FMO DATABASE

FMODB ID: Q123Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-313962.030154
FMO2-HF: Nuclear repulsion	283543.057509
FMO2-HF: Total energy	-30418.972645
FMO2-MP2: Total energy	-30502.394709

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.
-1.601	1.312	1.347	-1.007	-3.254	-0.001

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 : -0.005 / q_NPA : -0.014

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	-0.010	-0.007	2.277	-2.264	0.439	1.346	-0.982	-3.067	-0.001
4	A	1165	SER	0	-0.001	-0.002	4.093	0.341	0.551	0.001	-0.025	-0.187	0.000
5	A	1166	GLU	-1	-0.909	-0.949	7.725	-0.032	-0.032	0.000	0.000	0.000	0.000
6	A	1167	LEU	0	0.023	0.014	10.448	0.089	0.089	0.000	0.000	0.000	0.000
7	A	1168	SER	0	0.000	-0.006	9.282	0.034	0.034	0.000	0.000	0.000	0.000
8	A	1169	GLN	0	0.049	0.027	11.341	0.115	0.115	0.000	0.000	0.000	0.000
9	A	1170	GLY	0	0.011	0.005	13.132	0.012	0.012	0.000	0.000	0.000	0.000
10	A	1171	LEU	0	0.014	0.001	15.688	0.013	0.013	0.000	0.000	0.000	0.000
11	A	1172	ALA	0	-0.017	-0.002	15.312	0.008	0.008	0.000	0.000	0.000	0.000
12	A	1173	VAL	0	-0.003	-0.005	16.673	0.007	0.007	0.000	0.000	0.000	0.000
13	A	1174	GLU	-1	-0.832	-0.892	19.002	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	1175	LEU	0	-0.029	-0.018	20.183	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	1176	MET	0	-0.006	-0.004	20.913	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	1177	GLU	-1	-0.883	-0.949	22.798	0.071	0.071	0.000	0.000	0.000	0.000
17	A	1178	ARG	1	0.816	0.882	24.975	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	1179	VAL	0	0.008	0.003	25.518	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	1180	MET	0	-0.046	-0.001	26.846	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	1181	MET	0	0.020	-0.001	28.621	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	1182	GLU	-1	-0.918	-0.950	30.669	0.028	0.028	0.000	0.000	0.000	0.000
22	A	1183	PHE	0	0.047	0.030	31.132	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	1184	VAL	0	0.021	0.018	32.125	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	1185	ARG	1	0.861	0.926	34.536	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	1186	GLU	-1	-0.932	-0.966	35.294	0.043	0.043	0.000	0.000	0.000	0.000
26	A	1187	THR	0	-0.027	-0.026	36.141	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	1188	CYS	0	-0.062	-0.041	37.812	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	1189	SER	0	-0.037	-0.004	40.597	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	1190	GLN	0	0.060	0.035	42.036	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	1191	GLU	-1	-0.834	-0.914	42.155	0.044	0.044	0.000	0.000	0.000	0.000
31	A	1192	LEU	0	-0.033	-0.009	44.530	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	1193	LYS	1	0.885	0.932	46.440	-0.032	-0.032	0.000	0.000	0.000	0.000
33	A	1194	ASN	0	-0.012	-0.019	45.620	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	1195	ALA	0	0.001	0.017	48.605	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	1196	VAL	0	0.005	-0.003	50.405	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	1197	GLU	-1	-0.864	-0.908	51.863	0.026	0.026	0.000	0.000	0.000	0.000
37	A	1198	THR	0	-0.021	-0.025	52.335	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	1199	ASP	-1	-0.823	-0.888	54.584	0.023	0.023	0.000	0.000	0.000	0.000
39	A	1200	GLN	0	0.021	0.010	56.416	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	1201	ARG	1	0.795	0.871	53.368	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	1202	VAL	0	0.010	0.009	58.600	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	1203	ARG	1	0.786	0.873	57.310	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	1204	VAL	0	0.026	0.015	62.349	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	1205	ALA	0	0.010	0.010	63.776	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	1206	ARG	1	0.994	1.003	61.949	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	1207	CYS	0	-0.042	-0.025	65.728	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	1208	CYS	0	-0.059	-0.034	68.087	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	1209	GLU	-1	-0.934	-0.965	68.044	0.019	0.019	0.000	0.000	0.000	0.000
49	A	1210	ASP	-1	-0.910	-0.962	69.289	0.016	0.016	0.000	0.000	0.000	0.000
50	A	1211	VAL	0	-0.031	-0.021	72.437	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	1212	CYS	0	-0.034	-0.019	74.136	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	1213	ALA	0	-0.017	-0.005	75.389	0.000	0.000	0.000	0.000	0.000	0.000
53	A	1214	HIS	0	-0.020	-0.003	76.785	0.000	0.000	0.000	0.000	0.000	0.000
54	A	1215	LEU	0	-0.027	-0.019	77.726	0.000	0.000	0.000	0.000	0.000	0.000
55	A	1216	VAL	0	-0.010	0.002	80.107	0.000	0.000	0.000	0.000	0.000	0.000
56	A	1217	ASP	-1	-0.913	-0.963	80.789	0.012	0.012	0.000	0.000	0.000	0.000
57	A	1218	LEU	0	-0.003	0.002	82.733	0.000	0.000	0.000	0.000	0.000	0.000
58	A	1219	PHE	0	-0.017	-0.015	82.655	0.000	0.000	0.000	0.000	0.000	0.000
59	A	1220	LEU	0	0.059	0.040	85.860	0.000	0.000	0.000	0.000	0.000	0.000
60	A	1221	VAL	0	-0.035	-0.023	87.034	0.000	0.000	0.000	0.000	0.000	0.000
61	A	1222	GLU	-1	-0.904	-0.940	89.321	0.009	0.009	0.000	0.000	0.000	0.000
62	A	1223	GLU	-1	-0.883	-0.947	88.522	0.011	0.011	0.000	0.000	0.000	0.000
63	A	1224	ILE	0	-0.017	0.007	89.933	0.000	0.000	0.000	0.000	0.000	0.000
64	A	1225	PHE	0	-0.012	-0.015	93.490	0.000	0.000	0.000	0.000	0.000	0.000
65	A	1226	GLN	0	-0.075	-0.060	93.944	0.000	0.000	0.000	0.000	0.000	0.000
66	A	1227	THR	0	0.021	-0.007	95.167	0.000	0.000	0.000	0.000	0.000	0.000
67	A	1228	ALA	0	-0.038	-0.021	97.735	0.000	0.000	0.000	0.000	0.000	0.000
68	A	1229	LYS	1	0.811	0.914	98.639	-0.008	-0.008	0.000	0.000	0.000	0.000
69	A	1230	GLU	-1	-0.932	-0.945	100.896	0.008	0.008	0.000	0.000	0.000	0.000
70	A	1231	THR	0	-0.030	-0.016	101.271	0.000	0.000	0.000	0.000	0.000	0.000
71	A	1232	LEU	0	-0.094	-0.051	103.771	0.000	0.000	0.000	0.000	0.000	0.000
72	A	1233	GLN	0	-0.031	0.005	106.417	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)