FMO DATABASE

FMODB ID: ZY4QN

Calculation Name: 4DHX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DHX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NPA8

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	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	72
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-313972.071485
FMO2-HF: Nuclear repulsion	283553.621106
FMO2-HF: Total energy	-30418.450379
FMO2-MP2: Total energy	-30501.915585

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:1162:LEU)

Summations of interaction energy for fragment #1(A:1162: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.
-1.633	1.109	1.734	-1.293	-3.182	-0.002

Interaction energy analysis for fragmet #1(A:1162:LEU)

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 : -0.020

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	1164	LEU	0	-0.022	-0.005	2.088	-2.305	0.254	1.734	-1.271	-3.021	-0.002
4	A	1165	SER	0	0.017	0.010	4.344	0.361	0.544	0.000	-0.022	-0.161	0.000
5	A	1166	GLU	-1	-0.909	-0.950	8.026	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	1167	LEU	0	0.024	0.001	10.372	0.079	0.079	0.000	0.000	0.000	0.000
7	A	1168	SER	0	0.000	-0.014	9.551	0.032	0.032	0.000	0.000	0.000	0.000
8	A	1169	GLN	0	0.049	0.028	11.394	0.091	0.091	0.000	0.000	0.000	0.000
9	A	1170	GLY	0	0.014	0.004	13.121	0.014	0.014	0.000	0.000	0.000	0.000
10	A	1171	LEU	0	0.001	-0.002	15.279	0.005	0.005	0.000	0.000	0.000	0.000
11	A	1172	ALA	0	-0.007	-0.001	15.443	0.005	0.005	0.000	0.000	0.000	0.000
12	A	1173	VAL	0	-0.010	-0.005	16.776	0.006	0.006	0.000	0.000	0.000	0.000
13	A	1174	GLU	-1	-0.888	-0.940	19.111	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	1175	LEU	0	-0.036	-0.016	20.047	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	1176	MET	0	0.003	-0.003	21.071	-0.007	-0.007	0.000	0.000	0.000	0.000
16	A	1177	GLU	-1	-0.893	-0.951	22.880	0.077	0.077	0.000	0.000	0.000	0.000
17	A	1178	ARG	1	0.872	0.928	25.094	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	1179	VAL	0	0.020	0.015	25.363	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	1180	MET	0	-0.032	0.005	26.827	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	1181	MET	0	0.004	-0.007	28.595	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	1182	GLU	-1	-0.972	-0.994	30.880	0.032	0.032	0.000	0.000	0.000	0.000
22	A	1183	PHE	0	0.050	0.033	30.552	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	1184	VAL	0	0.012	0.014	32.278	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	1185	ARG	1	0.916	0.955	34.767	-0.033	-0.033	0.000	0.000	0.000	0.000
25	A	1186	GLU	-1	-0.926	-0.960	35.719	0.039	0.039	0.000	0.000	0.000	0.000
26	A	1187	THR	0	-0.019	-0.014	36.104	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	1188	CYS	0	-0.056	-0.038	38.061	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	1189	SER	0	-0.047	-0.014	40.782	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	1190	GLN	0	-0.014	-0.013	41.966	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	1191	GLU	-1	-0.918	-0.963	41.797	0.046	0.046	0.000	0.000	0.000	0.000
31	A	1192	LEU	0	-0.025	-0.009	44.507	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	1193	LYS	1	0.965	0.984	46.499	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	1194	ASN	0	0.058	0.030	45.747	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	1195	ALA	0	0.003	0.008	48.812	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	1196	VAL	0	0.002	-0.005	50.653	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1197	GLU	-1	-0.955	-0.968	51.985	0.024	0.024	0.000	0.000	0.000	0.000
37	A	1198	THR	0	-0.045	-0.046	52.528	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	1199	ASP	-1	-0.862	-0.932	54.758	0.023	0.023	0.000	0.000	0.000	0.000
39	A	1200	GLN	0	0.013	0.017	56.582	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	1201	ARG	1	0.921	0.960	54.251	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	1202	VAL	0	-0.007	0.008	58.340	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	1203	ARG	1	0.859	0.916	58.352	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	1204	VAL	0	0.014	0.015	62.630	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	1205	ALA	0	0.015	0.009	64.073	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1206	ARG	1	0.989	0.994	61.566	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	1207	CYS	0	-0.031	-0.018	66.027	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	1208	CYS	0	-0.050	-0.028	68.360	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	1209	GLU	-1	-0.949	-0.968	68.703	0.019	0.019	0.000	0.000	0.000	0.000
49	A	1210	ASP	-1	-0.911	-0.956	70.488	0.016	0.016	0.000	0.000	0.000	0.000
50	A	1211	VAL	0	-0.031	-0.019	72.626	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	1212	CYS	0	-0.049	-0.020	74.427	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	1213	ALA	0	0.008	-0.005	75.728	0.000	0.000	0.000	0.000	0.000	0.000
53	A	1214	HIS	0	-0.016	-0.001	77.109	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1215	LEU	0	-0.015	-0.010	78.473	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1216	VAL	0	-0.013	0.003	80.335	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1217	ASP	-1	-0.878	-0.945	80.810	0.012	0.012	0.000	0.000	0.000	0.000
57	A	1218	LEU	0	-0.014	0.002	83.134	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1219	PHE	0	-0.019	-0.033	82.628	0.000	0.000	0.000	0.000	0.000	0.000
59	A	1220	LEU	0	0.039	0.034	85.701	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1221	VAL	0	-0.053	-0.032	87.093	0.000	0.000	0.000	0.000	0.000	0.000
61	A	1222	GLU	-1	-0.973	-0.974	89.408	0.008	0.008	0.000	0.000	0.000	0.000
62	A	1223	GLU	-1	-0.888	-0.958	89.228	0.010	0.010	0.000	0.000	0.000	0.000
63	A	1224	ILE	0	-0.060	-0.030	89.852	0.000	0.000	0.000	0.000	0.000	0.000
64	A	1225	PHE	0	-0.047	-0.025	93.607	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1226	GLN	0	-0.013	-0.026	94.506	0.000	0.000	0.000	0.000	0.000	0.000
66	A	1227	THR	0	0.042	0.032	95.491	0.000	0.000	0.000	0.000	0.000	0.000
67	A	1228	ALA	0	-0.022	-0.011	97.868	0.000	0.000	0.000	0.000	0.000	0.000
68	A	1229	LYS	1	0.887	0.942	99.799	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	1230	GLU	-1	-0.921	-0.934	100.852	0.008	0.008	0.000	0.000	0.000	0.000
70	A	1231	THR	0	-0.081	-0.038	101.455	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1232	LEU	0	-0.111	-0.060	103.896	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1233	GLN	0	-0.008	0.011	106.716	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1162:LEU)