FMO DATABASE

FMODB ID: NNQKQ

Calculation Name: 3VVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VVV

Chain ID: A

ChEMBL ID:

UniProt ID: Q13137

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1005954.568416
FMO2-HF: Nuclear repulsion	958461.232422
FMO2-HF: Total energy	-47493.335994
FMO2-MP2: Total energy	-47633.289751

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:19:GLY)

Summations of interaction energy for fragment #1(A:19:GLY)

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.
-0.734	0.688	-0.006	-0.775	-0.64	0.004

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.022

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	21	SER	0	-0.003	0.004	3.815	-0.651	0.771	-0.006	-0.775	-0.640	0.004
4	A	22	GLN	0	0.005	0.004	5.789	0.657	0.657	0.000	0.000	0.000	0.000
5	A	23	VAL	0	-0.001	0.012	8.278	0.442	0.442	0.000	0.000	0.000	0.000
6	A	24	ILE	0	-0.006	-0.006	10.326	-0.239	-0.239	0.000	0.000	0.000	0.000
7	A	25	PHE	0	0.004	0.003	12.655	0.139	0.139	0.000	0.000	0.000	0.000
8	A	26	ASN	0	-0.051	-0.034	15.851	0.027	0.027	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.036	-0.001	19.071	0.027	0.027	0.000	0.000	0.000	0.000
10	A	28	VAL	0	-0.049	-0.003	17.965	0.014	0.014	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.876	-0.933	21.200	-0.281	-0.281	0.000	0.000	0.000	0.000
12	A	30	LYS	1	0.947	0.951	22.340	0.323	0.323	0.000	0.000	0.000	0.000
13	A	31	PHE	0	-0.023	-0.005	24.208	0.000	0.000	0.000	0.000	0.000	0.000
14	A	32	TYR	0	0.048	0.034	22.576	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	33	ILE	0	0.039	0.009	28.132	0.010	0.010	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.017	0.011	31.495	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	35	GLY	0	-0.021	-0.012	32.412	0.009	0.009	0.000	0.000	0.000	0.000
18	A	36	GLY	0	-0.001	0.011	32.420	0.009	0.009	0.000	0.000	0.000	0.000
19	A	37	ASP	-1	-0.823	-0.902	30.006	-0.185	-0.185	0.000	0.000	0.000	0.000
20	A	38	VAL	0	0.024	0.013	24.168	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	39	THR	0	-0.042	-0.012	24.726	0.003	0.003	0.000	0.000	0.000	0.000
22	A	40	CYS	0	-0.049	-0.004	19.181	-0.036	-0.036	0.000	0.000	0.000	0.000
23	A	41	HIS	0	0.037	0.013	20.850	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	42	TYR	0	-0.029	-0.028	15.828	-0.075	-0.075	0.000	0.000	0.000	0.000
25	A	43	THR	0	-0.022	0.000	15.630	0.091	0.091	0.000	0.000	0.000	0.000
26	A	44	PHE	0	0.025	0.011	13.639	-0.133	-0.133	0.000	0.000	0.000	0.000
27	A	45	THR	0	0.001	-0.018	9.798	0.095	0.095	0.000	0.000	0.000	0.000
28	A	46	GLN	0	-0.035	-0.031	12.540	0.046	0.046	0.000	0.000	0.000	0.000
29	A	47	HIS	0	0.010	-0.004	10.870	0.082	0.082	0.000	0.000	0.000	0.000
30	A	48	PHE	0	-0.028	0.006	9.690	0.025	0.025	0.000	0.000	0.000	0.000
31	A	49	ILE	0	-0.018	-0.012	11.817	0.056	0.056	0.000	0.000	0.000	0.000
32	A	50	PRO	0	-0.005	0.011	14.153	0.007	0.007	0.000	0.000	0.000	0.000
33	A	51	ARG	1	0.739	0.850	12.067	0.172	0.172	0.000	0.000	0.000	0.000
34	A	52	ARG	1	0.922	0.949	17.594	0.105	0.105	0.000	0.000	0.000	0.000
35	A	53	LYS	1	0.942	0.968	19.327	0.073	0.073	0.000	0.000	0.000	0.000
36	A	54	ASP	-1	-0.703	-0.824	14.716	-0.396	-0.396	0.000	0.000	0.000	0.000
37	A	55	TRP	0	-0.054	-0.031	15.432	0.014	0.014	0.000	0.000	0.000	0.000
38	A	56	ILE	0	0.001	0.008	15.210	-0.095	-0.095	0.000	0.000	0.000	0.000
39	A	57	GLY	0	0.016	0.007	15.973	0.074	0.074	0.000	0.000	0.000	0.000
40	A	58	ILE	0	-0.016	0.007	17.088	-0.070	-0.070	0.000	0.000	0.000	0.000
41	A	59	PHE	0	0.002	0.006	15.145	0.047	0.047	0.000	0.000	0.000	0.000
42	A	60	ARG	1	0.882	0.936	18.261	0.196	0.196	0.000	0.000	0.000	0.000
43	A	61	VAL	0	0.001	-0.020	16.400	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	62	GLY	0	-0.023	-0.017	15.934	0.052	0.052	0.000	0.000	0.000	0.000
45	A	63	TRP	0	-0.096	-0.031	10.392	0.070	0.070	0.000	0.000	0.000	0.000
46	A	64	LYS	1	0.948	0.962	14.778	0.070	0.070	0.000	0.000	0.000	0.000
47	A	65	THR	0	-0.049	-0.040	14.222	0.026	0.026	0.000	0.000	0.000	0.000
48	A	66	THR	0	0.032	-0.001	12.291	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	67	ARG	1	0.936	0.947	15.090	0.064	0.064	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.798	-0.872	18.003	-0.170	-0.170	0.000	0.000	0.000	0.000
51	A	69	TYR	0	-0.065	-0.002	18.248	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	70	TYR	0	0.023	0.013	19.652	0.032	0.032	0.000	0.000	0.000	0.000
53	A	71	THR	0	-0.022	-0.025	21.851	0.026	0.026	0.000	0.000	0.000	0.000
54	A	72	PHE	0	-0.032	-0.028	19.831	-0.038	-0.038	0.000	0.000	0.000	0.000
55	A	73	MET	0	-0.007	0.019	20.475	0.040	0.040	0.000	0.000	0.000	0.000
56	A	74	TRP	0	-0.023	-0.013	19.841	-0.034	-0.034	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.004	0.005	17.511	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	76	THR	0	-0.004	-0.036	19.677	0.037	0.037	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.065	-0.009	21.617	0.000	0.000	0.000	0.000	0.000	0.000
60	A	78	PRO	0	-0.003	-0.018	24.515	0.008	0.008	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.033	0.007	19.128	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	80	ASP	-1	-0.861	-0.928	23.072	-0.190	-0.190	0.000	0.000	0.000	0.000
63	A	81	LEU	0	0.046	0.024	22.323	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	82	ASN	0	-0.078	-0.059	21.538	0.015	0.015	0.000	0.000	0.000	0.000
65	A	83	ASN	0	-0.011	0.000	16.942	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	84	LYS	1	0.937	0.979	16.187	0.144	0.144	0.000	0.000	0.000	0.000
67	A	85	SER	0	0.017	-0.001	15.199	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	86	ALA	0	-0.075	-0.044	17.088	0.035	0.035	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.858	0.945	20.215	0.296	0.296	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.047	0.017	20.579	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	89	GLN	0	0.007	0.021	19.244	0.070	0.070	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.833	-0.927	21.472	-0.301	-0.301	0.000	0.000	0.000	0.000
73	A	91	VAL	0	-0.031	0.013	20.532	0.024	0.024	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.038	0.028	23.330	0.001	0.001	0.000	0.000	0.000	0.000
75	A	93	PHE	0	0.037	0.014	20.010	0.009	0.009	0.000	0.000	0.000	0.000
76	A	94	LYS	1	0.832	0.891	26.022	0.180	0.180	0.000	0.000	0.000	0.000
77	A	95	ALA	0	0.078	0.032	29.233	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	96	TYR	0	-0.067	-0.032	31.058	0.001	0.001	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.036	-0.030	27.240	0.007	0.007	0.000	0.000	0.000	0.000
80	A	98	LEU	0	-0.002	0.021	25.608	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	99	PRO	0	0.001	0.007	24.583	0.020	0.020	0.000	0.000	0.000	0.000
82	A	100	LYS	1	0.806	0.893	27.746	0.167	0.167	0.000	0.000	0.000	0.000
83	A	101	ASP	-1	-0.840	-0.877	27.398	-0.193	-0.193	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-0.880	-0.946	29.157	-0.178	-0.178	0.000	0.000	0.000	0.000
85	A	103	GLU	-1	-0.817	-0.872	24.476	-0.208	-0.208	0.000	0.000	0.000	0.000
86	A	104	TYR	0	-0.050	-0.028	21.045	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	105	TYR	0	-0.071	-0.079	19.992	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	106	GLN	0	-0.007	-0.001	12.997	0.001	0.001	0.000	0.000	0.000	0.000
89	A	107	PHE	0	0.057	0.023	16.177	0.042	0.042	0.000	0.000	0.000	0.000
90	A	108	CYS	0	-0.036	-0.018	11.823	-0.166	-0.166	0.000	0.000	0.000	0.000
91	A	109	TYR	0	-0.029	-0.042	11.223	0.139	0.139	0.000	0.000	0.000	0.000
92	A	110	VAL	0	-0.014	-0.004	10.499	-0.228	-0.228	0.000	0.000	0.000	0.000
93	A	111	ASP	-1	-0.748	-0.869	10.202	-0.249	-0.249	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.849	-0.942	12.506	-0.057	-0.057	0.000	0.000	0.000	0.000
95	A	113	ASP	-1	-0.867	-0.894	11.462	0.139	0.139	0.000	0.000	0.000	0.000
96	A	114	GLY	0	-0.049	-0.018	12.467	0.080	0.080	0.000	0.000	0.000	0.000
97	A	115	VAL	0	-0.046	-0.019	6.117	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	116	VAL	0	0.026	0.009	7.381	-0.094	-0.094	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.777	0.878	5.869	-0.082	-0.082	0.000	0.000	0.000	0.000
100	A	118	GLY	0	0.052	0.010	7.482	-0.333	-0.333	0.000	0.000	0.000	0.000
101	A	119	ALA	0	0.017	0.007	9.191	0.225	0.225	0.000	0.000	0.000	0.000
102	A	120	SER	0	-0.034	-0.008	11.263	-0.067	-0.067	0.000	0.000	0.000	0.000
103	A	121	ILE	0	-0.010	-0.001	14.537	-0.029	-0.029	0.000	0.000	0.000	0.000
104	A	122	PRO	0	0.004	0.001	16.559	0.010	0.010	0.000	0.000	0.000	0.000
105	A	123	PHE	0	-0.001	0.008	18.815	0.015	0.015	0.000	0.000	0.000	0.000
106	A	124	GLN	0	0.015	0.001	22.366	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.014	0.002	23.835	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	126	ARG	1	0.782	0.840	28.142	0.237	0.237	0.000	0.000	0.000	0.000
109	A	127	PRO	0	-0.029	-0.015	31.303	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.905	-0.943	32.453	-0.190	-0.190	0.000	0.000	0.000	0.000
111	A	129	ASN	0	-0.062	-0.041	31.815	0.006	0.006	0.000	0.000	0.000	0.000
112	A	130	GLU	-1	-0.909	-0.963	34.390	-0.134	-0.134	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.976	-0.986	31.827	-0.162	-0.162	0.000	0.000	0.000	0.000
114	A	132	ASP	-1	-0.843	-0.869	29.358	-0.235	-0.235	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)