FMO DATABASE

FMODB ID: JQGN9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1005288.454774
FMO2-HF: Nuclear repulsion	957794.977863
FMO2-HF: Total energy	-47493.476911
FMO2-MP2: Total energy	-47633.413375

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.
-0.333	0.853	-0.003	-0.653	-0.53	0.003

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 : 0.052 / q_NPA : 0.026

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	0.001	0.012	3.874	-0.442	0.744	-0.003	-0.653	-0.530	0.003
4	A	22	GLN	0	0.026	0.020	5.863	0.724	0.724	0.000	0.000	0.000	0.000
5	A	23	VAL	0	0.017	0.017	8.251	0.453	0.453	0.000	0.000	0.000	0.000
6	A	24	ILE	0	-0.011	-0.005	10.141	-0.265	-0.265	0.000	0.000	0.000	0.000
7	A	25	PHE	0	0.012	0.005	12.552	0.147	0.147	0.000	0.000	0.000	0.000
8	A	26	ASN	0	-0.048	-0.032	15.744	0.018	0.018	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.019	-0.006	18.958	0.026	0.026	0.000	0.000	0.000	0.000
10	A	28	VAL	0	-0.038	0.000	18.118	0.015	0.015	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.897	-0.938	21.306	-0.276	-0.276	0.000	0.000	0.000	0.000
12	A	30	LYS	1	0.958	0.955	22.551	0.302	0.302	0.000	0.000	0.000	0.000
13	A	31	PHE	0	-0.029	-0.008	23.992	0.000	0.000	0.000	0.000	0.000	0.000
14	A	32	TYR	0	0.054	0.031	22.351	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	33	ILE	0	0.049	0.016	27.783	0.010	0.010	0.000	0.000	0.000	0.000
16	A	34	PRO	0	-0.007	-0.002	31.463	0.000	0.000	0.000	0.000	0.000	0.000
17	A	35	GLY	0	-0.017	-0.006	32.293	0.010	0.010	0.000	0.000	0.000	0.000
18	A	36	GLY	0	0.001	0.014	32.540	0.009	0.009	0.000	0.000	0.000	0.000
19	A	37	ASP	-1	-0.824	-0.908	29.949	-0.180	-0.180	0.000	0.000	0.000	0.000
20	A	38	VAL	0	0.019	0.008	24.081	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	39	THR	0	-0.046	-0.028	24.972	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	40	CYS	0	-0.060	-0.016	19.304	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	41	HIS	0	0.019	0.000	20.948	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	42	TYR	0	-0.052	-0.045	15.881	-0.075	-0.075	0.000	0.000	0.000	0.000
25	A	43	THR	0	-0.011	0.002	15.844	0.091	0.091	0.000	0.000	0.000	0.000
26	A	44	PHE	0	0.021	0.011	13.768	-0.133	-0.133	0.000	0.000	0.000	0.000
27	A	45	THR	0	0.012	-0.020	9.573	0.096	0.096	0.000	0.000	0.000	0.000
28	A	46	GLN	0	-0.058	-0.045	12.629	0.066	0.066	0.000	0.000	0.000	0.000
29	A	47	HIS	0	0.006	-0.003	11.242	0.093	0.093	0.000	0.000	0.000	0.000
30	A	48	PHE	0	-0.016	0.012	10.200	0.012	0.012	0.000	0.000	0.000	0.000
31	A	49	ILE	0	-0.022	-0.022	12.342	0.066	0.066	0.000	0.000	0.000	0.000
32	A	50	PRO	0	-0.001	0.012	14.722	0.013	0.013	0.000	0.000	0.000	0.000
33	A	51	ARG	1	0.742	0.856	11.985	0.173	0.173	0.000	0.000	0.000	0.000
34	A	52	ARG	1	0.922	0.952	17.607	0.114	0.114	0.000	0.000	0.000	0.000
35	A	53	LYS	1	0.935	0.967	19.284	0.077	0.077	0.000	0.000	0.000	0.000
36	A	54	ASP	-1	-0.700	-0.832	14.598	-0.387	-0.387	0.000	0.000	0.000	0.000
37	A	55	TRP	0	-0.058	-0.031	15.335	0.018	0.018	0.000	0.000	0.000	0.000
38	A	56	ILE	0	0.004	0.011	15.024	-0.096	-0.096	0.000	0.000	0.000	0.000
39	A	57	GLY	0	0.005	0.004	15.890	0.074	0.074	0.000	0.000	0.000	0.000
40	A	58	ILE	0	-0.013	0.004	16.889	-0.070	-0.070	0.000	0.000	0.000	0.000
41	A	59	PHE	0	-0.012	-0.007	15.071	0.046	0.046	0.000	0.000	0.000	0.000
42	A	60	ARG	1	0.871	0.921	17.973	0.188	0.188	0.000	0.000	0.000	0.000
43	A	61	VAL	0	-0.008	-0.022	16.416	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	62	GLY	0	-0.018	-0.014	15.978	0.049	0.049	0.000	0.000	0.000	0.000
45	A	63	TRP	0	-0.089	-0.033	10.006	0.067	0.067	0.000	0.000	0.000	0.000
46	A	64	LYS	1	0.907	0.948	14.242	0.058	0.058	0.000	0.000	0.000	0.000
47	A	65	THR	0	-0.045	-0.047	13.674	0.040	0.040	0.000	0.000	0.000	0.000
48	A	66	THR	0	0.017	-0.001	11.741	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	67	ARG	1	0.934	0.951	14.544	0.053	0.053	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.794	-0.865	17.538	-0.144	-0.144	0.000	0.000	0.000	0.000
51	A	69	TYR	0	-0.047	-0.004	18.153	-0.015	-0.015	0.000	0.000	0.000	0.000
52	A	70	TYR	0	-0.016	0.000	19.599	0.032	0.032	0.000	0.000	0.000	0.000
53	A	71	THR	0	-0.027	-0.022	21.801	0.023	0.023	0.000	0.000	0.000	0.000
54	A	72	PHE	0	-0.032	-0.020	19.554	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	73	MET	0	0.000	0.017	20.270	0.040	0.040	0.000	0.000	0.000	0.000
56	A	74	TRP	0	-0.011	-0.012	19.626	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.011	0.002	17.526	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	76	THR	0	0.007	-0.018	19.503	0.030	0.030	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.052	-0.013	21.682	0.002	0.002	0.000	0.000	0.000	0.000
60	A	78	PRO	0	-0.016	-0.017	24.550	0.010	0.010	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.028	0.013	19.172	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	80	ASP	-1	-0.781	-0.883	23.166	-0.217	-0.217	0.000	0.000	0.000	0.000
63	A	81	LEU	0	0.043	0.027	22.526	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	82	ASN	0	-0.076	-0.059	21.756	0.015	0.015	0.000	0.000	0.000	0.000
65	A	83	ASN	0	-0.014	0.001	17.209	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	84	LYS	1	0.933	0.983	16.384	0.156	0.156	0.000	0.000	0.000	0.000
67	A	85	SER	0	0.022	0.006	15.312	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	86	ALA	0	-0.087	-0.049	17.256	0.031	0.031	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.819	0.905	20.387	0.297	0.297	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.052	0.027	20.510	-0.063	-0.063	0.000	0.000	0.000	0.000
71	A	89	GLN	0	-0.022	-0.004	19.508	0.064	0.064	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.811	-0.894	21.282	-0.302	-0.302	0.000	0.000	0.000	0.000
73	A	91	VAL	0	-0.017	0.023	20.371	0.026	0.026	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.035	0.018	23.242	0.004	0.004	0.000	0.000	0.000	0.000
75	A	93	PHE	0	0.027	0.016	19.693	0.016	0.016	0.000	0.000	0.000	0.000
76	A	94	LYS	1	0.835	0.889	25.664	0.179	0.179	0.000	0.000	0.000	0.000
77	A	95	ALA	0	0.065	0.020	29.143	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	96	TYR	0	-0.058	-0.023	30.975	0.001	0.001	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.031	-0.021	27.095	0.007	0.007	0.000	0.000	0.000	0.000
80	A	98	LEU	0	0.007	0.029	25.561	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	99	PRO	0	-0.004	0.002	24.366	0.019	0.019	0.000	0.000	0.000	0.000
82	A	100	LYS	1	0.767	0.871	27.489	0.164	0.164	0.000	0.000	0.000	0.000
83	A	101	ASP	-1	-0.782	-0.863	27.063	-0.177	-0.177	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-0.885	-0.942	28.274	-0.173	-0.173	0.000	0.000	0.000	0.000
85	A	103	GLU	-1	-0.791	-0.866	24.375	-0.200	-0.200	0.000	0.000	0.000	0.000
86	A	104	TYR	0	-0.037	-0.018	20.744	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	105	TYR	0	-0.071	-0.072	19.651	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	106	GLN	0	-0.015	0.001	12.603	0.007	0.007	0.000	0.000	0.000	0.000
89	A	107	PHE	0	0.062	0.029	16.163	0.043	0.043	0.000	0.000	0.000	0.000
90	A	108	CYS	0	-0.031	-0.016	11.698	-0.158	-0.158	0.000	0.000	0.000	0.000
91	A	109	TYR	0	-0.011	-0.032	11.149	0.142	0.142	0.000	0.000	0.000	0.000
92	A	110	VAL	0	-0.023	-0.013	10.416	-0.224	-0.224	0.000	0.000	0.000	0.000
93	A	111	ASP	-1	-0.734	-0.856	10.412	-0.256	-0.256	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.857	-0.949	12.653	-0.059	-0.059	0.000	0.000	0.000	0.000
95	A	113	ASP	-1	-0.863	-0.887	11.051	0.133	0.133	0.000	0.000	0.000	0.000
96	A	114	GLY	0	-0.037	-0.012	12.667	0.077	0.077	0.000	0.000	0.000	0.000
97	A	115	VAL	0	-0.040	-0.023	6.230	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	116	VAL	0	0.029	0.006	7.009	-0.083	-0.083	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.766	0.870	5.828	-0.051	-0.051	0.000	0.000	0.000	0.000
100	A	118	GLY	0	0.048	0.010	7.448	-0.333	-0.333	0.000	0.000	0.000	0.000
101	A	119	ALA	0	0.011	0.006	8.815	0.278	0.278	0.000	0.000	0.000	0.000
102	A	120	SER	0	-0.029	-0.007	11.265	-0.068	-0.068	0.000	0.000	0.000	0.000
103	A	121	ILE	0	0.000	-0.001	14.153	-0.041	-0.041	0.000	0.000	0.000	0.000
104	A	122	PRO	0	-0.002	0.005	16.035	0.011	0.011	0.000	0.000	0.000	0.000
105	A	123	PHE	0	0.001	0.010	18.256	0.013	0.013	0.000	0.000	0.000	0.000
106	A	124	GLN	0	0.020	0.010	21.938	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.021	-0.002	23.345	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	126	ARG	1	0.768	0.842	27.764	0.231	0.231	0.000	0.000	0.000	0.000
109	A	127	PRO	0	-0.022	-0.014	30.725	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.910	-0.949	31.956	-0.185	-0.185	0.000	0.000	0.000	0.000
111	A	129	ASN	0	-0.075	-0.048	31.123	0.004	0.004	0.000	0.000	0.000	0.000
112	A	130	GLU	-1	-0.915	-0.958	34.035	-0.129	-0.129	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.945	-0.974	31.501	-0.152	-0.152	0.000	0.000	0.000	0.000
114	A	132	ASP	-1	-0.855	-0.875	29.006	-0.231	-0.231	0.000	0.000	0.000	0.000

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