FMO DATABASE

FMODB ID: QYMQY

Calculation Name: 3NXA-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NXA

Chain ID: C

ChEMBL ID:

UniProt ID: Q96FQ6

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-692842.561564
FMO2-HF: Nuclear repulsion	653938.455943
FMO2-HF: Total energy	-38904.105622
FMO2-MP2: Total energy	-39019.055116

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(C:5:TYR)

Summations of interaction energy for fragment #1(C:5:TYR)

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.
-2.45	-3.181	-0.034	1.669	-0.904	0

Interaction energy analysis for fragmet #1(C:5:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.025

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].
3	C	7	GLU	-1	-0.840	-0.927	3.225	6.440	5.207	-0.032	1.750	-0.485
4	C	8	LEU	0	0.037	0.016	5.406	0.088	0.088	0.000	0.000	0.000
5	C	9	GLU	-1	-0.871	-0.901	4.573	-3.840	-3.664	-0.001	-0.038	-0.137
6	C	10	LYS	1	0.908	0.919	4.395	-4.168	-3.842	-0.001	-0.043	-0.282
7	C	11	ALA	0	-0.004	0.014	6.458	-0.399	-0.399	0.000	0.000	0.000
8	C	12	VAL	0	0.037	0.014	9.666	-0.112	-0.112	0.000	0.000	0.000
9	C	13	ILE	0	-0.024	0.007	6.749	-0.103	-0.103	0.000	0.000	0.000
10	C	14	VAL	0	0.021	0.009	9.840	-0.180	-0.180	0.000	0.000	0.000
11	C	15	LEU	0	0.015	-0.001	11.991	-0.154	-0.154	0.000	0.000	0.000
12	C	16	VAL	0	0.010	0.013	12.939	-0.086	-0.086	0.000	0.000	0.000
13	C	17	GLU	-1	-0.917	-0.954	12.644	0.208	0.208	0.000	0.000	0.000
14	C	18	ASN	0	-0.048	-0.056	15.337	-0.043	-0.043	0.000	0.000	0.000
15	C	19	PHE	0	-0.003	0.016	17.658	-0.043	-0.043	0.000	0.000	0.000
16	C	20	TYR	0	-0.033	-0.058	17.223	-0.039	-0.039	0.000	0.000	0.000
17	C	21	LYS	1	0.768	0.911	19.089	-0.344	-0.344	0.000	0.000	0.000
18	C	22	TYR	0	-0.063	-0.075	20.950	-0.023	-0.023	0.000	0.000	0.000
19	C	23	VAL	0	-0.008	0.022	22.924	-0.021	-0.021	0.000	0.000	0.000
20	C	24	SER	0	-0.100	-0.077	25.177	0.006	0.006	0.000	0.000	0.000
21	C	25	LYS	1	1.008	1.019	26.243	-0.117	-0.117	0.000	0.000	0.000
22	C	26	TYR	0	-0.009	-0.013	29.480	-0.003	-0.003	0.000	0.000	0.000
23	C	27	SER	0	-0.004	0.024	28.366	-0.009	-0.009	0.000	0.000	0.000
24	C	28	LEU	0	0.052	0.008	30.439	-0.007	-0.007	0.000	0.000	0.000
25	C	29	VAL	0	0.019	0.014	28.865	-0.010	-0.010	0.000	0.000	0.000
26	C	30	LYS	1	0.912	0.921	25.195	0.017	0.017	0.000	0.000	0.000
27	C	31	ASN	0	0.030	0.046	22.609	0.012	0.012	0.000	0.000	0.000
28	C	32	LYS	1	0.889	0.936	24.415	-0.010	-0.010	0.000	0.000	0.000
29	C	33	ILE	0	0.040	0.053	24.141	0.003	0.003	0.000	0.000	0.000
30	C	34	SER	0	-0.023	-0.020	27.066	-0.011	-0.011	0.000	0.000	0.000
31	C	35	LYS	1	0.893	0.903	29.594	-0.041	-0.041	0.000	0.000	0.000
32	C	36	SER	0	-0.054	-0.014	31.378	0.007	0.007	0.000	0.000	0.000
33	C	37	SER	0	0.070	0.034	27.504	0.003	0.003	0.000	0.000	0.000
34	C	38	PHE	0	0.034	0.017	24.714	0.015	0.015	0.000	0.000	0.000
35	C	39	ARG	1	0.877	0.916	27.312	-0.067	-0.067	0.000	0.000	0.000
36	C	40	GLU	-1	-0.901	-0.952	28.324	0.128	0.128	0.000	0.000	0.000
37	C	41	MET	0	0.026	0.036	22.436	0.016	0.016	0.000	0.000	0.000
38	C	42	LEU	0	-0.030	0.004	24.673	0.021	0.021	0.000	0.000	0.000
39	C	43	GLN	0	-0.037	-0.034	26.350	0.019	0.019	0.000	0.000	0.000
40	C	44	LYS	1	0.869	0.931	23.069	-0.311	-0.311	0.000	0.000	0.000
41	C	45	GLU	-1	-0.770	-0.830	20.801	0.361	0.361	0.000	0.000	0.000
42	C	46	LEU	0	-0.020	-0.029	20.540	0.031	0.031	0.000	0.000	0.000
43	C	47	ASN	0	-0.004	0.005	23.663	-0.006	-0.006	0.000	0.000	0.000
44	C	48	HIS	0	0.019	0.002	22.586	-0.032	-0.032	0.000	0.000	0.000
45	C	49	MET	0	-0.048	-0.036	19.517	-0.020	-0.020	0.000	0.000	0.000
46	C	50	LEU	0	0.038	0.037	24.360	-0.019	-0.019	0.000	0.000	0.000
47	C	51	SER	0	0.014	0.025	27.921	-0.018	-0.018	0.000	0.000	0.000
48	C	52	ASP	-1	-0.824	-0.911	29.958	0.109	0.109	0.000	0.000	0.000
49	C	53	THR	0	0.043	0.003	31.908	0.003	0.003	0.000	0.000	0.000
50	C	54	GLY	0	-0.019	-0.011	34.815	-0.004	-0.004	0.000	0.000	0.000
51	C	55	ASN	0	0.033	-0.004	29.449	-0.010	-0.010	0.000	0.000	0.000
52	C	56	ARG	1	0.866	0.956	30.776	-0.137	-0.137	0.000	0.000	0.000
53	C	57	LYS	1	0.812	0.899	31.713	-0.085	-0.085	0.000	0.000	0.000
54	C	58	ALA	0	-0.040	-0.012	31.925	-0.007	-0.007	0.000	0.000	0.000
55	C	59	ALA	0	0.031	0.010	28.931	-0.006	-0.006	0.000	0.000	0.000
56	C	60	ASP	-1	-0.767	-0.880	30.702	0.083	0.083	0.000	0.000	0.000
57	C	61	LYS	1	0.951	0.968	33.229	-0.064	-0.064	0.000	0.000	0.000
58	C	62	LEU	0	-0.006	-0.014	28.680	-0.009	-0.009	0.000	0.000	0.000
59	C	63	ILE	0	-0.016	0.027	28.865	-0.007	-0.007	0.000	0.000	0.000
60	C	64	GLN	0	0.001	0.014	32.464	-0.004	-0.004	0.000	0.000	0.000
61	C	65	ASN	0	-0.042	-0.028	35.215	-0.005	-0.005	0.000	0.000	0.000
62	C	66	LEU	0	-0.018	0.015	29.568	-0.006	-0.006	0.000	0.000	0.000
63	C	67	ASP	-1	-0.785	-0.893	33.551	0.013	0.013	0.000	0.000	0.000
64	C	68	ALA	0	-0.055	-0.043	33.343	0.001	0.001	0.000	0.000	0.000
65	C	69	ASN	0	-0.087	-0.041	30.902	-0.011	-0.011	0.000	0.000	0.000
66	C	70	HIS	0	0.120	0.063	31.082	0.003	0.003	0.000	0.000	0.000
67	C	71	ASP	-1	-0.901	-0.937	33.312	0.011	0.011	0.000	0.000	0.000
68	C	72	GLY	0	0.030	0.016	34.775	0.004	0.004	0.000	0.000	0.000
69	C	73	ARG	1	0.775	0.888	30.276	-0.022	-0.022	0.000	0.000	0.000
70	C	74	ILE	0	-0.004	-0.003	25.962	-0.009	-0.009	0.000	0.000	0.000
71	C	75	SER	0	-0.018	-0.057	25.205	0.004	0.004	0.000	0.000	0.000
72	C	76	PHE	0	0.063	0.016	16.431	0.016	0.016	0.000	0.000	0.000
73	C	77	ASP	-1	-0.877	-0.931	21.769	-0.024	-0.024	0.000	0.000	0.000
74	C	78	GLU	-1	-0.789	-0.831	23.146	0.027	0.027	0.000	0.000	0.000
75	C	79	TYR	0	-0.078	-0.071	17.863	0.014	0.014	0.000	0.000	0.000
76	C	80	TRP	0	0.049	0.030	14.858	0.025	0.025	0.000	0.000	0.000
77	C	81	THR	0	-0.048	-0.037	21.340	0.003	0.003	0.000	0.000	0.000
78	C	82	LEU	0	0.005	0.002	24.567	0.006	0.006	0.000	0.000	0.000
79	C	83	ILE	0	0.034	0.012	19.752	0.008	0.008	0.000	0.000	0.000
80	C	84	GLY	0	0.001	0.032	22.321	0.010	0.010	0.000	0.000	0.000
81	C	85	GLY	0	-0.010	-0.022	23.150	-0.004	-0.004	0.000	0.000	0.000
82	C	86	ILE	0	0.027	0.008	24.139	-0.001	-0.001	0.000	0.000	0.000
83	C	87	THR	0	-0.002	0.008	19.925	0.014	0.014	0.000	0.000	0.000
84	C	88	GLY	0	-0.103	-0.068	23.258	-0.003	-0.003	0.000	0.000	0.000
85	C	89	PRO	0	-0.013	-0.009	24.908	-0.003	-0.003	0.000	0.000	0.000
86	C	90	ILE	0	0.036	0.034	24.335	-0.003	-0.003	0.000	0.000	0.000
87	C	91	ALA	0	0.054	0.018	21.933	0.018	0.018	0.000	0.000	0.000
88	C	92	LYS	1	0.824	0.896	22.543	-0.092	-0.092	0.000	0.000	0.000
89	C	93	LEU	0	0.015	0.043	24.668	0.006	0.006	0.000	0.000	0.000
90	C	94	ILE	0	-0.008	-0.022	19.563	0.012	0.012	0.000	0.000	0.000
91	C	95	HIS	0	-0.003	-0.006	19.469	0.036	0.036	0.000	0.000	0.000
92	C	96	GLU	-1	-0.872	-0.946	21.363	0.126	0.126	0.000	0.000	0.000
93	C	97	GLN	0	-0.101	-0.046	22.636	-0.008	-0.008	0.000	0.000	0.000
94	C	98	GLU	-1	-0.899	-0.973	17.490	0.396	0.396	0.000	0.000	0.000
95	C	99	GLN	0	-0.060	0.001	20.363	-0.010	-0.010	0.000	0.000	0.000
96	C	100	GLN	0	-0.075	-0.052	22.306	0.004	0.004	0.000	0.000	0.000
97	C	101	SER	0	-0.012	0.026	20.683	-0.007	-0.007	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:5:TYR)