FMO DATABASE

FMODB ID: R5RM8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1738078.144334
FMO2-HF: Nuclear repulsion	1671691.222772
FMO2-HF: Total energy	-66386.921563
FMO2-MP2: Total energy	-66581.83971

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.
-137.334	-135.787	14.62	-8.355	-7.814	0.088

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 : -0.893 / 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	ARG	1	0.855	0.932	3.781	-32.611	-30.994	-0.009	-0.795	-0.814	0.003
4	A	137	PRO	0	0.053	0.033	6.338	0.446	0.446	0.000	0.000	0.000	0.000
5	A	138	VAL	0	-0.029	-0.001	8.027	-1.640	-1.640	0.000	0.000	0.000	0.000
6	A	139	VAL	0	0.002	0.005	11.189	-0.975	-0.975	0.000	0.000	0.000	0.000
7	A	140	ILE	0	0.005	-0.010	14.621	-0.390	-0.390	0.000	0.000	0.000	0.000
8	A	141	ASP	-1	-0.777	-0.851	17.597	12.199	12.199	0.000	0.000	0.000	0.000
9	A	142	GLY	0	0.039	0.000	21.213	-0.170	-0.170	0.000	0.000	0.000	0.000
10	A	143	SER	0	0.005	-0.014	22.730	-0.452	-0.452	0.000	0.000	0.000	0.000
11	A	144	ASN	0	0.012	0.029	23.883	0.049	0.049	0.000	0.000	0.000	0.000
12	A	145	VAL	0	0.044	0.017	20.845	-0.255	-0.255	0.000	0.000	0.000	0.000
13	A	146	ALA	0	-0.033	-0.030	24.291	-0.223	-0.223	0.000	0.000	0.000	0.000
14	A	147	MET	0	-0.060	-0.011	26.927	-0.354	-0.354	0.000	0.000	0.000	0.000
15	A	148	SER	0	-0.006	0.021	26.476	-0.375	-0.375	0.000	0.000	0.000	0.000
16	A	149	HIS	0	0.039	0.055	26.398	-0.340	-0.340	0.000	0.000	0.000	0.000
17	A	150	GLY	0	0.003	0.014	28.377	-0.281	-0.281	0.000	0.000	0.000	0.000
18	A	151	ASN	0	-0.034	-0.023	31.737	0.070	0.070	0.000	0.000	0.000	0.000
19	A	152	LYS	1	0.920	0.939	30.301	-10.352	-10.352	0.000	0.000	0.000	0.000
20	A	153	GLU	-1	-0.912	-0.946	34.129	8.139	8.139	0.000	0.000	0.000	0.000
21	A	154	VAL	0	-0.063	-0.042	33.684	-0.168	-0.168	0.000	0.000	0.000	0.000
22	A	155	PHE	0	0.020	0.002	26.991	0.292	0.292	0.000	0.000	0.000	0.000
23	A	156	SER	0	-0.003	-0.031	29.496	-0.207	-0.207	0.000	0.000	0.000	0.000
24	A	157	CYS	0	-0.006	-0.003	27.128	0.445	0.445	0.000	0.000	0.000	0.000
25	A	158	ARG	1	0.880	0.925	25.473	-10.662	-10.662	0.000	0.000	0.000	0.000
26	A	159	GLY	0	0.036	0.031	24.382	0.505	0.505	0.000	0.000	0.000	0.000
27	A	160	ILE	0	0.014	0.000	21.044	0.654	0.654	0.000	0.000	0.000	0.000
28	A	161	LEU	0	-0.018	-0.001	20.392	0.747	0.747	0.000	0.000	0.000	0.000
29	A	162	LEU	0	-0.042	-0.018	19.897	0.761	0.761	0.000	0.000	0.000	0.000
30	A	163	ALA	0	0.005	0.010	18.615	0.666	0.666	0.000	0.000	0.000	0.000
31	A	164	VAL	0	-0.009	-0.010	15.525	1.185	1.185	0.000	0.000	0.000	0.000
32	A	165	ASN	0	0.021	-0.018	15.072	1.779	1.779	0.000	0.000	0.000	0.000
33	A	166	TRP	0	0.023	0.028	12.896	1.330	1.330	0.000	0.000	0.000	0.000
34	A	167	PHE	0	0.010	-0.017	11.175	1.057	1.057	0.000	0.000	0.000	0.000
35	A	168	LEU	0	-0.037	-0.005	10.764	2.254	2.254	0.000	0.000	0.000	0.000
36	A	169	GLU	-1	-0.967	-0.978	11.469	19.317	19.317	0.000	0.000	0.000	0.000
37	A	170	ARG	1	0.846	0.941	9.293	-27.726	-27.726	0.000	0.000	0.000	0.000
38	A	171	GLY	0	-0.003	0.003	7.152	4.343	4.343	0.000	0.000	0.000	0.000
39	A	172	HIS	0	-0.015	-0.004	6.637	3.176	3.176	0.000	0.000	0.000	0.000
40	A	173	THR	0	-0.045	-0.038	6.938	-2.300	-2.300	0.000	0.000	0.000	0.000
41	A	174	ASP	-1	-0.945	-0.953	6.915	24.554	24.554	0.000	0.000	0.000	0.000
42	A	175	ILE	0	0.012	-0.001	8.596	0.332	0.332	0.000	0.000	0.000	0.000
43	A	176	THR	0	0.008	0.010	11.901	-1.297	-1.297	0.000	0.000	0.000	0.000
44	A	177	VAL	0	-0.027	-0.004	14.955	-0.096	-0.096	0.000	0.000	0.000	0.000
45	A	178	PHE	0	0.036	0.020	17.922	-0.515	-0.515	0.000	0.000	0.000	0.000
46	A	179	VAL	0	0.015	-0.001	21.161	-0.202	-0.202	0.000	0.000	0.000	0.000
47	A	180	PRO	0	0.059	0.048	24.772	-0.127	-0.127	0.000	0.000	0.000	0.000
48	A	181	SER	0	-0.016	-0.013	27.922	-0.148	-0.148	0.000	0.000	0.000	0.000
49	A	182	TRP	0	0.020	-0.004	29.452	-0.202	-0.202	0.000	0.000	0.000	0.000
50	A	183	ARG	1	0.970	1.002	29.210	-10.006	-10.006	0.000	0.000	0.000	0.000
51	A	184	LYS	1	0.892	0.970	28.571	-10.213	-10.213	0.000	0.000	0.000	0.000
52	A	185	GLU	-1	-0.971	-0.978	31.927	8.083	8.083	0.000	0.000	0.000	0.000
53	A	186	GLN	0	0.051	0.025	35.612	0.226	0.226	0.000	0.000	0.000	0.000
54	A	187	PRO	0	-0.002	0.013	36.584	-0.102	-0.102	0.000	0.000	0.000	0.000
55	A	188	ARG	1	0.929	0.954	38.280	-7.388	-7.388	0.000	0.000	0.000	0.000
56	A	189	PRO	0	0.032	-0.003	40.252	0.151	0.151	0.000	0.000	0.000	0.000
57	A	190	ASP	-1	-0.902	-0.938	40.962	7.648	7.648	0.000	0.000	0.000	0.000
58	A	191	VAL	0	-0.113	-0.052	36.034	0.201	0.201	0.000	0.000	0.000	0.000
59	A	192	PRO	0	0.026	0.034	36.691	0.112	0.112	0.000	0.000	0.000	0.000
60	A	193	ILE	0	-0.027	-0.026	30.657	0.250	0.250	0.000	0.000	0.000	0.000
61	A	194	THR	0	0.013	0.005	32.173	-0.210	-0.210	0.000	0.000	0.000	0.000
62	A	195	ASP	-1	-0.830	-0.937	29.802	10.389	10.389	0.000	0.000	0.000	0.000
63	A	196	GLN	0	-0.026	-0.039	29.677	0.191	0.191	0.000	0.000	0.000	0.000
64	A	197	HIS	0	-0.016	-0.011	29.080	0.021	0.021	0.000	0.000	0.000	0.000
65	A	198	ILE	0	0.046	0.023	24.391	0.224	0.224	0.000	0.000	0.000	0.000
66	A	199	LEU	0	-0.003	0.004	24.891	0.484	0.484	0.000	0.000	0.000	0.000
67	A	200	ARG	1	0.984	0.973	24.606	-9.462	-9.462	0.000	0.000	0.000	0.000
68	A	201	GLU	-1	-0.966	-0.963	24.031	12.420	12.420	0.000	0.000	0.000	0.000
69	A	202	LEU	0	0.023	-0.010	19.428	0.420	0.420	0.000	0.000	0.000	0.000
70	A	203	GLU	-1	-0.886	-0.940	20.276	12.032	12.032	0.000	0.000	0.000	0.000
71	A	204	LYS	1	0.928	0.971	21.339	-11.439	-11.439	0.000	0.000	0.000	0.000
72	A	205	LYS	1	0.898	0.941	18.451	-14.341	-14.341	0.000	0.000	0.000	0.000
73	A	206	LYS	1	0.888	0.943	16.526	-14.771	-14.771	0.000	0.000	0.000	0.000
74	A	207	ILE	0	0.054	0.047	15.143	0.585	0.585	0.000	0.000	0.000	0.000
75	A	208	LEU	0	-0.043	-0.002	16.902	0.220	0.220	0.000	0.000	0.000	0.000
76	A	209	VAL	0	0.023	-0.002	18.549	-0.404	-0.404	0.000	0.000	0.000	0.000
77	A	210	PHE	0	-0.030	-0.031	21.232	-0.236	-0.236	0.000	0.000	0.000	0.000
78	A	211	THR	0	0.009	0.017	23.558	-0.152	-0.152	0.000	0.000	0.000	0.000
79	A	212	PRO	0	-0.006	-0.015	25.781	-0.378	-0.378	0.000	0.000	0.000	0.000
80	A	213	SER	0	-0.010	-0.007	29.232	-0.116	-0.116	0.000	0.000	0.000	0.000
81	A	214	ARG	1	0.982	0.997	32.554	-8.050	-8.050	0.000	0.000	0.000	0.000
82	A	215	ARG	1	0.919	0.947	36.006	-7.635	-7.635	0.000	0.000	0.000	0.000
83	A	216	VAL	0	0.016	0.008	39.326	-0.030	-0.030	0.000	0.000	0.000	0.000
84	A	217	GLY	0	0.062	0.032	41.967	-0.048	-0.048	0.000	0.000	0.000	0.000
85	A	218	GLY	0	0.012	0.006	44.262	-0.081	-0.081	0.000	0.000	0.000	0.000
86	A	219	LYS	1	0.952	0.983	42.528	-6.754	-6.754	0.000	0.000	0.000	0.000
87	A	220	ARG	1	0.910	0.971	35.382	-8.311	-8.311	0.000	0.000	0.000	0.000
88	A	221	VAL	0	0.016	0.010	35.866	-0.062	-0.062	0.000	0.000	0.000	0.000
89	A	222	VAL	0	0.002	-0.028	30.832	0.075	0.075	0.000	0.000	0.000	0.000
90	A	223	CYS	0	-0.052	-0.016	29.278	-0.212	-0.212	0.000	0.000	0.000	0.000
91	A	224	TYR	0	0.019	0.002	28.437	0.094	0.094	0.000	0.000	0.000	0.000
92	A	225	ASP	-1	-0.809	-0.919	25.383	12.099	12.099	0.000	0.000	0.000	0.000
93	A	226	ASP	-1	-0.808	-0.904	23.770	11.607	11.607	0.000	0.000	0.000	0.000
94	A	227	ARG	1	0.858	0.925	22.906	-10.237	-10.237	0.000	0.000	0.000	0.000
95	A	228	PHE	0	-0.061	-0.028	21.445	0.246	0.246	0.000	0.000	0.000	0.000
96	A	229	ILE	0	0.012	0.017	18.650	0.706	0.706	0.000	0.000	0.000	0.000
97	A	230	VAL	0	0.046	0.014	18.012	0.869	0.869	0.000	0.000	0.000	0.000
98	A	231	LYS	1	0.892	0.962	18.251	-11.666	-11.666	0.000	0.000	0.000	0.000
99	A	232	LEU	0	0.057	0.026	14.363	0.273	0.273	0.000	0.000	0.000	0.000
100	A	233	ALA	0	0.029	0.034	13.646	1.086	1.086	0.000	0.000	0.000	0.000
101	A	234	TYR	0	-0.002	-0.014	13.565	1.149	1.149	0.000	0.000	0.000	0.000
102	A	235	GLU	-1	-0.966	-0.982	14.597	15.499	15.499	0.000	0.000	0.000	0.000
103	A	236	SER	0	-0.078	-0.046	10.363	0.796	0.796	0.000	0.000	0.000	0.000
104	A	237	ASP	-1	-0.908	-0.961	9.692	27.719	27.719	0.000	0.000	0.000	0.000
105	A	238	GLY	0	-0.006	-0.013	9.511	3.218	3.218	0.000	0.000	0.000	0.000
106	A	239	ILE	0	-0.069	-0.035	10.541	-0.896	-0.896	0.000	0.000	0.000	0.000
107	A	240	VAL	0	0.015	0.010	12.900	-0.341	-0.341	0.000	0.000	0.000	0.000
108	A	241	VAL	0	-0.007	-0.003	15.180	-0.242	-0.242	0.000	0.000	0.000	0.000
109	A	242	SER	0	-0.012	-0.024	17.789	-0.831	-0.831	0.000	0.000	0.000	0.000
110	A	243	ASN	0	0.006	0.000	21.540	0.645	0.645	0.000	0.000	0.000	0.000
111	A	244	ASP	-1	-0.876	-0.921	24.366	10.847	10.847	0.000	0.000	0.000	0.000
112	A	245	THR	0	0.005	-0.010	24.092	0.311	0.311	0.000	0.000	0.000	0.000
113	A	246	TYR	0	-0.007	-0.052	21.484	0.314	0.314	0.000	0.000	0.000	0.000
114	A	247	ARG	1	0.971	0.975	26.542	-10.008	-10.008	0.000	0.000	0.000	0.000
115	A	248	ASP	-1	-0.880	-0.944	29.327	9.471	9.471	0.000	0.000	0.000	0.000
116	A	249	LEU	0	-0.027	-0.016	24.484	-0.065	-0.065	0.000	0.000	0.000	0.000
117	A	250	GLN	0	-0.048	-0.038	25.309	0.007	0.007	0.000	0.000	0.000	0.000
118	A	251	GLY	0	-0.076	-0.030	27.168	-0.017	-0.017	0.000	0.000	0.000	0.000
119	A	252	GLU	-1	-0.856	-0.903	28.089	10.014	10.014	0.000	0.000	0.000	0.000
120	A	253	ARG	1	0.909	0.975	24.251	-11.625	-11.625	0.000	0.000	0.000	0.000
121	A	254	GLN	0	0.020	-0.015	25.958	0.062	0.062	0.000	0.000	0.000	0.000
122	A	255	GLU	-1	-0.828	-0.924	21.417	12.330	12.330	0.000	0.000	0.000	0.000
123	A	256	TRP	0	-0.032	-0.014	20.880	0.426	0.426	0.000	0.000	0.000	0.000
124	A	257	LYS	1	0.937	0.985	21.985	-10.404	-10.404	0.000	0.000	0.000	0.000
125	A	258	ARG	1	0.865	0.923	21.334	-12.318	-12.318	0.000	0.000	0.000	0.000
126	A	259	PHE	0	0.040	0.024	14.012	0.156	0.156	0.000	0.000	0.000	0.000
127	A	260	ILE	0	-0.034	-0.037	18.344	0.713	0.713	0.000	0.000	0.000	0.000
128	A	261	GLU	-1	-0.922	-0.948	20.713	12.548	12.548	0.000	0.000	0.000	0.000
129	A	262	GLU	-1	-0.959	-0.972	17.151	16.860	16.860	0.000	0.000	0.000	0.000
130	A	263	ARG	1	0.830	0.911	10.718	-21.723	-21.723	0.000	0.000	0.000	0.000
131	A	264	LEU	0	-0.037	0.001	16.021	0.640	0.640	0.000	0.000	0.000	0.000
132	A	265	LEU	0	-0.032	-0.011	14.757	0.265	0.265	0.000	0.000	0.000	0.000
133	A	266	MET	0	-0.003	0.000	17.938	-0.417	-0.417	0.000	0.000	0.000	0.000
134	A	267	TYR	0	-0.037	-0.039	20.341	0.588	0.588	0.000	0.000	0.000	0.000
135	A	268	SER	0	-0.010	0.003	22.398	-0.909	-0.909	0.000	0.000	0.000	0.000
136	A	269	PHE	0	-0.007	-0.002	23.134	0.552	0.552	0.000	0.000	0.000	0.000
137	A	270	VAL	0	-0.039	-0.023	26.057	-0.492	-0.492	0.000	0.000	0.000	0.000
138	A	271	ASN	0	-0.001	0.001	27.789	0.003	0.003	0.000	0.000	0.000	0.000
139	A	272	ASP	-1	-0.779	-0.886	26.034	11.366	11.366	0.000	0.000	0.000	0.000
140	A	273	LYS	1	0.949	0.976	22.004	-13.558	-13.558	0.000	0.000	0.000	0.000
141	A	274	PHE	0	0.019	0.009	17.065	-0.361	-0.361	0.000	0.000	0.000	0.000
142	A	275	MET	0	-0.047	-0.042	20.471	0.281	0.281	0.000	0.000	0.000	0.000
143	A	276	PRO	0	0.041	0.030	16.647	-0.671	-0.671	0.000	0.000	0.000	0.000
144	A	277	PRO	0	0.002	0.014	19.459	-0.035	-0.035	0.000	0.000	0.000	0.000
145	A	278	ASP	-1	-0.835	-0.942	17.514	18.935	18.935	0.000	0.000	0.000	0.000
146	A	279	ASP	-1	-1.003	-1.000	17.542	15.621	15.621	0.000	0.000	0.000	0.000
147	A	280	PRO	0	-0.043	-0.016	15.522	-0.772	-0.772	0.000	0.000	0.000	0.000
148	A	281	LEU	0	-0.014	0.000	17.193	-0.592	-0.592	0.000	0.000	0.000	0.000
149	A	282	GLY	0	0.025	0.025	20.478	-0.632	-0.632	0.000	0.000	0.000	0.000
150	A	283	ARG	1	0.948	0.955	21.501	-13.306	-13.306	0.000	0.000	0.000	0.000
151	A	284	HIS	0	-0.030	-0.021	22.500	0.402	0.402	0.000	0.000	0.000	0.000
152	A	285	GLY	0	0.017	0.029	19.295	0.208	0.208	0.000	0.000	0.000	0.000
153	A	286	PRO	0	-0.048	-0.019	13.792	-0.023	-0.023	0.000	0.000	0.000	0.000
154	A	287	SER	0	0.056	0.021	13.228	-0.209	-0.209	0.000	0.000	0.000	0.000
155	A	288	LEU	0	0.084	0.037	13.342	1.572	1.572	0.000	0.000	0.000	0.000
156	A	289	ASP	-1	-0.918	-0.974	10.037	27.599	27.599	0.000	0.000	0.000	0.000
157	A	290	ASN	0	-0.027	-0.030	8.682	6.654	6.654	0.000	0.000	0.000	0.000
158	A	291	PHE	0	-0.039	0.010	9.543	1.989	1.989	0.000	0.000	0.000	0.000
159	A	292	LEU	0	-0.005	-0.008	9.143	0.760	0.760	0.000	0.000	0.000	0.000
160	A	293	ARG	1	0.893	0.964	2.513	-75.052	-71.184	0.675	-2.289	-2.255	0.030
161	A	294	LYS	1	0.908	0.946	1.964	-82.115	-86.053	13.954	-5.271	-4.745	0.055
162	A	295	LYS	1	0.915	0.940	5.226	-37.151	-37.151	0.000	0.000	0.000	0.000
163	A	296	PRO	0	0.033	0.048	6.090	6.271	6.271	0.000	0.000	0.000	0.000

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