FMO DATABASE

FMODB ID: R87Y8

Calculation Name: 4YTW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YTW

Chain ID: B

ChEMBL ID:

UniProt ID: O60200

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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1476795.347275
FMO2-HF: Nuclear repulsion	1409199.054065
FMO2-HF: Total energy	-67596.29321
FMO2-MP2: Total energy	-67793.176678

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(B:1:MET)

Summations of interaction energy for fragment #1(B: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.
-9.153	-6.562	10.251	-5.116	-7.729	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.012

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	B	3	LEU	0	-0.001	0.008	2.583	-2.124	0.543	1.379	-0.963	-3.084	0.003
4	B	4	LEU	0	-0.004	-0.014	4.828	0.071	0.135	-0.001	-0.004	-0.059	0.000
5	B	5	HIS	0	0.021	0.019	7.581	-0.120	-0.120	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.904	0.941	11.536	-0.117	-0.117	0.000	0.000	0.000	0.000
7	B	7	SER	0	-0.012	0.009	15.178	-0.006	-0.006	0.000	0.000	0.000	0.000
8	B	8	THR	0	0.047	0.026	18.530	0.006	0.006	0.000	0.000	0.000	0.000
9	B	9	HIS	0	-0.044	-0.010	22.130	-0.008	-0.008	0.000	0.000	0.000	0.000
10	B	10	ILE	0	0.053	0.027	25.180	0.003	0.003	0.000	0.000	0.000	0.000
11	B	11	PHE	0	-0.023	-0.006	26.241	-0.002	-0.002	0.000	0.000	0.000	0.000
12	B	12	PRO	0	0.039	0.041	31.008	0.001	0.001	0.000	0.000	0.000	0.000
13	B	13	THR	0	-0.032	-0.034	34.106	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	14	ASP	-1	-0.769	-0.876	34.729	0.037	0.037	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.070	0.019	30.777	0.001	0.001	0.000	0.000	0.000	0.000
16	B	16	ALA	0	0.011	0.022	34.164	0.002	0.002	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.036	-0.029	35.919	0.000	0.000	0.000	0.000	0.000	0.000
18	B	18	VAL	0	-0.002	0.006	29.549	0.001	0.001	0.000	0.000	0.000	0.000
19	B	19	SER	0	-0.007	-0.021	30.763	0.002	0.002	0.000	0.000	0.000	0.000
20	B	20	ARG	1	0.972	0.987	31.785	-0.032	-0.032	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.019	0.006	31.504	0.000	0.000	0.000	0.000	0.000	0.000
22	B	22	PHE	0	0.002	0.003	23.881	0.001	0.001	0.000	0.000	0.000	0.000
23	B	23	PHE	0	-0.020	-0.033	28.846	0.002	0.002	0.000	0.000	0.000	0.000
24	B	24	ASN	0	-0.052	-0.018	31.070	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	25	ARG	1	0.935	1.003	23.389	-0.072	-0.072	0.000	0.000	0.000	0.000
26	B	26	TYR	0	-0.023	0.022	23.900	0.000	0.000	0.000	0.000	0.000	0.000
27	B	27	PRO	0	0.060	0.014	30.218	0.000	0.000	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.035	-0.018	27.181	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	29	PRO	0	0.028	0.001	29.420	0.002	0.002	0.000	0.000	0.000	0.000
30	B	30	TYR	0	0.031	0.021	26.029	-0.002	-0.002	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.082	-0.035	24.447	0.007	0.007	0.000	0.000	0.000	0.000
32	B	32	PRO	0	0.033	0.023	25.453	0.001	0.001	0.000	0.000	0.000	0.000
33	B	33	HIS	0	-0.077	-0.044	21.708	-0.002	-0.002	0.000	0.000	0.000	0.000
34	B	34	VAL	0	-0.026	-0.003	23.608	0.003	0.003	0.000	0.000	0.000	0.000
35	B	35	LEU	0	-0.010	-0.009	25.415	-0.004	-0.004	0.000	0.000	0.000	0.000
36	B	36	SER	0	0.030	0.012	27.158	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.035	-0.028	26.861	0.005	0.005	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.883	-0.915	28.563	0.038	0.038	0.000	0.000	0.000	0.000
39	B	39	THR	0	-0.049	-0.044	29.076	0.005	0.005	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.021	-0.005	26.994	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	41	SER	0	0.016	0.001	28.950	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.934	0.947	30.841	-0.051	-0.051	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.044	-0.001	32.052	-0.002	-0.002	0.000	0.000	0.000	0.000
44	B	44	VAL	0	0.037	0.028	34.254	0.002	0.002	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.751	-0.869	32.605	0.070	0.070	0.000	0.000	0.000	0.000
46	B	46	GLN	0	0.019	-0.016	35.419	-0.001	-0.001	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.998	-0.990	32.967	0.075	0.075	0.000	0.000	0.000	0.000
48	B	48	GLY	0	-0.019	0.004	36.917	-0.002	-0.002	0.000	0.000	0.000	0.000
49	B	49	ASN	0	-0.013	-0.011	32.452	-0.004	-0.004	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.039	-0.012	33.102	0.000	0.000	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.856	0.928	26.905	-0.083	-0.083	0.000	0.000	0.000	0.000
52	B	52	THR	0	0.009	-0.002	29.006	-0.006	-0.006	0.000	0.000	0.000	0.000
53	B	53	THR	0	-0.014	0.002	24.677	0.009	0.009	0.000	0.000	0.000	0.000
54	B	54	ARG	1	0.748	0.832	25.719	-0.067	-0.067	0.000	0.000	0.000	0.000
55	B	55	LEU	0	0.006	0.008	23.309	0.007	0.007	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.016	0.006	22.863	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	57	LYS	1	0.965	1.015	23.092	-0.028	-0.028	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.915	0.961	18.434	-0.085	-0.085	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.058	0.029	21.155	0.003	0.003	0.000	0.000	0.000	0.000
60	B	60	GLY	0	-0.009	-0.032	19.052	0.010	0.010	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.956	0.972	18.631	-0.010	-0.010	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.011	0.021	13.643	0.014	0.014	0.000	0.000	0.000	0.000
63	B	63	PRO	0	0.037	0.019	11.857	-0.018	-0.018	0.000	0.000	0.000	0.000
64	B	64	THR	0	0.038	-0.001	14.747	-0.017	-0.017	0.000	0.000	0.000	0.000
65	B	65	TRP	0	0.054	0.021	7.314	-0.015	-0.015	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.006	0.003	10.245	-0.033	-0.033	0.000	0.000	0.000	0.000
67	B	67	LYS	1	0.936	0.957	12.813	0.038	0.038	0.000	0.000	0.000	0.000
68	B	68	PRO	0	0.019	0.030	14.825	0.007	0.007	0.000	0.000	0.000	0.000
69	B	69	PHE	0	-0.032	-0.021	11.860	-0.014	-0.014	0.000	0.000	0.000	0.000
70	B	70	LEU	0	-0.051	-0.022	10.985	0.005	0.005	0.000	0.000	0.000	0.000
71	B	71	ARG	1	0.972	0.993	14.882	0.026	0.026	0.000	0.000	0.000	0.000
72	B	72	GLY	0	0.023	-0.001	17.671	0.007	0.007	0.000	0.000	0.000	0.000
73	B	73	ILE	0	-0.047	-0.024	15.009	0.003	0.003	0.000	0.000	0.000	0.000
74	B	74	THR	0	0.024	0.003	18.982	0.002	0.002	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.913	-0.949	20.733	0.030	0.030	0.000	0.000	0.000	0.000
76	B	76	THR	0	-0.086	-0.034	16.324	0.005	0.005	0.000	0.000	0.000	0.000
77	B	77	TRP	0	0.052	0.036	19.402	0.001	0.001	0.000	0.000	0.000	0.000
78	B	78	ILE	0	-0.020	-0.022	17.969	0.009	0.009	0.000	0.000	0.000	0.000
79	B	79	ILE	0	-0.001	0.019	18.725	-0.007	-0.007	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.806	-0.895	20.259	0.081	0.081	0.000	0.000	0.000	0.000
81	B	81	VAL	0	-0.004	-0.002	21.641	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	82	SER	0	-0.011	-0.016	23.461	0.002	0.002	0.000	0.000	0.000	0.000
83	B	83	VAL	0	-0.009	-0.012	26.034	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	84	VAL	0	-0.009	-0.004	28.538	0.001	0.001	0.000	0.000	0.000	0.000
85	B	85	ASN	0	0.056	0.031	31.280	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	86	PRO	0	0.007	-0.017	33.302	-0.001	-0.001	0.000	0.000	0.000	0.000
87	B	87	ALA	0	0.018	0.024	36.483	-0.003	-0.003	0.000	0.000	0.000	0.000
88	B	88	ASN	0	0.017	-0.004	31.358	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	89	SER	0	-0.009	0.011	33.835	-0.001	-0.001	0.000	0.000	0.000	0.000
90	B	90	THR	0	0.004	0.007	28.126	0.002	0.002	0.000	0.000	0.000	0.000
91	B	91	MET	0	-0.043	-0.013	27.109	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	92	LYS	1	0.959	0.989	23.741	-0.102	-0.102	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.031	-0.033	22.234	-0.002	-0.002	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.023	-0.057	14.405	0.004	0.004	0.000	0.000	0.000	0.000
95	B	95	THR	0	0.015	0.020	17.669	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	96	ARG	1	0.955	0.983	13.931	-0.119	-0.119	0.000	0.000	0.000	0.000
97	B	97	ASN	0	-0.015	0.001	11.965	0.006	0.006	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.023	-0.029	15.059	0.003	0.003	0.000	0.000	0.000	0.000
99	B	99	ASP	-1	-0.787	-0.890	16.459	0.051	0.051	0.000	0.000	0.000	0.000
100	B	100	HIS	0	0.023	-0.014	13.595	-0.002	-0.002	0.000	0.000	0.000	0.000
101	B	101	THR	0	-0.005	-0.001	10.898	-0.007	-0.007	0.000	0.000	0.000	0.000
102	B	102	GLY	0	-0.003	0.014	9.133	-0.051	-0.051	0.000	0.000	0.000	0.000
103	B	103	ILE	0	-0.045	-0.014	8.689	-0.132	-0.132	0.000	0.000	0.000	0.000
104	B	104	MET	0	0.010	0.019	4.416	-0.443	-0.209	0.004	-0.044	-0.195	0.000
105	B	105	LYS	1	0.938	0.999	7.557	-0.213	-0.213	0.000	0.000	0.000	0.000
106	B	106	VAL	0	0.003	-0.005	8.647	0.000	0.000	0.000	0.000	0.000	0.000
107	B	107	GLU	-1	-0.893	-0.924	10.725	0.205	0.205	0.000	0.000	0.000	0.000
108	B	108	GLU	-1	-0.867	-0.914	12.459	0.132	0.132	0.000	0.000	0.000	0.000
109	B	109	TYR	0	-0.044	-0.025	14.824	-0.006	-0.006	0.000	0.000	0.000	0.000
110	B	110	THR	0	0.014	-0.004	17.630	0.001	0.001	0.000	0.000	0.000	0.000
111	B	111	THR	0	-0.050	-0.011	20.439	0.000	0.000	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.002	0.007	23.601	-0.001	-0.001	0.000	0.000	0.000	0.000
113	B	113	GLN	0	0.024	-0.010	26.886	0.006	0.006	0.000	0.000	0.000	0.000
114	B	114	PHE	0	-0.012	0.006	29.417	-0.002	-0.002	0.000	0.000	0.000	0.000
115	B	115	ASP	-1	-0.822	-0.897	32.306	0.043	0.043	0.000	0.000	0.000	0.000
116	B	116	SER	0	0.006	-0.026	34.148	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	117	ALA	0	-0.023	0.003	36.715	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	118	THR	0	-0.033	-0.035	34.462	-0.002	-0.002	0.000	0.000	0.000	0.000
119	B	119	SER	0	-0.057	-0.016	36.994	-0.002	-0.002	0.000	0.000	0.000	0.000
120	B	120	SER	0	-0.014	-0.001	32.901	-0.002	-0.002	0.000	0.000	0.000	0.000
121	B	121	THR	0	-0.038	-0.024	29.328	0.003	0.003	0.000	0.000	0.000	0.000
122	B	122	ILE	0	0.003	0.006	25.956	-0.001	-0.001	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.008	-0.010	24.016	0.004	0.004	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.858	-0.920	21.010	0.072	0.072	0.000	0.000	0.000	0.000
125	B	125	SER	0	0.001	-0.026	17.440	0.004	0.004	0.000	0.000	0.000	0.000
126	B	126	ARG	1	0.858	0.921	14.255	-0.158	-0.158	0.000	0.000	0.000	0.000
127	B	127	VAL	0	0.046	0.025	10.581	0.004	0.004	0.000	0.000	0.000	0.000
128	B	128	LYS	1	0.926	0.969	7.261	-0.405	-0.405	0.000	0.000	0.000	0.000
129	B	129	PHE	0	0.003	0.007	5.508	0.050	0.050	0.000	0.000	0.000	0.000
130	B	130	SER	0	-0.008	-0.024	4.452	-0.740	-0.525	-0.001	-0.080	-0.135	0.000
131	B	131	SER	0	-0.009	-0.054	2.882	0.700	1.868	0.032	-0.388	-0.812	0.001
132	B	132	GLY	0	0.064	0.039	1.957	-6.987	-9.096	8.837	-3.580	-3.148	-0.038
133	B	133	PHE	0	0.012	0.028	3.899	0.412	0.565	0.002	-0.041	-0.114	0.000
134	B	134	ASN	0	-0.027	-0.017	4.351	-0.558	-0.359	-0.001	-0.016	-0.182	0.000
135	B	135	MET	0	0.007	-0.003	6.265	0.127	0.127	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.027	0.016	9.007	0.051	0.051	0.000	0.000	0.000	0.000
137	B	137	ILE	0	-0.009	-0.010	8.589	0.071	0.071	0.000	0.000	0.000	0.000
138	B	138	LYS	1	0.970	0.977	8.011	0.698	0.698	0.000	0.000	0.000	0.000
139	B	139	SER	0	0.067	0.035	12.472	0.048	0.048	0.000	0.000	0.000	0.000
140	B	140	LYS	1	0.990	1.007	13.791	0.277	0.277	0.000	0.000	0.000	0.000
141	B	141	VAL	0	-0.021	-0.007	12.874	0.021	0.021	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.936	-0.967	15.912	-0.123	-0.123	0.000	0.000	0.000	0.000
143	B	143	ASP	-1	-0.851	-0.923	18.451	-0.151	-0.151	0.000	0.000	0.000	0.000
144	B	144	TRP	0	-0.023	-0.012	19.004	0.018	0.018	0.000	0.000	0.000	0.000
145	B	145	SER	0	-0.004	-0.017	19.149	0.016	0.016	0.000	0.000	0.000	0.000
146	B	146	ARG	1	0.898	0.951	21.456	0.145	0.145	0.000	0.000	0.000	0.000
147	B	147	THR	0	0.000	0.000	23.989	0.016	0.016	0.000	0.000	0.000	0.000
148	B	148	LYS	1	0.860	0.949	24.261	0.148	0.148	0.000	0.000	0.000	0.000
149	B	149	PHE	0	0.010	0.001	25.831	0.009	0.009	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.875	-0.941	27.667	-0.069	-0.069	0.000	0.000	0.000	0.000
151	B	151	GLU	-1	-0.874	-0.948	28.788	-0.103	-0.103	0.000	0.000	0.000	0.000
152	B	152	ASN	0	-0.011	-0.033	28.187	0.008	0.008	0.000	0.000	0.000	0.000
153	B	153	VAL	0	-0.007	0.020	31.597	0.006	0.006	0.000	0.000	0.000	0.000
154	B	154	LYS	1	0.909	0.949	33.659	0.072	0.072	0.000	0.000	0.000	0.000
155	B	155	LYS	1	0.953	0.980	32.881	0.086	0.086	0.000	0.000	0.000	0.000
156	B	156	SER	0	-0.009	0.011	35.197	0.004	0.004	0.000	0.000	0.000	0.000
157	B	157	ARG	1	0.998	0.998	37.030	0.055	0.055	0.000	0.000	0.000	0.000
158	B	158	MET	0	-0.037	-0.030	39.442	0.002	0.002	0.000	0.000	0.000	0.000
159	B	159	GLY	0	0.034	0.030	39.988	0.002	0.002	0.000	0.000	0.000	0.000
160	B	160	MET	0	0.006	-0.005	40.599	0.002	0.002	0.000	0.000	0.000	0.000
161	B	161	ALA	0	0.004	0.006	42.935	0.002	0.002	0.000	0.000	0.000	0.000
162	B	162	PHE	0	-0.020	-0.008	44.639	0.002	0.002	0.000	0.000	0.000	0.000
163	B	163	VAL	0	-0.024	-0.026	44.360	0.002	0.002	0.000	0.000	0.000	0.000
164	B	164	ILE	0	0.020	0.008	46.100	0.001	0.001	0.000	0.000	0.000	0.000
165	B	165	GLN	0	0.008	0.008	48.900	0.001	0.001	0.000	0.000	0.000	0.000
166	B	166	LYS	1	0.892	0.959	48.158	0.043	0.043	0.000	0.000	0.000	0.000
167	B	167	LEU	0	-0.086	-0.056	49.437	0.001	0.001	0.000	0.000	0.000	0.000
168	B	168	GLU	-1	-0.970	-0.954	52.893	-0.026	-0.026	0.000	0.000	0.000	0.000

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