FMO DATABASE

FMODB ID: 8J16Y

Calculation Name: 1NYH-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYH

Chain ID: A

ChEMBL ID:

UniProt ID: P11978

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:

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	78
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-329260.47803
FMO2-HF: Nuclear repulsion	298892.095932
FMO2-HF: Total energy	-30368.382099
FMO2-MP2: Total energy	-30455.938818

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:1270:ACE )

Summations of interaction energy for fragment #1(A:1270:ACE )

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.
0.242	1.247	0.176	-0.517	-0.663	0

Interaction energy analysis for fragmet #1(A:1270:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / 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	1272	SER	0	0.035	0.036	3.851	1.248	2.001	-0.005	-0.359	-0.388
4	A	1273	PHE	0	0.067	0.013	6.089	0.106	0.106	0.000	0.000	0.000
5	A	1274	VAL	0	0.011	0.005	7.836	0.129	0.129	0.000	0.000	0.000
6	A	1275	ASP	-1	-0.831	-0.927	6.080	-0.880	-0.880	0.000	0.000	0.000
7	A	1276	ILE	0	-0.086	-0.030	2.784	-0.079	0.173	0.181	-0.158	-0.275
8	A	1277	VAL	0	-0.021	-0.022	6.274	0.091	0.091	0.000	0.000	0.000
9	A	1278	LEU	0	0.049	0.021	9.978	0.041	0.041	0.000	0.000	0.000
10	A	1279	SER	0	0.014	0.023	6.916	0.061	0.061	0.000	0.000	0.000
11	A	1280	LYS	1	0.910	0.956	8.534	-0.549	-0.549	0.000	0.000	0.000
12	A	1281	ALA	0	0.001	0.010	10.917	-0.012	-0.012	0.000	0.000	0.000
13	A	1282	ALA	0	0.006	-0.005	12.088	-0.005	-0.005	0.000	0.000	0.000
14	A	1283	SER	0	0.018	0.003	11.643	0.010	0.010	0.000	0.000	0.000
15	A	1284	ALA	0	0.001	0.006	13.711	-0.007	-0.007	0.000	0.000	0.000
16	A	1285	LEU	0	-0.028	-0.011	16.437	-0.010	-0.010	0.000	0.000	0.000
17	A	1286	ASP	-1	-0.817	-0.913	16.019	0.110	0.110	0.000	0.000	0.000
18	A	1287	GLU	-1	-0.934	-0.972	16.277	0.210	0.210	0.000	0.000	0.000
19	A	1288	LYS	1	0.806	0.895	19.367	-0.099	-0.099	0.000	0.000	0.000
20	A	1289	GLU	-1	-0.888	-0.950	21.369	0.024	0.024	0.000	0.000	0.000
21	A	1290	LYS	1	0.884	0.946	18.226	-0.125	-0.125	0.000	0.000	0.000
22	A	1291	GLN	0	-0.020	-0.005	23.438	-0.001	-0.001	0.000	0.000	0.000
23	A	1292	LEU	0	0.014	0.009	25.796	-0.005	-0.005	0.000	0.000	0.000
24	A	1293	ALA	0	0.015	0.008	26.379	-0.005	-0.005	0.000	0.000	0.000
25	A	1294	VAL	0	-0.030	-0.012	27.256	-0.003	-0.003	0.000	0.000	0.000
26	A	1295	ALA	0	-0.010	-0.007	29.744	-0.003	-0.003	0.000	0.000	0.000
27	A	1296	ASN	0	0.015	-0.013	30.460	-0.005	-0.005	0.000	0.000	0.000
28	A	1297	GLU	-1	-0.865	-0.895	32.260	0.030	0.030	0.000	0.000	0.000
29	A	1298	ILE	0	0.002	-0.002	33.595	-0.002	-0.002	0.000	0.000	0.000
30	A	1299	ILE	0	-0.006	0.010	34.649	-0.002	-0.002	0.000	0.000	0.000
31	A	1300	ARG	1	0.886	0.939	35.946	-0.027	-0.027	0.000	0.000	0.000
32	A	1301	SER	0	0.002	-0.017	38.147	-0.002	-0.002	0.000	0.000	0.000
33	A	1302	LEU	0	0.018	-0.002	39.845	-0.001	-0.001	0.000	0.000	0.000
34	A	1303	SER	0	-0.008	0.001	41.485	-0.002	-0.002	0.000	0.000	0.000
35	A	1304	ASP	-1	-0.928	-0.952	42.870	0.019	0.019	0.000	0.000	0.000
36	A	1305	GLU	-1	-1.009	-0.997	44.349	0.026	0.026	0.000	0.000	0.000
37	A	1306	VAL	0	0.011	-0.001	45.980	-0.001	-0.001	0.000	0.000	0.000
38	A	1307	MET	0	0.047	0.025	47.269	-0.001	-0.001	0.000	0.000	0.000
39	A	1308	ARG	1	0.895	0.933	45.043	-0.021	-0.021	0.000	0.000	0.000
40	A	1309	ASN	0	-0.026	-0.011	49.481	-0.001	-0.001	0.000	0.000	0.000
41	A	1310	GLU	-1	-0.930	-0.963	51.429	0.014	0.014	0.000	0.000	0.000
42	A	1311	ILE	0	-0.006	0.004	52.923	-0.001	-0.001	0.000	0.000	0.000
43	A	1312	ARG	1	0.956	0.971	54.178	-0.019	-0.019	0.000	0.000	0.000
44	A	1313	ILE	0	-0.036	-0.016	55.396	0.000	0.000	0.000	0.000	0.000
45	A	1314	THR	0	0.045	0.025	58.075	-0.001	-0.001	0.000	0.000	0.000
46	A	1315	SER	0	-0.032	-0.011	59.494	0.000	0.000	0.000	0.000	0.000
47	A	1316	LEU	0	0.023	0.018	59.586	0.000	0.000	0.000	0.000	0.000
48	A	1317	GLN	0	0.024	0.011	61.765	0.000	0.000	0.000	0.000	0.000
49	A	1318	GLY	0	0.001	0.019	63.997	-0.001	-0.001	0.000	0.000	0.000
50	A	1319	ASP	-1	-0.885	-0.958	64.431	0.012	0.012	0.000	0.000	0.000
51	A	1320	LEU	0	-0.084	-0.040	66.486	0.000	0.000	0.000	0.000	0.000
52	A	1321	THR	0	-0.041	-0.039	67.884	0.000	0.000	0.000	0.000	0.000
53	A	1322	PHE	0	0.041	0.016	69.947	0.000	0.000	0.000	0.000	0.000
54	A	1323	THR	0	0.024	0.010	70.389	0.000	0.000	0.000	0.000	0.000
55	A	1324	LYS	1	0.962	0.982	70.304	-0.011	-0.011	0.000	0.000	0.000
56	A	1325	LYS	1	0.970	1.007	74.311	-0.007	-0.007	0.000	0.000	0.000
57	A	1326	CYS	0	-0.042	-0.021	75.311	0.000	0.000	0.000	0.000	0.000
58	A	1327	LEU	0	-0.030	-0.018	76.670	0.000	0.000	0.000	0.000	0.000
59	A	1328	GLU	-1	-0.945	-0.983	78.324	0.007	0.007	0.000	0.000	0.000
60	A	1329	ASN	0	-0.005	-0.012	80.304	0.000	0.000	0.000	0.000	0.000
61	A	1330	ALA	0	0.024	0.009	81.529	0.000	0.000	0.000	0.000	0.000
62	A	1331	ARG	1	0.903	0.948	81.360	-0.009	-0.009	0.000	0.000	0.000
63	A	1332	SER	0	0.035	0.028	84.195	0.000	0.000	0.000	0.000	0.000
64	A	1333	GLN	0	-0.001	-0.006	84.624	0.000	0.000	0.000	0.000	0.000
65	A	1334	ILE	0	-0.027	0.002	85.160	0.000	0.000	0.000	0.000	0.000
66	A	1335	SER	0	0.072	0.034	88.571	0.000	0.000	0.000	0.000	0.000
67	A	1336	GLU	-1	-0.961	-0.978	90.512	0.006	0.006	0.000	0.000	0.000
68	A	1337	LYS	1	0.858	0.915	90.175	-0.007	-0.007	0.000	0.000	0.000
69	A	1338	ASP	-1	-0.838	-0.921	92.198	0.007	0.007	0.000	0.000	0.000
70	A	1339	ALA	0	-0.025	0.000	94.191	0.000	0.000	0.000	0.000	0.000
71	A	1340	LYS	1	0.897	0.927	96.599	-0.005	-0.005	0.000	0.000	0.000
72	A	1341	ILE	0	-0.003	0.011	95.828	0.000	0.000	0.000	0.000	0.000
73	A	1342	ASN	0	0.022	-0.008	97.533	0.000	0.000	0.000	0.000	0.000
74	A	1343	LYS	1	0.932	0.980	100.034	-0.005	-0.005	0.000	0.000	0.000
75	A	1344	LEU	0	-0.120	-0.053	101.730	0.000	0.000	0.000	0.000	0.000
76	A	1345	MET	0	0.008	0.003	100.331	0.000	0.000	0.000	0.000	0.000
77	A	1346	GLU	-1	-0.940	-0.964	104.618	0.005	0.005	0.000	0.000	0.000
78	A	1347	NME	0	-0.069	-0.018	107.471	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1270:ACE )