FMO DATABASE

FMODB ID: 7224K

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

Total energy (hartree)

FMO2-HF: Electronic energy	-743980.80997
FMO2-HF: Nuclear repulsion	704299.882644
FMO2-HF: Total energy	-39680.927326
FMO2-MP2: Total energy	-39794.75244

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.
-96.851	-88.301	14.621	-10.257	-12.914	-0.102

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 : 0.922 / q_NPA : 0.964

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	0.897	0.963	2.917	22.844	25.191	0.095	-1.073	-1.369	0.004
4	B	13	ALA	0	0.035	0.012	2.847	2.323	3.334	0.230	-0.355	-0.886	-0.001
5	B	14	GLU	-1	-0.874	-0.935	3.294	-37.517	-36.023	0.044	-0.734	-0.804	-0.004
6	B	15	LYS	1	0.963	0.983	6.020	21.372	21.372	0.000	0.000	0.000	0.000
7	B	16	VAL	0	-0.017	-0.009	7.612	2.162	2.162	0.000	0.000	0.000	0.000
8	B	17	GLU	-1	-0.828	-0.918	7.827	-24.233	-24.233	0.000	0.000	0.000	0.000
9	B	18	CYS	0	-0.082	-0.041	9.874	1.776	1.776	0.000	0.000	0.000	0.000
10	B	19	ALA	0	-0.025	-0.001	11.952	1.295	1.295	0.000	0.000	0.000	0.000
11	B	20	LEU	0	-0.020	0.004	11.478	1.181	1.181	0.000	0.000	0.000	0.000
12	B	21	LYS	1	0.859	0.922	11.544	21.628	21.628	0.000	0.000	0.000	0.000
13	B	22	GLY	0	-0.040	-0.016	15.451	0.263	0.263	0.000	0.000	0.000	0.000
14	B	23	GLY	0	-0.017	0.007	18.359	0.662	0.662	0.000	0.000	0.000	0.000
15	B	24	ILE	0	-0.019	-0.016	19.919	-0.208	-0.208	0.000	0.000	0.000	0.000
16	B	25	PHE	0	-0.020	-0.017	17.148	0.131	0.131	0.000	0.000	0.000	0.000
17	B	26	ARG	1	0.843	0.882	22.741	9.035	9.035	0.000	0.000	0.000	0.000
18	B	27	GLY	0	0.022	0.012	25.511	-0.135	-0.135	0.000	0.000	0.000	0.000
19	B	28	THR	0	-0.021	-0.008	26.970	0.077	0.077	0.000	0.000	0.000	0.000
20	B	29	LEU	0	0.023	0.030	24.026	0.005	0.005	0.000	0.000	0.000	0.000
21	B	30	PRO	0	0.011	0.004	27.308	0.286	0.286	0.000	0.000	0.000	0.000
22	B	31	ALA	0	0.019	0.018	29.896	-0.233	-0.233	0.000	0.000	0.000	0.000
23	B	32	ALA	0	-0.011	-0.012	32.559	0.250	0.250	0.000	0.000	0.000	0.000
24	B	33	ASP	-1	-0.875	-0.949	30.612	-9.045	-9.045	0.000	0.000	0.000	0.000
25	B	34	CYS	0	-0.015	-0.003	33.252	0.212	0.212	0.000	0.000	0.000	0.000
26	B	35	PRO	0	-0.045	-0.017	35.718	-0.035	-0.035	0.000	0.000	0.000	0.000
27	B	36	GLY	0	-0.008	-0.011	32.631	-0.086	-0.086	0.000	0.000	0.000	0.000
28	B	37	ILE	0	0.022	0.016	30.245	0.186	0.186	0.000	0.000	0.000	0.000
29	B	38	ASP	-1	-0.814	-0.861	30.026	-9.236	-9.236	0.000	0.000	0.000	0.000
30	B	39	THR	0	0.004	-0.012	25.397	-0.025	-0.025	0.000	0.000	0.000	0.000
31	B	40	THR	0	-0.019	-0.021	25.752	-0.081	-0.081	0.000	0.000	0.000	0.000
32	B	41	VAL	0	0.014	0.011	19.750	0.021	0.021	0.000	0.000	0.000	0.000
33	B	42	THR	0	-0.024	-0.018	21.194	0.266	0.266	0.000	0.000	0.000	0.000
34	B	43	PHE	0	0.052	0.033	15.709	-0.152	-0.152	0.000	0.000	0.000	0.000
35	B	44	ASN	0	0.010	0.002	17.693	0.127	0.127	0.000	0.000	0.000	0.000
36	B	45	ALA	0	0.033	-0.008	16.378	-0.803	-0.803	0.000	0.000	0.000	0.000
37	B	46	ASP	-1	-0.811	-0.882	15.963	-15.168	-15.168	0.000	0.000	0.000	0.000
38	B	47	GLY	0	0.047	0.043	14.953	-0.621	-0.621	0.000	0.000	0.000	0.000
39	B	48	THR	0	-0.077	-0.067	15.773	0.327	0.327	0.000	0.000	0.000	0.000
40	B	49	ALA	0	0.001	-0.017	18.337	-0.269	-0.269	0.000	0.000	0.000	0.000
41	B	50	GLN	0	-0.060	-0.024	20.316	0.555	0.555	0.000	0.000	0.000	0.000
42	B	51	LYS	1	0.822	0.895	22.813	10.984	10.984	0.000	0.000	0.000	0.000
43	B	52	VAL	0	0.007	0.003	25.138	0.242	0.242	0.000	0.000	0.000	0.000
44	B	53	GLU	-1	-0.812	-0.874	27.687	-10.322	-10.322	0.000	0.000	0.000	0.000
45	B	54	LEU	0	-0.009	0.000	30.839	0.269	0.269	0.000	0.000	0.000	0.000
46	B	64	PRO	0	0.019	-0.016	33.933	0.065	0.065	0.000	0.000	0.000	0.000
47	B	65	LEU	0	-0.002	0.034	31.985	-0.040	-0.040	0.000	0.000	0.000	0.000
48	B	66	THR	0	-0.007	-0.009	29.331	-0.234	-0.234	0.000	0.000	0.000	0.000
49	B	67	TYR	0	-0.049	-0.048	25.778	-0.030	-0.030	0.000	0.000	0.000	0.000
50	B	68	ARG	1	0.862	0.915	22.398	12.104	12.104	0.000	0.000	0.000	0.000
51	B	69	GLY	0	0.048	0.011	21.631	0.117	0.117	0.000	0.000	0.000	0.000
52	B	70	THR	0	-0.037	-0.012	17.154	0.148	0.148	0.000	0.000	0.000	0.000
53	B	71	TRP	0	-0.059	-0.025	11.194	-0.138	-0.138	0.000	0.000	0.000	0.000
54	B	72	MET	0	0.004	0.020	9.660	0.164	0.164	0.000	0.000	0.000	0.000
55	B	73	VAL	0	0.008	0.003	6.757	1.424	1.424	0.000	0.000	0.000	0.000
56	B	74	ARG	1	0.799	0.895	6.669	20.178	20.178	0.000	0.000	0.000	0.000
57	B	75	GLU	-1	-0.847	-0.953	2.180	-105.195	-103.240	13.897	-7.047	-8.805	-0.087
58	B	76	ASP	-1	-0.814	-0.897	2.745	-28.339	-26.596	0.355	-1.048	-1.050	-0.014
59	B	77	GLY	0	-0.038	-0.042	5.262	2.576	2.576	0.000	0.000	0.000	0.000
60	B	78	ILE	0	-0.048	-0.022	6.204	2.294	2.294	0.000	0.000	0.000	0.000
61	B	79	VAL	0	-0.010	-0.001	9.254	-1.801	-1.801	0.000	0.000	0.000	0.000
62	B	80	GLU	-1	-0.822	-0.917	11.693	-19.397	-19.397	0.000	0.000	0.000	0.000
63	B	81	LEU	0	0.001	0.000	14.210	-0.352	-0.352	0.000	0.000	0.000	0.000
64	B	82	SER	0	-0.017	-0.013	17.285	0.381	0.381	0.000	0.000	0.000	0.000
65	B	83	LEU	0	0.006	0.013	19.668	0.141	0.141	0.000	0.000	0.000	0.000
66	B	84	VAL	0	0.010	0.019	23.180	-0.050	-0.050	0.000	0.000	0.000	0.000
67	B	85	SER	0	-0.028	-0.014	26.165	0.577	0.577	0.000	0.000	0.000	0.000
68	B	95	LYS	1	0.913	0.954	15.892	17.390	17.390	0.000	0.000	0.000	0.000
69	B	96	GLU	-1	-0.811	-0.873	19.643	-12.027	-12.027	0.000	0.000	0.000	0.000
70	B	97	LEU	0	-0.030	-0.016	14.222	-0.922	-0.922	0.000	0.000	0.000	0.000
71	B	98	TYR	0	-0.035	-0.052	14.594	1.022	1.022	0.000	0.000	0.000	0.000
72	B	99	GLU	-1	-0.793	-0.881	12.680	-16.320	-16.320	0.000	0.000	0.000	0.000
73	B	100	LEU	0	-0.018	-0.007	11.604	0.760	0.760	0.000	0.000	0.000	0.000
74	B	101	ILE	0	-0.026	-0.002	13.120	-0.317	-0.317	0.000	0.000	0.000	0.000
75	B	102	ASP	-1	-0.785	-0.879	15.827	-12.454	-12.454	0.000	0.000	0.000	0.000
76	B	103	SER	0	-0.026	-0.026	15.698	-0.572	-0.572	0.000	0.000	0.000	0.000
77	B	104	ASN	0	-0.029	-0.011	16.710	-0.345	-0.345	0.000	0.000	0.000	0.000
78	B	105	SER	0	0.010	-0.014	17.665	0.813	0.813	0.000	0.000	0.000	0.000
79	B	106	VAL	0	0.001	0.008	15.124	-0.809	-0.809	0.000	0.000	0.000	0.000
80	B	107	ARG	1	0.834	0.905	16.876	14.249	14.249	0.000	0.000	0.000	0.000
81	B	108	TYR	0	0.021	0.013	17.488	-0.578	-0.578	0.000	0.000	0.000	0.000
82	B	109	MET	0	-0.045	-0.018	13.852	0.119	0.119	0.000	0.000	0.000	0.000
83	B	110	GLY	0	0.012	0.007	18.663	0.400	0.400	0.000	0.000	0.000	0.000
84	B	111	ALA	0	0.038	0.017	19.769	-0.329	-0.329	0.000	0.000	0.000	0.000
85	B	112	PRO	0	-0.003	-0.022	17.271	-0.140	-0.140	0.000	0.000	0.000	0.000
86	B	113	GLY	0	-0.002	0.010	18.715	0.485	0.485	0.000	0.000	0.000	0.000
87	B	114	ALA	0	-0.024	-0.003	20.718	0.548	0.548	0.000	0.000	0.000	0.000
88	B	115	GLY	0	0.036	0.026	19.705	-0.034	-0.034	0.000	0.000	0.000	0.000
89	B	116	LYS	1	0.919	0.958	20.408	11.481	11.481	0.000	0.000	0.000	0.000
90	B	117	PRO	0	0.001	-0.014	20.723	-0.120	-0.120	0.000	0.000	0.000	0.000
91	B	118	SER	0	0.003	0.015	21.730	0.114	0.114	0.000	0.000	0.000	0.000
92	B	119	LYS	1	1.011	0.993	23.449	9.985	9.985	0.000	0.000	0.000	0.000
93	B	120	GLU	-1	-0.938	-0.972	24.454	-9.049	-9.049	0.000	0.000	0.000	0.000
94	B	121	MET	0	0.020	0.018	26.755	0.162	0.162	0.000	0.000	0.000	0.000
95	B	122	ALA	0	-0.035	-0.017	21.752	-0.107	-0.107	0.000	0.000	0.000	0.000
96	B	123	PRO	0	0.006	-0.011	23.264	-0.273	-0.273	0.000	0.000	0.000	0.000
97	B	124	PHE	0	0.025	0.014	25.041	-0.048	-0.048	0.000	0.000	0.000	0.000
98	B	125	TYR	0	-0.009	-0.001	22.686	-0.046	-0.046	0.000	0.000	0.000	0.000
99	B	126	VAL	0	-0.046	-0.015	21.027	-0.616	-0.616	0.000	0.000	0.000	0.000
100	B	127	LEU	0	-0.018	0.003	21.061	0.380	0.380	0.000	0.000	0.000	0.000
101	B	128	LYS	1	0.856	0.904	20.990	10.874	10.874	0.000	0.000	0.000	0.000
102	B	129	LYS	1	0.845	0.932	17.376	14.272	14.272	0.000	0.000	0.000	0.000
103	B	130	THR	0	-0.024	-0.006	22.445	0.298	0.298	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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