FMO DATABASE

FMODB ID: MVZ5Z

Calculation Name: 3QYC-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 3QYC

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID:
Warning: Undefined array key "Uniprot" in /home/FMODBwui_src/fmodbwui/detail.php on line 453

Warning: Undefined array key "Uniprot" in /home/FMODBwui_src/fmodbwui/detail.php on line 453

Base Structure: X-ray

Registration Date: 2023-06-26

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-954806.71047
FMO2-HF: Nuclear repulsion	907313.265229
FMO2-HF: Total energy	-47493.445241
FMO2-MP2: Total energy	-47627.980665

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:4:VAL)

Summations of interaction energy for fragment #1(A:4:VAL)

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.
-18.5	-7.345	8.625	-6.991	-12.788	-0.044

Interaction energy analysis for fragmet #1(A:4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : 0.002

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	6	LEU	0	0.017	0.006	3.353	-1.203	0.819	-0.009	-0.885	-1.127	0.003
4	A	7	VAL	0	0.021	0.003	5.615	-0.054	-0.054	0.000	0.000	0.000	0.000
5	A	8	GLU	-1	-0.783	-0.890	9.423	-0.054	-0.054	0.000	0.000	0.000	0.000
6	A	9	SER	0	-0.031	-0.014	12.135	0.044	0.044	0.000	0.000	0.000	0.000
7	A	10	GLY	0	0.029	0.002	15.598	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	11	GLY	0	0.021	0.022	18.387	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	12	GLY	0	-0.016	-0.014	19.982	0.019	0.019	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.049	-0.023	23.626	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.029	-0.004	26.857	0.007	0.007	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.995	0.993	29.050	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	16	PRO	0	0.029	0.003	31.197	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.024	-0.002	31.995	0.004	0.004	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.017	-0.003	30.209	0.001	0.001	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.050	-0.046	26.672	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.018	0.016	22.433	0.009	0.009	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.926	0.964	18.526	-0.114	-0.114	0.000	0.000	0.000	0.000
19	A	22	LEU	0	0.005	0.028	16.074	0.023	0.023	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.025	-0.040	14.518	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	24	CYS	0	-0.039	-0.002	8.448	0.044	0.044	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.021	0.031	9.515	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	26	ALA	0	0.036	0.011	4.533	-0.048	-0.012	-0.001	-0.007	-0.028	0.000
24	A	27	SER	0	-0.051	-0.028	4.451	-0.082	0.062	-0.001	-0.031	-0.112	0.000
25	A	28	GLY	0	0.038	0.017	2.605	-0.146	1.507	1.153	-1.311	-1.495	-0.012
26	A	29	VAL	0	0.023	0.010	2.389	-2.416	-1.727	1.783	-0.469	-2.003	0.001
27	A	30	ARG	1	0.840	0.906	4.488	-0.381	-0.285	-0.001	-0.014	-0.081	0.000
28	A	31	LEU	0	0.047	0.024	6.234	-0.261	-0.261	0.000	0.000	0.000	0.000
29	A	32	SER	0	-0.043	-0.035	7.175	-0.138	-0.138	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.055	-0.011	6.260	0.022	0.022	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.058	0.020	2.270	-0.320	0.751	2.863	-1.183	-2.751	-0.010
32	A	35	ASP	-1	-0.764	-0.868	7.862	-0.250	-0.250	0.000	0.000	0.000	0.000
33	A	36	MET	0	-0.041	-0.007	6.492	-0.207	-0.207	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.010	-0.011	10.125	0.085	0.085	0.000	0.000	0.000	0.000
35	A	38	TRP	0	0.022	0.011	11.363	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.011	-0.004	13.451	0.005	0.005	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.781	0.871	15.661	0.131	0.131	0.000	0.000	0.000	0.000
38	A	41	GLN	0	0.002	-0.010	18.412	-0.029	-0.029	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.003	0.011	20.744	0.017	0.017	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.024	-0.010	24.169	-0.008	-0.008	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.004	0.008	26.651	0.001	0.001	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.863	0.936	24.952	0.112	0.112	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.044	0.027	23.091	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.010	-0.011	16.399	0.012	0.012	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.769	-0.848	19.598	-0.129	-0.129	0.000	0.000	0.000	0.000
46	A	49	TRP	0	0.053	0.020	12.959	0.011	0.011	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.008	0.014	17.799	0.020	0.020	0.000	0.000	0.000	0.000
48	A	51	SER	0	-0.022	-0.041	17.262	0.023	0.023	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.024	0.008	14.541	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.033	-0.011	13.360	0.050	0.050	0.000	0.000	0.000	0.000
51	A	54	SER	0	0.066	0.036	13.143	-0.045	-0.045	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.001	-0.018	11.288	0.079	0.079	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.029	-0.015	12.612	0.060	0.060	0.000	0.000	0.000	0.000
54	A	57	GLY	0	-0.017	-0.009	15.639	0.041	0.041	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.011	-0.003	17.183	0.009	0.009	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.017	-0.015	18.633	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.017	-0.010	17.954	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	61	TYR	0	-0.006	-0.003	18.107	0.004	0.004	0.000	0.000	0.000	0.000
59	A	62	TYR	0	0.020	0.020	19.808	0.006	0.006	0.000	0.000	0.000	0.000
60	A	63	ALA	0	0.059	0.049	21.937	0.005	0.005	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.833	-0.924	23.719	-0.116	-0.116	0.000	0.000	0.000	0.000
62	A	65	SER	0	-0.052	-0.022	24.725	0.010	0.010	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.015	-0.012	22.088	0.012	0.012	0.000	0.000	0.000	0.000
64	A	67	LYS	1	0.857	0.922	25.539	0.138	0.138	0.000	0.000	0.000	0.000
65	A	68	GLY	0	-0.006	0.011	26.467	0.007	0.007	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.747	0.839	26.962	0.070	0.070	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.014	-0.005	21.126	0.012	0.012	0.000	0.000	0.000	0.000
68	A	71	THR	0	-0.050	-0.033	22.007	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	72	ILE	0	0.001	0.021	14.263	0.020	0.020	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.009	-0.010	16.859	0.012	0.012	0.000	0.000	0.000	0.000
71	A	74	ARG	1	0.802	0.892	9.674	0.289	0.289	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.746	-0.822	13.759	0.145	0.145	0.000	0.000	0.000	0.000
73	A	76	ASN	0	0.077	0.032	11.644	0.045	0.045	0.000	0.000	0.000	0.000
74	A	77	SER	0	-0.104	-0.071	12.286	0.060	0.060	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.864	0.910	13.642	-0.138	-0.138	0.000	0.000	0.000	0.000
76	A	79	ASN	0	0.024	0.039	8.009	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.048	0.022	9.009	0.082	0.082	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.003	0.008	9.808	-0.055	-0.055	0.000	0.000	0.000	0.000
79	A	82	TYR	0	-0.022	-0.034	12.293	0.056	0.056	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.006	0.000	15.538	-0.039	-0.039	0.000	0.000	0.000	0.000
81	A	84	GLN	0	-0.007	0.004	17.863	0.024	0.024	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.034	-0.010	20.810	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	86	ASN	0	0.062	0.025	23.564	0.021	0.021	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.010	-0.010	27.336	-0.007	-0.007	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.003	0.015	24.299	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	89	ARG	1	0.898	0.935	28.438	0.061	0.061	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.063	0.031	28.783	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.835	-0.918	28.572	-0.055	-0.055	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.772	-0.835	24.737	-0.073	-0.073	0.000	0.000	0.000	0.000
90	A	93	THR	0	-0.030	-0.002	23.931	0.004	0.004	0.000	0.000	0.000	0.000
91	A	94	ALA	0	-0.014	-0.017	21.174	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	95	VAL	0	0.028	0.028	16.608	0.021	0.021	0.000	0.000	0.000	0.000
93	A	96	TYR	0	-0.043	-0.044	16.218	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	97	TYR	0	0.051	0.021	11.800	0.043	0.043	0.000	0.000	0.000	0.000
95	A	98	CYS	0	-0.086	-0.048	9.621	0.001	0.001	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.013	0.011	7.342	-0.012	-0.012	0.000	0.000	0.000	0.000
97	A	100	THR	0	0.052	0.016	3.432	-0.184	0.031	0.009	-0.042	-0.182	0.000
98	A	101	LEU	0	-0.067	-0.035	6.761	0.075	0.075	0.000	0.000	0.000	0.000
99	A	102	PRO	0	-0.016	-0.025	8.321	-0.206	-0.206	0.000	0.000	0.000	0.000
100	A	103	ASP	-1	-0.868	-0.911	7.888	-1.270	-1.270	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.035	-0.019	10.714	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.020	0.005	12.780	0.097	0.097	0.000	0.000	0.000	0.000
103	A	106	PRO	0	-0.013	0.004	15.702	0.016	0.016	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.013	0.006	18.432	0.040	0.040	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.940	-0.971	14.629	-0.626	-0.626	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.062	-0.048	16.250	0.054	0.054	0.000	0.000	0.000	0.000
107	A	111	THR	0	0.001	-0.001	10.826	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	112	TYR	0	-0.031	-0.030	7.761	0.107	0.107	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.021	0.001	3.132	-0.211	0.172	0.050	-0.107	-0.326	0.001
110	A	114	ASP	-1	-0.864	-0.932	2.808	-5.031	-3.844	0.281	-0.468	-1.000	-0.004
111	A	115	ALA	0	0.014	0.011	2.621	-6.249	-3.631	0.889	-1.618	-1.889	-0.022
112	A	116	SER	0	-0.035	-0.026	2.555	-0.780	0.106	1.610	-0.836	-1.660	-0.001
113	A	117	TRP	0	-0.007	-0.022	4.415	0.446	0.601	-0.001	-0.020	-0.134	0.000
114	A	118	GLY	0	0.010	0.017	6.483	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	119	GLN	0	-0.030	-0.011	8.044	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	120	GLY	0	-0.005	-0.005	11.298	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	121	THR	0	-0.048	-0.032	13.559	0.059	0.059	0.000	0.000	0.000	0.000
118	A	122	MET	0	-0.013	0.009	16.533	-0.035	-0.035	0.000	0.000	0.000	0.000
119	A	123	VAL	0	0.020	0.008	19.775	0.018	0.018	0.000	0.000	0.000	0.000
120	A	124	THR	0	-0.002	-0.004	22.392	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	125	VAL	0	0.006	0.006	26.158	0.009	0.009	0.000	0.000	0.000	0.000
122	A	126	SER	0	0.008	-0.005	28.839	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	127	SER	0	-0.011	-0.023	32.232	0.005	0.005	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.013	0.028	35.588	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:4:VAL)