FMO DATABASE

FMODB ID: R5G28

Calculation Name: 1NYH-A-Xray372

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: 2023-06-20

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-325985.332937
FMO2-HF: Nuclear repulsion	295786.719002
FMO2-HF: Total energy	-30198.613934
FMO2-MP2: Total energy	-30285.547464

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:1271:LEU)

Summations of interaction energy for fragment #1(A:1271:LEU)

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.
-8.114	-1.624	2.901	-3.988	-5.405	-0.027

Interaction energy analysis for fragmet #1(A:1271:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.016

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	1273	PHE	0	0.025	-0.003	3.745	-2.078	-0.042	-0.001	-1.137	-0.899	0.005
4	A	1274	VAL	0	0.022	0.005	6.104	0.502	0.502	0.000	0.000	0.000	0.000
5	A	1275	ASP	-1	-0.753	-0.884	2.597	-8.754	-5.193	2.608	-2.562	-3.608	-0.033
6	A	1276	ILE	0	-0.032	0.005	2.764	0.279	1.109	0.295	-0.287	-0.838	0.001
7	A	1277	VAL	0	0.005	0.005	5.103	0.611	0.674	-0.001	-0.002	-0.060	0.000
8	A	1278	LEU	0	0.001	-0.001	7.707	0.296	0.296	0.000	0.000	0.000	0.000
9	A	1279	SER	0	-0.016	-0.018	5.943	0.452	0.452	0.000	0.000	0.000	0.000
10	A	1280	LYS	1	0.814	0.893	8.415	0.278	0.278	0.000	0.000	0.000	0.000
11	A	1281	ALA	0	0.008	0.008	10.699	0.088	0.088	0.000	0.000	0.000	0.000
12	A	1282	ALA	0	0.013	0.002	11.689	0.064	0.064	0.000	0.000	0.000	0.000
13	A	1283	SER	0	-0.059	-0.048	11.961	0.074	0.074	0.000	0.000	0.000	0.000
14	A	1284	ALA	0	0.007	0.007	13.842	0.024	0.024	0.000	0.000	0.000	0.000
15	A	1285	LEU	0	-0.002	0.003	16.310	0.013	0.013	0.000	0.000	0.000	0.000
16	A	1286	ASP	-1	-0.807	-0.888	16.438	0.120	0.120	0.000	0.000	0.000	0.000
17	A	1287	GLU	-1	-0.820	-0.896	15.598	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	1288	LYS	1	0.853	0.920	19.644	0.066	0.066	0.000	0.000	0.000	0.000
19	A	1289	GLU	-1	-0.873	-0.943	21.577	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	1290	LYS	1	0.819	0.895	19.023	-0.105	-0.105	0.000	0.000	0.000	0.000
21	A	1291	GLN	0	0.004	0.009	24.248	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	1292	LEU	0	0.015	0.020	26.077	0.001	0.001	0.000	0.000	0.000	0.000
23	A	1293	ALA	0	0.020	0.013	27.086	0.001	0.001	0.000	0.000	0.000	0.000
24	A	1294	VAL	0	-0.009	-0.008	28.208	0.002	0.002	0.000	0.000	0.000	0.000
25	A	1295	ALA	0	0.000	0.000	30.333	0.000	0.000	0.000	0.000	0.000	0.000
26	A	1296	ASN	0	-0.035	-0.031	31.034	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	1297	GLU	-1	-0.834	-0.886	33.012	0.029	0.029	0.000	0.000	0.000	0.000
28	A	1298	ILE	0	-0.008	-0.006	33.895	0.000	0.000	0.000	0.000	0.000	0.000
29	A	1299	ILE	0	0.015	0.007	35.290	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	1300	ARG	1	0.859	0.926	36.666	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	1301	SER	0	0.008	-0.003	38.901	0.001	0.001	0.000	0.000	0.000	0.000
32	A	1302	LEU	0	0.005	-0.001	40.100	0.000	0.000	0.000	0.000	0.000	0.000
33	A	1303	SER	0	-0.031	-0.025	41.672	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	1304	ASP	-1	-0.856	-0.888	43.528	0.016	0.016	0.000	0.000	0.000	0.000
35	A	1305	GLU	-1	-0.928	-0.970	44.979	0.009	0.009	0.000	0.000	0.000	0.000
36	A	1306	VAL	0	-0.005	0.001	46.604	0.000	0.000	0.000	0.000	0.000	0.000
37	A	1307	MET	0	0.039	0.028	47.558	0.000	0.000	0.000	0.000	0.000	0.000
38	A	1308	ARG	1	0.805	0.862	46.574	-0.016	-0.016	0.000	0.000	0.000	0.000
39	A	1309	ASN	0	-0.052	-0.030	49.909	0.000	0.000	0.000	0.000	0.000	0.000
40	A	1310	GLU	-1	-0.910	-0.950	52.010	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	1311	ILE	0	0.000	0.012	53.608	0.000	0.000	0.000	0.000	0.000	0.000
42	A	1312	ARG	1	0.945	0.973	55.025	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	1313	ILE	0	-0.015	-0.014	56.555	0.000	0.000	0.000	0.000	0.000	0.000
44	A	1314	THR	0	-0.004	-0.016	58.193	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1315	SER	0	-0.065	-0.032	60.204	0.000	0.000	0.000	0.000	0.000	0.000
46	A	1316	LEU	0	0.008	0.007	60.014	0.000	0.000	0.000	0.000	0.000	0.000
47	A	1317	GLN	0	-0.010	-0.004	62.005	0.000	0.000	0.000	0.000	0.000	0.000
48	A	1318	GLY	0	0.035	0.039	64.812	0.000	0.000	0.000	0.000	0.000	0.000
49	A	1319	ASP	-1	-0.834	-0.912	64.603	0.007	0.007	0.000	0.000	0.000	0.000
50	A	1320	LEU	0	-0.024	-0.004	67.288	0.000	0.000	0.000	0.000	0.000	0.000
51	A	1321	THR	0	-0.046	-0.043	68.575	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	1322	PHE	0	0.029	0.009	70.688	0.000	0.000	0.000	0.000	0.000	0.000
53	A	1323	THR	0	0.001	-0.009	71.007	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1324	LYS	1	0.928	0.960	70.504	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1325	LYS	1	0.846	0.915	75.012	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	1326	CYS	0	-0.034	-0.015	75.897	0.000	0.000	0.000	0.000	0.000	0.000
57	A	1327	LEU	0	-0.007	-0.004	77.412	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1328	GLU	-1	-0.807	-0.889	79.156	0.001	0.001	0.000	0.000	0.000	0.000
59	A	1329	ASN	0	0.020	0.027	81.089	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1330	ALA	0	0.039	0.017	82.174	0.000	0.000	0.000	0.000	0.000	0.000
61	A	1331	ARG	1	0.907	0.944	82.236	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	1332	SER	0	-0.004	0.002	84.972	0.000	0.000	0.000	0.000	0.000	0.000
63	A	1333	GLN	0	0.044	0.020	85.756	0.000	0.000	0.000	0.000	0.000	0.000
64	A	1334	ILE	0	-0.035	-0.016	85.648	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1335	SER	0	0.048	0.030	89.319	0.000	0.000	0.000	0.000	0.000	0.000
66	A	1336	GLU	-1	-0.943	-0.973	89.941	0.002	0.002	0.000	0.000	0.000	0.000
67	A	1337	LYS	1	0.809	0.893	90.288	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	1338	ASP	-1	-0.835	-0.911	92.150	0.002	0.002	0.000	0.000	0.000	0.000
69	A	1339	ALA	0	-0.018	0.003	95.127	0.000	0.000	0.000	0.000	0.000	0.000
70	A	1340	LYS	1	0.886	0.928	97.072	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	1341	ILE	0	0.018	0.010	96.846	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1342	ASN	0	-0.013	-0.026	97.713	0.000	0.000	0.000	0.000	0.000	0.000
73	A	1343	LYS	1	0.956	0.982	101.006	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	1344	LEU	0	-0.081	-0.043	102.153	0.000	0.000	0.000	0.000	0.000	0.000
75	A	1345	MET	0	-0.023	0.001	102.417	0.000	0.000	0.000	0.000	0.000	0.000
76	A	1346	GLU	-1	-1.014	-0.988	105.332	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:1271:LEU)