FMO DATABASE

FMODB ID: 535QZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1044553.464592
FMO2-HF: Nuclear repulsion	995414.345389
FMO2-HF: Total energy	-49139.119203
FMO2-MP2: Total energy	-49284.007611

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.
-12.189	-3.169	7.435	-5.122	-11.329	-0.018

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 : 0.017 / q_NPA : 0.012

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	0.059	0.006	3.111	-2.929	0.078	0.106	-1.674	-1.438	0.002
4	A	4	LEU	0	-0.003	0.013	5.842	0.308	0.308	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.903	0.935	2.280	-4.262	-3.252	3.439	-1.109	-3.340	0.004
6	A	6	HIS	0	0.030	0.016	2.632	-2.968	0.899	3.222	-2.003	-5.086	-0.023
7	A	7	LEU	0	-0.011	0.003	3.757	0.099	0.260	0.006	0.026	-0.192	0.000
8	A	8	GLN	0	-0.037	-0.027	6.268	0.606	0.606	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.037	0.011	2.732	-2.168	-1.207	0.663	-0.358	-1.265	-0.001
10	A	10	LEU	0	0.001	0.019	5.188	-0.302	-0.288	-0.001	-0.004	-0.008	0.000
11	A	11	GLN	0	0.017	-0.001	7.437	0.093	0.093	0.000	0.000	0.000	0.000
12	A	12	ASN	0	-0.017	-0.011	7.387	-0.214	-0.214	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.041	0.028	5.546	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.751	-0.867	9.418	-0.165	-0.165	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.804	0.897	12.516	-0.311	-0.311	0.000	0.000	0.000	0.000
16	A	16	ILE	0	0.016	0.015	10.066	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.010	-0.004	12.830	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.050	-0.017	15.215	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.015	-0.005	17.092	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.000	-0.009	17.525	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.039	-0.012	19.027	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.023	-0.009	21.471	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.046	-0.018	21.877	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.038	-0.015	23.014	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.029	0.018	24.434	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.120	0.050	25.944	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.799	0.873	20.482	-0.026	-0.026	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.007	0.000	22.378	-0.020	-0.020	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.877	-0.921	23.929	-0.044	-0.044	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.821	-0.890	20.696	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.012	0.021	18.118	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	32	HIS	1	0.873	0.954	20.510	0.064	0.064	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.076	-0.041	22.651	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.010	-0.001	17.590	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.066	-0.032	15.746	-0.040	-0.040	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.802	-0.905	19.940	-0.097	-0.097	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.039	0.013	20.469	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.006	-0.002	20.523	0.002	0.002	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.789	-0.856	17.283	-0.334	-0.334	0.000	0.000	0.000	0.000
40	A	40	PHE	0	0.058	0.048	15.436	-0.062	-0.062	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.107	-0.074	10.891	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.073	-0.058	14.300	0.012	0.012	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.025	0.001	16.042	0.026	0.026	0.000	0.000	0.000	0.000
44	A	44	PRO	0	-0.015	-0.009	18.945	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.012	-0.001	14.409	0.048	0.048	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.037	0.031	18.393	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.027	-0.020	20.388	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.052	0.018	20.709	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	PHE	0	0.016	0.001	20.172	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.864	-0.929	22.228	-0.052	-0.052	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.052	-0.026	25.491	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.020	0.001	24.010	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.012	-0.006	24.597	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.805	0.899	27.206	0.033	0.033	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.000	0.003	28.551	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	HIS	0	-0.007	-0.016	28.587	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.974	-0.990	29.852	-0.047	-0.047	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.877	-0.912	32.883	0.009	0.009	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.926	-0.956	34.167	0.010	0.010	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.106	-0.039	33.476	0.008	0.008	0.000	0.000	0.000	0.000
61	A	61	PRO	0	-0.008	-0.011	31.041	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.004	0.003	25.003	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.800	-0.903	26.618	0.105	0.105	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.782	-0.905	26.003	0.170	0.170	0.000	0.000	0.000	0.000
65	A	65	ASN	0	-0.081	-0.047	28.172	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.015	-0.003	30.900	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.011	0.001	25.269	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.723	0.813	26.943	-0.158	-0.158	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.087	-0.041	30.534	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.793	0.875	31.603	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	71	MET	0	0.021	0.047	28.491	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.027	-0.010	29.451	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.971	0.981	32.335	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.877	-0.921	32.756	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.786	0.881	27.766	0.010	0.010	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.057	0.017	28.479	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	ILE	0	-0.033	-0.018	22.678	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.855	0.919	21.388	-0.128	-0.128	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.779	-0.875	23.938	0.178	0.178	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.886	-0.949	21.064	0.230	0.230	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.765	-0.850	19.078	0.222	0.222	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.005	0.000	19.860	0.008	0.008	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.041	0.018	21.518	0.008	0.008	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.038	-0.018	16.582	0.028	0.028	0.000	0.000	0.000	0.000
85	A	85	ILE	0	-0.047	-0.020	16.797	0.040	0.040	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.024	0.002	18.408	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	ALA	0	-0.026	-0.002	19.466	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.034	0.002	14.470	0.069	0.069	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.027	-0.010	14.943	-0.048	-0.048	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.017	0.008	15.116	0.013	0.013	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.040	-0.021	11.928	0.054	0.054	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.910	-0.950	16.164	0.129	0.129	0.000	0.000	0.000	0.000
93	A	93	ASN	0	-0.086	-0.056	15.804	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	94	ILE	0	0.064	0.037	14.074	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.886	-0.937	14.361	-0.159	-0.159	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.002	-0.002	10.859	-0.056	-0.056	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.043	0.014	7.907	-0.040	-0.040	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.009	0.001	11.012	-0.054	-0.054	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.867	-0.907	12.991	-0.749	-0.749	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.900	-0.962	6.363	-1.369	-1.369	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.016	0.002	10.378	-0.097	-0.097	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.842	0.908	12.149	0.281	0.281	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.047	-0.050	11.749	-0.083	-0.083	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.005	-0.014	9.953	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	105	SER	0	-0.089	-0.072	11.908	0.046	0.046	0.000	0.000	0.000	0.000
106	A	106	ILE	0	0.012	0.008	15.480	0.037	0.037	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.897	0.956	11.878	1.149	1.149	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.847	0.929	12.982	0.506	0.506	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.845	0.912	16.253	0.370	0.370	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.005	0.009	18.211	0.033	0.033	0.000	0.000	0.000	0.000
111	A	111	PHE	0	-0.007	-0.020	14.083	0.009	0.009	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.027	0.023	19.148	0.034	0.034	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.004	0.012	21.872	0.034	0.034	0.000	0.000	0.000	0.000
114	A	114	ALA	0	-0.004	-0.016	21.477	0.023	0.023	0.000	0.000	0.000	0.000
115	A	115	ASN	0	-0.028	0.000	20.892	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	116	THR	0	0.016	-0.005	24.462	0.026	0.026	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.020	-0.009	26.669	0.021	0.021	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.832	0.909	22.340	0.383	0.383	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.833	-0.922	26.031	-0.278	-0.278	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.027	-0.004	29.989	0.018	0.018	0.000	0.000	0.000	0.000
121	A	121	ALA	0	-0.037	-0.005	32.012	0.012	0.012	0.000	0.000	0.000	0.000
122	A	122	HIS	0	-0.111	-0.050	33.078	0.014	0.014	0.000	0.000	0.000	0.000

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