FMO DATABASE

FMODB ID: 94LK2

Calculation Name: 5V3N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5V3N

Chain ID: A

ChEMBL ID:

UniProt ID: P25651

Base Structure: X-ray

Registration Date: 2023-06-22

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	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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-889102.608841
FMO2-HF: Nuclear repulsion	844379.766784
FMO2-HF: Total energy	-44722.842057
FMO2-MP2: Total energy	-44854.74507

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:70:ASN)

Summations of interaction energy for fragment #1(A:70:ASN)

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.
-3.274	0.55	1.145	-1.55	-3.419	0.006

Interaction energy analysis for fragmet #1(A:70:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : -0.004

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	72	GLU	-1	-0.780	-0.852	3.295	-1.027	0.702	-0.002	-0.714	-1.013	0.001
4	A	73	VAL	0	0.040	0.031	3.253	-0.532	0.439	0.066	-0.270	-0.767	0.001
5	A	74	ILE	0	-0.005	0.002	2.386	-1.352	-0.228	1.081	-0.566	-1.639	0.004
6	A	75	LYS	1	0.829	0.885	5.954	-0.363	-0.363	0.000	0.000	0.000	0.000
7	A	76	ASP	-1	-0.785	-0.856	8.055	0.515	0.515	0.000	0.000	0.000	0.000
8	A	77	LEU	0	-0.029	-0.007	8.273	-0.097	-0.097	0.000	0.000	0.000	0.000
9	A	78	TYR	0	-0.014	-0.022	9.114	-0.141	-0.141	0.000	0.000	0.000	0.000
10	A	79	GLU	-1	-0.864	-0.904	12.207	0.224	0.224	0.000	0.000	0.000	0.000
11	A	80	TYR	0	-0.067	-0.074	11.447	-0.072	-0.072	0.000	0.000	0.000	0.000
12	A	81	LEU	0	-0.038	0.002	12.857	-0.029	-0.029	0.000	0.000	0.000	0.000
13	A	82	CYS	0	-0.074	-0.037	15.318	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	83	ASN	0	0.019	0.038	17.229	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	84	VAL	0	-0.008	-0.017	16.085	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	85	ARG	1	0.826	0.895	10.189	-0.290	-0.290	0.000	0.000	0.000	0.000
17	A	86	VAL	0	0.000	0.004	14.062	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	87	HIS	0	-0.021	-0.021	13.327	0.004	0.004	0.000	0.000	0.000	0.000
19	A	88	LYS	1	0.892	0.947	13.458	0.004	0.004	0.000	0.000	0.000	0.000
20	A	89	SER	0	-0.025	-0.023	15.336	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	90	TYR	0	-0.069	-0.021	17.478	0.013	0.013	0.000	0.000	0.000	0.000
22	A	91	GLU	-1	-0.927	-0.960	20.173	-0.133	-0.133	0.000	0.000	0.000	0.000
23	A	92	ASP	-1	-0.820	-0.894	23.303	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	93	ASP	-1	-0.947	-0.975	26.988	-0.048	-0.048	0.000	0.000	0.000	0.000
25	A	94	SER	0	-0.077	-0.045	29.080	0.001	0.001	0.000	0.000	0.000	0.000
26	A	95	GLY	0	0.008	-0.012	27.097	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	96	LEU	0	0.006	0.024	19.253	0.002	0.002	0.000	0.000	0.000	0.000
28	A	97	TRP	0	-0.017	-0.013	22.201	0.011	0.011	0.000	0.000	0.000	0.000
29	A	98	PHE	0	-0.024	-0.013	16.255	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	99	ASP	-1	-0.842	-0.908	18.739	0.010	0.010	0.000	0.000	0.000	0.000
31	A	100	ILE	0	-0.018	-0.016	17.967	0.004	0.004	0.000	0.000	0.000	0.000
32	A	101	SER	0	0.023	0.002	18.680	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	102	GLN	0	-0.023	0.004	19.268	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	103	GLY	0	0.023	-0.012	21.244	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	104	THR	0	-0.016	-0.005	21.003	0.029	0.029	0.000	0.000	0.000	0.000
36	A	105	HIS	0	0.078	0.006	19.846	-0.026	-0.026	0.000	0.000	0.000	0.000
37	A	106	SER	0	-0.051	-0.016	23.678	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	107	GLY	0	-0.004	-0.018	25.036	0.019	0.019	0.000	0.000	0.000	0.000
39	A	108	GLY	0	-0.039	-0.014	27.439	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	109	SER	0	0.019	0.010	29.928	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	110	SER	0	-0.021	-0.012	27.396	0.005	0.005	0.000	0.000	0.000	0.000
42	A	111	ASP	-1	-0.876	-0.932	27.725	0.109	0.109	0.000	0.000	0.000	0.000
43	A	112	ASP	-1	-0.913	-0.927	30.079	0.110	0.110	0.000	0.000	0.000	0.000
44	A	113	TYR	0	-0.030	-0.018	25.108	0.010	0.010	0.000	0.000	0.000	0.000
45	A	114	SER	0	-0.053	-0.032	25.771	-0.017	-0.017	0.000	0.000	0.000	0.000
46	A	115	ILE	0	0.021	0.020	21.646	0.005	0.005	0.000	0.000	0.000	0.000
47	A	116	MET	0	-0.001	0.021	24.695	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	117	ASP	-1	-0.770	-0.848	22.823	0.088	0.088	0.000	0.000	0.000	0.000
49	A	118	TYR	0	-0.064	-0.074	22.741	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	119	LYS	1	0.862	0.928	22.895	0.007	0.007	0.000	0.000	0.000	0.000
51	A	120	LEU	0	-0.041	-0.027	21.619	0.003	0.003	0.000	0.000	0.000	0.000
52	A	121	GLY	0	0.072	0.027	23.296	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	122	PHE	0	-0.052	-0.033	21.689	0.001	0.001	0.000	0.000	0.000	0.000
54	A	123	VAL	0	0.056	0.030	25.932	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	124	LYS	1	0.840	0.908	28.558	0.098	0.098	0.000	0.000	0.000	0.000
56	A	125	GLY	0	0.058	0.040	31.480	0.006	0.006	0.000	0.000	0.000	0.000
57	A	126	GLN	0	0.022	-0.010	34.251	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	127	ALA	0	-0.015	-0.016	35.864	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	128	GLN	0	-0.004	0.010	32.477	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	129	VAL	0	0.030	0.020	31.576	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	130	THR	0	-0.044	-0.023	25.584	0.002	0.002	0.000	0.000	0.000	0.000
62	A	131	GLU	-1	-0.892	-0.932	28.841	-0.052	-0.052	0.000	0.000	0.000	0.000
63	A	132	VAL	0	-0.024	-0.011	25.909	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	133	ILE	0	0.000	0.011	27.859	0.007	0.007	0.000	0.000	0.000	0.000
65	A	134	TYR	0	-0.031	-0.030	26.736	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	135	ALA	0	0.065	0.019	27.774	0.001	0.001	0.000	0.000	0.000	0.000
67	A	136	PRO	0	0.045	0.052	27.693	0.003	0.003	0.000	0.000	0.000	0.000
68	A	137	VAL	0	-0.048	-0.045	25.025	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	138	LEU	0	0.018	-0.011	27.953	0.005	0.005	0.000	0.000	0.000	0.000
70	A	139	LYS	1	0.861	0.928	30.474	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	140	GLN	0	-0.017	0.001	26.811	0.002	0.002	0.000	0.000	0.000	0.000
72	A	141	ARG	1	0.735	0.856	26.197	-0.074	-0.074	0.000	0.000	0.000	0.000
73	A	142	SER	0	0.034	-0.008	30.744	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	143	THR	0	0.028	-0.010	33.756	0.001	0.001	0.000	0.000	0.000	0.000
75	A	144	GLU	-1	-0.916	-0.948	35.327	0.060	0.060	0.000	0.000	0.000	0.000
76	A	145	GLU	-1	-0.718	-0.801	28.704	0.080	0.080	0.000	0.000	0.000	0.000
77	A	146	LEU	0	-0.021	-0.012	32.729	0.000	0.000	0.000	0.000	0.000	0.000
78	A	147	TYR	0	0.010	0.012	34.426	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	148	SER	0	0.010	0.009	32.596	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	149	LEU	0	0.016	0.009	28.801	0.000	0.000	0.000	0.000	0.000	0.000
81	A	150	GLN	0	-0.045	-0.028	32.921	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	151	SER	0	-0.084	-0.031	35.679	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	152	LYS	1	0.826	0.912	30.242	-0.097	-0.097	0.000	0.000	0.000	0.000
84	A	153	LEU	0	-0.016	-0.012	29.481	0.000	0.000	0.000	0.000	0.000	0.000
85	A	154	PRO	0	-0.041	-0.010	32.941	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	155	GLU	-1	-0.806	-0.923	35.199	0.019	0.019	0.000	0.000	0.000	0.000
87	A	156	TYR	0	0.053	0.015	32.805	0.002	0.002	0.000	0.000	0.000	0.000
88	A	157	LEU	0	-0.043	-0.014	29.810	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	158	PHE	0	-0.016	0.000	31.884	0.003	0.003	0.000	0.000	0.000	0.000
90	A	159	GLU	-1	-0.951	-0.967	34.325	0.005	0.005	0.000	0.000	0.000	0.000
91	A	160	THR	0	-0.054	-0.032	32.231	0.000	0.000	0.000	0.000	0.000	0.000
92	A	161	LEU	0	-0.034	-0.009	31.916	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	162	SER	0	-0.019	-0.032	31.916	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	163	PHE	0	-0.022	-0.011	26.796	0.004	0.004	0.000	0.000	0.000	0.000
95	A	164	PRO	0	0.098	0.061	30.500	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	165	LEU	0	0.045	0.008	23.351	0.004	0.004	0.000	0.000	0.000	0.000
97	A	166	SER	0	-0.030	-0.017	25.923	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	167	SER	0	-0.008	-0.013	27.467	0.003	0.003	0.000	0.000	0.000	0.000
99	A	168	LEU	0	0.007	0.019	21.150	0.011	0.011	0.000	0.000	0.000	0.000
100	A	169	ASN	0	0.019	0.010	21.739	0.011	0.011	0.000	0.000	0.000	0.000
101	A	170	GLN	0	0.028	0.016	23.934	0.011	0.011	0.000	0.000	0.000	0.000
102	A	171	PHE	0	0.021	0.016	26.056	0.011	0.011	0.000	0.000	0.000	0.000
103	A	172	TYR	0	-0.008	-0.014	19.535	0.000	0.000	0.000	0.000	0.000	0.000
104	A	173	ASN	0	0.005	-0.021	23.964	0.022	0.022	0.000	0.000	0.000	0.000
105	A	174	LYS	1	0.885	0.958	25.650	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	175	ILE	0	0.046	0.043	25.361	0.006	0.006	0.000	0.000	0.000	0.000
107	A	176	ALA	0	0.012	0.011	23.282	0.008	0.008	0.000	0.000	0.000	0.000
108	A	177	LYS	1	0.921	0.948	25.091	-0.051	-0.051	0.000	0.000	0.000	0.000
109	A	178	SER	0	-0.063	-0.044	28.094	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	179	LEU	0	-0.001	-0.008	25.057	0.001	0.001	0.000	0.000	0.000	0.000
111	A	180	ASN	0	-0.021	-0.006	23.471	0.010	0.010	0.000	0.000	0.000	0.000
112	A	181	LYS	1	0.851	0.947	27.594	-0.054	-0.054	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:70:ASN)