FMO DATABASE

FMODB ID: 5J87Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1265211.745619
FMO2-HF: Nuclear repulsion	1205501.27817
FMO2-HF: Total energy	-59710.46745
FMO2-MP2: Total energy	-59878.75891

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.
-8.834	-7.261	5.737	-3.639	-3.673	-0.004

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 : 0.023 / 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	0.930	0.951	3.613	-6.036	-4.110	0.013	-0.877	-1.063	0.004
4	A	188	ILE	0	0.026	0.009	2.029	-0.812	-1.623	5.723	-2.650	-2.262	-0.008
5	A	189	GLU	-1	-0.893	-0.939	3.935	-2.199	-1.741	0.001	-0.112	-0.348	0.000
6	A	190	ALA	0	-0.034	-0.016	6.077	0.406	0.406	0.000	0.000	0.000	0.000
7	A	191	MET	0	-0.081	-0.039	7.070	0.129	0.129	0.000	0.000	0.000	0.000
8	A	192	ASP	-1	-0.841	-0.927	8.372	-0.549	-0.549	0.000	0.000	0.000	0.000
9	A	193	PRO	0	-0.003	-0.012	9.882	0.062	0.062	0.000	0.000	0.000	0.000
10	A	194	ALA	0	0.057	0.065	11.878	0.040	0.040	0.000	0.000	0.000	0.000
11	A	195	THR	0	0.007	-0.009	10.991	0.052	0.052	0.000	0.000	0.000	0.000
12	A	196	VAL	0	-0.029	-0.008	13.109	0.061	0.061	0.000	0.000	0.000	0.000
13	A	197	GLU	-1	-0.898	-0.951	15.453	-0.149	-0.149	0.000	0.000	0.000	0.000
14	A	198	GLN	0	-0.054	-0.017	16.005	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	199	GLN	0	-0.056	-0.035	14.799	0.050	0.050	0.000	0.000	0.000	0.000
16	A	200	GLU	-1	-0.835	-0.920	19.279	0.022	0.022	0.000	0.000	0.000	0.000
17	A	201	HIS	0	0.027	0.011	21.283	0.004	0.004	0.000	0.000	0.000	0.000
18	A	202	TRP	0	-0.074	-0.035	22.087	0.007	0.007	0.000	0.000	0.000	0.000
19	A	203	PHE	0	0.018	-0.008	23.412	0.008	0.008	0.000	0.000	0.000	0.000
20	A	204	GLU	-1	-0.880	-0.945	25.287	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	205	LYS	1	0.826	0.917	25.718	0.085	0.085	0.000	0.000	0.000	0.000
22	A	206	ALA	0	0.023	0.025	27.734	0.003	0.003	0.000	0.000	0.000	0.000
23	A	207	LEU	0	0.034	0.015	29.452	0.003	0.003	0.000	0.000	0.000	0.000
24	A	208	ARG	1	0.966	0.993	30.640	0.042	0.042	0.000	0.000	0.000	0.000
25	A	209	ASP	-1	-0.960	-0.983	31.428	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	210	LYS	1	0.842	0.913	31.671	0.016	0.016	0.000	0.000	0.000	0.000
27	A	211	LYS	1	0.824	0.914	34.962	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	212	GLY	0	0.005	0.024	35.991	0.001	0.001	0.000	0.000	0.000	0.000
29	A	213	PHE	0	-0.055	-0.026	34.361	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	214	ILE	0	0.001	-0.011	33.371	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	215	ILE	0	-0.009	0.005	27.778	0.004	0.004	0.000	0.000	0.000	0.000
32	A	216	LYS	1	0.865	0.930	31.430	0.006	0.006	0.000	0.000	0.000	0.000
33	A	217	GLN	0	-0.007	-0.009	26.490	0.007	0.007	0.000	0.000	0.000	0.000
34	A	218	MET	0	-0.045	0.001	30.454	0.000	0.000	0.000	0.000	0.000	0.000
35	A	219	LYS	1	0.887	0.932	30.087	0.008	0.008	0.000	0.000	0.000	0.000
36	A	220	GLU	-1	-0.951	-0.976	25.665	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	221	ASP	-1	-0.923	-0.948	28.746	0.023	0.023	0.000	0.000	0.000	0.000
38	A	222	GLY	0	0.082	0.035	28.680	0.002	0.002	0.000	0.000	0.000	0.000
39	A	223	ALA	0	-0.047	-0.030	28.032	0.000	0.000	0.000	0.000	0.000	0.000
40	A	224	CYS	0	-0.096	-0.038	29.090	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	225	LEU	0	0.092	0.042	32.080	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	226	PHE	0	0.029	-0.013	33.755	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	227	ARG	1	0.881	0.933	33.372	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	228	ALA	0	0.041	0.014	33.074	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	229	VAL	0	0.019	0.003	35.172	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	230	ALA	0	0.013	0.015	38.349	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	231	ASP	-1	-0.861	-0.929	37.291	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	232	GLN	0	0.026	0.030	37.509	0.000	0.000	0.000	0.000	0.000	0.000
49	A	233	VAL	0	-0.069	-0.029	40.237	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	234	TYR	0	-0.031	-0.035	43.031	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	235	GLY	0	-0.006	0.022	41.899	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	236	ASP	-1	-0.871	-0.957	41.155	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	237	GLN	0	0.085	0.048	34.250	0.005	0.005	0.000	0.000	0.000	0.000
54	A	238	ASP	-1	-0.893	-0.940	38.705	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	239	MET	0	-0.027	0.004	40.639	0.001	0.001	0.000	0.000	0.000	0.000
56	A	240	HIS	0	0.023	-0.006	38.097	0.002	0.002	0.000	0.000	0.000	0.000
57	A	241	GLU	-1	-0.966	-0.993	40.088	0.014	0.014	0.000	0.000	0.000	0.000
58	A	242	VAL	0	-0.017	0.000	42.289	0.002	0.002	0.000	0.000	0.000	0.000
59	A	243	VAL	0	0.016	0.020	40.532	0.002	0.002	0.000	0.000	0.000	0.000
60	A	244	ARG	1	0.972	0.993	38.953	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	245	LYS	1	0.867	0.925	41.581	-0.014	-0.014	0.000	0.000	0.000	0.000
62	A	246	HIS	0	0.068	0.037	45.085	0.002	0.002	0.000	0.000	0.000	0.000
63	A	247	CYS	0	0.013	0.024	41.323	0.002	0.002	0.000	0.000	0.000	0.000
64	A	248	MET	0	-0.064	-0.036	39.250	0.002	0.002	0.000	0.000	0.000	0.000
65	A	249	ASP	-1	-0.917	-0.962	44.360	0.024	0.024	0.000	0.000	0.000	0.000
66	A	250	TYR	0	-0.040	-0.044	45.967	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	251	LEU	0	-0.001	-0.010	41.057	0.001	0.001	0.000	0.000	0.000	0.000
68	A	252	MET	0	-0.034	-0.006	45.687	0.001	0.001	0.000	0.000	0.000	0.000
69	A	253	LYS	1	0.909	0.946	48.113	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	254	ASN	0	-0.058	-0.012	48.072	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	255	ALA	0	0.025	0.013	47.297	0.002	0.002	0.000	0.000	0.000	0.000
72	A	256	ASP	-1	-0.888	-0.947	47.374	0.038	0.038	0.000	0.000	0.000	0.000
73	A	257	TYR	0	-0.017	-0.003	44.591	0.003	0.003	0.000	0.000	0.000	0.000
74	A	258	PHE	0	0.020	-0.018	42.691	0.003	0.003	0.000	0.000	0.000	0.000
75	A	259	SER	0	-0.036	-0.010	43.073	0.003	0.003	0.000	0.000	0.000	0.000
76	A	260	ASN	0	-0.066	-0.023	43.806	0.003	0.003	0.000	0.000	0.000	0.000
77	A	261	TYR	0	-0.109	-0.030	38.447	0.005	0.005	0.000	0.000	0.000	0.000
78	A	279	HIS	0	0.027	0.007	31.349	0.002	0.002	0.000	0.000	0.000	0.000
79	A	280	GLY	0	-0.005	-0.004	32.971	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	281	ASN	0	0.095	0.021	30.321	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	282	HIS	0	0.020	0.013	33.901	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	283	ILE	0	-0.001	0.005	35.576	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	284	GLU	-1	-0.917	-0.971	36.074	0.043	0.043	0.000	0.000	0.000	0.000
84	A	285	MET	0	-0.063	-0.023	32.121	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	286	GLN	0	-0.031	-0.018	38.207	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	287	ALA	0	0.018	0.009	41.132	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	288	MET	0	-0.019	-0.023	37.997	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	289	ALA	0	0.023	0.019	41.720	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	290	GLU	-1	-0.848	-0.908	43.472	0.032	0.032	0.000	0.000	0.000	0.000
90	A	291	MET	0	-0.084	-0.024	44.119	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	292	TYR	0	-0.042	-0.037	42.828	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	293	ASN	0	0.006	0.004	47.239	0.000	0.000	0.000	0.000	0.000	0.000
93	A	294	ARG	1	0.881	0.941	43.365	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	295	PRO	0	0.047	0.022	42.071	0.002	0.002	0.000	0.000	0.000	0.000
95	A	296	VAL	0	-0.011	0.014	36.759	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	297	GLU	-1	-0.843	-0.900	35.943	0.023	0.023	0.000	0.000	0.000	0.000
97	A	298	VAL	0	0.000	-0.007	30.176	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	299	TYR	0	-0.021	-0.038	30.104	0.003	0.003	0.000	0.000	0.000	0.000
99	A	300	GLN	0	-0.011	-0.019	23.783	0.011	0.011	0.000	0.000	0.000	0.000
100	A	301	TYR	0	0.034	0.038	18.237	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	302	SER	0	-0.028	-0.025	22.484	0.016	0.016	0.000	0.000	0.000	0.000
102	A	303	THR	0	0.017	0.008	19.163	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	304	GLY	0	-0.013	0.000	22.576	0.001	0.001	0.000	0.000	0.000	0.000
104	A	305	THR	0	-0.017	-0.031	25.736	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	306	SER	0	-0.030	-0.017	29.023	0.001	0.001	0.000	0.000	0.000	0.000
106	A	307	ALA	0	0.084	0.056	26.258	0.003	0.003	0.000	0.000	0.000	0.000
107	A	308	VAL	0	-0.078	-0.041	28.226	0.000	0.000	0.000	0.000	0.000	0.000
108	A	309	GLU	-1	-0.861	-0.929	31.060	0.015	0.015	0.000	0.000	0.000	0.000
109	A	310	PRO	0	0.005	0.019	31.642	0.004	0.004	0.000	0.000	0.000	0.000
110	A	311	ILE	0	-0.056	-0.033	28.026	0.004	0.004	0.000	0.000	0.000	0.000
111	A	312	ASN	0	-0.032	-0.032	31.466	0.005	0.005	0.000	0.000	0.000	0.000
112	A	313	THR	0	-0.002	0.003	34.558	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	314	PHE	0	-0.044	-0.012	35.041	0.004	0.004	0.000	0.000	0.000	0.000
114	A	315	HIS	0	0.040	0.013	40.086	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	316	GLY	0	0.073	0.043	43.796	0.001	0.001	0.000	0.000	0.000	0.000
116	A	317	ILE	0	-0.044	-0.017	46.474	0.001	0.001	0.000	0.000	0.000	0.000
117	A	318	HIS	0	-0.028	-0.020	50.030	0.001	0.001	0.000	0.000	0.000	0.000
118	A	319	GLN	0	0.006	-0.002	48.336	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	320	ASN	0	-0.063	-0.035	49.489	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	321	GLU	-1	-0.930	-0.973	49.523	0.010	0.010	0.000	0.000	0.000	0.000
121	A	322	ASP	-1	-0.950	-0.947	47.760	0.009	0.009	0.000	0.000	0.000	0.000
122	A	323	GLU	-1	-0.862	-0.917	42.675	0.006	0.006	0.000	0.000	0.000	0.000
123	A	324	PRO	0	-0.004	-0.001	40.635	0.001	0.001	0.000	0.000	0.000	0.000
124	A	325	ILE	0	-0.025	-0.004	38.253	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	326	ARG	1	0.779	0.878	35.716	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	327	VAL	0	-0.007	-0.014	32.297	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	328	SER	0	0.012	-0.011	27.838	0.003	0.003	0.000	0.000	0.000	0.000
128	A	329	TYR	0	-0.053	-0.027	23.492	0.006	0.006	0.000	0.000	0.000	0.000
129	A	330	HIS	0	0.060	0.029	22.936	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	331	ARG	1	0.895	0.941	19.435	-0.155	-0.155	0.000	0.000	0.000	0.000
131	A	332	ASN	0	0.030	0.025	19.022	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	333	ILE	0	0.010	0.004	13.546	0.022	0.022	0.000	0.000	0.000	0.000
133	A	334	HIS	0	0.028	0.018	16.922	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	335	TYR	0	-0.021	-0.003	11.747	0.038	0.038	0.000	0.000	0.000	0.000
135	A	336	ASN	0	0.014	0.003	17.275	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	337	SER	0	-0.020	-0.014	18.119	0.003	0.003	0.000	0.000	0.000	0.000
137	A	338	VAL	0	0.006	-0.003	16.957	0.010	0.010	0.000	0.000	0.000	0.000
138	A	339	VAL	0	0.014	0.006	19.762	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	340	ASN	0	0.000	-0.013	22.102	0.019	0.019	0.000	0.000	0.000	0.000
140	A	341	PRO	0	-0.023	-0.005	23.992	-0.009	-0.009	0.000	0.000	0.000	0.000
141	A	342	ASN	0	-0.003	0.018	25.879	-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)