FMO DATABASE

FMODB ID: VR8M1

Calculation Name: 3N50-B-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N50

Chain ID: B

ChEMBL ID:

UniProt ID: Q9H4W6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	156
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1312886.186628
FMO2-HF: Nuclear repulsion	1253715.618145
FMO2-HF: Total energy	-59170.568483
FMO2-MP2: Total energy	-59344.780861

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:251:ACE )

Summations of interaction energy for fragment #1(B:251:ACE )

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.
1.573	2.439	-0.006	-0.407	-0.453	0

Interaction energy analysis for fragmet #1(B:251:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.000

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].
3	B	253	THR	0	-0.017	0.001	3.827	1.002	1.868	-0.006	-0.407	-0.453
4	B	254	PRO	0	0.024	0.015	7.036	-0.015	-0.015	0.000	0.000	0.000
5	B	255	CYS	0	-0.044	-0.014	9.749	0.017	0.017	0.000	0.000	0.000
6	B	256	ILE	0	0.055	0.006	12.593	0.052	0.052	0.000	0.000	0.000
7	B	257	LYS	1	0.904	0.946	13.865	0.283	0.283	0.000	0.000	0.000
8	B	258	ALA	0	-0.003	-0.003	17.882	0.014	0.014	0.000	0.000	0.000
9	B	259	ILE	0	-0.021	0.000	20.406	-0.001	-0.001	0.000	0.000	0.000
10	B	260	SER	0	-0.031	0.020	23.024	0.004	0.004	0.000	0.000	0.000
11	B	261	PRO	0	0.078	0.018	25.770	0.005	0.005	0.000	0.000	0.000
12	B	262	SER	0	0.029	0.001	27.087	-0.003	-0.003	0.000	0.000	0.000
13	B	263	GLU	-1	-0.957	-0.983	28.132	-0.047	-0.047	0.000	0.000	0.000
14	B	264	GLY	0	-0.006	-0.001	31.282	0.003	0.003	0.000	0.000	0.000
15	B	265	TRP	0	0.050	0.035	32.840	-0.001	-0.001	0.000	0.000	0.000
16	B	266	THR	0	0.022	0.001	34.297	-0.001	-0.001	0.000	0.000	0.000
17	B	267	THR	0	0.041	0.025	35.436	0.000	0.000	0.000	0.000	0.000
18	B	268	GLY	0	-0.041	-0.010	32.413	0.002	0.002	0.000	0.000	0.000
19	B	269	GLY	0	-0.048	-0.032	31.515	0.002	0.002	0.000	0.000	0.000
20	B	270	ALA	0	-0.021	-0.005	30.760	0.003	0.003	0.000	0.000	0.000
21	B	271	THR	0	-0.016	-0.014	26.454	-0.001	-0.001	0.000	0.000	0.000
22	B	272	VAL	0	-0.012	-0.001	23.460	-0.003	-0.003	0.000	0.000	0.000
23	B	273	ILE	0	-0.024	-0.013	20.944	0.005	0.005	0.000	0.000	0.000
24	B	274	ILE	0	-0.008	-0.006	17.366	-0.011	-0.011	0.000	0.000	0.000
25	B	275	ILE	0	0.041	0.010	17.466	0.008	0.008	0.000	0.000	0.000
26	B	276	GLY	0	0.011	-0.006	14.471	-0.018	-0.018	0.000	0.000	0.000
27	B	277	ASP	-1	-0.895	-0.929	9.500	-0.321	-0.321	0.000	0.000	0.000
28	B	278	ASN	0	-0.037	-0.027	5.942	0.000	0.000	0.000	0.000	0.000
29	B	279	PHE	0	-0.022	0.003	8.126	0.045	0.045	0.000	0.000	0.000
30	B	280	PHE	0	-0.004	-0.022	8.465	0.076	0.076	0.000	0.000	0.000
31	B	281	ASP	-1	-0.881	-0.941	11.532	0.084	0.084	0.000	0.000	0.000
32	B	282	GLY	0	0.024	0.015	13.749	0.020	0.020	0.000	0.000	0.000
33	B	283	LEU	0	-0.095	-0.025	12.048	-0.020	-0.020	0.000	0.000	0.000
34	B	284	GLN	0	-0.016	-0.019	14.825	0.006	0.006	0.000	0.000	0.000
35	B	285	VAL	0	0.004	0.003	16.916	-0.026	-0.026	0.000	0.000	0.000
36	B	286	VAL	0	-0.024	-0.019	18.940	0.015	0.015	0.000	0.000	0.000
37	B	287	PHE	0	0.054	0.015	21.538	-0.012	-0.012	0.000	0.000	0.000
38	B	288	GLY	0	0.026	0.011	24.602	0.009	0.009	0.000	0.000	0.000
39	B	289	THR	0	-0.030	-0.022	24.461	-0.006	-0.006	0.000	0.000	0.000
40	B	290	MET	0	-0.041	-0.011	25.393	0.005	0.005	0.000	0.000	0.000
41	B	291	LEU	0	-0.009	0.007	19.812	-0.006	-0.006	0.000	0.000	0.000
42	B	292	VAL	0	-0.001	0.012	22.221	0.008	0.008	0.000	0.000	0.000
43	B	293	TRP	0	0.014	-0.008	19.442	-0.008	-0.008	0.000	0.000	0.000
44	B	294	SER	0	-0.065	-0.039	17.921	-0.010	-0.010	0.000	0.000	0.000
45	B	295	GLU	-1	-0.817	-0.895	19.321	0.035	0.035	0.000	0.000	0.000
46	B	296	LEU	0	-0.004	-0.007	13.570	-0.016	-0.016	0.000	0.000	0.000
47	B	297	ILE	0	-0.040	-0.002	17.470	0.010	0.010	0.000	0.000	0.000
48	B	298	THR	0	0.026	-0.002	15.777	0.008	0.008	0.000	0.000	0.000
49	B	299	PRO	0	0.046	0.016	10.271	-0.022	-0.022	0.000	0.000	0.000
50	B	300	HIS	1	0.850	0.915	11.477	0.098	0.098	0.000	0.000	0.000
51	B	301	ALA	0	-0.010	-0.003	14.123	-0.019	-0.019	0.000	0.000	0.000
52	B	302	ILE	0	0.038	0.029	14.516	0.022	0.022	0.000	0.000	0.000
53	B	303	ARG	1	0.880	0.943	18.081	-0.022	-0.022	0.000	0.000	0.000
54	B	304	VAL	0	0.036	0.015	20.913	0.007	0.007	0.000	0.000	0.000
55	B	305	GLN	0	0.019	0.003	23.459	0.000	0.000	0.000	0.000	0.000
56	B	306	THR	0	-0.026	-0.003	26.896	-0.001	-0.001	0.000	0.000	0.000
57	B	307	PRO	0	0.027	0.032	26.611	0.006	0.006	0.000	0.000	0.000
58	B	308	PRO	0	0.024	0.018	29.542	-0.004	-0.004	0.000	0.000	0.000
59	B	309	ARG	1	0.908	0.959	30.950	0.048	0.048	0.000	0.000	0.000
60	B	310	HIS	0	0.028	0.008	33.845	0.001	0.001	0.000	0.000	0.000
61	B	311	ILE	0	-0.017	-0.002	35.194	0.001	0.001	0.000	0.000	0.000
62	B	312	PRO	0	0.037	0.011	35.300	-0.003	-0.003	0.000	0.000	0.000
63	B	313	GLY	0	0.013	0.013	34.672	0.000	0.000	0.000	0.000	0.000
64	B	314	VAL	0	-0.011	-0.003	28.988	-0.001	-0.001	0.000	0.000	0.000
65	B	315	VAL	0	-0.043	-0.014	26.312	0.002	0.002	0.000	0.000	0.000
66	B	316	GLU	-1	-0.927	-0.973	23.457	-0.129	-0.129	0.000	0.000	0.000
67	B	317	VAL	0	-0.023	-0.013	20.254	0.006	0.006	0.000	0.000	0.000
68	B	318	THR	0	-0.004	0.001	17.896	-0.017	-0.017	0.000	0.000	0.000
69	B	319	LEU	0	0.016	0.018	13.376	0.017	0.017	0.000	0.000	0.000
70	B	320	SER	0	-0.017	-0.010	15.067	-0.020	-0.020	0.000	0.000	0.000
71	B	321	TYR	0	0.078	0.031	10.785	0.014	0.014	0.000	0.000	0.000
72	B	322	LYS	1	0.966	0.992	13.801	-0.114	-0.114	0.000	0.000	0.000
73	B	323	SER	0	0.020	0.006	15.916	-0.002	-0.002	0.000	0.000	0.000
74	B	324	LYS	1	0.948	1.005	10.826	0.238	0.238	0.000	0.000	0.000
75	B	325	GLN	0	-0.010	-0.010	14.590	-0.005	-0.005	0.000	0.000	0.000
76	B	326	PHE	0	0.001	-0.030	9.305	-0.059	-0.059	0.000	0.000	0.000
77	B	327	CYS	0	0.014	-0.001	13.700	0.022	0.022	0.000	0.000	0.000
78	B	328	LYS	1	1.004	0.997	15.543	0.182	0.182	0.000	0.000	0.000
79	B	329	GLY	0	-0.010	0.003	17.244	0.019	0.019	0.000	0.000	0.000
80	B	330	ALA	0	-0.037	-0.014	16.543	0.000	0.000	0.000	0.000	0.000
81	B	331	PRO	0	0.007	0.024	18.114	-0.011	-0.011	0.000	0.000	0.000
82	B	332	GLY	0	0.017	0.016	20.336	0.003	0.003	0.000	0.000	0.000
83	B	333	ARG	1	0.916	0.948	21.865	0.118	0.118	0.000	0.000	0.000
84	B	334	PHE	0	0.024	0.020	25.586	0.001	0.001	0.000	0.000	0.000
85	B	335	VAL	0	0.023	0.008	27.558	-0.001	-0.001	0.000	0.000	0.000
86	B	336	TYR	0	-0.065	-0.044	29.343	0.001	0.001	0.000	0.000	0.000
87	B	337	THR	0	0.052	0.004	33.665	-0.002	-0.002	0.000	0.000	0.000
88	B	338	ALA	0	0.003	-0.003	37.214	0.002	0.002	0.000	0.000	0.000
89	B	339	LEU	0	-0.017	-0.004	40.112	0.000	0.000	0.000	0.000	0.000
90	B	340	ASN	0	0.001	-0.003	41.583	0.001	0.001	0.000	0.000	0.000
91	B	341	GLU	-1	-0.866	-0.936	45.191	-0.015	-0.015	0.000	0.000	0.000
92	B	342	PRO	0	-0.021	-0.008	44.368	-0.001	-0.001	0.000	0.000	0.000
93	B	343	THR	0	0.029	0.016	40.839	0.000	0.000	0.000	0.000	0.000
94	B	344	ILE	0	0.057	0.012	43.072	0.001	0.001	0.000	0.000	0.000
95	B	345	ASP	-1	-0.911	-0.963	38.231	-0.013	-0.013	0.000	0.000	0.000
96	B	346	TYR	0	-0.058	-0.020	37.447	0.002	0.002	0.000	0.000	0.000
97	B	347	GLY	0	0.056	0.019	39.856	0.001	0.001	0.000	0.000	0.000
98	B	348	PHE	0	0.006	-0.002	39.526	0.002	0.002	0.000	0.000	0.000
99	B	349	GLN	0	-0.022	-0.004	34.492	0.002	0.002	0.000	0.000	0.000
100	B	350	ARG	1	0.930	0.974	37.020	0.009	0.009	0.000	0.000	0.000
101	B	351	LEU	0	0.050	-0.001	39.366	0.002	0.002	0.000	0.000	0.000
102	B	352	GLN	0	-0.051	-0.018	34.926	0.004	0.004	0.000	0.000	0.000
103	B	353	LYS	1	0.927	0.978	35.097	0.007	0.007	0.000	0.000	0.000
104	B	354	VAL	0	-0.053	-0.032	37.112	0.001	0.001	0.000	0.000	0.000
105	B	355	ILE	0	-0.035	0.007	40.615	0.001	0.001	0.000	0.000	0.000
106	B	356	PRO	0	0.011	0.004	40.307	0.001	0.001	0.000	0.000	0.000
107	B	357	ARG	1	0.853	0.901	35.128	-0.020	-0.020	0.000	0.000	0.000
108	B	358	HIS	0	0.026	0.022	40.762	0.001	0.001	0.000	0.000	0.000
109	B	359	PRO	0	0.006	-0.010	40.340	0.001	0.001	0.000	0.000	0.000
110	B	360	GLY	0	0.010	0.010	38.614	0.000	0.000	0.000	0.000	0.000
111	B	361	ASP	-1	-0.796	-0.881	38.537	0.016	0.016	0.000	0.000	0.000
112	B	362	PRO	0	0.008	-0.004	35.482	0.002	0.002	0.000	0.000	0.000
113	B	363	GLU	-1	-0.899	-0.932	28.354	0.030	0.030	0.000	0.000	0.000
114	B	364	ARG	1	0.915	0.954	32.179	-0.004	-0.004	0.000	0.000	0.000
115	B	365	LEU	0	-0.007	-0.002	34.440	0.000	0.000	0.000	0.000	0.000
116	B	366	PRO	0	0.038	0.014	38.233	-0.002	-0.002	0.000	0.000	0.000
117	B	367	LYS	1	0.979	0.973	38.028	0.005	0.005	0.000	0.000	0.000
118	B	368	GLU	-1	-0.876	-0.938	41.990	0.006	0.006	0.000	0.000	0.000
119	B	369	VAL	0	0.036	0.016	42.463	0.000	0.000	0.000	0.000	0.000
120	B	370	LEU	0	-0.060	-0.019	39.420	0.000	0.000	0.000	0.000	0.000
121	B	371	LEU	0	0.030	0.006	43.707	0.000	0.000	0.000	0.000	0.000
122	B	372	LYS	1	0.869	0.940	47.008	-0.007	-0.007	0.000	0.000	0.000
123	B	373	ARG	1	0.854	0.914	41.564	-0.012	-0.012	0.000	0.000	0.000
124	B	374	ALA	0	-0.013	-0.011	46.434	0.000	0.000	0.000	0.000	0.000
125	B	375	ALA	0	0.008	0.009	48.101	0.000	0.000	0.000	0.000	0.000
126	B	376	ASP	-1	-0.794	-0.884	50.591	0.007	0.007	0.000	0.000	0.000
127	B	377	LEU	0	-0.057	-0.041	47.062	0.000	0.000	0.000	0.000	0.000
128	B	378	VAL	0	-0.030	-0.016	50.810	0.000	0.000	0.000	0.000	0.000
129	B	379	GLU	-1	-0.926	-0.947	53.301	0.003	0.003	0.000	0.000	0.000
130	B	380	ALA	0	-0.031	-0.027	54.190	0.000	0.000	0.000	0.000	0.000
131	B	381	LEU	0	-0.046	-0.018	53.576	0.000	0.000	0.000	0.000	0.000
132	B	382	TYR	0	-0.014	-0.025	56.275	0.000	0.000	0.000	0.000	0.000
133	B	383	GLY	0	-0.004	0.032	59.422	0.000	0.000	0.000	0.000	0.000
134	B	384	MET	0	-0.023	-0.009	54.081	0.001	0.001	0.000	0.000	0.000
135	B	385	PRO	0	0.030	0.010	59.598	0.000	0.000	0.000	0.000	0.000
136	B	386	HIS	0	-0.002	0.017	61.758	0.000	0.000	0.000	0.000	0.000
137	B	387	ASN	0	0.016	-0.024	60.992	-0.001	-0.001	0.000	0.000	0.000
138	B	388	ASN	0	-0.035	-0.022	55.971	0.000	0.000	0.000	0.000	0.000
139	B	389	GLN	0	0.006	0.009	56.298	0.000	0.000	0.000	0.000	0.000
140	B	390	GLU	-1	-0.852	-0.931	57.008	-0.002	-0.002	0.000	0.000	0.000
141	B	391	ILE	0	-0.031	-0.006	53.376	-0.001	-0.001	0.000	0.000	0.000
142	B	392	ILE	0	-0.022	-0.011	51.482	-0.001	-0.001	0.000	0.000	0.000
143	B	393	LEU	0	0.034	0.007	52.290	-0.001	-0.001	0.000	0.000	0.000
144	B	394	LYS	1	0.901	0.969	52.422	0.004	0.004	0.000	0.000	0.000
145	B	395	ARG	1	0.924	0.955	48.475	-0.001	-0.001	0.000	0.000	0.000
146	B	396	ALA	0	-0.012	-0.010	48.885	-0.001	-0.001	0.000	0.000	0.000
147	B	397	ALA	0	0.013	0.004	49.398	-0.001	-0.001	0.000	0.000	0.000
148	B	398	ASP	-1	-0.791	-0.885	48.627	-0.007	-0.007	0.000	0.000	0.000
149	B	399	ILE	0	-0.113	-0.069	43.960	-0.001	-0.001	0.000	0.000	0.000
150	B	400	ALA	0	-0.047	-0.035	45.460	-0.001	-0.001	0.000	0.000	0.000
151	B	401	GLU	-1	-0.913	-0.953	47.184	-0.012	-0.012	0.000	0.000	0.000
152	B	402	ALA	0	-0.028	-0.006	43.839	-0.001	-0.001	0.000	0.000	0.000
153	B	403	LEU	0	-0.148	-0.065	40.631	-0.001	-0.001	0.000	0.000	0.000
154	B	404	TYR	0	-0.017	-0.009	43.066	-0.002	-0.002	0.000	0.000	0.000
155	B	405	SER	0	0.018	0.006	45.732	0.000	0.000	0.000	0.000	0.000
156	B	406	NME	0	-0.008	0.011	47.513	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:251:ACE )