FMO DATABASE

FMODB ID: 944Q2

Calculation Name: 4U3Q-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: B

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2023-06-21

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-742408.594175
FMO2-HF: Nuclear repulsion	702728.216325
FMO2-HF: Total energy	-39680.37785
FMO2-MP2: Total energy	-39794.164774

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(B:10:LYS)

Summations of interaction energy for fragment #1(B:10:LYS)

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.
-54.671	-48.402	0.367	-2.679	-3.956	-0.002

Interaction energy analysis for fragmet #1(B:10:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.024 / q_NPA : 0.995

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	B	12	LYS	1	0.935	0.977	3.067	21.395	23.896	0.035	-1.194	-1.342	0.005
4	B	13	ALA	0	0.058	0.010	2.925	2.364	3.144	0.073	-0.223	-0.630	-0.001
5	B	14	GLU	-1	-0.833	-0.904	4.259	-33.748	-33.366	-0.001	-0.071	-0.310	0.000
6	B	15	LYS	1	0.938	0.978	6.101	21.391	21.391	0.000	0.000	0.000	0.000
7	B	16	VAL	0	-0.043	-0.023	7.871	2.063	2.063	0.000	0.000	0.000	0.000
8	B	17	GLU	-1	-0.900	-0.961	6.738	-28.082	-28.082	0.000	0.000	0.000	0.000
9	B	18	CYS	0	-0.098	-0.056	9.797	1.859	1.859	0.000	0.000	0.000	0.000
10	B	19	ALA	0	-0.048	-0.020	12.122	1.211	1.211	0.000	0.000	0.000	0.000
11	B	20	LEU	0	-0.011	0.004	12.109	1.115	1.115	0.000	0.000	0.000	0.000
12	B	21	LYS	1	0.955	0.989	12.093	20.883	20.883	0.000	0.000	0.000	0.000
13	B	22	GLY	0	-0.058	-0.027	15.813	0.192	0.192	0.000	0.000	0.000	0.000
14	B	23	GLY	0	-0.051	-0.015	18.509	0.672	0.672	0.000	0.000	0.000	0.000
15	B	24	ILE	0	-0.007	-0.014	20.032	-0.186	-0.186	0.000	0.000	0.000	0.000
16	B	25	PHE	0	-0.031	-0.030	17.582	0.194	0.194	0.000	0.000	0.000	0.000
17	B	26	ARG	1	0.861	0.885	22.743	8.972	8.972	0.000	0.000	0.000	0.000
18	B	27	GLY	0	0.007	-0.002	25.689	-0.126	-0.126	0.000	0.000	0.000	0.000
19	B	28	THR	0	-0.019	-0.001	27.050	0.055	0.055	0.000	0.000	0.000	0.000
20	B	29	LEU	0	-0.011	0.014	24.571	-0.058	-0.058	0.000	0.000	0.000	0.000
21	B	30	PRO	0	0.030	0.012	27.733	0.283	0.283	0.000	0.000	0.000	0.000
22	B	31	ALA	0	0.013	0.017	30.512	-0.187	-0.187	0.000	0.000	0.000	0.000
23	B	32	ALA	0	-0.014	-0.016	32.561	0.226	0.226	0.000	0.000	0.000	0.000
24	B	33	ASP	-1	-0.910	-0.966	31.499	-8.537	-8.537	0.000	0.000	0.000	0.000
25	B	34	CYS	0	-0.022	0.000	33.935	0.201	0.201	0.000	0.000	0.000	0.000
26	B	35	PRO	0	-0.053	-0.023	36.174	-0.050	-0.050	0.000	0.000	0.000	0.000
27	B	36	GLY	0	-0.007	-0.008	33.117	-0.088	-0.088	0.000	0.000	0.000	0.000
28	B	37	ILE	0	0.022	0.011	30.453	0.163	0.163	0.000	0.000	0.000	0.000
29	B	38	ASP	-1	-0.832	-0.878	30.211	-9.073	-9.073	0.000	0.000	0.000	0.000
30	B	39	THR	0	-0.001	-0.010	25.558	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	40	THR	0	-0.027	-0.023	25.656	-0.052	-0.052	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.008	0.003	19.912	0.006	0.006	0.000	0.000	0.000	0.000
33	B	42	THR	0	-0.021	-0.008	21.635	0.043	0.043	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.049	0.022	15.974	-0.098	-0.098	0.000	0.000	0.000	0.000
35	B	44	ASN	0	-0.008	-0.006	18.159	0.203	0.203	0.000	0.000	0.000	0.000
36	B	45	ALA	0	0.032	-0.008	16.210	-0.759	-0.759	0.000	0.000	0.000	0.000
37	B	46	ASP	-1	-0.851	-0.893	16.038	-14.806	-14.806	0.000	0.000	0.000	0.000
38	B	47	GLY	0	0.027	0.022	15.077	-0.449	-0.449	0.000	0.000	0.000	0.000
39	B	48	THR	0	-0.070	-0.061	15.979	0.268	0.268	0.000	0.000	0.000	0.000
40	B	49	ALA	0	0.010	-0.014	18.614	-0.269	-0.269	0.000	0.000	0.000	0.000
41	B	50	GLN	0	-0.047	-0.016	20.551	0.377	0.377	0.000	0.000	0.000	0.000
42	B	51	LYS	1	0.856	0.946	23.372	10.777	10.777	0.000	0.000	0.000	0.000
43	B	52	VAL	0	-0.003	0.003	25.410	0.241	0.241	0.000	0.000	0.000	0.000
44	B	53	GLU	-1	-0.824	-0.912	28.078	-9.890	-9.890	0.000	0.000	0.000	0.000
45	B	54	LEU	0	0.014	0.010	30.813	0.249	0.249	0.000	0.000	0.000	0.000
46	B	64	PRO	0	0.034	-0.007	34.346	0.048	0.048	0.000	0.000	0.000	0.000
47	B	65	LEU	0	-0.050	0.002	32.205	0.012	0.012	0.000	0.000	0.000	0.000
48	B	66	THR	0	0.002	0.001	29.104	-0.229	-0.229	0.000	0.000	0.000	0.000
49	B	67	TYR	0	-0.029	-0.011	25.996	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	68	ARG	1	0.919	0.939	24.027	11.669	11.669	0.000	0.000	0.000	0.000
51	B	69	GLY	0	0.022	0.011	21.830	0.110	0.110	0.000	0.000	0.000	0.000
52	B	70	THR	0	-0.023	-0.003	16.944	0.139	0.139	0.000	0.000	0.000	0.000
53	B	71	TRP	0	-0.046	-0.026	11.311	-0.044	-0.044	0.000	0.000	0.000	0.000
54	B	72	MET	0	0.002	0.020	9.461	0.172	0.172	0.000	0.000	0.000	0.000
55	B	73	VAL	0	0.012	0.009	6.525	1.372	1.372	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.840	0.936	6.848	18.266	18.266	0.000	0.000	0.000	0.000
57	B	75	GLU	-1	-0.931	-0.980	2.827	-60.896	-58.885	0.249	-0.854	-1.405	-0.003
58	B	76	ASP	-1	-0.836	-0.915	3.468	-23.770	-23.175	0.011	-0.337	-0.269	-0.003
59	B	77	GLY	0	-0.039	-0.025	5.836	1.725	1.725	0.000	0.000	0.000	0.000
60	B	78	ILE	0	-0.058	-0.033	6.705	1.683	1.683	0.000	0.000	0.000	0.000
61	B	79	VAL	0	-0.010	-0.005	9.548	-1.401	-1.401	0.000	0.000	0.000	0.000
62	B	80	GLU	-1	-0.885	-0.955	11.969	-17.685	-17.685	0.000	0.000	0.000	0.000
63	B	81	LEU	0	-0.013	0.000	14.185	-0.284	-0.284	0.000	0.000	0.000	0.000
64	B	82	SER	0	-0.015	-0.018	17.531	0.432	0.432	0.000	0.000	0.000	0.000
65	B	83	LEU	0	-0.001	0.003	20.089	0.084	0.084	0.000	0.000	0.000	0.000
66	B	84	VAL	0	-0.011	-0.001	23.557	0.030	0.030	0.000	0.000	0.000	0.000
67	B	85	SER	0	0.011	0.013	26.673	0.392	0.392	0.000	0.000	0.000	0.000
68	B	95	LYS	1	0.935	0.967	16.871	15.713	15.713	0.000	0.000	0.000	0.000
69	B	96	GLU	-1	-0.874	-0.940	19.031	-11.624	-11.624	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.022	-0.018	14.300	-0.762	-0.762	0.000	0.000	0.000	0.000
71	B	98	TYR	0	-0.028	-0.029	14.559	1.038	1.038	0.000	0.000	0.000	0.000
72	B	99	GLU	-1	-0.841	-0.923	12.675	-16.260	-16.260	0.000	0.000	0.000	0.000
73	B	100	LEU	0	-0.033	-0.009	11.741	0.624	0.624	0.000	0.000	0.000	0.000
74	B	101	ILE	0	-0.043	-0.007	13.565	-0.232	-0.232	0.000	0.000	0.000	0.000
75	B	102	ASP	-1	-0.802	-0.904	15.774	-12.702	-12.702	0.000	0.000	0.000	0.000
76	B	103	SER	0	-0.043	-0.040	15.831	-0.559	-0.559	0.000	0.000	0.000	0.000
77	B	104	ASN	0	-0.041	-0.015	16.859	-0.231	-0.231	0.000	0.000	0.000	0.000
78	B	105	SER	0	-0.005	-0.009	18.408	0.734	0.734	0.000	0.000	0.000	0.000
79	B	106	VAL	0	0.018	0.021	15.565	-0.702	-0.702	0.000	0.000	0.000	0.000
80	B	107	ARG	1	0.902	0.948	17.033	13.798	13.798	0.000	0.000	0.000	0.000
81	B	108	TYR	0	0.017	0.014	17.722	-0.669	-0.669	0.000	0.000	0.000	0.000
82	B	109	MET	0	-0.055	-0.022	14.550	0.162	0.162	0.000	0.000	0.000	0.000
83	B	110	GLY	0	0.023	0.011	19.039	0.397	0.397	0.000	0.000	0.000	0.000
84	B	111	ALA	0	0.054	0.038	19.665	-0.422	-0.422	0.000	0.000	0.000	0.000
85	B	112	PRO	0	0.006	-0.019	17.246	-0.136	-0.136	0.000	0.000	0.000	0.000
86	B	113	GLY	0	-0.002	0.011	18.505	0.398	0.398	0.000	0.000	0.000	0.000
87	B	114	ALA	0	-0.032	-0.009	20.446	0.549	0.549	0.000	0.000	0.000	0.000
88	B	115	GLY	0	0.016	0.014	19.685	0.057	0.057	0.000	0.000	0.000	0.000
89	B	116	LYS	1	0.954	0.974	20.441	11.013	11.013	0.000	0.000	0.000	0.000
90	B	117	PRO	0	-0.005	-0.017	20.999	-0.083	-0.083	0.000	0.000	0.000	0.000
91	B	118	SER	0	0.008	0.020	22.002	0.131	0.131	0.000	0.000	0.000	0.000
92	B	119	LYS	1	1.041	1.005	24.020	9.532	9.532	0.000	0.000	0.000	0.000
93	B	120	GLU	-1	-0.966	-0.985	25.028	-8.690	-8.690	0.000	0.000	0.000	0.000
94	B	121	MET	0	0.034	0.020	26.741	0.174	0.174	0.000	0.000	0.000	0.000
95	B	122	ALA	0	-0.010	-0.005	22.208	-0.130	-0.130	0.000	0.000	0.000	0.000
96	B	123	PRO	0	-0.025	-0.026	23.743	-0.260	-0.260	0.000	0.000	0.000	0.000
97	B	124	PHE	0	0.019	0.014	25.456	-0.022	-0.022	0.000	0.000	0.000	0.000
98	B	125	TYR	0	0.010	0.003	22.662	0.062	0.062	0.000	0.000	0.000	0.000
99	B	126	VAL	0	-0.050	-0.018	21.360	-0.525	-0.525	0.000	0.000	0.000	0.000
100	B	127	LEU	0	-0.020	0.000	20.779	0.357	0.357	0.000	0.000	0.000	0.000
101	B	128	LYS	1	0.948	0.968	21.329	10.037	10.037	0.000	0.000	0.000	0.000
102	B	129	LYS	1	0.952	0.995	18.937	13.488	13.488	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.032	-0.009	22.770	0.333	0.333	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:10:LYS)