FMO DATABASE

FMODB ID: GN3Y1

Calculation Name: 3QKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKB

Chain ID: A

ChEMBL ID:

UniProt ID: Q03GF5

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-609874.547652
FMO2-HF: Nuclear repulsion	573499.344535
FMO2-HF: Total energy	-36375.203117
FMO2-MP2: Total energy	-36481.257508

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:-2:PHE)

Summations of interaction energy for fragment #1(A:-2:PHE)

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.
-23.066	-19.121	13.241	-7.09	-10.096	0.023

Interaction energy analysis for fragmet #1(A:-2:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.025

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	0	GLY	0	-0.015	0.001	3.882	-2.028	0.509	-0.025	-1.385	-1.128	0.000
4	A	1	MET	0	-0.019	0.028	5.137	0.212	0.212	0.000	0.000	0.000	0.000
5	A	2	PHE	0	-0.004	0.005	6.729	0.129	0.129	0.000	0.000	0.000	0.000
6	A	3	ILE	0	-0.005	-0.013	10.531	-0.072	-0.072	0.000	0.000	0.000	0.000
7	A	4	THR	0	-0.019	-0.001	13.108	0.052	0.052	0.000	0.000	0.000	0.000
8	A	5	THR	0	0.038	0.023	16.944	-0.010	-0.010	0.000	0.000	0.000	0.000
9	A	6	GLU	-1	-0.845	-0.910	20.091	-0.088	-0.088	0.000	0.000	0.000	0.000
10	A	7	GLY	0	0.034	0.017	19.682	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	8	ILE	0	-0.008	-0.008	16.375	0.008	0.008	0.000	0.000	0.000	0.000
12	A	9	ASN	0	-0.024	-0.013	20.602	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	10	ALA	0	0.000	-0.005	19.030	0.011	0.011	0.000	0.000	0.000	0.000
14	A	11	GLY	0	0.026	0.022	20.869	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	12	TYR	0	-0.028	-0.019	16.929	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	13	THR	0	0.000	0.007	17.054	0.010	0.010	0.000	0.000	0.000	0.000
17	A	14	ILE	0	-0.005	-0.014	16.355	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.777	0.893	11.288	0.589	0.589	0.000	0.000	0.000	0.000
19	A	16	ASP	-1	-0.812	-0.908	15.513	-0.153	-0.153	0.000	0.000	0.000	0.000
20	A	17	VAL	0	-0.087	-0.041	16.029	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	18	VAL	0	-0.017	-0.001	12.480	0.003	0.003	0.000	0.000	0.000	0.000
22	A	19	GLU	-1	-0.778	-0.897	15.697	-0.110	-0.110	0.000	0.000	0.000	0.000
23	A	20	ALA	0	-0.022	-0.005	14.606	0.010	0.010	0.000	0.000	0.000	0.000
24	A	21	THR	0	-0.001	0.003	16.695	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	22	SER	0	-0.024	-0.016	17.071	0.007	0.007	0.000	0.000	0.000	0.000
26	A	23	SER	0	-0.011	-0.007	19.002	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	24	LEU	0	-0.011	0.011	21.487	0.004	0.004	0.000	0.000	0.000	0.000
28	A	25	MET	0	-0.010	-0.001	23.897	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	26	LEU	0	0.004	0.018	27.338	0.001	0.001	0.000	0.000	0.000	0.000
30	A	27	ALA	0	0.055	0.025	29.799	0.001	0.001	0.000	0.000	0.000	0.000
31	A	28	SER	0	-0.024	-0.031	32.120	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	29	GLU	-1	-0.898	-0.949	34.371	0.002	0.002	0.000	0.000	0.000	0.000
33	A	30	ASP	-1	-0.864	-0.928	31.224	0.002	0.002	0.000	0.000	0.000	0.000
34	A	31	ILE	0	-0.030	-0.007	32.404	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	32	ASP	-1	-0.795	-0.884	34.480	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	33	LYS	1	0.789	0.887	29.799	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	34	TYR	0	0.001	-0.028	28.846	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	35	ASN	0	0.015	0.011	26.598	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	36	MET	0	-0.013	-0.006	24.586	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	37	PHE	0	0.002	-0.015	23.243	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	38	ASP	-1	-0.912	-0.953	21.612	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	39	GLN	0	-0.018	-0.019	18.814	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	40	LEU	0	0.001	0.016	17.486	-0.012	-0.012	0.000	0.000	0.000	0.000
44	A	41	PHE	0	0.060	0.039	17.682	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	42	ASP	-1	-0.824	-0.902	14.480	-0.148	-0.148	0.000	0.000	0.000	0.000
46	A	43	GLU	-1	-0.836	-0.904	13.064	-0.077	-0.077	0.000	0.000	0.000	0.000
47	A	44	ALA	0	-0.013	-0.009	12.979	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	45	LYS	1	0.845	0.914	12.393	0.110	0.110	0.000	0.000	0.000	0.000
49	A	46	GLN	0	0.028	0.015	7.023	-0.090	-0.090	0.000	0.000	0.000	0.000
50	A	47	LYS	1	0.801	0.883	8.340	0.020	0.020	0.000	0.000	0.000	0.000
51	A	48	LEU	0	-0.027	-0.004	10.281	0.027	0.027	0.000	0.000	0.000	0.000
52	A	49	LYS	1	0.912	0.954	6.301	0.655	0.655	0.000	0.000	0.000	0.000
53	A	50	LYS	1	0.819	0.901	2.205	-15.159	-16.256	10.384	-3.407	-5.879	0.048
54	A	51	LYS	1	0.841	0.893	6.755	0.286	0.286	0.000	0.000	0.000	0.000
55	A	52	ALA	0	0.030	0.012	8.349	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	53	ASP	-1	-0.883	-0.933	2.525	-5.693	-3.188	2.882	-2.298	-3.089	-0.025
57	A	54	LEU	0	-0.027	-0.024	5.616	0.043	0.043	0.000	0.000	0.000	0.000
58	A	55	LEU	0	-0.009	0.017	8.188	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	56	GLU	-1	-0.949	-0.968	7.203	-0.842	-0.842	0.000	0.000	0.000	0.000
60	A	57	GLY	0	0.018	0.015	8.285	0.175	0.175	0.000	0.000	0.000	0.000
61	A	58	ASP	-1	-0.841	-0.923	7.459	-0.759	-0.759	0.000	0.000	0.000	0.000
62	A	59	GLY	0	-0.017	-0.032	8.361	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	60	ILE	0	-0.047	-0.010	10.127	0.032	0.032	0.000	0.000	0.000	0.000
64	A	61	ILE	0	-0.014	-0.009	12.978	0.033	0.033	0.000	0.000	0.000	0.000
65	A	62	GLY	0	-0.006	-0.003	16.743	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	63	LEU	0	-0.062	-0.018	15.904	0.007	0.007	0.000	0.000	0.000	0.000
67	A	64	LYS	1	0.805	0.889	18.485	0.120	0.120	0.000	0.000	0.000	0.000
68	A	65	TYR	0	0.001	-0.021	17.155	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	66	ASN	0	-0.006	0.010	22.278	0.001	0.001	0.000	0.000	0.000	0.000
70	A	67	THR	0	0.010	-0.005	23.924	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	68	GLU	-1	-0.830	-0.891	26.195	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	69	VAL	0	0.027	0.012	28.058	0.000	0.000	0.000	0.000	0.000	0.000
73	A	70	VAL	0	-0.030	-0.004	29.271	0.000	0.000	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.904	-0.956	31.869	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	72	VAL	0	-0.034	-0.035	33.783	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	73	ASN	0	-0.066	-0.042	36.583	0.000	0.000	0.000	0.000	0.000	0.000
77	A	74	GLY	0	0.036	0.029	39.856	0.001	0.001	0.000	0.000	0.000	0.000
78	A	75	ALA	0	0.024	0.021	38.058	0.001	0.001	0.000	0.000	0.000	0.000
79	A	76	PRO	0	0.031	0.016	33.596	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	77	LYS	1	0.829	0.913	31.992	0.006	0.006	0.000	0.000	0.000	0.000
81	A	78	PHE	0	0.002	-0.009	26.928	0.002	0.002	0.000	0.000	0.000	0.000
82	A	79	LEU	0	0.002	0.036	25.574	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	80	VAL	0	-0.001	-0.019	23.866	0.001	0.001	0.000	0.000	0.000	0.000
84	A	81	VAL	0	0.035	0.022	20.120	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	82	HIS	1	0.788	0.844	20.268	0.056	0.056	0.000	0.000	0.000	0.000
86	A	83	GLY	0	0.038	0.022	18.136	0.002	0.002	0.000	0.000	0.000	0.000
87	A	84	TYR	0	-0.033	-0.030	17.214	0.000	0.000	0.000	0.000	0.000	0.000
88	A	85	GLY	0	0.040	0.025	16.650	0.007	0.007	0.000	0.000	0.000	0.000
89	A	86	THR	0	-0.016	-0.002	16.610	0.004	0.004	0.000	0.000	0.000	0.000
90	A	87	VAL	0	-0.006	0.009	10.855	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	88	ILE	0	-0.033	-0.021	12.767	0.043	0.043	0.000	0.000	0.000	0.000
92	A	89	LEU	0	0.010	0.012	11.115	-0.099	-0.099	0.000	0.000	0.000	0.000
93	A	90	ILE	0	-0.007	-0.011	12.992	0.063	0.063	0.000	0.000	0.000	0.000
94	A	91	ASP	-1	-0.996	-0.997	15.147	-0.142	-0.142	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:PHE)