FMO DATABASE

FMODB ID: YVJ52

Calculation Name: 3TMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TMO

Chain ID: A

ChEMBL ID:

UniProt ID: Q96G74

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	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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1266688.449872
FMO2-HF: Nuclear repulsion	1206977.039961
FMO2-HF: Total energy	-59711.409911
FMO2-MP2: Total energy	-59879.695482

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:185:ALA)

Summations of interaction energy for fragment #1(A:185:ALA)

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.
-10.004	-6.64	1.636	-1.921	-3.08	0.001

Interaction energy analysis for fragmet #1(A:185:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.008

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	187	ARG	1	0.933	0.951	3.616	-5.798	-3.893	0.013	-0.864	-1.054	0.004
4	A	188	ILE	0	0.017	-0.001	2.343	-1.741	-0.775	1.622	-0.934	-1.654	-0.003
5	A	189	GLU	-1	-0.881	-0.932	3.977	-2.663	-2.170	0.001	-0.123	-0.372	0.000
6	A	190	ALA	0	-0.039	-0.020	6.112	0.404	0.404	0.000	0.000	0.000	0.000
7	A	191	MET	0	-0.072	-0.034	7.002	0.126	0.126	0.000	0.000	0.000	0.000
8	A	192	ASP	-1	-0.841	-0.911	8.368	-0.570	-0.570	0.000	0.000	0.000	0.000
9	A	193	PRO	0	-0.003	-0.012	9.905	0.057	0.057	0.000	0.000	0.000	0.000
10	A	194	ALA	0	0.039	0.041	11.909	0.034	0.034	0.000	0.000	0.000	0.000
11	A	195	THR	0	-0.003	-0.010	10.833	0.056	0.056	0.000	0.000	0.000	0.000
12	A	196	VAL	0	-0.024	-0.005	13.028	0.059	0.059	0.000	0.000	0.000	0.000
13	A	197	GLU	-1	-0.889	-0.945	15.473	-0.135	-0.135	0.000	0.000	0.000	0.000
14	A	198	GLN	0	-0.055	-0.018	16.116	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	199	GLN	0	-0.045	-0.019	14.648	0.050	0.050	0.000	0.000	0.000	0.000
16	A	200	GLU	-1	-0.795	-0.895	19.303	0.025	0.025	0.000	0.000	0.000	0.000
17	A	201	HIS	0	0.002	-0.001	21.314	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	202	TRP	0	-0.063	-0.032	22.114	0.008	0.008	0.000	0.000	0.000	0.000
19	A	203	PHE	0	0.008	-0.006	23.436	0.008	0.008	0.000	0.000	0.000	0.000
20	A	204	GLU	-1	-0.860	-0.927	25.309	-0.045	-0.045	0.000	0.000	0.000	0.000
21	A	205	LYS	1	0.792	0.898	25.934	0.088	0.088	0.000	0.000	0.000	0.000
22	A	206	ALA	0	0.040	0.023	27.701	0.003	0.003	0.000	0.000	0.000	0.000
23	A	207	LEU	0	0.038	0.019	29.478	0.003	0.003	0.000	0.000	0.000	0.000
24	A	208	ARG	1	0.862	0.925	30.785	0.042	0.042	0.000	0.000	0.000	0.000
25	A	209	ASP	-1	-0.884	-0.931	31.469	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	210	LYS	1	0.849	0.920	31.838	0.023	0.023	0.000	0.000	0.000	0.000
27	A	211	LYS	1	0.803	0.882	34.683	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	212	GLY	0	-0.008	0.017	36.009	0.001	0.001	0.000	0.000	0.000	0.000
29	A	213	PHE	0	-0.052	-0.028	34.363	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	214	ILE	0	-0.007	-0.017	33.378	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	215	ILE	0	0.010	0.014	28.088	0.004	0.004	0.000	0.000	0.000	0.000
32	A	216	LYS	1	0.834	0.902	31.452	0.003	0.003	0.000	0.000	0.000	0.000
33	A	217	GLN	0	0.009	0.000	26.624	0.009	0.009	0.000	0.000	0.000	0.000
34	A	218	MET	0	-0.046	0.000	30.449	0.001	0.001	0.000	0.000	0.000	0.000
35	A	219	LYS	1	0.787	0.869	30.039	0.003	0.003	0.000	0.000	0.000	0.000
36	A	220	GLU	-1	-0.937	-0.969	25.076	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	221	ASP	-1	-0.937	-0.962	28.751	0.029	0.029	0.000	0.000	0.000	0.000
38	A	222	GLY	0	0.042	0.023	28.666	0.002	0.002	0.000	0.000	0.000	0.000
39	A	223	ALA	0	-0.031	-0.019	28.047	0.000	0.000	0.000	0.000	0.000	0.000
40	A	224	CYS	0	-0.078	-0.038	29.081	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	225	LEU	0	0.093	0.049	32.078	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	226	PHE	0	0.025	-0.011	33.753	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	227	ARG	1	0.864	0.907	33.167	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	228	ALA	0	0.042	0.010	33.070	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	229	VAL	0	0.022	0.005	35.178	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	230	ALA	0	0.014	0.016	38.353	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	231	ASP	-1	-0.837	-0.909	37.354	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	232	GLN	0	0.019	0.022	37.569	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	233	VAL	0	-0.074	-0.031	40.246	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	234	TYR	0	-0.031	-0.035	43.040	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	235	GLY	0	0.001	0.025	41.915	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	236	ASP	-1	-0.864	-0.950	41.122	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	237	GLN	0	0.091	0.057	34.218	0.005	0.005	0.000	0.000	0.000	0.000
54	A	238	ASP	-1	-0.832	-0.884	38.713	0.001	0.001	0.000	0.000	0.000	0.000
55	A	239	MET	0	-0.007	0.011	40.646	0.001	0.001	0.000	0.000	0.000	0.000
56	A	240	HIS	0	0.026	-0.003	37.462	0.001	0.001	0.000	0.000	0.000	0.000
57	A	241	GLU	-1	-0.830	-0.914	40.090	0.023	0.023	0.000	0.000	0.000	0.000
58	A	242	VAL	0	-0.012	-0.004	42.286	0.002	0.002	0.000	0.000	0.000	0.000
59	A	243	VAL	0	0.023	0.022	40.553	0.001	0.001	0.000	0.000	0.000	0.000
60	A	244	ARG	1	0.891	0.943	39.070	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	245	LYS	1	0.824	0.906	41.576	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	246	HIS	0	0.063	0.030	45.078	0.002	0.002	0.000	0.000	0.000	0.000
63	A	247	CYS	0	0.015	0.025	41.444	0.002	0.002	0.000	0.000	0.000	0.000
64	A	248	MET	0	-0.051	-0.025	39.229	0.002	0.002	0.000	0.000	0.000	0.000
65	A	249	ASP	-1	-0.831	-0.902	44.346	0.025	0.025	0.000	0.000	0.000	0.000
66	A	250	TYR	0	-0.025	-0.044	45.826	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	251	LEU	0	0.004	-0.007	41.068	0.001	0.001	0.000	0.000	0.000	0.000
68	A	252	MET	0	-0.040	-0.009	45.672	0.001	0.001	0.000	0.000	0.000	0.000
69	A	253	LYS	1	0.776	0.861	48.097	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	254	ASN	0	-0.050	-0.009	48.048	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	255	ALA	0	0.018	0.009	47.278	0.002	0.002	0.000	0.000	0.000	0.000
72	A	256	ASP	-1	-0.892	-0.947	47.353	0.040	0.040	0.000	0.000	0.000	0.000
73	A	257	TYR	0	-0.020	-0.002	45.137	0.003	0.003	0.000	0.000	0.000	0.000
74	A	258	PHE	0	0.040	0.002	42.858	0.003	0.003	0.000	0.000	0.000	0.000
75	A	259	SER	0	-0.034	-0.013	43.052	0.003	0.003	0.000	0.000	0.000	0.000
76	A	260	ASN	0	-0.126	-0.055	43.781	0.003	0.003	0.000	0.000	0.000	0.000
77	A	261	TYR	0	-0.075	-0.020	38.362	0.005	0.005	0.000	0.000	0.000	0.000
78	A	279	HIS	0	0.029	0.009	31.880	0.003	0.003	0.000	0.000	0.000	0.000
79	A	280	GLY	0	-0.005	-0.008	32.954	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	281	ASN	0	0.048	0.007	31.145	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	282	HIS	0	0.055	0.023	33.889	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	283	ILE	0	-0.004	0.000	35.564	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	284	GLU	-1	-0.890	-0.954	35.723	0.044	0.044	0.000	0.000	0.000	0.000
84	A	285	MET	0	-0.058	-0.026	32.046	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	286	GLN	0	-0.040	-0.032	38.205	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	287	ALA	0	0.018	0.012	41.124	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	288	MET	0	-0.014	-0.021	37.845	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	289	ALA	0	0.023	0.019	41.689	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	290	GLU	-1	-0.820	-0.879	43.469	0.033	0.033	0.000	0.000	0.000	0.000
90	A	291	MET	0	-0.077	-0.019	44.001	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	292	TYR	0	-0.050	-0.037	43.000	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	293	ASN	0	0.010	0.007	47.239	0.000	0.000	0.000	0.000	0.000	0.000
93	A	294	ARG	1	0.881	0.943	43.368	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	295	PRO	0	0.057	0.029	41.979	0.002	0.002	0.000	0.000	0.000	0.000
95	A	296	VAL	0	-0.014	0.009	36.817	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	297	GLU	-1	-0.841	-0.888	36.074	0.022	0.022	0.000	0.000	0.000	0.000
97	A	298	VAL	0	0.011	-0.001	30.207	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	299	TYR	0	-0.013	-0.042	30.149	0.002	0.002	0.000	0.000	0.000	0.000
99	A	300	GLN	0	-0.012	-0.015	24.190	0.009	0.009	0.000	0.000	0.000	0.000
100	A	301	TYR	0	0.003	0.003	18.119	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	302	SER	0	-0.032	-0.029	22.469	0.017	0.017	0.000	0.000	0.000	0.000
102	A	303	THR	0	0.026	0.014	19.150	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	304	GLY	0	-0.011	0.001	22.576	0.000	0.000	0.000	0.000	0.000	0.000
104	A	305	THR	0	-0.011	-0.031	25.736	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	306	SER	0	-0.034	-0.013	29.023	0.001	0.001	0.000	0.000	0.000	0.000
106	A	307	ALA	0	0.080	0.053	26.270	0.004	0.004	0.000	0.000	0.000	0.000
107	A	308	VAL	0	-0.064	-0.034	28.239	0.001	0.001	0.000	0.000	0.000	0.000
108	A	309	GLU	-1	-0.821	-0.887	31.075	0.012	0.012	0.000	0.000	0.000	0.000
109	A	310	PRO	0	-0.005	0.013	31.650	0.003	0.003	0.000	0.000	0.000	0.000
110	A	311	ILE	0	-0.046	-0.029	27.880	0.003	0.003	0.000	0.000	0.000	0.000
111	A	312	ASN	0	-0.030	-0.028	31.467	0.005	0.005	0.000	0.000	0.000	0.000
112	A	313	THR	0	-0.005	0.000	34.556	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	314	PHE	0	-0.039	-0.009	34.977	0.004	0.004	0.000	0.000	0.000	0.000
114	A	315	HIS	0	0.047	0.015	40.083	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	316	GLY	0	0.064	0.040	43.793	0.001	0.001	0.000	0.000	0.000	0.000
116	A	317	ILE	0	-0.046	-0.022	46.471	0.001	0.001	0.000	0.000	0.000	0.000
117	A	318	HIS	0	-0.038	-0.023	50.026	0.001	0.001	0.000	0.000	0.000	0.000
118	A	319	GLN	0	-0.015	-0.010	48.220	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	320	ASN	0	-0.049	-0.031	49.236	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	321	GLU	-1	-0.921	-0.969	49.530	0.010	0.010	0.000	0.000	0.000	0.000
121	A	322	ASP	-1	-0.971	-0.963	47.826	0.009	0.009	0.000	0.000	0.000	0.000
122	A	323	GLU	-1	-0.820	-0.901	42.675	0.007	0.007	0.000	0.000	0.000	0.000
123	A	324	PRO	0	-0.026	-0.001	40.733	0.001	0.001	0.000	0.000	0.000	0.000
124	A	325	ILE	0	-0.028	-0.003	38.353	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	326	ARG	1	0.756	0.864	35.686	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	327	VAL	0	-0.017	-0.020	32.610	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	328	SER	0	-0.009	-0.031	27.670	0.003	0.003	0.000	0.000	0.000	0.000
128	A	329	TYR	0	-0.045	-0.021	23.596	0.006	0.006	0.000	0.000	0.000	0.000
129	A	330	HIS	0	0.050	0.026	23.030	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	331	ARG	1	0.895	0.941	19.714	-0.162	-0.162	0.000	0.000	0.000	0.000
131	A	332	ASN	0	0.035	0.025	19.024	0.003	0.003	0.000	0.000	0.000	0.000
132	A	333	ILE	0	0.008	0.003	13.660	0.023	0.023	0.000	0.000	0.000	0.000
133	A	334	HIS	0	0.024	0.008	16.920	-0.029	-0.029	0.000	0.000	0.000	0.000
134	A	335	TYR	0	-0.025	-0.004	11.911	0.044	0.044	0.000	0.000	0.000	0.000
135	A	336	ASN	0	0.011	0.010	17.266	-0.028	-0.028	0.000	0.000	0.000	0.000
136	A	337	SER	0	-0.004	-0.006	18.101	0.005	0.005	0.000	0.000	0.000	0.000
137	A	338	VAL	0	0.003	-0.005	16.768	0.008	0.008	0.000	0.000	0.000	0.000
138	A	339	VAL	0	0.010	0.006	19.734	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	340	ASN	0	0.018	-0.003	22.151	0.022	0.022	0.000	0.000	0.000	0.000
140	A	341	PRO	0	-0.025	-0.005	24.056	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	342	ASN	0	-0.016	0.009	25.421	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:185:ALA)