FMO DATABASE

FMODB ID: K3N83

Calculation Name: 3V33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V33

Chain ID: A

ChEMBL ID:

UniProt ID: Q5D1E8

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	163
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1741232.495345
FMO2-HF: Nuclear repulsion	1674844.164848
FMO2-HF: Total energy	-66388.330498
FMO2-MP2: Total energy	-66583.326306

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:ASP)

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

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.
-180.177	-194.542	45.285	-17.552	-13.365	0.18

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.814 / q_NPA : -0.870

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	ARG	1	0.781	0.889	3.552	-32.942	-31.353	0.051	-0.793	-0.846	0.002
4	A	137	PRO	0	0.038	0.030	6.203	-0.466	-0.466	0.000	0.000	0.000	0.000
5	A	138	VAL	0	-0.030	-0.006	8.267	-1.116	-1.116	0.000	0.000	0.000	0.000
6	A	139	VAL	0	-0.002	0.008	11.338	-1.223	-1.223	0.000	0.000	0.000	0.000
7	A	140	ILE	0	-0.010	-0.012	14.670	-0.217	-0.217	0.000	0.000	0.000	0.000
8	A	141	ASP	-1	-0.738	-0.831	17.575	12.153	12.153	0.000	0.000	0.000	0.000
9	A	142	GLY	0	0.046	0.002	21.233	-0.219	-0.219	0.000	0.000	0.000	0.000
10	A	143	SER	0	-0.048	-0.047	22.667	-0.521	-0.521	0.000	0.000	0.000	0.000
11	A	144	ASN	0	0.004	0.023	24.006	-0.070	-0.070	0.000	0.000	0.000	0.000
12	A	145	VAL	0	0.027	0.008	20.804	-0.285	-0.285	0.000	0.000	0.000	0.000
13	A	146	ALA	0	-0.030	-0.020	24.279	-0.194	-0.194	0.000	0.000	0.000	0.000
14	A	147	MET	0	-0.038	0.000	27.061	-0.340	-0.340	0.000	0.000	0.000	0.000
15	A	148	SER	0	0.005	0.025	26.189	-0.406	-0.406	0.000	0.000	0.000	0.000
16	A	149	HIS	0	-0.002	0.031	26.474	-0.218	-0.218	0.000	0.000	0.000	0.000
17	A	150	GLY	0	0.004	0.005	28.421	-0.306	-0.306	0.000	0.000	0.000	0.000
18	A	151	ASN	0	-0.051	-0.048	31.904	0.087	0.087	0.000	0.000	0.000	0.000
19	A	152	LYS	1	0.891	0.927	30.630	-10.231	-10.231	0.000	0.000	0.000	0.000
20	A	153	GLU	-1	-0.885	-0.907	34.153	8.011	8.011	0.000	0.000	0.000	0.000
21	A	154	VAL	0	-0.061	-0.042	34.017	-0.160	-0.160	0.000	0.000	0.000	0.000
22	A	155	PHE	0	0.040	-0.005	27.203	0.281	0.281	0.000	0.000	0.000	0.000
23	A	156	SER	0	-0.002	-0.016	29.672	-0.215	-0.215	0.000	0.000	0.000	0.000
24	A	157	CYS	0	-0.014	-0.013	27.043	0.429	0.429	0.000	0.000	0.000	0.000
25	A	158	ARG	1	0.833	0.876	25.518	-10.302	-10.302	0.000	0.000	0.000	0.000
26	A	159	GLY	0	0.037	0.026	24.673	0.452	0.452	0.000	0.000	0.000	0.000
27	A	160	ILE	0	0.013	0.000	20.888	0.638	0.638	0.000	0.000	0.000	0.000
28	A	161	LEU	0	-0.011	0.002	20.319	0.681	0.681	0.000	0.000	0.000	0.000
29	A	162	LEU	0	-0.013	0.002	20.240	0.662	0.662	0.000	0.000	0.000	0.000
30	A	163	ALA	0	-0.001	0.006	18.759	0.644	0.644	0.000	0.000	0.000	0.000
31	A	164	VAL	0	-0.016	-0.016	15.828	1.129	1.129	0.000	0.000	0.000	0.000
32	A	165	ASN	0	-0.063	-0.047	15.466	0.995	0.995	0.000	0.000	0.000	0.000
33	A	166	TRP	0	0.052	0.031	13.200	1.238	1.238	0.000	0.000	0.000	0.000
34	A	167	PHE	0	0.012	-0.008	11.538	1.068	1.068	0.000	0.000	0.000	0.000
35	A	168	LEU	0	-0.031	-0.012	11.475	1.852	1.852	0.000	0.000	0.000	0.000
36	A	169	GLU	-1	-0.930	-0.961	12.385	17.842	17.842	0.000	0.000	0.000	0.000
37	A	170	ARG	1	0.788	0.887	9.232	-27.731	-27.731	0.000	0.000	0.000	0.000
38	A	171	GLY	0	-0.004	0.007	8.191	3.521	3.521	0.000	0.000	0.000	0.000
39	A	172	HIS	0	-0.038	-0.019	7.329	2.278	2.278	0.000	0.000	0.000	0.000
40	A	173	THR	0	-0.039	-0.035	7.157	-2.047	-2.047	0.000	0.000	0.000	0.000
41	A	174	ASP	-1	-0.924	-0.952	6.680	27.341	27.341	0.000	0.000	0.000	0.000
42	A	175	ILE	0	0.025	0.002	8.518	0.605	0.605	0.000	0.000	0.000	0.000
43	A	176	THR	0	-0.059	-0.027	11.877	-1.092	-1.092	0.000	0.000	0.000	0.000
44	A	177	VAL	0	-0.009	0.006	15.085	-0.076	-0.076	0.000	0.000	0.000	0.000
45	A	178	PHE	0	0.019	0.011	18.056	-0.414	-0.414	0.000	0.000	0.000	0.000
46	A	179	VAL	0	0.038	0.007	21.317	-0.152	-0.152	0.000	0.000	0.000	0.000
47	A	180	PRO	0	0.025	0.029	24.984	-0.122	-0.122	0.000	0.000	0.000	0.000
48	A	181	SER	0	-0.021	-0.027	28.227	-0.270	-0.270	0.000	0.000	0.000	0.000
49	A	182	TRP	0	0.002	-0.010	29.402	-0.177	-0.177	0.000	0.000	0.000	0.000
50	A	183	ARG	1	0.916	0.979	29.301	-9.744	-9.744	0.000	0.000	0.000	0.000
51	A	184	LYS	1	0.793	0.904	27.432	-10.514	-10.514	0.000	0.000	0.000	0.000
52	A	185	GLU	-1	-0.818	-0.879	32.084	7.893	7.893	0.000	0.000	0.000	0.000
53	A	186	GLN	0	0.034	0.023	35.731	0.184	0.184	0.000	0.000	0.000	0.000
54	A	187	PRO	0	-0.020	0.001	36.495	-0.089	-0.089	0.000	0.000	0.000	0.000
55	A	188	ARG	1	0.851	0.896	38.285	-7.381	-7.381	0.000	0.000	0.000	0.000
56	A	189	PRO	0	0.039	0.002	40.272	0.168	0.168	0.000	0.000	0.000	0.000
57	A	190	ASP	-1	-0.801	-0.875	40.776	7.546	7.546	0.000	0.000	0.000	0.000
58	A	191	VAL	0	-0.089	-0.039	36.049	0.183	0.183	0.000	0.000	0.000	0.000
59	A	192	PRO	0	0.032	0.031	36.430	0.149	0.149	0.000	0.000	0.000	0.000
60	A	193	ILE	0	-0.036	-0.032	30.982	0.267	0.267	0.000	0.000	0.000	0.000
61	A	194	THR	0	0.007	-0.002	31.912	-0.263	-0.263	0.000	0.000	0.000	0.000
62	A	195	ASP	-1	-0.817	-0.922	29.746	10.193	10.193	0.000	0.000	0.000	0.000
63	A	196	GLN	0	-0.032	-0.032	29.496	0.158	0.158	0.000	0.000	0.000	0.000
64	A	197	HIS	0	0.001	0.006	28.962	-0.056	-0.056	0.000	0.000	0.000	0.000
65	A	198	ILE	0	0.047	0.023	24.282	0.212	0.212	0.000	0.000	0.000	0.000
66	A	199	LEU	0	0.006	0.007	24.638	0.450	0.450	0.000	0.000	0.000	0.000
67	A	200	ARG	1	0.964	0.972	24.688	-9.186	-9.186	0.000	0.000	0.000	0.000
68	A	201	GLU	-1	-0.899	-0.925	24.050	12.247	12.247	0.000	0.000	0.000	0.000
69	A	202	LEU	0	0.036	0.001	19.272	0.365	0.365	0.000	0.000	0.000	0.000
70	A	203	GLU	-1	-0.808	-0.871	20.185	11.501	11.501	0.000	0.000	0.000	0.000
71	A	204	LYS	1	0.909	0.951	21.569	-11.015	-11.015	0.000	0.000	0.000	0.000
72	A	205	LYS	1	0.833	0.896	18.730	-13.425	-13.425	0.000	0.000	0.000	0.000
73	A	206	LYS	1	0.893	0.947	16.668	-13.973	-13.973	0.000	0.000	0.000	0.000
74	A	207	ILE	0	0.069	0.053	14.855	0.425	0.425	0.000	0.000	0.000	0.000
75	A	208	LEU	0	-0.053	-0.009	16.777	0.274	0.274	0.000	0.000	0.000	0.000
76	A	209	VAL	0	0.027	0.006	18.452	-0.451	-0.451	0.000	0.000	0.000	0.000
77	A	210	PHE	0	-0.009	-0.022	21.137	-0.140	-0.140	0.000	0.000	0.000	0.000
78	A	211	THR	0	-0.004	-0.001	23.695	-0.232	-0.232	0.000	0.000	0.000	0.000
79	A	212	PRO	0	0.027	0.019	25.777	-0.416	-0.416	0.000	0.000	0.000	0.000
80	A	213	SER	0	-0.045	-0.027	29.131	-0.108	-0.108	0.000	0.000	0.000	0.000
81	A	214	ARG	1	0.945	0.979	32.418	-7.935	-7.935	0.000	0.000	0.000	0.000
82	A	215	ARG	1	0.862	0.903	35.955	-7.668	-7.668	0.000	0.000	0.000	0.000
83	A	216	VAL	0	0.011	-0.005	39.683	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	217	GLY	0	0.056	0.035	42.368	-0.037	-0.037	0.000	0.000	0.000	0.000
85	A	218	GLY	0	0.006	0.009	44.524	-0.080	-0.080	0.000	0.000	0.000	0.000
86	A	219	LYS	1	0.953	0.974	42.624	-6.540	-6.540	0.000	0.000	0.000	0.000
87	A	220	ARG	1	0.897	0.950	35.676	-8.220	-8.220	0.000	0.000	0.000	0.000
88	A	221	VAL	0	-0.003	-0.002	36.059	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	222	VAL	0	0.002	-0.016	31.730	0.083	0.083	0.000	0.000	0.000	0.000
90	A	223	CYS	0	-0.029	0.000	29.048	-0.167	-0.167	0.000	0.000	0.000	0.000
91	A	224	TYR	0	0.000	-0.007	28.512	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	225	ASP	-1	-0.740	-0.856	25.170	12.159	12.159	0.000	0.000	0.000	0.000
93	A	226	ASP	-1	-0.763	-0.897	23.756	11.698	11.698	0.000	0.000	0.000	0.000
94	A	227	ARG	1	0.815	0.883	22.995	-10.102	-10.102	0.000	0.000	0.000	0.000
95	A	228	PHE	0	-0.045	-0.028	21.479	0.165	0.165	0.000	0.000	0.000	0.000
96	A	229	ILE	0	-0.001	0.008	18.959	0.725	0.725	0.000	0.000	0.000	0.000
97	A	230	VAL	0	0.038	0.014	18.111	0.871	0.871	0.000	0.000	0.000	0.000
98	A	231	LYS	1	0.846	0.946	18.378	-12.439	-12.439	0.000	0.000	0.000	0.000
99	A	232	LEU	0	0.025	0.016	14.495	0.344	0.344	0.000	0.000	0.000	0.000
100	A	233	ALA	0	0.032	0.032	13.687	1.167	1.167	0.000	0.000	0.000	0.000
101	A	234	TYR	0	0.013	0.005	13.536	1.295	1.295	0.000	0.000	0.000	0.000
102	A	235	GLU	-1	-0.908	-0.975	14.781	15.132	15.132	0.000	0.000	0.000	0.000
103	A	236	SER	0	-0.065	-0.048	10.460	0.659	0.659	0.000	0.000	0.000	0.000
104	A	237	ASP	-1	-0.800	-0.871	9.393	30.169	30.169	0.000	0.000	0.000	0.000
105	A	238	GLY	0	0.036	0.015	9.329	2.892	2.892	0.000	0.000	0.000	0.000
106	A	239	ILE	0	-0.046	-0.016	10.732	-0.079	-0.079	0.000	0.000	0.000	0.000
107	A	240	VAL	0	0.007	0.000	12.963	-0.496	-0.496	0.000	0.000	0.000	0.000
108	A	241	VAL	0	0.006	0.004	15.089	-0.458	-0.458	0.000	0.000	0.000	0.000
109	A	242	SER	0	-0.018	-0.047	17.734	-0.876	-0.876	0.000	0.000	0.000	0.000
110	A	243	ASN	0	0.012	-0.002	21.527	0.744	0.744	0.000	0.000	0.000	0.000
111	A	244	ASP	-1	-0.849	-0.901	24.615	10.805	10.805	0.000	0.000	0.000	0.000
112	A	245	THR	0	-0.026	-0.036	24.234	0.371	0.371	0.000	0.000	0.000	0.000
113	A	246	TYR	0	0.007	-0.039	21.608	0.282	0.282	0.000	0.000	0.000	0.000
114	A	247	ARG	1	0.905	0.942	26.754	-10.359	-10.359	0.000	0.000	0.000	0.000
115	A	248	ASP	-1	-0.872	-0.932	29.558	9.605	9.605	0.000	0.000	0.000	0.000
116	A	249	LEU	0	-0.011	-0.011	24.527	-0.064	-0.064	0.000	0.000	0.000	0.000
117	A	250	GLN	0	-0.048	-0.028	25.675	-0.213	-0.213	0.000	0.000	0.000	0.000
118	A	251	GLY	0	-0.015	-0.005	27.340	-0.064	-0.064	0.000	0.000	0.000	0.000
119	A	252	GLU	-1	-0.818	-0.848	28.371	10.212	10.212	0.000	0.000	0.000	0.000
120	A	253	ARG	1	0.823	0.906	24.633	-11.422	-11.422	0.000	0.000	0.000	0.000
121	A	254	GLN	0	0.039	0.015	25.606	0.359	0.359	0.000	0.000	0.000	0.000
122	A	255	GLU	-1	-0.819	-0.915	21.592	12.499	12.499	0.000	0.000	0.000	0.000
123	A	256	TRP	0	0.000	-0.013	20.954	0.398	0.398	0.000	0.000	0.000	0.000
124	A	257	LYS	1	0.860	0.951	21.817	-10.729	-10.729	0.000	0.000	0.000	0.000
125	A	258	ARG	1	0.865	0.931	20.679	-12.817	-12.817	0.000	0.000	0.000	0.000
126	A	259	PHE	0	0.038	0.021	13.861	0.306	0.306	0.000	0.000	0.000	0.000
127	A	260	ILE	0	-0.038	-0.027	18.135	0.632	0.632	0.000	0.000	0.000	0.000
128	A	261	GLU	-1	-0.880	-0.945	20.332	12.900	12.900	0.000	0.000	0.000	0.000
129	A	262	GLU	-1	-0.931	-0.962	16.586	17.215	17.215	0.000	0.000	0.000	0.000
130	A	263	ARG	1	0.727	0.842	10.460	-22.848	-22.848	0.000	0.000	0.000	0.000
131	A	264	LEU	0	-0.042	-0.003	15.825	0.637	0.637	0.000	0.000	0.000	0.000
132	A	265	LEU	0	-0.039	-0.020	14.338	0.561	0.561	0.000	0.000	0.000	0.000
133	A	266	MET	0	0.019	0.011	17.906	-0.375	-0.375	0.000	0.000	0.000	0.000
134	A	267	TYR	0	-0.037	-0.039	20.200	0.601	0.601	0.000	0.000	0.000	0.000
135	A	268	SER	0	-0.038	-0.011	22.137	-0.979	-0.979	0.000	0.000	0.000	0.000
136	A	269	PHE	0	0.007	0.001	23.294	0.581	0.581	0.000	0.000	0.000	0.000
137	A	270	VAL	0	-0.006	0.008	26.262	-0.514	-0.514	0.000	0.000	0.000	0.000
138	A	271	ASN	0	0.001	-0.012	28.076	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	272	ASP	-1	-0.741	-0.842	26.390	11.206	11.206	0.000	0.000	0.000	0.000
140	A	273	LYS	1	0.863	0.907	22.146	-13.364	-13.364	0.000	0.000	0.000	0.000
141	A	274	PHE	0	0.039	0.021	17.094	-0.274	-0.274	0.000	0.000	0.000	0.000
142	A	275	MET	0	0.004	0.022	20.389	0.128	0.128	0.000	0.000	0.000	0.000
143	A	276	PRO	0	0.057	0.040	16.373	-0.678	-0.678	0.000	0.000	0.000	0.000
144	A	277	PRO	0	0.002	0.015	19.080	-0.099	-0.099	0.000	0.000	0.000	0.000
145	A	278	ASP	-1	-0.859	-0.951	16.972	18.463	18.463	0.000	0.000	0.000	0.000
146	A	279	ASP	-1	-0.931	-0.975	16.938	16.163	16.163	0.000	0.000	0.000	0.000
147	A	280	PRO	0	-0.039	-0.012	15.101	-0.833	-0.833	0.000	0.000	0.000	0.000
148	A	281	LEU	0	-0.028	0.003	17.106	-0.492	-0.492	0.000	0.000	0.000	0.000
149	A	282	GLY	0	0.024	0.029	20.391	-0.734	-0.734	0.000	0.000	0.000	0.000
150	A	283	ARG	1	0.932	0.943	21.412	-13.774	-13.774	0.000	0.000	0.000	0.000
151	A	284	HIS	0	-0.017	-0.005	22.382	0.401	0.401	0.000	0.000	0.000	0.000
152	A	285	GLY	0	0.013	0.025	18.833	0.207	0.207	0.000	0.000	0.000	0.000
153	A	286	PRO	0	-0.043	-0.019	13.281	0.012	0.012	0.000	0.000	0.000	0.000
154	A	287	SER	0	0.063	0.024	13.539	0.017	0.017	0.000	0.000	0.000	0.000
155	A	288	LEU	0	0.014	0.001	12.952	2.228	2.228	0.000	0.000	0.000	0.000
156	A	289	ASP	-1	-0.836	-0.907	9.158	28.894	28.894	0.000	0.000	0.000	0.000
157	A	290	ASN	0	-0.053	-0.045	8.278	6.878	6.878	0.000	0.000	0.000	0.000
158	A	291	PHE	0	-0.025	-0.001	9.265	2.353	2.353	0.000	0.000	0.000	0.000
159	A	292	LEU	0	0.021	0.010	8.551	0.695	0.695	0.000	0.000	0.000	0.000
160	A	293	ARG	1	0.798	0.886	1.726	-120.731	-133.037	31.937	-11.691	-7.940	0.134
161	A	294	LYS	1	0.904	0.934	1.954	-82.380	-86.215	13.299	-5.063	-4.400	0.044
162	A	295	LYS	1	0.918	0.947	4.983	-41.521	-41.418	-0.001	-0.005	-0.096	0.000
163	A	296	PRO	0	0.042	0.046	5.310	10.935	11.019	-0.001	0.000	-0.083	0.000

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