FMO DATABASE

FMODB ID: YY5J2

Calculation Name: 3V67-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: 3V67

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: Q87KW6

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	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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1215160.3348
FMO2-HF: Nuclear repulsion	1161182.683581
FMO2-HF: Total energy	-53977.651219
FMO2-MP2: Total energy	-54137.137044

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:41:PRO)

Summations of interaction energy for fragment #1(A:41:PRO)

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.
-0.737	3.26	-0.033	-2.059	-1.905	0.008

Interaction energy analysis for fragmet #1(A:41:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.079 / q_NPA : 0.041

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	43	LYS	1	0.993	0.995	3.514	-1.539	2.458	-0.033	-2.059	-1.905	0.008
4	A	44	ALA	0	0.013	0.025	7.052	0.114	0.114	0.000	0.000	0.000	0.000
5	A	45	ARG	1	0.936	0.968	9.885	0.605	0.605	0.000	0.000	0.000	0.000
6	A	46	ASP	-1	-0.754	-0.874	12.823	-0.147	-0.147	0.000	0.000	0.000	0.000
7	A	47	ILE	0	-0.087	-0.042	16.592	-0.028	-0.028	0.000	0.000	0.000	0.000
8	A	48	PRO	0	0.001	0.006	17.991	0.008	0.008	0.000	0.000	0.000	0.000
9	A	49	ASP	-1	-0.794	-0.895	21.118	-0.103	-0.103	0.000	0.000	0.000	0.000
10	A	50	GLU	-1	-0.912	-0.956	23.850	-0.117	-0.117	0.000	0.000	0.000	0.000
11	A	51	HIS	0	-0.037	-0.026	19.889	0.017	0.017	0.000	0.000	0.000	0.000
12	A	52	TYR	0	0.018	-0.001	21.799	0.015	0.015	0.000	0.000	0.000	0.000
13	A	53	GLN	0	0.067	0.034	23.360	0.016	0.016	0.000	0.000	0.000	0.000
14	A	54	ARG	1	0.919	0.973	25.695	0.066	0.066	0.000	0.000	0.000	0.000
15	A	55	ILE	0	-0.034	-0.031	20.677	0.009	0.009	0.000	0.000	0.000	0.000
16	A	56	ILE	0	0.020	0.006	25.039	0.011	0.011	0.000	0.000	0.000	0.000
17	A	57	GLU	-1	-0.868	-0.930	27.405	-0.037	-0.037	0.000	0.000	0.000	0.000
18	A	58	THR	0	-0.104	-0.058	26.855	0.007	0.007	0.000	0.000	0.000	0.000
19	A	59	ARG	1	0.835	0.885	26.553	0.008	0.008	0.000	0.000	0.000	0.000
20	A	60	ASP	-1	-0.808	-0.884	28.522	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	61	ALA	0	-0.047	-0.014	31.941	0.003	0.003	0.000	0.000	0.000	0.000
22	A	62	ILE	0	-0.061	-0.037	28.056	0.003	0.003	0.000	0.000	0.000	0.000
23	A	63	GLN	0	0.057	0.019	31.051	0.007	0.007	0.000	0.000	0.000	0.000
24	A	64	ASN	0	0.038	0.016	33.297	0.004	0.004	0.000	0.000	0.000	0.000
25	A	65	LYS	1	0.860	0.956	35.004	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	66	TYR	0	-0.097	-0.074	33.052	0.000	0.000	0.000	0.000	0.000	0.000
27	A	67	SER	0	0.064	0.048	36.621	0.003	0.003	0.000	0.000	0.000	0.000
28	A	68	LYS	1	0.935	0.968	38.292	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	69	GLU	-1	-0.925	-0.961	37.058	0.027	0.027	0.000	0.000	0.000	0.000
30	A	70	THR	0	0.066	0.028	37.845	0.001	0.001	0.000	0.000	0.000	0.000
31	A	71	ASP	-1	-0.858	-0.916	36.166	0.046	0.046	0.000	0.000	0.000	0.000
32	A	72	LEU	0	0.078	0.019	29.032	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	73	GLY	0	0.046	0.023	31.813	0.000	0.000	0.000	0.000	0.000	0.000
34	A	74	ARG	1	0.884	0.940	32.840	-0.033	-0.033	0.000	0.000	0.000	0.000
35	A	75	ILE	0	-0.011	-0.002	31.184	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	76	LEU	0	-0.022	-0.003	27.054	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	77	PHE	0	0.014	0.011	29.683	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	78	ARG	1	0.950	0.963	31.897	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	79	VAL	0	-0.026	0.004	27.807	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	80	GLU	-1	-0.885	-0.897	25.072	0.046	0.046	0.000	0.000	0.000	0.000
41	A	81	GLY	0	0.055	0.019	28.620	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	82	ASN	0	-0.005	-0.005	31.220	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	83	ARG	1	0.742	0.882	23.567	0.010	0.010	0.000	0.000	0.000	0.000
44	A	84	ALA	0	0.054	0.030	29.105	0.005	0.005	0.000	0.000	0.000	0.000
45	A	85	GLY	0	0.021	0.006	28.166	0.002	0.002	0.000	0.000	0.000	0.000
46	A	86	LYS	1	0.929	0.956	23.030	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	87	HIS	0	0.008	-0.003	22.795	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	88	ASP	-1	-0.802	-0.849	24.645	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	89	PRO	0	0.046	0.029	23.736	0.000	0.000	0.000	0.000	0.000	0.000
50	A	90	ARG	1	0.875	0.908	23.785	0.013	0.013	0.000	0.000	0.000	0.000
51	A	91	PRO	0	0.055	0.035	22.193	0.004	0.004	0.000	0.000	0.000	0.000
52	A	92	ARG	1	0.829	0.918	20.669	-0.037	-0.037	0.000	0.000	0.000	0.000
53	A	93	VAL	0	0.026	0.019	21.239	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	94	PHE	0	-0.065	-0.032	18.550	0.008	0.008	0.000	0.000	0.000	0.000
55	A	95	PHE	0	0.082	0.020	21.399	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	96	SER	0	0.012	0.037	19.585	0.010	0.010	0.000	0.000	0.000	0.000
57	A	97	ASP	-1	-0.738	-0.837	21.699	0.124	0.124	0.000	0.000	0.000	0.000
58	A	98	TYR	0	0.018	-0.014	21.806	0.005	0.005	0.000	0.000	0.000	0.000
59	A	99	ASN	0	-0.026	-0.018	22.395	0.006	0.006	0.000	0.000	0.000	0.000
60	A	100	GLY	0	0.004	0.018	18.389	0.018	0.018	0.000	0.000	0.000	0.000
61	A	101	ASN	0	-0.075	-0.047	18.381	0.039	0.039	0.000	0.000	0.000	0.000
62	A	102	VAL	0	-0.013	-0.017	17.172	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	103	LEU	0	-0.034	-0.016	20.270	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.107	-0.127	21.926	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	105	THR	0	-0.024	-0.002	24.772	0.004	0.004	0.000	0.000	0.000	0.000
66	A	106	ASP	-1	-0.924	-0.950	23.868	0.089	0.089	0.000	0.000	0.000	0.000
67	A	107	LYS	1	0.926	0.968	23.288	-0.040	-0.040	0.000	0.000	0.000	0.000
68	A	108	ARG	1	0.910	0.911	23.303	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	109	SER	0	-0.062	-0.019	19.370	0.002	0.002	0.000	0.000	0.000	0.000
70	A	110	ASN	0	0.126	0.043	18.334	0.022	0.022	0.000	0.000	0.000	0.000
71	A	111	PHE	0	-0.050	-0.026	11.254	0.027	0.027	0.000	0.000	0.000	0.000
72	A	112	GLN	0	0.023	0.016	14.403	0.025	0.025	0.000	0.000	0.000	0.000
73	A	113	LEU	0	0.064	0.046	15.899	0.000	0.000	0.000	0.000	0.000	0.000
74	A	114	ARG	1	0.959	0.990	12.563	-0.148	-0.148	0.000	0.000	0.000	0.000
75	A	115	ALA	0	-0.029	-0.009	11.012	0.053	0.053	0.000	0.000	0.000	0.000
76	A	116	MET	0	-0.004	0.007	11.655	0.016	0.016	0.000	0.000	0.000	0.000
77	A	117	GLN	0	0.101	0.050	13.719	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	118	ASN	0	0.006	0.027	6.964	-0.107	-0.107	0.000	0.000	0.000	0.000
79	A	119	PHE	0	-0.021	0.028	10.085	0.056	0.056	0.000	0.000	0.000	0.000
80	A	120	VAL	0	0.056	0.018	11.133	0.005	0.005	0.000	0.000	0.000	0.000
81	A	121	THR	0	-0.058	-0.031	11.791	0.038	0.038	0.000	0.000	0.000	0.000
82	A	122	SER	0	-0.082	-0.082	8.214	0.147	0.147	0.000	0.000	0.000	0.000
83	A	123	ILE	0	-0.089	-0.032	10.070	-0.050	-0.050	0.000	0.000	0.000	0.000
84	A	124	GLU	-1	-0.959	-0.969	9.657	0.136	0.136	0.000	0.000	0.000	0.000
85	A	125	ASP	-1	-0.825	-0.932	13.902	0.047	0.047	0.000	0.000	0.000	0.000
86	A	126	TYR	0	-0.001	-0.008	16.837	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	127	ASN	0	-0.058	-0.022	19.389	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	128	LYS	1	0.931	0.963	17.515	0.005	0.005	0.000	0.000	0.000	0.000
89	A	129	PRO	0	0.000	0.026	17.307	0.000	0.000	0.000	0.000	0.000	0.000
90	A	130	LYS	1	0.844	0.928	13.292	0.132	0.132	0.000	0.000	0.000	0.000
91	A	131	GLN	0	0.030	-0.005	13.348	0.061	0.061	0.000	0.000	0.000	0.000
92	A	132	ARG	1	0.918	0.963	6.575	-0.142	-0.142	0.000	0.000	0.000	0.000
93	A	133	LEU	0	0.010	0.008	8.525	0.074	0.074	0.000	0.000	0.000	0.000
94	A	134	TYR	0	-0.072	-0.076	7.522	-0.200	-0.200	0.000	0.000	0.000	0.000
95	A	135	GLY	0	0.026	0.012	8.071	0.071	0.071	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.979	0.985	9.849	0.188	0.188	0.000	0.000	0.000	0.000
97	A	137	TYR	0	-0.022	0.000	12.226	0.020	0.020	0.000	0.000	0.000	0.000
98	A	138	MET	0	0.008	0.020	12.247	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	139	ILE	0	-0.021	-0.005	12.559	0.040	0.040	0.000	0.000	0.000	0.000
100	A	140	ALA	0	0.011	0.006	13.579	-0.030	-0.030	0.000	0.000	0.000	0.000
101	A	141	GLY	0	0.022	0.036	16.224	0.023	0.023	0.000	0.000	0.000	0.000
102	A	142	PRO	0	0.039	0.014	16.240	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	143	VAL	0	0.004	-0.017	19.143	-0.011	-0.011	0.000	0.000	0.000	0.000
104	A	144	PRO	0	0.052	0.033	22.771	0.007	0.007	0.000	0.000	0.000	0.000
105	A	145	ILE	0	-0.045	-0.020	25.578	-0.010	-0.010	0.000	0.000	0.000	0.000
106	A	146	VAL	0	0.060	0.037	28.040	0.007	0.007	0.000	0.000	0.000	0.000
107	A	147	LEU	0	-0.056	-0.038	28.719	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	148	ALA	0	0.000	-0.004	32.276	0.004	0.004	0.000	0.000	0.000	0.000
109	A	149	ASP	-1	-0.903	-0.945	35.253	0.032	0.032	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.052	-0.013	31.026	0.005	0.005	0.000	0.000	0.000	0.000
111	A	151	GLU	-1	-0.926	-0.963	28.799	0.044	0.044	0.000	0.000	0.000	0.000
112	A	152	LEU	0	-0.066	-0.038	25.634	0.010	0.010	0.000	0.000	0.000	0.000
113	A	153	LEU	0	-0.025	-0.004	20.470	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	154	MET	0	-0.034	-0.006	22.665	0.007	0.007	0.000	0.000	0.000	0.000
115	A	155	TYR	0	-0.003	-0.040	16.602	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	156	VAL	0	0.010	0.003	18.735	0.002	0.002	0.000	0.000	0.000	0.000
117	A	157	GLY	0	0.012	0.009	17.062	-0.014	-0.014	0.000	0.000	0.000	0.000
118	A	158	PHE	0	-0.006	-0.025	17.132	0.007	0.007	0.000	0.000	0.000	0.000
119	A	159	LYS	1	0.921	0.964	16.508	0.097	0.097	0.000	0.000	0.000	0.000
120	A	160	TRP	0	0.022	-0.002	12.582	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	161	ASN	0	-0.064	-0.065	15.653	-0.021	-0.021	0.000	0.000	0.000	0.000
122	A	162	GLU	-1	-0.948	-0.966	13.012	-0.404	-0.404	0.000	0.000	0.000	0.000
123	A	163	PRO	0	0.036	0.024	16.179	0.021	0.021	0.000	0.000	0.000	0.000
124	A	164	PRO	0	0.013	0.017	18.872	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	165	PRO	0	0.003	0.008	19.504	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	166	LEU	0	0.018	0.009	20.292	0.020	0.020	0.000	0.000	0.000	0.000
127	A	167	LEU	0	-0.004	0.004	21.748	-0.017	-0.017	0.000	0.000	0.000	0.000
128	A	168	LEU	0	-0.015	-0.012	22.408	0.015	0.015	0.000	0.000	0.000	0.000
129	A	169	ARG	1	0.900	0.935	23.564	0.125	0.125	0.000	0.000	0.000	0.000
130	A	170	LEU	0	0.056	0.028	24.087	0.001	0.001	0.000	0.000	0.000	0.000
131	A	171	PHE	0	-0.037	-0.016	26.351	0.005	0.005	0.000	0.000	0.000	0.000
132	A	172	ASP	-1	-0.903	-0.937	29.014	-0.125	-0.125	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:41:PRO)