FMO DATABASE

FMODB ID: YYK62

Calculation Name: 4NTQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NTQ

Chain ID: A

ChEMBL ID:

UniProt ID: D5CBA0

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

Total energy (hartree)

FMO2-HF: Electronic energy	-469674.553443
FMO2-HF: Nuclear repulsion	440043.172124
FMO2-HF: Total energy	-29631.381319
FMO2-MP2: Total energy	-29719.253268

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:160:LEU)

Summations of interaction energy for fragment #1(A:160: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.
-7.336	-6.818	15.813	-4.032	-12.3	-0.01

Interaction energy analysis for fragmet #1(A:160:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / 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	162	GLY	0	0.035	0.014	2.961	-2.061	0.861	0.199	-1.536	-1.586	-0.003
4	A	163	LYS	1	0.912	0.952	5.393	-0.033	0.041	-0.001	-0.001	-0.072	0.000
5	A	164	GLU	-1	-0.837	-0.924	7.260	0.033	0.033	0.000	0.000	0.000	0.000
6	A	165	ALA	0	0.008	0.013	4.571	0.261	0.342	-0.001	-0.009	-0.071	0.000
7	A	166	GLN	0	0.019	-0.004	6.697	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	167	GLU	-1	-0.840	-0.919	10.015	0.441	0.441	0.000	0.000	0.000	0.000
9	A	168	ALA	0	-0.035	-0.012	7.542	0.010	0.010	0.000	0.000	0.000	0.000
10	A	169	ALA	0	-0.002	-0.013	9.271	-0.027	-0.027	0.000	0.000	0.000	0.000
11	A	170	SER	0	-0.031	-0.009	10.591	-0.144	-0.144	0.000	0.000	0.000	0.000
12	A	171	ASN	0	-0.010	-0.009	12.745	-0.162	-0.162	0.000	0.000	0.000	0.000
13	A	172	LEU	0	-0.064	-0.023	10.119	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	173	GLY	0	0.019	0.021	14.124	-0.059	-0.059	0.000	0.000	0.000	0.000
15	A	174	PHE	0	-0.015	-0.022	12.925	-0.064	-0.064	0.000	0.000	0.000	0.000
16	A	175	ASP	-1	-0.846	-0.926	14.157	0.494	0.494	0.000	0.000	0.000	0.000
17	A	176	ARG	1	0.860	0.939	16.252	-0.298	-0.298	0.000	0.000	0.000	0.000
18	A	177	ARG	1	0.900	0.928	10.667	-0.186	-0.186	0.000	0.000	0.000	0.000
19	A	178	ILE	0	-0.040	-0.025	13.638	-0.069	-0.069	0.000	0.000	0.000	0.000
20	A	179	PRO	0	-0.062	-0.017	13.083	0.024	0.024	0.000	0.000	0.000	0.000
21	A	180	PRO	0	0.032	0.013	11.815	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	181	GLN	0	0.002	0.007	14.629	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	182	LYS	1	0.968	0.975	17.567	-0.055	-0.055	0.000	0.000	0.000	0.000
24	A	183	ALA	0	-0.017	0.015	20.587	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	184	PRO	0	0.017	0.006	21.743	0.001	0.001	0.000	0.000	0.000	0.000
26	A	185	PHE	0	-0.002	-0.009	18.218	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	186	ASN	0	0.103	0.036	16.206	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	187	SER	0	0.006	0.014	13.860	0.045	0.045	0.000	0.000	0.000	0.000
29	A	188	HIS	0	0.013	0.006	12.447	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	189	GLY	0	0.043	0.015	9.903	0.029	0.029	0.000	0.000	0.000	0.000
31	A	190	GLN	0	-0.022	-0.018	5.656	0.154	0.154	0.000	0.000	0.000	0.000
32	A	191	PRO	0	-0.043	-0.001	6.999	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	192	VAL	0	0.020	0.009	9.159	0.100	0.100	0.000	0.000	0.000	0.000
34	A	193	PHE	0	-0.024	-0.014	7.314	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	194	TYR	0	-0.026	-0.016	12.431	0.012	0.012	0.000	0.000	0.000	0.000
36	A	195	ASP	-1	-0.831	-0.923	16.082	0.514	0.514	0.000	0.000	0.000	0.000
37	A	196	GLY	0	-0.007	0.019	17.931	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	197	LYS	1	0.887	0.946	19.896	-0.312	-0.312	0.000	0.000	0.000	0.000
39	A	198	ASN	0	-0.008	-0.024	16.718	-0.069	-0.069	0.000	0.000	0.000	0.000
40	A	199	TYR	0	0.026	0.011	13.780	0.005	0.005	0.000	0.000	0.000	0.000
41	A	200	ILE	0	0.017	0.032	9.578	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	201	THR	0	0.030	0.013	6.769	-0.126	-0.126	0.000	0.000	0.000	0.000
43	A	202	PRO	0	-0.017	-0.007	2.268	-0.913	-0.324	1.530	-0.637	-1.481	0.002
44	A	203	ASP	-1	-0.890	-0.964	3.926	-1.177	-0.756	0.008	-0.132	-0.296	-0.001
45	A	204	ILE	0	-0.006	-0.019	2.128	-3.942	-2.517	5.108	-2.390	-4.143	-0.012
46	A	205	ASP	-1	-0.904	-0.937	3.073	0.101	-0.554	-0.016	1.012	-0.341	-0.001
47	A	206	SER	0	-0.011	-0.013	5.591	-0.399	-0.399	0.000	0.000	0.000	0.000
48	A	207	HIS	0	-0.021	-0.015	7.996	-0.077	-0.077	0.000	0.000	0.000	0.000
49	A	208	ASN	0	-0.063	-0.006	2.529	-3.022	-1.037	0.263	-0.918	-1.331	-0.006
50	A	209	VAL	0	-0.007	-0.013	5.441	0.584	0.584	0.000	0.000	0.000	0.000
51	A	210	THR	0	-0.020	-0.027	4.689	-0.545	-0.506	-0.001	-0.006	-0.032	0.000
52	A	211	ASN	0	-0.008	-0.010	2.106	0.635	-0.368	8.540	-5.071	-2.467	0.012
53	A	212	GLY	0	0.056	0.045	2.989	3.011	-2.531	0.185	5.661	-0.305	-0.001
54	A	213	TRP	0	0.006	-0.007	4.918	0.895	1.077	-0.001	-0.005	-0.175	0.000
55	A	214	LYS	1	0.823	0.923	7.462	-0.637	-0.637	0.000	0.000	0.000	0.000
56	A	215	MET	0	0.046	0.030	9.731	0.043	0.043	0.000	0.000	0.000	0.000
57	A	216	PHE	0	-0.032	-0.024	10.720	-0.120	-0.120	0.000	0.000	0.000	0.000
58	A	217	ASN	0	0.062	0.017	15.434	0.013	0.013	0.000	0.000	0.000	0.000
59	A	218	SER	0	0.039	0.020	18.926	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	219	LYS	1	0.902	0.944	21.285	-0.170	-0.170	0.000	0.000	0.000	0.000
61	A	220	GLY	0	0.052	0.027	17.572	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	221	LYS	1	0.929	0.966	17.728	-0.157	-0.157	0.000	0.000	0.000	0.000
63	A	222	ARG	1	0.950	0.990	12.478	-0.131	-0.131	0.000	0.000	0.000	0.000
64	A	223	ILE	0	-0.019	-0.023	15.970	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	224	GLY	0	0.009	0.009	15.299	0.011	0.011	0.000	0.000	0.000	0.000
66	A	225	THR	0	-0.036	-0.026	9.759	0.012	0.012	0.000	0.000	0.000	0.000
67	A	226	TYR	0	-0.042	-0.029	10.310	-0.122	-0.122	0.000	0.000	0.000	0.000
68	A	227	ASP	-1	-0.734	-0.862	8.827	1.206	1.206	0.000	0.000	0.000	0.000
69	A	228	SER	0	-0.012	-0.020	7.399	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	229	GLY	0	0.014	0.011	8.810	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	230	LEU	0	-0.074	-0.031	10.905	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	231	ASN	0	0.010	0.018	13.216	-0.203	-0.203	0.000	0.000	0.000	0.000
73	A	232	ARG	1	0.876	0.929	13.580	-0.236	-0.236	0.000	0.000	0.000	0.000
74	A	233	ILE	0	-0.006	0.011	11.340	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	234	LYS	1	0.975	0.977	11.552	-0.105	-0.105	0.000	0.000	0.000	0.000
76	A	235	ASP	-1	-0.868	-0.910	14.361	0.237	0.237	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:160:LEU)