FMO DATABASE

FMODB ID: VQJ31

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1270087.996014
FMO2-HF: Nuclear repulsion	1210376.15778
FMO2-HF: Total energy	-59711.838234
FMO2-MP2: Total energy	-59880.128206

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.
-13.56	-8.23	0.753	-2.665	-3.417	-0.01

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 : -0.007 / q_NPA : -0.006

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	0.923	0.954	3.514	-5.042	-2.973	0.009	-0.989	-1.090	0.003
4	A	188	ILE	0	0.028	0.013	2.610	-1.271	-0.093	0.400	-0.488	-1.089	-0.001
5	A	189	GLU	-1	-0.875	-0.945	2.815	-7.449	-5.366	0.344	-1.188	-1.238	-0.012
6	A	190	ALA	0	-0.044	-0.021	6.231	0.399	0.399	0.000	0.000	0.000	0.000
7	A	191	MET	0	-0.085	-0.037	7.643	0.227	0.227	0.000	0.000	0.000	0.000
8	A	192	ASP	-1	-0.883	-0.923	8.306	-0.676	-0.676	0.000	0.000	0.000	0.000
9	A	193	PRO	0	0.024	0.012	9.944	0.052	0.052	0.000	0.000	0.000	0.000
10	A	194	ALA	0	0.052	0.037	12.152	0.034	0.034	0.000	0.000	0.000	0.000
11	A	195	THR	0	-0.015	-0.026	10.360	0.088	0.088	0.000	0.000	0.000	0.000
12	A	196	VAL	0	-0.016	0.006	13.112	0.065	0.065	0.000	0.000	0.000	0.000
13	A	197	GLU	-1	-0.895	-0.954	15.451	-0.155	-0.155	0.000	0.000	0.000	0.000
14	A	198	GLN	0	-0.048	-0.021	15.328	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	199	GLN	0	-0.040	-0.018	14.579	0.054	0.054	0.000	0.000	0.000	0.000
16	A	200	GLU	-1	-0.784	-0.896	19.148	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	201	HIS	0	-0.002	0.001	21.261	0.001	0.001	0.000	0.000	0.000	0.000
18	A	202	TRP	0	-0.046	-0.021	21.731	0.006	0.006	0.000	0.000	0.000	0.000
19	A	203	PHE	0	0.018	0.007	23.408	0.009	0.009	0.000	0.000	0.000	0.000
20	A	204	GLU	-1	-0.842	-0.911	25.410	-0.067	-0.067	0.000	0.000	0.000	0.000
21	A	205	LYS	1	0.784	0.888	25.697	0.120	0.120	0.000	0.000	0.000	0.000
22	A	206	ALA	0	0.053	0.019	27.259	0.005	0.005	0.000	0.000	0.000	0.000
23	A	207	LEU	0	0.029	0.006	29.056	0.005	0.005	0.000	0.000	0.000	0.000
24	A	208	ARG	1	0.854	0.929	30.419	0.066	0.066	0.000	0.000	0.000	0.000
25	A	209	ASP	-1	-0.881	-0.930	30.817	-0.066	-0.066	0.000	0.000	0.000	0.000
26	A	210	LYS	1	0.806	0.893	31.836	0.049	0.049	0.000	0.000	0.000	0.000
27	A	211	LYS	1	0.811	0.896	34.670	0.016	0.016	0.000	0.000	0.000	0.000
28	A	212	GLY	0	-0.014	0.012	36.230	0.002	0.002	0.000	0.000	0.000	0.000
29	A	213	PHE	0	-0.020	-0.010	34.522	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	214	ILE	0	-0.001	-0.017	33.076	-0.006	-0.006	0.000	0.000	0.000	0.000
31	A	215	ILE	0	0.013	0.014	27.672	0.005	0.005	0.000	0.000	0.000	0.000
32	A	216	LYS	1	0.796	0.887	30.943	0.011	0.011	0.000	0.000	0.000	0.000
33	A	217	GLN	0	0.024	0.012	26.602	0.012	0.012	0.000	0.000	0.000	0.000
34	A	218	MET	0	-0.068	-0.020	29.976	0.003	0.003	0.000	0.000	0.000	0.000
35	A	219	LYS	1	0.798	0.881	29.917	0.006	0.006	0.000	0.000	0.000	0.000
36	A	220	GLU	-1	-0.906	-0.952	24.825	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	221	ASP	-1	-0.919	-0.968	28.988	0.029	0.029	0.000	0.000	0.000	0.000
38	A	222	GLY	0	0.007	0.005	29.080	0.002	0.002	0.000	0.000	0.000	0.000
39	A	223	ALA	0	-0.002	-0.004	28.283	0.000	0.000	0.000	0.000	0.000	0.000
40	A	224	CYS	0	-0.073	-0.024	29.614	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	225	LEU	0	0.078	0.033	33.038	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	226	PHE	0	0.026	-0.009	34.017	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	227	ARG	1	0.856	0.913	33.279	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	228	ALA	0	0.066	0.022	33.405	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	229	VAL	0	0.002	-0.019	35.534	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	230	ALA	0	-0.006	0.005	38.684	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	231	ASP	-1	-0.802	-0.886	37.720	-0.014	-0.014	0.000	0.000	0.000	0.000
48	A	232	GLN	0	0.010	0.015	37.879	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	233	VAL	0	-0.020	0.003	40.607	0.000	0.000	0.000	0.000	0.000	0.000
50	A	234	TYR	0	-0.023	-0.016	43.385	0.000	0.000	0.000	0.000	0.000	0.000
51	A	235	GLY	0	0.005	0.021	42.367	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	236	ASP	-1	-0.855	-0.950	40.892	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	237	GLN	0	0.073	0.052	34.302	0.004	0.004	0.000	0.000	0.000	0.000
54	A	238	ASP	-1	-0.839	-0.903	38.485	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	239	MET	0	-0.031	-0.003	40.403	0.003	0.003	0.000	0.000	0.000	0.000
56	A	240	HIS	0	0.046	0.021	37.222	0.000	0.000	0.000	0.000	0.000	0.000
57	A	241	GLU	-1	-0.788	-0.860	40.331	0.023	0.023	0.000	0.000	0.000	0.000
58	A	242	VAL	0	-0.022	-0.009	42.596	0.002	0.002	0.000	0.000	0.000	0.000
59	A	243	VAL	0	0.035	0.027	40.945	0.001	0.001	0.000	0.000	0.000	0.000
60	A	244	ARG	1	0.863	0.914	39.145	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	245	LYS	1	0.822	0.895	41.745	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	246	HIS	0	0.049	0.018	45.387	0.002	0.002	0.000	0.000	0.000	0.000
63	A	247	CYS	0	0.016	0.019	41.894	0.001	0.001	0.000	0.000	0.000	0.000
64	A	248	MET	0	-0.035	-0.006	39.564	0.002	0.002	0.000	0.000	0.000	0.000
65	A	249	ASP	-1	-0.828	-0.899	44.659	0.022	0.022	0.000	0.000	0.000	0.000
66	A	250	TYR	0	-0.024	-0.045	46.321	0.000	0.000	0.000	0.000	0.000	0.000
67	A	251	LEU	0	-0.002	-0.009	41.378	0.001	0.001	0.000	0.000	0.000	0.000
68	A	252	MET	0	-0.038	-0.013	46.001	0.001	0.001	0.000	0.000	0.000	0.000
69	A	253	LYS	1	0.747	0.849	48.435	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	254	ASN	0	-0.011	0.004	48.426	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	255	ALA	0	0.012	0.010	47.577	0.002	0.002	0.000	0.000	0.000	0.000
72	A	256	ASP	-1	-0.918	-0.959	47.892	0.035	0.035	0.000	0.000	0.000	0.000
73	A	257	TYR	0	-0.028	0.005	45.775	0.002	0.002	0.000	0.000	0.000	0.000
74	A	258	PHE	0	0.053	0.001	43.022	0.003	0.003	0.000	0.000	0.000	0.000
75	A	259	SER	0	-0.030	-0.013	43.366	0.003	0.003	0.000	0.000	0.000	0.000
76	A	260	ASN	0	-0.104	-0.042	44.640	0.003	0.003	0.000	0.000	0.000	0.000
77	A	261	TYR	0	-0.084	-0.031	38.491	0.004	0.004	0.000	0.000	0.000	0.000
78	A	279	HIS	0	0.027	0.005	32.159	0.003	0.003	0.000	0.000	0.000	0.000
79	A	280	GLY	0	-0.023	-0.018	33.018	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	281	ASN	0	0.005	-0.014	31.809	0.002	0.002	0.000	0.000	0.000	0.000
81	A	282	HIS	0	0.049	0.027	34.557	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	283	ILE	0	0.003	0.001	36.106	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	284	GLU	-1	-0.839	-0.923	35.747	0.039	0.039	0.000	0.000	0.000	0.000
84	A	285	MET	0	-0.040	-0.019	32.280	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	286	GLN	0	-0.031	-0.031	38.537	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	287	ALA	0	0.025	0.013	41.547	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	288	MET	0	-0.029	-0.024	38.023	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	289	ALA	0	0.013	0.014	41.951	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	290	GLU	-1	-0.821	-0.876	43.717	0.025	0.025	0.000	0.000	0.000	0.000
90	A	291	MET	0	-0.075	-0.019	44.235	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	292	TYR	0	-0.045	-0.035	43.441	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	293	ASN	0	-0.040	-0.023	47.744	0.000	0.000	0.000	0.000	0.000	0.000
93	A	294	ARG	1	0.845	0.916	43.093	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	295	PRO	0	0.022	0.014	42.481	0.002	0.002	0.000	0.000	0.000	0.000
95	A	296	VAL	0	-0.021	0.001	37.287	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	297	GLU	-1	-0.789	-0.846	36.421	0.005	0.005	0.000	0.000	0.000	0.000
97	A	298	VAL	0	-0.010	-0.019	30.803	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	299	TYR	0	-0.019	-0.041	30.237	0.000	0.000	0.000	0.000	0.000	0.000
99	A	300	GLN	0	-0.028	-0.033	24.101	0.013	0.013	0.000	0.000	0.000	0.000
100	A	301	TYR	0	0.012	0.010	18.030	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	302	SER	0	-0.029	-0.021	22.188	0.019	0.019	0.000	0.000	0.000	0.000
102	A	303	THR	0	0.011	0.000	18.982	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	304	GLY	0	0.013	0.018	22.294	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	305	THR	0	-0.016	-0.033	25.813	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	306	SER	0	-0.013	-0.003	29.111	0.003	0.003	0.000	0.000	0.000	0.000
106	A	307	ALA	0	0.036	0.031	26.143	0.004	0.004	0.000	0.000	0.000	0.000
107	A	308	VAL	0	-0.030	-0.004	28.149	0.000	0.000	0.000	0.000	0.000	0.000
108	A	309	GLU	-1	-0.829	-0.897	30.857	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	310	PRO	0	-0.027	0.000	31.690	0.002	0.002	0.000	0.000	0.000	0.000
110	A	311	ILE	0	-0.023	-0.014	27.992	0.003	0.003	0.000	0.000	0.000	0.000
111	A	312	ASN	0	-0.013	-0.009	31.689	0.005	0.005	0.000	0.000	0.000	0.000
112	A	313	THR	0	-0.041	-0.027	34.828	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	314	PHE	0	-0.001	0.018	35.238	0.003	0.003	0.000	0.000	0.000	0.000
114	A	315	HIS	0	0.034	0.004	40.321	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	316	GLY	0	0.058	0.041	44.070	0.002	0.002	0.000	0.000	0.000	0.000
116	A	317	ILE	0	-0.036	-0.017	47.176	0.001	0.001	0.000	0.000	0.000	0.000
117	A	318	HIS	0	-0.035	-0.021	50.593	0.000	0.000	0.000	0.000	0.000	0.000
118	A	319	GLN	0	-0.002	0.002	48.446	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	320	ASN	0	-0.086	-0.066	49.495	0.001	0.001	0.000	0.000	0.000	0.000
120	A	321	GLU	-1	-0.915	-0.959	49.735	0.000	0.000	0.000	0.000	0.000	0.000
121	A	322	ASP	-1	-0.935	-0.944	48.436	0.001	0.001	0.000	0.000	0.000	0.000
122	A	323	GLU	-1	-0.817	-0.899	43.065	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	324	PRO	0	-0.013	0.003	41.145	0.001	0.001	0.000	0.000	0.000	0.000
124	A	325	ILE	0	-0.023	0.005	38.553	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	326	ARG	1	0.724	0.828	35.814	0.006	0.006	0.000	0.000	0.000	0.000
126	A	327	VAL	0	-0.021	-0.017	32.994	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	328	SER	0	-0.016	-0.033	27.824	0.001	0.001	0.000	0.000	0.000	0.000
128	A	329	TYR	0	-0.034	-0.014	23.918	0.007	0.007	0.000	0.000	0.000	0.000
129	A	330	HIS	0	0.058	0.021	23.496	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	331	ARG	1	0.884	0.931	19.657	-0.131	-0.131	0.000	0.000	0.000	0.000
131	A	332	ASN	0	0.020	0.020	19.052	0.002	0.002	0.000	0.000	0.000	0.000
132	A	333	ILE	0	0.012	0.014	13.858	0.031	0.031	0.000	0.000	0.000	0.000
133	A	334	HIS	0	0.010	0.002	17.063	-0.029	-0.029	0.000	0.000	0.000	0.000
134	A	335	TYR	0	-0.018	-0.009	11.458	0.017	0.017	0.000	0.000	0.000	0.000
135	A	336	ASN	0	0.005	0.005	17.524	-0.037	-0.037	0.000	0.000	0.000	0.000
136	A	337	SER	0	0.007	0.001	18.543	0.022	0.022	0.000	0.000	0.000	0.000
137	A	338	VAL	0	0.018	0.008	16.817	0.001	0.001	0.000	0.000	0.000	0.000
138	A	339	VAL	0	-0.011	-0.006	19.945	0.000	0.000	0.000	0.000	0.000	0.000
139	A	340	ASN	0	0.026	0.002	22.516	0.018	0.018	0.000	0.000	0.000	0.000
140	A	341	PRO	0	-0.020	-0.010	24.365	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	342	ASN	0	-0.033	0.006	25.683	-0.014	-0.014	0.000	0.000	0.000	0.000

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