FMO DATABASE

FMODB ID: LZR19

Calculation Name: 3QYC-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3QYC

Chain ID: A

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

Total energy (hartree)

FMO2-HF: Electronic energy	-954414.917467
FMO2-HF: Nuclear repulsion	906921.865039
FMO2-HF: Total energy	-47493.052429
FMO2-MP2: Total energy	-47627.606435

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.
-11.092	-9.39	20.581	-7.811	-14.467	-0.036

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 : -0.010 / q_NPA : -0.003

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	0.016	0.005	3.365	-1.680	0.861	0.001	-1.090	-1.451	0.003
4	A	7	VAL	0	0.038	0.017	5.182	0.007	0.018	-0.001	-0.002	-0.007	0.000
5	A	8	GLU	-1	-0.780	-0.897	8.865	-0.195	-0.195	0.000	0.000	0.000	0.000
6	A	9	SER	0	-0.033	-0.016	11.665	0.040	0.040	0.000	0.000	0.000	0.000
7	A	10	GLY	0	0.009	-0.008	15.046	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	11	GLY	0	-0.003	0.013	17.823	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	12	GLY	0	0.015	-0.003	19.528	0.020	0.020	0.000	0.000	0.000	0.000
10	A	13	LEU	0	-0.038	-0.009	23.107	-0.013	-0.013	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.021	-0.001	26.123	0.007	0.007	0.000	0.000	0.000	0.000
12	A	15	LYS	1	0.988	0.992	28.372	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	16	PRO	0	0.017	-0.001	30.666	-0.002	-0.002	0.000	0.000	0.000	0.000
14	A	17	GLY	0	-0.022	-0.006	31.241	0.004	0.004	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.030	-0.014	29.502	0.002	0.002	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.056	-0.050	26.129	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.029	0.016	21.906	0.010	0.010	0.000	0.000	0.000	0.000
18	A	21	ARG	1	0.944	0.986	18.383	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	22	LEU	0	-0.014	0.013	15.606	0.020	0.020	0.000	0.000	0.000	0.000
20	A	23	SER	0	-0.049	-0.033	13.776	0.001	0.001	0.000	0.000	0.000	0.000
21	A	24	CYS	0	-0.007	-0.002	7.911	0.006	0.006	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.025	0.028	8.581	-0.039	-0.039	0.000	0.000	0.000	0.000
23	A	26	ALA	0	0.050	0.019	3.587	-0.215	-0.041	0.008	-0.047	-0.134	0.000
24	A	27	SER	0	-0.056	-0.024	4.297	0.020	0.221	-0.001	-0.049	-0.151	0.000
25	A	28	GLY	0	0.035	0.005	2.520	-0.598	1.055	1.597	-1.512	-1.737	-0.015
26	A	29	VAL	0	0.028	0.014	2.032	0.728	-3.705	10.101	-1.626	-4.042	0.006
27	A	30	ARG	1	0.831	0.914	4.018	-0.494	-0.249	0.000	-0.055	-0.191	0.000
28	A	31	LEU	0	0.074	0.024	5.704	-0.256	-0.256	0.000	0.000	0.000	0.000
29	A	32	SER	0	-0.059	-0.040	6.614	-0.136	-0.136	0.000	0.000	0.000	0.000
30	A	33	ALA	0	-0.031	-0.004	6.239	0.040	0.040	0.000	0.000	0.000	0.000
31	A	34	TYR	0	0.057	0.029	2.300	0.181	-2.236	8.206	-1.826	-3.963	-0.017
32	A	35	ASP	-1	-0.778	-0.875	7.417	-0.369	-0.369	0.000	0.000	0.000	0.000
33	A	36	MET	0	-0.059	-0.038	6.080	-0.220	-0.220	0.000	0.000	0.000	0.000
34	A	37	ALA	0	-0.002	-0.008	9.733	0.110	0.110	0.000	0.000	0.000	0.000
35	A	38	TRP	0	-0.001	0.006	11.442	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	39	VAL	0	0.017	0.008	13.848	0.018	0.018	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.801	0.898	15.783	0.170	0.170	0.000	0.000	0.000	0.000
38	A	41	GLN	0	-0.004	-0.010	18.441	-0.022	-0.022	0.000	0.000	0.000	0.000
39	A	42	ALA	0	0.012	0.010	20.831	0.016	0.016	0.000	0.000	0.000	0.000
40	A	43	PRO	0	0.020	-0.012	24.168	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	44	GLY	0	0.005	0.008	26.491	0.003	0.003	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.925	0.979	25.694	0.124	0.124	0.000	0.000	0.000	0.000
43	A	46	GLY	0	0.042	0.021	23.844	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.027	-0.015	17.033	0.008	0.008	0.000	0.000	0.000	0.000
45	A	48	GLU	-1	-0.825	-0.907	19.922	-0.164	-0.164	0.000	0.000	0.000	0.000
46	A	49	TRP	0	0.021	0.018	13.539	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	50	VAL	0	-0.016	-0.005	17.602	0.033	0.033	0.000	0.000	0.000	0.000
48	A	51	SER	0	-0.041	-0.052	17.027	0.027	0.027	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.042	0.018	14.224	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	53	ILE	0	-0.059	-0.016	12.684	0.062	0.062	0.000	0.000	0.000	0.000
51	A	54	SER	0	0.081	0.046	12.705	-0.058	-0.058	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.040	0.014	11.071	0.077	0.077	0.000	0.000	0.000	0.000
53	A	56	SER	0	-0.037	-0.026	12.286	0.050	0.050	0.000	0.000	0.000	0.000
54	A	57	GLY	0	0.013	-0.004	15.469	0.039	0.039	0.000	0.000	0.000	0.000
55	A	58	GLY	0	-0.041	-0.008	16.714	0.019	0.019	0.000	0.000	0.000	0.000
56	A	59	SER	0	-0.027	-0.013	18.134	0.010	0.010	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.008	-0.014	17.519	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	61	TYR	0	0.028	0.026	18.001	0.007	0.007	0.000	0.000	0.000	0.000
59	A	62	TYR	0	-0.011	0.003	19.370	0.000	0.000	0.000	0.000	0.000	0.000
60	A	63	ALA	0	0.049	0.051	21.785	0.005	0.005	0.000	0.000	0.000	0.000
61	A	64	ASP	-1	-0.876	-0.961	23.388	-0.137	-0.137	0.000	0.000	0.000	0.000
62	A	65	SER	0	-0.078	-0.031	25.209	0.011	0.011	0.000	0.000	0.000	0.000
63	A	66	VAL	0	-0.002	-0.003	22.070	0.012	0.012	0.000	0.000	0.000	0.000
64	A	67	LYS	1	1.014	1.016	25.516	0.130	0.130	0.000	0.000	0.000	0.000
65	A	68	GLY	0	-0.048	-0.019	26.418	0.009	0.009	0.000	0.000	0.000	0.000
66	A	69	ARG	1	0.740	0.855	26.818	0.099	0.099	0.000	0.000	0.000	0.000
67	A	70	PHE	0	0.020	-0.003	20.774	0.009	0.009	0.000	0.000	0.000	0.000
68	A	71	THR	0	-0.041	-0.019	21.211	0.000	0.000	0.000	0.000	0.000	0.000
69	A	72	ILE	0	-0.002	0.011	13.872	0.013	0.013	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.023	-0.015	16.458	0.016	0.016	0.000	0.000	0.000	0.000
71	A	74	ARG	1	0.828	0.911	9.070	0.390	0.390	0.000	0.000	0.000	0.000
72	A	75	ASP	-1	-0.777	-0.850	13.414	0.064	0.064	0.000	0.000	0.000	0.000
73	A	76	ASN	0	0.055	0.005	11.178	0.014	0.014	0.000	0.000	0.000	0.000
74	A	77	SER	0	-0.110	-0.064	11.385	0.062	0.062	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.949	0.972	12.940	-0.089	-0.089	0.000	0.000	0.000	0.000
76	A	79	ASN	0	0.007	0.030	7.456	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.004	-0.006	8.563	0.063	0.063	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.005	0.012	9.475	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	82	TYR	0	-0.036	-0.046	11.847	0.039	0.039	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.023	0.012	15.040	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	84	GLN	0	-0.037	-0.015	17.332	0.025	0.025	0.000	0.000	0.000	0.000
82	A	85	MET	0	-0.019	0.000	19.959	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	86	ASN	0	0.074	0.033	23.065	0.020	0.020	0.000	0.000	0.000	0.000
84	A	87	SER	0	0.002	-0.002	26.787	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.008	0.000	24.085	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	89	ARG	1	0.966	0.982	28.189	0.083	0.083	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.082	0.044	28.516	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.908	-0.961	28.802	-0.074	-0.074	0.000	0.000	0.000	0.000
89	A	92	ASP	-1	-0.786	-0.869	24.609	-0.105	-0.105	0.000	0.000	0.000	0.000
90	A	93	THR	0	-0.021	0.003	23.804	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	94	ALA	0	-0.016	-0.024	21.300	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	95	VAL	0	0.017	0.030	16.540	0.017	0.017	0.000	0.000	0.000	0.000
93	A	96	TYR	0	-0.061	-0.062	15.960	-0.032	-0.032	0.000	0.000	0.000	0.000
94	A	97	TYR	0	0.049	0.013	11.867	0.035	0.035	0.000	0.000	0.000	0.000
95	A	98	CYS	0	-0.067	-0.013	9.073	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	99	VAL	0	0.022	0.005	7.666	-0.052	-0.052	0.000	0.000	0.000	0.000
97	A	100	THR	0	0.073	0.029	3.461	-0.216	-0.016	0.006	-0.040	-0.167	0.000
98	A	101	LEU	0	-0.090	-0.047	6.840	0.080	0.080	0.000	0.000	0.000	0.000
99	A	102	PRO	0	-0.032	-0.026	9.117	-0.100	-0.100	0.000	0.000	0.000	0.000
100	A	103	ASP	-1	-0.859	-0.897	8.774	-1.019	-1.019	0.000	0.000	0.000	0.000
101	A	104	LEU	0	-0.052	-0.039	11.054	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	105	CYS	0	-0.023	-0.005	12.834	0.075	0.075	0.000	0.000	0.000	0.000
103	A	106	PRO	0	-0.031	0.004	15.707	0.017	0.017	0.000	0.000	0.000	0.000
104	A	107	GLY	0	0.029	0.003	18.810	0.035	0.035	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.944	-0.981	14.926	-0.493	-0.493	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.057	-0.036	16.938	0.047	0.047	0.000	0.000	0.000	0.000
107	A	111	THR	0	0.013	0.002	11.204	0.015	0.015	0.000	0.000	0.000	0.000
108	A	112	TYR	0	-0.028	-0.010	8.181	0.077	0.077	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.031	-0.004	3.239	-0.332	0.045	0.038	-0.110	-0.305	0.001
110	A	114	ASP	-1	-0.859	-0.930	3.406	-2.871	-2.402	0.019	-0.147	-0.340	-0.001
111	A	115	ALA	0	-0.016	-0.012	2.802	-3.900	-2.186	0.355	-0.990	-1.079	-0.012
112	A	116	SER	0	-0.023	-0.026	2.652	-0.711	0.146	0.253	-0.310	-0.799	-0.001
113	A	117	TRP	0	0.002	-0.011	4.777	0.419	0.529	-0.001	-0.007	-0.101	0.000
114	A	118	GLY	0	0.005	0.019	7.370	0.009	0.009	0.000	0.000	0.000	0.000
115	A	119	GLN	0	-0.024	-0.015	8.296	0.054	0.054	0.000	0.000	0.000	0.000
116	A	120	GLY	0	-0.005	-0.004	11.431	0.013	0.013	0.000	0.000	0.000	0.000
117	A	121	THR	0	-0.052	-0.027	13.596	0.062	0.062	0.000	0.000	0.000	0.000
118	A	122	MET	0	-0.019	0.001	16.263	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	123	VAL	0	0.021	0.014	19.600	0.018	0.018	0.000	0.000	0.000	0.000
120	A	124	THR	0	-0.013	-0.014	22.095	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	125	VAL	0	0.004	0.007	25.799	0.010	0.010	0.000	0.000	0.000	0.000
122	A	126	SER	0	0.003	-0.011	28.311	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	127	SER	0	-0.035	-0.027	31.729	0.005	0.005	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.036	0.032	35.026	-0.002	-0.002	0.000	0.000	0.000	0.000

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