FMO DATABASE

FMODB ID: GNVN1

Calculation Name: 3BT3-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3BT3

Chain ID: A

ChEMBL ID:
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UniProt ID: A9KJQ6

Base Structure: X-ray

Registration Date: 2023-03-14

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1125380.272596
FMO2-HF: Nuclear repulsion	1072549.207392
FMO2-HF: Total energy	-52831.065204
FMO2-MP2: Total energy	-52983.855815

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:134:GLU)

Summations of interaction energy for fragment #1(A:134:GLU)

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.
80.704	79.666	19.548	-6.212	-12.297	-0.02

Interaction energy analysis for fragmet #1(A:134:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.947

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	136	GLY	0	-0.025	-0.005	3.771	-5.145	-2.753	-0.019	-1.125	-1.247	0.004
4	A	137	TYR	0	-0.003	-0.002	2.351	-3.108	-9.065	18.808	-3.768	-9.084	-0.018
5	A	138	VAL	0	0.017	0.013	2.767	8.406	10.717	0.759	-1.258	-1.811	-0.006
6	A	139	VAL	0	0.024	0.007	4.019	-6.839	-6.623	0.000	-0.061	-0.155	0.000
7	A	140	ARG	1	0.904	0.952	6.185	-29.312	-29.312	0.000	0.000	0.000	0.000
8	A	141	GLU	-1	-0.802	-0.894	9.538	18.647	18.647	0.000	0.000	0.000	0.000
9	A	142	ASN	0	-0.065	-0.050	10.136	0.889	0.889	0.000	0.000	0.000	0.000
10	A	143	GLY	0	0.036	0.048	12.200	-0.241	-0.241	0.000	0.000	0.000	0.000
11	A	144	PRO	0	-0.002	0.001	15.892	0.345	0.345	0.000	0.000	0.000	0.000
12	A	145	VAL	0	0.013	0.007	17.019	-0.517	-0.517	0.000	0.000	0.000	0.000
13	A	146	TYR	0	-0.017	-0.028	19.575	-0.196	-0.196	0.000	0.000	0.000	0.000
14	A	147	PHE	0	-0.039	-0.016	20.938	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	148	THR	0	0.020	-0.005	25.855	-0.359	-0.359	0.000	0.000	0.000	0.000
16	A	149	LYS	1	0.915	0.954	29.415	-9.187	-9.187	0.000	0.000	0.000	0.000
17	A	150	ASP	-1	-0.871	-0.941	32.540	8.447	8.447	0.000	0.000	0.000	0.000
18	A	151	MET	0	0.000	0.037	28.212	0.065	0.065	0.000	0.000	0.000	0.000
19	A	152	ASP	-1	-0.760	-0.871	31.467	9.068	9.068	0.000	0.000	0.000	0.000
20	A	153	LYS	1	0.909	0.968	34.280	-8.853	-8.853	0.000	0.000	0.000	0.000
21	A	154	THR	0	-0.031	-0.045	29.060	-0.092	-0.092	0.000	0.000	0.000	0.000
22	A	155	VAL	0	0.023	-0.001	29.537	0.173	0.173	0.000	0.000	0.000	0.000
23	A	156	LYS	1	0.984	0.999	31.731	-8.424	-8.424	0.000	0.000	0.000	0.000
24	A	157	TRP	0	0.022	0.030	30.430	0.014	0.014	0.000	0.000	0.000	0.000
25	A	158	PHE	0	-0.014	-0.026	26.914	0.034	0.034	0.000	0.000	0.000	0.000
26	A	159	GLU	-1	-0.941	-0.958	31.713	9.431	9.431	0.000	0.000	0.000	0.000
27	A	160	GLU	-1	-0.980	-1.005	33.914	8.018	8.018	0.000	0.000	0.000	0.000
28	A	161	ILE	0	-0.060	-0.020	34.893	-0.154	-0.154	0.000	0.000	0.000	0.000
29	A	162	LEU	0	-0.044	-0.039	29.293	0.010	0.010	0.000	0.000	0.000	0.000
30	A	163	GLY	0	-0.020	0.014	32.100	0.150	0.150	0.000	0.000	0.000	0.000
31	A	164	TRP	0	-0.060	-0.038	24.213	0.450	0.450	0.000	0.000	0.000	0.000
32	A	165	SER	0	0.022	0.006	28.797	-0.480	-0.480	0.000	0.000	0.000	0.000
33	A	166	GLY	0	-0.001	-0.014	28.163	0.490	0.490	0.000	0.000	0.000	0.000
34	A	167	ASP	-1	-0.958	-0.966	27.964	10.169	10.169	0.000	0.000	0.000	0.000
35	A	168	ILE	0	-0.071	-0.034	27.744	0.427	0.427	0.000	0.000	0.000	0.000
36	A	169	VAL	0	0.037	0.017	25.087	-0.194	-0.194	0.000	0.000	0.000	0.000
37	A	170	ALA	0	-0.033	-0.020	27.673	-0.176	-0.176	0.000	0.000	0.000	0.000
38	A	171	ARG	1	0.769	0.863	29.408	-8.902	-8.902	0.000	0.000	0.000	0.000
39	A	172	ASP	-1	-0.753	-0.860	32.323	8.955	8.955	0.000	0.000	0.000	0.000
40	A	173	ASP	-1	-0.967	-1.001	33.753	8.315	8.315	0.000	0.000	0.000	0.000
41	A	174	GLU	-1	-1.012	-1.001	36.899	7.728	7.728	0.000	0.000	0.000	0.000
42	A	175	GLY	0	-0.041	-0.007	36.951	-0.165	-0.165	0.000	0.000	0.000	0.000
43	A	176	PHE	0	-0.040	-0.013	33.959	0.093	0.093	0.000	0.000	0.000	0.000
44	A	177	GLY	0	-0.013	0.000	30.854	0.108	0.108	0.000	0.000	0.000	0.000
45	A	178	ASP	-1	-0.888	-0.966	27.544	10.251	10.251	0.000	0.000	0.000	0.000
46	A	179	TYR	0	-0.038	-0.058	19.915	0.384	0.384	0.000	0.000	0.000	0.000
47	A	180	GLY	0	0.054	0.007	24.653	-0.525	-0.525	0.000	0.000	0.000	0.000
48	A	181	CYS	0	-0.089	-0.013	22.617	0.631	0.631	0.000	0.000	0.000	0.000
49	A	182	VAL	0	0.053	0.031	24.167	-0.528	-0.528	0.000	0.000	0.000	0.000
50	A	183	PHE	0	0.011	-0.024	23.110	0.853	0.853	0.000	0.000	0.000	0.000
51	A	184	ASP	-1	-0.888	-0.940	23.543	12.878	12.878	0.000	0.000	0.000	0.000
52	A	185	TYR	0	-0.035	-0.003	20.883	0.017	0.017	0.000	0.000	0.000	0.000
53	A	186	PRO	0	0.045	0.008	26.927	-0.068	-0.068	0.000	0.000	0.000	0.000
54	A	187	SER	0	0.079	0.019	27.584	0.328	0.328	0.000	0.000	0.000	0.000
55	A	188	GLU	-1	-1.001	-0.990	27.858	10.391	10.391	0.000	0.000	0.000	0.000
56	A	189	VAL	0	-0.044	-0.024	23.056	0.224	0.224	0.000	0.000	0.000	0.000
57	A	190	ALA	0	0.063	0.022	22.264	0.032	0.032	0.000	0.000	0.000	0.000
58	A	191	VAL	0	-0.040	0.001	22.908	0.253	0.253	0.000	0.000	0.000	0.000
59	A	192	ALA	0	-0.071	-0.045	24.387	-0.091	-0.091	0.000	0.000	0.000	0.000
60	A	193	HIS	-1	-0.912	-1.025	18.766	15.936	15.936	0.000	0.000	0.000	0.000
61	A	194	LEU	0	-0.049	-0.050	19.452	0.110	0.110	0.000	0.000	0.000	0.000
62	A	195	THR	0	-0.063	0.055	14.355	-0.112	-0.112	0.000	0.000	0.000	0.000
63	A	196	PRO	0	-0.130	-0.093	14.301	1.516	1.516	0.000	0.000	0.000	0.000
64	A	197	PHE	0	0.144	0.114	16.170	-1.009	-1.009	0.000	0.000	0.000	0.000
65	A	198	ARG	1	0.869	0.933	16.222	-14.817	-14.817	0.000	0.000	0.000	0.000
66	A	199	GLY	0	0.054	0.042	18.316	-0.482	-0.482	0.000	0.000	0.000	0.000
67	A	200	PHE	0	-0.070	-0.039	19.781	0.801	0.801	0.000	0.000	0.000	0.000
68	A	201	HIS	0	0.024	0.023	15.907	-1.220	-1.220	0.000	0.000	0.000	0.000
69	A	202	LEU	0	-0.046	-0.030	21.008	-0.074	-0.074	0.000	0.000	0.000	0.000
70	A	203	PHE	0	0.028	0.007	18.906	0.070	0.070	0.000	0.000	0.000	0.000
71	A	204	LYS	1	0.898	0.958	24.740	-10.008	-10.008	0.000	0.000	0.000	0.000
72	A	205	GLY	0	-0.047	-0.034	27.074	0.250	0.250	0.000	0.000	0.000	0.000
73	A	206	GLU	-1	-0.981	-1.005	28.546	9.301	9.301	0.000	0.000	0.000	0.000
74	A	207	PRO	0	0.031	0.032	27.970	0.420	0.420	0.000	0.000	0.000	0.000
75	A	208	ILE	0	-0.005	-0.003	22.837	-0.030	-0.030	0.000	0.000	0.000	0.000
76	A	209	LYS	1	0.943	0.972	27.183	-10.061	-10.061	0.000	0.000	0.000	0.000
77	A	210	GLY	0	0.022	0.006	27.827	0.200	0.200	0.000	0.000	0.000	0.000
78	A	211	VAL	0	-0.039	-0.027	23.278	-0.124	-0.124	0.000	0.000	0.000	0.000
79	A	212	ALA	0	0.001	0.004	23.301	0.380	0.380	0.000	0.000	0.000	0.000
80	A	213	GLY	0	0.035	0.015	21.809	0.570	0.570	0.000	0.000	0.000	0.000
81	A	214	PHE	0	-0.061	-0.027	19.258	-0.647	-0.647	0.000	0.000	0.000	0.000
82	A	215	MET	0	0.007	0.014	20.442	0.817	0.817	0.000	0.000	0.000	0.000
83	A	216	MET	0	-0.008	0.002	20.289	-0.514	-0.514	0.000	0.000	0.000	0.000
84	A	217	ILE	0	-0.020	-0.019	23.133	0.170	0.170	0.000	0.000	0.000	0.000
85	A	218	GLU	-1	-0.927	-0.962	26.081	11.626	11.626	0.000	0.000	0.000	0.000
86	A	219	GLY	0	-0.025	0.002	28.751	-0.182	-0.182	0.000	0.000	0.000	0.000
87	A	220	ILE	0	-0.006	-0.020	30.223	-0.158	-0.158	0.000	0.000	0.000	0.000
88	A	221	ASP	-1	-0.848	-0.920	32.492	8.709	8.709	0.000	0.000	0.000	0.000
89	A	222	ALA	0	-0.029	-0.014	34.579	-0.226	-0.226	0.000	0.000	0.000	0.000
90	A	223	LEU	0	0.035	0.026	30.253	-0.160	-0.160	0.000	0.000	0.000	0.000
91	A	224	HIS	0	0.013	0.000	34.088	-0.333	-0.333	0.000	0.000	0.000	0.000
92	A	225	LYS	1	0.917	0.963	36.459	-7.844	-7.844	0.000	0.000	0.000	0.000
93	A	226	TYR	0	-0.009	0.010	35.164	-0.199	-0.199	0.000	0.000	0.000	0.000
94	A	227	VAL	0	0.025	0.011	34.403	-0.110	-0.110	0.000	0.000	0.000	0.000
95	A	228	LYS	1	0.877	0.945	37.396	-8.038	-8.038	0.000	0.000	0.000	0.000
96	A	229	GLU	-1	-0.919	-0.971	40.818	7.321	7.321	0.000	0.000	0.000	0.000
97	A	230	ASN	0	-0.106	-0.039	38.098	-0.341	-0.341	0.000	0.000	0.000	0.000
98	A	231	GLY	0	-0.015	0.000	41.191	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	232	TRP	0	-0.052	-0.010	35.863	-0.149	-0.149	0.000	0.000	0.000	0.000
100	A	233	ASP	-1	-0.825	-0.948	40.107	7.481	7.481	0.000	0.000	0.000	0.000
101	A	234	GLN	0	-0.125	-0.046	37.455	0.058	0.058	0.000	0.000	0.000	0.000
102	A	235	ILE	0	0.006	-0.007	34.077	0.333	0.333	0.000	0.000	0.000	0.000
103	A	236	SER	0	-0.027	-0.003	34.478	-0.133	-0.133	0.000	0.000	0.000	0.000
104	A	237	ASP	-1	-0.895	-0.958	36.425	8.030	8.030	0.000	0.000	0.000	0.000
105	A	238	ILE	0	-0.026	-0.013	33.909	0.258	0.258	0.000	0.000	0.000	0.000
106	A	239	TYR	0	-0.039	-0.021	31.525	-0.178	-0.178	0.000	0.000	0.000	0.000
107	A	240	THR	0	-0.019	-0.025	32.679	0.303	0.303	0.000	0.000	0.000	0.000
108	A	241	GLN	0	-0.003	-0.003	28.317	-0.325	-0.325	0.000	0.000	0.000	0.000
109	A	242	PRO	0	-0.026	-0.023	29.724	0.001	0.001	0.000	0.000	0.000	0.000
110	A	243	TRP	0	-0.071	-0.032	24.314	0.036	0.036	0.000	0.000	0.000	0.000
111	A	244	GLY	0	0.027	0.026	26.346	0.389	0.389	0.000	0.000	0.000	0.000
112	A	245	ALA	0	0.006	-0.001	26.687	0.190	0.190	0.000	0.000	0.000	0.000
113	A	246	ARG	1	0.837	0.921	28.812	-9.516	-9.516	0.000	0.000	0.000	0.000
114	A	247	GLU	-1	-0.741	-0.867	27.806	12.025	12.025	0.000	0.000	0.000	0.000
115	A	248	CYS	0	-0.030	0.012	30.206	-0.476	-0.476	0.000	0.000	0.000	0.000
116	A	249	SER	0	-0.024	-0.015	29.978	0.379	0.379	0.000	0.000	0.000	0.000
117	A	250	ILE	0	0.031	0.015	30.544	-0.390	-0.390	0.000	0.000	0.000	0.000
118	A	251	THR	0	-0.002	0.007	31.085	0.427	0.427	0.000	0.000	0.000	0.000
119	A	252	THR	0	0.036	0.007	29.379	-0.316	-0.316	0.000	0.000	0.000	0.000
120	A	253	THR	0	-0.016	-0.003	32.677	-0.262	-0.262	0.000	0.000	0.000	0.000
121	A	254	ASP	-1	-0.835	-0.886	30.912	9.834	9.834	0.000	0.000	0.000	0.000
122	A	255	GLY	0	-0.020	-0.004	32.846	-0.010	-0.010	0.000	0.000	0.000	0.000
123	A	256	CYS	0	-0.056	-0.008	27.328	-0.012	-0.012	0.000	0.000	0.000	0.000
124	A	257	ILE	0	-0.003	0.009	28.346	-0.224	-0.224	0.000	0.000	0.000	0.000
125	A	258	LEU	0	0.003	0.003	25.523	0.627	0.627	0.000	0.000	0.000	0.000
126	A	259	ARG	1	0.801	0.869	24.776	-12.827	-12.827	0.000	0.000	0.000	0.000
127	A	260	PHE	0	0.046	0.024	25.359	0.529	0.529	0.000	0.000	0.000	0.000
128	A	261	PHE	0	-0.005	-0.020	21.071	-0.390	-0.390	0.000	0.000	0.000	0.000
129	A	262	GLU	-1	-0.760	-0.878	26.232	10.874	10.874	0.000	0.000	0.000	0.000
130	A	263	SER	0	-0.026	-0.012	25.483	-0.132	-0.132	0.000	0.000	0.000	0.000
131	A	264	ILE	0	-0.040	-0.016	27.511	-0.324	-0.324	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:134:GLU)