FMO DATABASE

FMODB ID: V2151

Calculation Name: 3GXV-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GXV

Chain ID: A

ChEMBL ID:

UniProt ID: O25916

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1042386.994894
FMO2-HF: Nuclear repulsion	993229.882405
FMO2-HF: Total energy	-49157.112488
FMO2-MP2: Total energy	-49302.177147

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:1:MET )

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

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.
-11.907	-10.794	16.113	-6.868	-10.357	-0.005

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.035

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

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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	3	HIS	0	0.086	0.006	2.968	-3.188	-0.881	0.182	-1.231	-1.258	-0.004
4	A	4	LEU	0	0.006	0.006	5.602	0.308	0.308	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.907	0.975	1.847	-5.674	-10.225	13.268	-4.054	-4.663	0.009
6	A	6	HIS	0	0.037	0.013	2.502	0.354	3.056	2.165	-1.355	-3.511	-0.010
7	A	7	LEU	0	-0.041	-0.006	4.399	-0.365	-0.272	0.004	0.001	-0.098	0.000
8	A	8	GLN	0	-0.029	-0.027	6.903	0.180	0.180	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.006	-0.001	3.360	-1.461	-0.900	0.494	-0.227	-0.828	0.000
10	A	10	LEU	0	0.010	0.025	6.358	-0.472	-0.471	0.000	-0.002	0.001	0.000
11	A	11	GLN	0	-0.003	-0.019	9.016	-0.139	-0.139	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.021	0.003	8.491	-0.080	-0.080	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.028	0.019	6.385	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.732	-0.858	10.495	-0.091	-0.091	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.850	0.946	13.826	-0.162	-0.162	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.021	0.013	10.752	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.010	0.005	13.711	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.054	-0.031	16.104	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.007	0.006	17.928	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.021	0.001	18.466	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.048	-0.013	19.951	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.028	-0.012	22.442	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.043	-0.019	22.602	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.043	-0.018	23.519	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.047	0.029	24.746	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.081	0.033	26.289	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.960	0.982	20.859	0.151	0.151	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.014	0.005	23.263	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.926	-0.969	24.530	-0.111	-0.111	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.929	-0.961	21.605	-0.192	-0.192	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.011	0.003	18.828	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	32	HIS	1	0.882	0.941	21.047	0.115	0.115	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.083	-0.032	23.372	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.023	-0.009	18.173	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.061	-0.035	16.470	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.824	-0.905	20.866	-0.107	-0.107	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.024	0.001	21.511	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.027	-0.023	21.580	0.000	0.000	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.856	-0.901	18.236	-0.206	-0.206	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.003	0.001	16.678	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.107	-0.059	11.769	0.022	0.022	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.086	-0.067	15.305	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.041	0.003	16.967	-0.011	-0.011	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.028	-0.018	19.761	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.003	-0.016	15.477	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.031	0.021	19.744	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.019	-0.025	21.817	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.053	0.029	22.128	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.002	-0.003	21.438	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.950	-0.989	23.505	-0.053	-0.053	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.066	-0.031	26.692	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.029	0.004	25.411	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.020	-0.005	25.660	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.909	0.955	28.424	0.047	0.047	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.001	0.011	29.646	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	HIS	0	0.045	0.011	29.388	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.993	-0.988	31.408	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-1.028	-1.012	33.897	-0.031	-0.031	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.960	-0.976	34.809	-0.050	-0.050	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.104	-0.036	34.559	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.020	-0.013	32.228	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.009	0.004	26.040	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.817	-0.917	28.030	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.925	-0.991	27.086	0.039	0.039	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.081	-0.035	29.233	0.006	0.006	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.014	-0.020	32.299	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.020	0.013	26.755	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.862	0.928	28.211	-0.044	-0.044	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.029	-0.004	31.878	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.958	0.979	33.387	0.019	0.019	0.000	0.000	0.000	0.000
71	A	71	MET	0	0.002	0.038	29.756	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.058	-0.024	30.430	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.963	0.972	33.482	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.949	-0.950	34.446	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.894	0.956	27.908	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.070	0.006	30.033	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.033	-0.026	24.154	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.917	0.955	24.237	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.786	-0.907	25.157	0.072	0.072	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.909	-0.959	22.031	0.166	0.166	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.823	-0.894	20.322	0.131	0.131	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.006	-0.011	21.061	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.010	0.011	22.287	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.024	-0.015	17.694	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.053	-0.017	18.122	0.008	0.008	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.011	-0.004	19.608	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.017	0.001	20.295	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.033	0.004	15.484	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.032	-0.020	15.422	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.019	0.014	15.443	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.010	0.001	11.985	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.922	-0.958	16.107	-0.151	-0.151	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.046	-0.041	15.714	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.043	0.017	14.127	-0.055	-0.055	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.901	-0.953	14.610	-0.354	-0.354	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.022	0.011	10.406	-0.016	-0.016	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.026	0.008	8.016	-0.051	-0.051	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.023	0.009	11.317	0.024	0.024	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.878	-0.929	12.855	-0.625	-0.625	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.916	-0.974	6.849	-1.481	-1.481	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.034	-0.012	10.806	0.049	0.049	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.910	0.965	13.083	0.284	0.284	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.048	-0.037	11.575	0.103	0.103	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.036	-0.027	11.179	0.018	0.018	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.078	-0.062	13.043	0.046	0.046	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.014	0.003	16.661	0.027	0.027	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.921	0.963	12.138	0.754	0.754	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.957	0.993	14.099	0.216	0.216	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.947	0.979	17.101	0.219	0.219	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.014	0.012	18.552	0.019	0.019	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.008	-0.013	14.290	0.013	0.013	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.006	0.011	19.330	0.024	0.024	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.023	0.007	22.073	0.018	0.018	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.002	-0.009	21.479	0.011	0.011	0.000	0.000	0.000	0.000
115	A	115	ASN	0	-0.036	-0.045	20.485	0.006	0.006	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.048	0.010	24.205	0.013	0.013	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.032	0.000	26.123	0.009	0.009	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.878	0.966	21.761	0.174	0.174	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.929	-0.960	27.102	-0.074	-0.074	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.014	0.001	29.832	0.011	0.011	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.012	0.007	31.669	0.005	0.005	0.000	0.000	0.000	0.000
122	A	122	HIS	1	0.875	0.957	32.834	0.066	0.066	0.000	0.000	0.000	0.000
123	A	123	NME	0	-0.027	-0.029	32.401	0.002	0.002	0.000	0.000	0.000	0.000

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