	-0.465	0.000	0.000	0.000	0.000
34	C	52	THR	0	-0.145	-0.093	19.832	0.025	0.025	0.000	0.000	0.000	0.000
35	C	53	ASP	-1	-0.855	-0.935	21.592	-0.146	-0.146	0.000	0.000	0.000	0.000
36	C	54	LEU	0	-0.036	-0.010	18.554	-0.016	-0.016	0.000	0.000	0.000	0.000
37	C	55	TYR	0	-0.040	-0.028	19.059	-0.002	-0.002	0.000	0.000	0.000	0.000
38	C	56	PHE	0	-0.011	0.022	18.969	0.013	0.013	0.000	0.000	0.000	0.000
39	C	57	LEU	0	0.002	-0.024	13.241	-0.042	-0.042	0.000	0.000	0.000	0.000
40	C	58	TYR	0	-0.054	-0.008	16.124	0.048	0.048	0.000	0.000	0.000	0.000
41	C	59	ASN	0	-0.032	-0.003	12.164	-0.059	-0.059	0.000	0.000	0.000	0.000
42	C	60	LEU	0	0.059	0.010	12.288	0.063	0.063	0.000	0.000	0.000	0.000
43	C	61	ILE	0	-0.014	-0.003	9.401	-0.120	-0.120	0.000	0.000	0.000	0.000
44	C	62	ILE	0	0.003	0.009	10.929	0.065	0.065	0.000	0.000	0.000	0.000
45	C	63	SER	0	-0.006	-0.028	11.255	-0.019	-0.019	0.000	0.000	0.000	0.000
46	C	64	GLU	-1	-0.878	-0.930	12.274	0.164	0.164	0.000	0.000	0.000	0.000
47	C	65	GLU	-1	-0.879	-0.936	14.146	0.152	0.152	0.000	0.000	0.000	0.000
48	C	66	ASP	-1	-0.856	-0.924	14.881	0.053	0.053	0.000	0.000	0.000	0.000
49	C	67	PHE	0	-0.065	-0.046	15.130	-0.046	-0.046	0.000	0.000	0.000	0.000
50	C	68	GLN	0	0.000	-0.011	17.104	-0.038	-0.038	0.000	0.000	0.000	0.000
51	C	69	SER	0	0.034	0.014	20.371	-0.010	-0.010	0.000	0.000	0.000	0.000
52	C	70	LEU	0	-0.075	-0.017	17.196	-0.011	-0.011	0.000	0.000	0.000	0.000
53	C	71	LYS	1	0.813	0.906	20.519	0.023	0.023	0.000	0.000	0.000	0.000
54	C	72	VAL	0	-0.040	-0.014	22.065	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	73	GLN	0	-0.098	-0.066	22.623	-0.003	-0.003	0.000	0.000	0.000	0.000
56	C	74	GLN	0	-0.051	-0.040	22.120	0.003	0.003	0.000	0.000	0.000	0.000
57	C	75	GLY	0	0.023	0.024	25.454	-0.012	-0.012	0.000	0.000	0.000	0.000
58	C	76	LEU	0	-0.004	0.005	19.766	0.003	0.003	0.000	0.000	0.000	0.000
59	C	77	LEU	0	-0.010	0.009	22.836	-0.013	-0.013	0.000	0.000	0.000	0.000
60	C	78	ILE	0	-0.028	-0.012	18.447	0.016	0.016	0.000	0.000	0.000	0.000
61	C	79	ASP	-1	-0.807	-0.922	17.516	0.018	0.018	0.000	0.000	0.000	0.000
62	C	80	PHE	0	0.038	0.023	9.215	-0.067	-0.067	0.000	0.000	0.000	0.000
63	C	81	THR	0	0.000	-0.007	12.911	-0.089	-0.089	0.000	0.000	0.000	0.000
64	C	82	SER	0	-0.001	-0.013	14.081	-0.064	-0.064	0.000	0.000	0.000	0.000
65	C	83	PHE	0	-0.009	0.008	13.381	-0.048	-0.048	0.000	0.000	0.000	0.000
66	C	84	PRO	0	0.057	0.029	10.709	-0.026	-0.026	0.000	0.000	0.000	0.000
67	C	85	GLN	0	-0.005	-0.003	12.933	-0.086	-0.086	0.000	0.000	0.000	0.000
68	C	86	LYS	1	0.865	0.933	15.401	0.300	0.300	0.000	0.000	0.000	0.000
69	C	87	PHE	0	0.024	-0.004	13.776	0.017	0.017	0.000	0.000	0.000	0.000
70	C	88	ILE	0	0.031	0.006	11.753	0.017	0.017	0.000	0.000	0.000	0.000
71	C	89	ASP	-1	-0.819	-0.891	16.242	-0.343	-0.343	0.000	0.000	0.000	0.000
72	C	90	LEU	0	-0.034	-0.016	19.673	0.030	0.030	0.000	0.000	0.000	0.000
73	C	91	LEU	0	-0.005	0.008	15.481	0.028	0.028	0.000	0.000	0.000	0.000
74	C	92	GLU	-1	-0.793	-0.884	18.275	-0.519	-0.519	0.000	0.000	0.000	0.000
75	C	93	GLN	0	-0.011	0.004	20.981	0.022	0.022	0.000	0.000	0.000	0.000
76	C	94	CYS	0	-0.055	-0.020	22.342	0.027	0.027	0.000	0.000	0.000	0.000
77	C	95	ILE	0	-0.024	-0.011	19.054	0.016	0.016	0.000	0.000	0.000	0.000
78	C	96	CYS	0	-0.090	-0.047	23.623	0.019	0.019	0.000	0.000	0.000	0.000
79	C	97	GLU	-1	-0.827	-0.908	26.512	-0.167	-0.167	0.000	0.000	0.000	0.000
80	C	98	GLN	0	-0.014	0.002	23.902	-0.001	-0.001	0.000	0.000	0.000	0.000
81	C	99	ASP	-1	-0.960	-0.975	28.452	-0.217	-0.217	0.000	0.000	0.000	0.000
82	C	100	LYS	1	0.875	0.952	31.397	0.194	0.194	0.000	0.000	0.000	0.000
83	C	101	GLU	-1	-0.903	-0.959	33.597	-0.141	-0.141	0.000	0.000	0.000	0.000
84	C	102	ASN	0	-0.086	-0.055	35.200	0.001	0.001	0.000	0.000	0.000	0.000
85	C	103	PRO	0	-0.021	0.004	29.725	0.001	0.001	0.000	0.000	0.000	0.000
86	C	104	ARG	1	0.943	0.972	30.979	0.165	0.165	0.000	0.000	0.000	0.000
87	C	105	PHE	0	0.014	0.025	25.503	-0.001	-0.001	0.000	0.000	0.000	0.000
88	C	106	LEU	0	-0.006	-0.009	26.419	-0.006	-0.006	0.000	0.000	0.000	0.000
89	C	107	LEU	0	0.015	0.011	19.634	0.004	0.004	0.000	0.000	0.000	0.000
90	C	108	GLN	0	-0.039	-0.022	24.046	0.022	0.022	0.000	0.000	0.000	0.000
91	C	109	LEU	0	0.012	0.004	21.027	-0.017	-0.017	0.000	0.000	0.000	0.000
92	C	110	SER	0	0.013	0.012	24.204	0.016	0.016	0.000	0.000	0.000	0.000
93	C	111	SER	0	0.011	0.023	25.607	0.003	0.003	0.000	0.000	0.000	0.000
94	C	119	SER	0	-0.005	-0.009	25.456	0.002	0.002	0.000	0.000	0.000	0.000
95	C	120	PRO	0	0.044	0.000	22.381	-0.014	-0.014	0.000	0.000	0.000	0.000
96	C	121	SER	0	-0.030	0.004	22.043	0.007	0.007	0.000	0.000	0.000	0.000
97	C	122	ASN	0	-0.049	-0.043	21.840	-0.006	-0.006	0.000	0.000	0.000	0.000
98	C	123	LEU	0	0.017	0.021	17.538	0.000	0.000	0.000	0.000	0.000	0.000
99	C	124	ASN	0	0.020	0.008	21.352	0.005	0.005	0.000	0.000	0.000	0.000
100	C	125	ILE	0	0.004	0.009	19.581	-0.008	-0.008	0.000	0.000	0.000	0.000
101	C	126	VAL	0	-0.030	-0.018	23.776	0.017	0.017	0.000	0.000	0.000	0.000
102	C	127	GLU	-1	-0.889	-0.955	27.544	-0.172	-0.172	0.000	0.000	0.000	0.000
103	C	128	THR	0	-0.096	-0.058	29.883	0.017	0.017	0.000	0.000	0.000	0.000
104	C	137	LEU	0	0.040	0.024	19.046	-0.001	-0.001	0.000	0.000	0.000	0.000
105	C	138	SER	0	-0.071	-0.066	21.953	0.005	0.005	0.000	0.000	0.000	0.000
106	C	139	LEU	0	0.022	0.024	15.852	0.007	0.007	0.000	0.000	0.000	0.000
107	C	140	LYS	1	0.988	0.989	19.866	0.076	0.076	0.000	0.000	0.000	0.000
108	C	141	LEU	0	0.000	0.011	15.706	0.009	0.009	0.000	0.000	0.000	0.000
109	C	142	LEU	0	0.031	0.007	16.711	0.033	0.033	0.000	0.000	0.000	0.000
110	C	143	PRO	0	-0.007	0.008	17.669	-0.032	-0.032	0.000	0.000	0.000	0.000
111	C	144	GLY	0	-0.037	-0.030	16.690	0.042	0.042	0.000	0.000	0.000	0.000

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