FMO DATABASE

FMODB ID: N35RQ

Calculation Name: 4NY6-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NY6

Chain ID: A

ChEMBL ID:

UniProt ID: P19614

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:

Apendix: None

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	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-419340.388831
FMO2-HF: Nuclear repulsion	391223.226597
FMO2-HF: Total energy	-28117.162234
FMO2-MP2: Total energy	-28194.839878

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:ASN )

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

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.
-21.152	-28.996	21.572	-7.65	-6.078	0.042

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.018

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	ALA	0	0.021	0.019	3.502	2.355	3.537	0.008	-0.522	-0.668	0.001
4	A	4	SER	0	0.018	-0.009	6.508	0.296	0.296	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.004	-0.003	9.566	-0.294	-0.294	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.027	-0.004	11.226	0.212	0.212	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.006	0.009	14.042	-0.143	-0.143	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.047	-0.042	17.604	0.000	0.000	0.000	0.000	0.000	0.000
9	A	9	GLN	0	-0.015	-0.017	18.871	-0.053	-0.053	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.013	0.002	21.687	0.037	0.037	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.010	0.002	20.377	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.003	-0.005	24.507	0.035	0.035	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.018	0.006	27.552	0.004	0.004	0.000	0.000	0.000	0.000
14	A	14	ASN	0	0.005	0.018	28.919	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.016	0.018	28.080	-0.032	-0.032	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.018	-0.003	27.249	0.021	0.021	0.000	0.000	0.000	0.000
17	A	17	LEU	0	0.037	0.022	21.161	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.041	0.015	24.177	-0.034	-0.034	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.062	0.012	20.634	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.015	0.006	20.811	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	21	MET	0	-0.058	-0.005	21.411	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	MET	0	-0.038	0.009	17.014	0.077	0.077	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.860	0.921	13.582	-0.249	-0.249	0.000	0.000	0.000	0.000
24	A	24	SER	0	0.013	0.006	9.876	0.126	0.126	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.748	-0.828	8.427	0.157	0.157	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.026	0.012	1.998	0.030	-0.190	2.318	-0.846	-1.252	-0.003
27	A	27	VAL	0	-0.015	0.010	5.133	0.073	0.140	0.000	-0.002	-0.064	0.000
28	A	28	THR	0	-0.025	0.006	6.338	1.427	1.427	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.030	-0.006	8.721	-0.649	-0.649	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.019	0.000	5.849	-0.127	-0.127	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.013	-0.002	8.929	-0.461	-0.461	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.051	-0.024	10.803	0.038	0.038	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.045	0.019	9.744	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.016	-0.002	9.959	-0.092	-0.092	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.868	-0.928	10.481	-0.796	-0.796	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.808	-0.896	13.374	0.216	0.216	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.018	-0.015	14.403	0.047	0.047	0.000	0.000	0.000	0.000
38	A	38	PRO	0	-0.022	-0.023	17.481	0.033	0.033	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.856	0.930	17.771	-0.165	-0.165	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.014	0.004	17.051	0.033	0.033	0.000	0.000	0.000	0.000
41	A	41	VAL	0	-0.046	-0.005	21.242	0.017	0.017	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.019	-0.028	24.053	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.068	0.020	23.094	0.012	0.012	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.025	0.001	25.598	0.015	0.015	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.031	0.028	22.678	0.027	0.027	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.055	-0.041	24.813	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.897	0.944	22.606	-0.608	-0.608	0.000	0.000	0.000	0.000
48	A	48	ALA	0	0.003	-0.005	25.450	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	VAL	0	0.003	0.001	19.517	0.050	0.050	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.015	-0.003	21.269	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.054	0.033	19.622	0.042	0.042	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.002	0.007	16.017	0.032	0.032	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.019	-0.002	15.105	0.149	0.149	0.000	0.000	0.000	0.000
54	A	54	THR	0	0.004	0.012	11.635	-0.212	-0.212	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.002	0.002	14.124	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	56	MET	0	0.027	0.012	13.003	0.104	0.104	0.000	0.000	0.000	0.000
57	A	57	PRO	0	0.034	0.002	14.956	-0.131	-0.131	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.855	-0.924	17.990	0.728	0.728	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.060	-0.002	18.578	-0.087	-0.087	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.012	0.016	19.928	-0.068	-0.068	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.860	0.930	22.679	-0.236	-0.236	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.033	0.012	25.598	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.076	-0.042	15.732	0.027	0.027	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.037	0.019	20.584	0.048	0.048	0.000	0.000	0.000	0.000
65	A	65	ALA	-1	-0.926	-0.943	16.176	0.246	0.246	0.000	0.000	0.000	0.000
66	A	101	HOH	0	-0.006	-0.007	5.670	-0.745	-0.745	0.000	0.000	0.000	0.000
67	A	102	HOH	0	0.004	0.002	20.831	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	103	HOH	0	-0.043	-0.028	22.226	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	104	HOH	0	0.012	0.008	18.593	0.008	0.008	0.000	0.000	0.000	0.000
70	A	105	HOH	0	-0.020	-0.018	12.902	0.061	0.061	0.000	0.000	0.000	0.000
71	A	106	HOH	0	-0.003	-0.009	26.630	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	107	HOH	0	-0.003	-0.002	15.653	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	108	HOH	0	-0.011	-0.004	7.949	-0.183	-0.183	0.000	0.000	0.000	0.000
74	A	109	HOH	0	-0.009	-0.031	11.563	-0.168	-0.168	0.000	0.000	0.000	0.000
75	A	110	HOH	0	0.009	-0.001	25.818	0.003	0.003	0.000	0.000	0.000	0.000
76	A	111	HOH	0	-0.027	-0.023	31.873	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	112	HOH	0	0.012	-0.002	23.747	0.002	0.002	0.000	0.000	0.000	0.000
78	A	113	HOH	0	0.000	0.000	23.116	-0.014	-0.014	0.000	0.000	0.000	0.000
79	A	114	HOH	0	-0.028	-0.033	26.973	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	115	HOH	0	0.016	0.009	26.764	0.006	0.006	0.000	0.000	0.000	0.000
81	A	116	HOH	0	0.032	0.008	7.555	-0.117	-0.117	0.000	0.000	0.000	0.000
82	A	117	HOH	0	0.013	0.005	18.261	-0.057	-0.057	0.000	0.000	0.000	0.000
83	A	118	HOH	0	0.020	0.006	17.533	-0.017	-0.017	0.000	0.000	0.000	0.000
84	A	119	HOH	0	0.001	0.001	21.078	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	120	HOH	0	0.020	0.013	11.930	0.113	0.113	0.000	0.000	0.000	0.000
86	A	121	HOH	0	0.031	0.021	15.008	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	122	HOH	0	-0.044	-0.039	12.510	-0.049	-0.049	0.000	0.000	0.000	0.000
88	A	123	HOH	0	-0.011	-0.009	6.653	-0.295	-0.295	0.000	0.000	0.000	0.000
89	A	124	HOH	0	0.031	0.019	29.860	0.005	0.005	0.000	0.000	0.000	0.000
90	A	125	HOH	0	0.038	0.021	28.885	0.005	0.005	0.000	0.000	0.000	0.000
91	A	126	HOH	0	0.011	0.002	29.885	0.002	0.002	0.000	0.000	0.000	0.000
92	A	127	HOH	0	-0.039	-0.029	24.073	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	128	HOH	0	-0.004	-0.003	28.186	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	129	HOH	0	-0.025	-0.024	19.598	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	130	HOH	0	-0.029	-0.025	19.655	0.011	0.011	0.000	0.000	0.000	0.000
96	A	131	HOH	0	-0.009	-0.006	30.886	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	132	HOH	0	0.007	-0.013	1.748	-16.345	-25.458	19.244	-6.158	-3.973	0.043
98	A	133	HOH	0	-0.035	-0.030	28.591	0.002	0.002	0.000	0.000	0.000	0.000
99	A	134	HOH	0	-0.006	-0.011	6.380	-0.306	-0.306	0.000	0.000	0.000	0.000
100	A	135	HOH	0	0.018	0.006	25.571	0.008	0.008	0.000	0.000	0.000	0.000
101	A	136	HOH	0	-0.033	-0.024	29.890	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	137	HOH	0	0.016	0.008	3.811	-3.935	-3.695	0.002	-0.122	-0.121	0.001
103	A	138	HOH	0	0.004	-0.009	6.205	-0.974	-0.974	0.000	0.000	0.000	0.000
104	A	139	HOH	0	-0.040	-0.030	13.132	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	140	HOH	0	0.034	0.022	24.783	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	141	HOH	0	0.004	0.001	20.747	0.012	0.012	0.000	0.000	0.000	0.000
107	A	142	HOH	0	-0.040	-0.031	8.926	-0.100	-0.100	0.000	0.000	0.000	0.000

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