FMO DATABASE

FMODB ID: K3VZ3

Calculation Name: 3GXV-A-Xray372

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: 2023-03-14

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	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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1041126.471316
FMO2-HF: Nuclear repulsion	991989.017716
FMO2-HF: Total energy	-49137.4536
FMO2-MP2: Total energy	-49282.422314

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.
-11.767	-10.681	16.274	-6.96	-10.399	-0.003

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 : -0.006 / q_NPA : -0.036

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	3	HIS	0	0.088	0.007	2.968	-3.209	-0.895	0.179	-1.225	-1.268	-0.003
4	A	4	LEU	0	0.005	0.005	5.602	0.302	0.302	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.905	0.973	1.847	-5.570	-10.136	13.416	-4.171	-4.679	0.010
6	A	6	HIS	0	0.036	0.013	2.502	0.400	3.091	2.164	-1.337	-3.517	-0.010
7	A	7	LEU	0	-0.035	-0.004	4.399	-0.340	-0.245	0.003	0.001	-0.099	0.000
8	A	8	GLN	0	-0.031	-0.028	6.903	0.173	0.173	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.004	-0.002	3.338	-1.452	-0.897	0.513	-0.227	-0.841	0.000
10	A	10	LEU	0	0.013	0.026	6.358	-0.447	-0.450	-0.001	-0.001	0.005	0.000
11	A	11	GLN	0	-0.006	-0.020	9.016	-0.140	-0.140	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.021	0.003	8.491	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.026	0.019	6.385	-0.036	-0.036	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.733	-0.858	10.495	-0.086	-0.086	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.854	0.947	13.826	-0.166	-0.166	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.019	0.012	10.751	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.006	0.006	13.711	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.056	-0.031	16.104	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.007	0.005	17.928	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.020	0.001	18.466	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.047	-0.013	19.951	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.027	-0.012	22.442	0.005	0.005	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.042	-0.020	22.602	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.044	-0.018	23.519	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.048	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	26.287	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.958	0.982	20.859	0.147	0.147	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.016	0.004	23.263	-0.016	-0.016	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.925	-0.968	24.530	-0.108	-0.108	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.929	-0.961	21.605	-0.187	-0.187	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.009	0.004	18.828	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	32	HIS	1	0.880	0.941	21.047	0.111	0.111	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.083	-0.033	23.374	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.022	-0.008	18.175	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.058	-0.033	16.470	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.825	-0.905	20.866	-0.105	-0.105	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.021	0.000	21.511	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.025	-0.023	21.580	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.856	-0.901	18.236	-0.201	-0.201	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.004	0.001	16.678	-0.023	-0.023	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.107	-0.058	11.769	0.021	0.021	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.086	-0.067	15.305	0.017	0.017	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.043	0.004	16.967	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.031	-0.020	19.761	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.004	-0.015	15.477	0.007	0.007	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.030	0.021	19.744	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.025	-0.027	21.817	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.057	0.031	22.128	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.002	-0.004	21.438	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.949	-0.988	23.505	-0.052	-0.052	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.067	-0.032	26.692	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.030	0.004	25.411	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.018	-0.004	25.660	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.906	0.954	28.424	0.045	0.045	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.001	0.012	29.646	0.002	0.002	0.000	0.000	0.000	0.000
56	A	56	HIS	0	0.044	0.010	29.388	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.991	-0.988	31.408	-0.076	-0.076	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-1.029	-1.012	33.897	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.961	-0.977	34.809	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.104	-0.035	34.559	0.004	0.004	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.023	-0.014	32.228	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	ILE	0	0.016	0.006	26.040	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.821	-0.918	28.030	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.923	-0.990	27.086	0.040	0.040	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	0.011	-0.021	32.299	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.016	0.014	26.755	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.860	0.927	28.211	-0.045	-0.045	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.029	-0.005	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	0.018	0.018	0.000	0.000	0.000	0.000
71	A	71	MET	0	0.000	0.038	29.756	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.053	-0.022	30.430	0.001	0.001	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.960	0.971	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	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.897	0.957	27.908	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.067	0.004	30.033	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.035	-0.026	24.155	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.924	0.958	24.237	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.792	-0.910	25.157	0.072	0.072	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.909	-0.960	22.031	0.164	0.164	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.821	-0.893	20.322	0.132	0.132	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.006	-0.011	21.061	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.007	0.010	22.287	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.023	-0.015	17.694	0.001	0.001	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.052	-0.015	18.122	0.009	0.009	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.012	-0.004	19.608	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.020	0.000	20.295	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.034	0.004	15.484	0.017	0.017	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.029	-0.019	15.421	-0.020	-0.020	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.020	0.014	15.443	-0.022	-0.022	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.013	0.000	11.986	0.003	0.003	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.924	-0.958	16.107	-0.146	-0.146	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.045	-0.041	15.714	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.040	0.016	14.127	-0.053	-0.053	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.898	-0.952	14.610	-0.345	-0.345	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.023	0.012	10.406	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.022	0.007	8.016	-0.049	-0.049	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.026	0.009	11.317	0.021	0.021	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.881	-0.930	12.855	-0.613	-0.613	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.916	-0.974	6.849	-1.445	-1.445	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.031	-0.011	10.806	0.044	0.044	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.910	0.965	13.083	0.277	0.277	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.049	-0.037	11.575	0.101	0.101	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.035	-0.027	11.179	0.015	0.015	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.077	-0.063	13.043	0.041	0.041	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.016	0.004	16.661	0.026	0.026	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.919	0.963	12.138	0.746	0.746	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.957	0.993	14.099	0.207	0.207	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.947	0.979	17.101	0.214	0.214	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.013	0.013	18.552	0.018	0.018	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.004	-0.015	14.290	0.010	0.010	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.007	0.011	19.330	0.022	0.022	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.021	0.007	22.073	0.017	0.017	0.000	0.000	0.000	0.000
114	A	114	ALA	0	0.001	-0.010	21.479	0.011	0.011	0.000	0.000	0.000	0.000
115	A	115	ASN	0	-0.040	-0.046	20.485	0.005	0.005	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.049	0.009	24.205	0.012	0.012	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.036	-0.003	26.122	0.009	0.009	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.878	0.965	21.761	0.173	0.173	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.935	-0.965	27.102	-0.076	-0.076	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.029	-0.008	29.832	0.011	0.011	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.052	-0.010	31.671	0.004	0.004	0.000	0.000	0.000	0.000
122	A	122	HIS	0	-0.065	-0.029	32.781	0.010	0.010	0.000	0.000	0.000	0.000

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