FMO DATABASE

FMODB ID: MV31Z

Calculation Name: 3N3E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3E

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UUZ6

Base Structure: X-ray

Registration Date: 2023-06-21

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-777443.980284
FMO2-HF: Nuclear repulsion	735596.22054
FMO2-HF: Total energy	-41847.759745
FMO2-MP2: Total energy	-41970.431541

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:61:GLY)

Summations of interaction energy for fragment #1(A:61: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.
-0.801	0.76	-0.006	-0.795	-0.76	0

Interaction energy analysis for fragmet #1(A:61:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : -0.011

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].
3	A	63	SER	0	0.032	0.033	3.573	-0.754	0.807	-0.006	-0.795	-0.760
4	A	64	GLU	-1	-0.873	-0.924	4.983	1.708	1.708	0.000	0.000	0.000
5	A	65	VAL	0	-0.009	-0.004	6.522	-0.375	-0.375	0.000	0.000	0.000
6	A	66	ARG	1	0.873	0.941	8.332	0.368	0.368	0.000	0.000	0.000
7	A	67	SER	0	0.019	0.007	12.455	-0.031	-0.031	0.000	0.000	0.000
8	A	68	ASP	-1	-0.748	-0.832	16.151	0.006	0.006	0.000	0.000	0.000
9	A	69	ARG	1	0.887	0.934	19.112	0.002	0.002	0.000	0.000	0.000
10	A	70	GLU	-1	-0.858	-0.919	21.805	-0.006	-0.006	0.000	0.000	0.000
11	A	71	LYS	1	0.851	0.900	17.670	0.043	0.043	0.000	0.000	0.000
12	A	72	PHE	0	-0.020	-0.005	15.001	0.024	0.024	0.000	0.000	0.000
13	A	73	THR	0	-0.010	-0.011	12.559	-0.031	-0.031	0.000	0.000	0.000
14	A	74	VAL	0	-0.012	0.004	10.558	0.096	0.096	0.000	0.000	0.000
15	A	75	TYR	0	0.009	0.005	7.928	-0.059	-0.059	0.000	0.000	0.000
16	A	76	LEU	0	-0.024	-0.022	7.566	0.026	0.026	0.000	0.000	0.000
17	A	77	ASP	-1	-0.880	-0.941	6.475	-1.589	-1.589	0.000	0.000	0.000
18	A	78	VAL	0	-0.052	-0.037	8.491	0.114	0.114	0.000	0.000	0.000
19	A	79	LYS	1	0.994	0.996	8.658	1.051	1.051	0.000	0.000	0.000
20	A	80	HIS	0	-0.051	-0.041	12.764	0.016	0.016	0.000	0.000	0.000
21	A	81	PHE	0	-0.050	-0.001	13.857	0.069	0.069	0.000	0.000	0.000
22	A	82	SER	0	0.005	0.002	17.160	-0.018	-0.018	0.000	0.000	0.000
23	A	83	PRO	0	0.029	-0.019	19.972	0.002	0.002	0.000	0.000	0.000
24	A	84	ASP	-1	-0.884	-0.930	21.315	-0.104	-0.104	0.000	0.000	0.000
25	A	85	GLU	-1	-0.918	-0.928	20.079	-0.172	-0.172	0.000	0.000	0.000
26	A	86	LEU	0	-0.033	-0.027	15.665	0.000	0.000	0.000	0.000	0.000
27	A	87	SER	0	0.013	0.015	19.440	0.012	0.012	0.000	0.000	0.000
28	A	88	VAL	0	-0.003	-0.015	17.816	0.008	0.008	0.000	0.000	0.000
29	A	89	LYS	1	0.951	0.980	20.282	-0.009	-0.009	0.000	0.000	0.000
30	A	90	VAL	0	-0.033	-0.002	21.112	0.013	0.013	0.000	0.000	0.000
31	A	91	THR	0	0.012	-0.001	22.624	-0.014	-0.014	0.000	0.000	0.000
32	A	92	ASP	-1	-0.890	-0.938	23.269	0.110	0.110	0.000	0.000	0.000
33	A	93	ASP	-1	-0.830	-0.879	23.721	0.118	0.118	0.000	0.000	0.000
34	A	94	TYR	0	-0.030	-0.025	17.778	0.058	0.058	0.000	0.000	0.000
35	A	95	VAL	0	0.002	0.005	17.152	-0.027	-0.027	0.000	0.000	0.000
36	A	96	GLU	-1	-0.918	-0.972	17.045	0.119	0.119	0.000	0.000	0.000
37	A	97	ILE	0	-0.014	-0.018	13.370	-0.031	-0.031	0.000	0.000	0.000
38	A	98	GLN	0	-0.019	-0.006	15.903	0.018	0.018	0.000	0.000	0.000
39	A	99	GLY	0	0.059	0.032	16.487	-0.028	-0.028	0.000	0.000	0.000
40	A	100	LYS	1	0.920	0.964	17.421	0.088	0.088	0.000	0.000	0.000
41	A	101	HIS	1	0.824	0.899	17.495	0.218	0.218	0.000	0.000	0.000
42	A	102	GLY	0	-0.025	-0.014	19.345	0.008	0.008	0.000	0.000	0.000
43	A	103	GLU	-1	-0.888	-0.933	18.975	-0.261	-0.261	0.000	0.000	0.000
44	A	104	ARG	1	0.984	0.976	22.572	0.103	0.103	0.000	0.000	0.000
45	A	105	GLN	0	-0.066	-0.034	20.073	-0.019	-0.019	0.000	0.000	0.000
46	A	106	ASP	-1	-0.896	-0.955	24.069	-0.095	-0.095	0.000	0.000	0.000
47	A	107	ASP	-1	-0.903	-0.943	26.351	-0.058	-0.058	0.000	0.000	0.000
48	A	108	HIS	0	-0.064	-0.028	29.639	0.004	0.004	0.000	0.000	0.000
49	A	109	GLY	0	0.034	0.037	25.826	0.006	0.006	0.000	0.000	0.000
50	A	110	TYR	0	-0.046	-0.044	23.990	-0.008	-0.008	0.000	0.000	0.000
51	A	111	ILE	0	-0.006	0.015	17.599	0.009	0.009	0.000	0.000	0.000
52	A	112	SER	0	0.013	-0.008	20.294	-0.013	-0.013	0.000	0.000	0.000
53	A	113	ARG	1	0.897	0.949	13.484	0.234	0.234	0.000	0.000	0.000
54	A	114	GLU	-1	-0.842	-0.924	16.501	-0.024	-0.024	0.000	0.000	0.000
55	A	115	PHE	0	-0.074	-0.028	12.912	0.022	0.022	0.000	0.000	0.000
56	A	116	HIS	0	0.041	0.012	14.911	-0.014	-0.014	0.000	0.000	0.000
57	A	117	ARG	1	0.888	0.954	6.926	-0.405	-0.405	0.000	0.000	0.000
58	A	118	ARG	1	0.980	1.000	13.915	-0.231	-0.231	0.000	0.000	0.000
59	A	119	TYR	0	-0.041	-0.048	8.873	0.016	0.016	0.000	0.000	0.000
60	A	120	ARG	1	0.940	0.971	15.134	-0.406	-0.406	0.000	0.000	0.000
61	A	121	LEU	0	0.005	0.005	17.291	0.020	0.020	0.000	0.000	0.000
62	A	122	PRO	0	-0.031	-0.008	18.291	0.001	0.001	0.000	0.000	0.000
63	A	123	SER	0	0.020	-0.001	21.370	-0.014	-0.014	0.000	0.000	0.000
64	A	124	ASN	0	-0.005	-0.001	23.339	-0.001	-0.001	0.000	0.000	0.000
65	A	125	VAL	0	-0.017	0.003	19.913	-0.010	-0.010	0.000	0.000	0.000
66	A	126	ASP	-1	-0.776	-0.867	23.341	0.018	0.018	0.000	0.000	0.000
67	A	127	GLN	0	0.022	-0.023	23.871	-0.017	-0.017	0.000	0.000	0.000
68	A	128	SER	0	-0.073	-0.038	25.122	-0.013	-0.013	0.000	0.000	0.000
69	A	129	ALA	0	0.008	0.005	25.636	-0.010	-0.010	0.000	0.000	0.000
70	A	130	ILE	0	-0.070	-0.025	19.745	-0.011	-0.011	0.000	0.000	0.000
71	A	131	THR	0	-0.019	-0.004	20.854	-0.014	-0.014	0.000	0.000	0.000
72	A	132	CYS	0	-0.015	-0.007	16.901	-0.002	-0.002	0.000	0.000	0.000
73	A	133	THR	0	0.009	0.014	17.378	0.011	0.011	0.000	0.000	0.000
74	A	134	LEU	0	0.014	0.010	15.208	-0.032	-0.032	0.000	0.000	0.000
75	A	135	SER	0	0.035	0.017	14.290	0.039	0.039	0.000	0.000	0.000
76	A	136	ALA	0	-0.057	-0.046	16.968	-0.009	-0.009	0.000	0.000	0.000
77	A	137	ASP	-1	-0.924	-0.952	13.756	-0.536	-0.536	0.000	0.000	0.000
78	A	138	GLY	0	-0.020	-0.009	13.117	-0.102	-0.102	0.000	0.000	0.000
79	A	139	LEU	0	-0.033	-0.005	8.987	-0.106	-0.106	0.000	0.000	0.000
80	A	140	LEU	0	0.010	0.008	11.588	0.143	0.143	0.000	0.000	0.000
81	A	141	THR	0	0.015	-0.008	11.822	-0.070	-0.070	0.000	0.000	0.000
82	A	142	LEU	0	-0.024	-0.007	13.821	0.039	0.039	0.000	0.000	0.000
83	A	143	CYS	0	-0.042	-0.030	15.362	0.023	0.023	0.000	0.000	0.000
84	A	144	GLY	0	0.091	0.031	18.036	0.004	0.004	0.000	0.000	0.000
85	A	145	PRO	0	0.014	0.011	20.176	0.015	0.015	0.000	0.000	0.000
86	A	146	LYS	1	0.823	0.904	19.318	-0.096	-0.096	0.000	0.000	0.000
87	A	147	THR	0	0.003	0.011	24.279	-0.008	-0.008	0.000	0.000	0.000
88	A	148	SER	0	-0.047	-0.028	28.019	0.009	0.009	0.000	0.000	0.000
89	A	149	GLY	0	0.000	0.000	30.786	-0.006	-0.006	0.000	0.000	0.000
90	A	150	ILE	0	-0.008	-0.012	33.648	0.005	0.005	0.000	0.000	0.000
91	A	151	ASP	-1	-0.913	-0.951	33.765	0.021	0.021	0.000	0.000	0.000
92	A	152	ALA	0	0.008	-0.002	29.878	0.000	0.000	0.000	0.000	0.000
93	A	153	GLY	0	0.017	0.014	28.935	0.001	0.001	0.000	0.000	0.000
94	A	154	ARG	1	0.771	0.849	28.088	-0.082	-0.082	0.000	0.000	0.000
95	A	155	GLY	0	0.009	-0.012	28.153	-0.004	-0.004	0.000	0.000	0.000
96	A	156	ASP	-1	-0.838	-0.908	26.969	0.056	0.056	0.000	0.000	0.000
97	A	157	ARG	1	0.821	0.912	24.579	0.007	0.007	0.000	0.000	0.000
98	A	158	THR	0	-0.003	-0.003	25.122	0.005	0.005	0.000	0.000	0.000
99	A	159	ILE	0	-0.069	-0.040	21.018	-0.001	-0.001	0.000	0.000	0.000
100	A	160	PRO	0	0.006	0.004	23.070	-0.008	-0.008	0.000	0.000	0.000
101	A	161	VAL	0	0.035	0.014	19.255	-0.007	-0.007	0.000	0.000	0.000
102	A	162	THR	0	-0.009	0.000	21.470	0.004	0.004	0.000	0.000	0.000
103	A	163	ARG	1	0.883	0.934	19.750	0.244	0.244	0.000	0.000	0.000
104	A	164	GLU	-1	-0.852	-0.906	17.381	-0.314	-0.314	0.000	0.000	0.000
105	A	165	ASP	-1	-0.956	-0.969	21.819	-0.202	-0.202	0.000	0.000	0.000
106	A	166	LYS	1	0.938	0.953	18.631	0.302	0.302	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:61:GLY)