FMO DATABASE

FMODB ID: 1418Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1214925.59187
FMO2-HF: Nuclear repulsion	1160946.348377
FMO2-HF: Total energy	-53979.243494
FMO2-MP2: Total energy	-54138.682853

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.
0.313	2.413	-0.006	-1.012	-1.082	0.004

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 : 0.073 / q_NPA : 0.019

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	0.930	0.953	3.200	-0.419	1.681	-0.006	-1.012	-1.082	0.004
4	A	44	ALA	0	0.039	0.033	6.965	0.044	0.044	0.000	0.000	0.000	0.000
5	A	45	ARG	1	0.941	0.972	10.207	-0.020	-0.020	0.000	0.000	0.000	0.000
6	A	46	ASP	-1	-0.739	-0.861	12.591	0.181	0.181	0.000	0.000	0.000	0.000
7	A	47	ILE	0	-0.036	-0.005	16.351	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	48	PRO	0	-0.001	0.005	18.387	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	49	ASP	-1	-0.828	-0.913	21.460	0.067	0.067	0.000	0.000	0.000	0.000
10	A	50	GLU	-1	-0.860	-0.938	23.893	0.037	0.037	0.000	0.000	0.000	0.000
11	A	51	HIS	0	-0.065	-0.040	21.492	0.011	0.011	0.000	0.000	0.000	0.000
12	A	52	TYR	0	-0.009	-0.006	22.432	0.018	0.018	0.000	0.000	0.000	0.000
13	A	53	GLN	0	0.021	0.002	23.859	0.010	0.010	0.000	0.000	0.000	0.000
14	A	54	ARG	1	0.868	0.924	26.151	-0.054	-0.054	0.000	0.000	0.000	0.000
15	A	55	ILE	0	-0.019	-0.012	21.142	0.004	0.004	0.000	0.000	0.000	0.000
16	A	56	ILE	0	0.018	0.015	25.503	0.006	0.006	0.000	0.000	0.000	0.000
17	A	57	GLU	-1	-0.776	-0.859	28.163	0.060	0.060	0.000	0.000	0.000	0.000
18	A	58	THR	0	-0.076	-0.060	27.378	0.002	0.002	0.000	0.000	0.000	0.000
19	A	59	ARG	1	0.812	0.880	27.363	-0.120	-0.120	0.000	0.000	0.000	0.000
20	A	60	ASP	-1	-0.753	-0.861	29.226	0.095	0.095	0.000	0.000	0.000	0.000
21	A	61	ALA	0	-0.022	0.003	32.686	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	62	ILE	0	-0.051	-0.031	28.761	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	63	GLN	0	0.050	0.023	32.015	0.004	0.004	0.000	0.000	0.000	0.000
24	A	64	ASN	0	0.002	-0.014	34.431	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	65	LYS	1	0.874	0.964	35.606	-0.075	-0.075	0.000	0.000	0.000	0.000
26	A	66	TYR	0	-0.032	-0.054	33.225	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	67	SER	0	0.029	0.013	37.356	0.001	0.001	0.000	0.000	0.000	0.000
28	A	68	LYS	1	0.854	0.933	39.230	-0.066	-0.066	0.000	0.000	0.000	0.000
29	A	69	GLU	-1	-0.799	-0.848	37.815	0.072	0.072	0.000	0.000	0.000	0.000
30	A	70	THR	0	0.079	0.031	38.491	0.003	0.003	0.000	0.000	0.000	0.000
31	A	71	ASP	-1	-0.818	-0.903	36.776	0.094	0.094	0.000	0.000	0.000	0.000
32	A	72	LEU	0	0.082	0.034	29.653	0.000	0.000	0.000	0.000	0.000	0.000
33	A	73	GLY	0	0.049	0.028	32.516	0.005	0.005	0.000	0.000	0.000	0.000
34	A	74	ARG	1	0.804	0.870	33.406	-0.078	-0.078	0.000	0.000	0.000	0.000
35	A	75	ILE	0	-0.004	-0.002	31.876	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	76	LEU	0	0.006	0.009	27.424	0.000	0.000	0.000	0.000	0.000	0.000
37	A	77	PHE	0	-0.013	-0.002	30.411	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	78	ARG	1	0.847	0.894	32.622	-0.078	-0.078	0.000	0.000	0.000	0.000
39	A	79	VAL	0	0.000	0.029	28.142	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	80	GLU	-1	-0.697	-0.808	25.503	0.156	0.156	0.000	0.000	0.000	0.000
41	A	81	GLY	0	0.037	0.016	28.909	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	82	ASN	0	-0.065	-0.027	30.940	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	83	ARG	1	0.777	0.905	23.815	-0.098	-0.098	0.000	0.000	0.000	0.000
44	A	84	ALA	0	0.089	0.038	29.361	0.001	0.001	0.000	0.000	0.000	0.000
45	A	85	GLY	0	-0.006	-0.021	28.557	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	86	LYS	1	0.927	0.970	23.561	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	87	HIS	0	0.038	-0.005	23.751	0.015	0.015	0.000	0.000	0.000	0.000
48	A	88	ASP	-1	-0.777	-0.841	25.137	0.056	0.056	0.000	0.000	0.000	0.000
49	A	89	PRO	0	0.036	0.020	24.415	0.009	0.009	0.000	0.000	0.000	0.000
50	A	90	ARG	1	0.823	0.893	24.397	-0.061	-0.061	0.000	0.000	0.000	0.000
51	A	91	PRO	0	0.045	0.013	22.376	0.006	0.006	0.000	0.000	0.000	0.000
52	A	92	ARG	1	0.777	0.890	21.247	-0.184	-0.184	0.000	0.000	0.000	0.000
53	A	93	VAL	0	0.026	0.021	21.557	0.017	0.017	0.000	0.000	0.000	0.000
54	A	94	PHE	0	-0.027	-0.020	19.170	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	95	PHE	0	0.058	0.012	22.358	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	96	SER	0	0.003	0.005	20.566	0.028	0.028	0.000	0.000	0.000	0.000
57	A	97	ASP	-1	-0.702	-0.817	22.723	0.246	0.246	0.000	0.000	0.000	0.000
58	A	98	TYR	0	0.016	0.003	22.821	0.027	0.027	0.000	0.000	0.000	0.000
59	A	99	ASN	0	-0.059	-0.039	23.166	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	100	GLY	0	0.035	0.029	19.199	0.022	0.022	0.000	0.000	0.000	0.000
61	A	101	ASN	0	-0.092	-0.054	19.066	0.049	0.049	0.000	0.000	0.000	0.000
62	A	102	VAL	0	0.007	-0.010	17.962	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	103	LEU	0	-0.041	-0.009	21.061	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.089	-0.080	22.360	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	105	THR	0	-0.005	0.002	25.247	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	106	ASP	-1	-0.899	-0.956	23.478	0.164	0.164	0.000	0.000	0.000	0.000
67	A	107	LYS	1	0.814	0.885	24.392	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	108	ARG	1	0.908	0.951	23.676	-0.071	-0.071	0.000	0.000	0.000	0.000
69	A	109	SER	0	-0.063	-0.036	19.998	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	110	ASN	0	0.106	0.057	19.259	0.027	0.027	0.000	0.000	0.000	0.000
71	A	111	PHE	0	-0.012	0.000	12.101	0.031	0.031	0.000	0.000	0.000	0.000
72	A	112	GLN	0	0.019	0.004	15.069	0.048	0.048	0.000	0.000	0.000	0.000
73	A	113	LEU	0	0.046	0.040	16.242	0.039	0.039	0.000	0.000	0.000	0.000
74	A	114	ARG	1	0.922	0.952	13.350	-0.195	-0.195	0.000	0.000	0.000	0.000
75	A	115	ALA	0	-0.016	-0.001	11.467	0.106	0.106	0.000	0.000	0.000	0.000
76	A	116	MET	0	-0.015	0.006	12.297	0.116	0.116	0.000	0.000	0.000	0.000
77	A	117	GLN	0	0.036	0.008	14.925	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	118	ASN	0	0.027	0.015	8.188	0.250	0.250	0.000	0.000	0.000	0.000
79	A	119	PHE	0	-0.028	0.002	11.230	0.198	0.198	0.000	0.000	0.000	0.000
80	A	120	VAL	0	0.063	0.027	12.277	0.037	0.037	0.000	0.000	0.000	0.000
81	A	121	THR	0	-0.053	-0.029	11.994	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	122	SER	0	-0.088	-0.061	9.220	0.331	0.331	0.000	0.000	0.000	0.000
83	A	123	ILE	0	-0.076	-0.019	10.878	0.020	0.020	0.000	0.000	0.000	0.000
84	A	124	GLU	-1	-0.752	-0.843	9.786	0.801	0.801	0.000	0.000	0.000	0.000
85	A	125	ASP	-1	-0.779	-0.884	13.753	0.194	0.194	0.000	0.000	0.000	0.000
86	A	126	TYR	0	0.001	-0.011	16.894	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	127	ASN	0	-0.020	0.007	19.525	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	128	LYS	1	0.793	0.870	17.417	-0.227	-0.227	0.000	0.000	0.000	0.000
89	A	129	PRO	0	0.016	0.023	17.522	0.039	0.039	0.000	0.000	0.000	0.000
90	A	130	LYS	1	0.799	0.898	13.582	-0.226	-0.226	0.000	0.000	0.000	0.000
91	A	131	GLN	0	-0.029	-0.045	13.696	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	132	ARG	1	0.780	0.867	7.749	-1.163	-1.163	0.000	0.000	0.000	0.000
93	A	133	LEU	0	0.010	0.005	9.040	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	134	TYR	0	-0.049	-0.046	7.738	0.011	0.011	0.000	0.000	0.000	0.000
95	A	135	GLY	0	0.027	0.012	8.730	-0.029	-0.029	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.861	0.909	10.471	0.114	0.114	0.000	0.000	0.000	0.000
97	A	137	TYR	0	-0.033	-0.012	12.868	0.005	0.005	0.000	0.000	0.000	0.000
98	A	138	MET	0	0.011	0.022	12.494	0.053	0.053	0.000	0.000	0.000	0.000
99	A	139	ILE	0	-0.017	-0.009	12.860	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	140	ALA	0	0.029	0.009	14.138	0.031	0.031	0.000	0.000	0.000	0.000
101	A	141	GLY	0	0.025	0.033	16.845	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	142	PRO	0	0.039	0.019	17.049	0.032	0.032	0.000	0.000	0.000	0.000
103	A	143	VAL	0	-0.003	-0.015	19.999	-0.018	-0.018	0.000	0.000	0.000	0.000
104	A	144	PRO	0	0.045	0.033	23.588	0.007	0.007	0.000	0.000	0.000	0.000
105	A	145	ILE	0	-0.060	-0.032	26.470	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	146	VAL	0	0.053	0.039	29.149	0.007	0.007	0.000	0.000	0.000	0.000
107	A	147	LEU	0	-0.045	-0.029	29.540	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	148	ALA	0	-0.004	-0.007	33.381	0.004	0.004	0.000	0.000	0.000	0.000
109	A	149	ASP	-1	-0.920	-0.951	36.445	0.089	0.089	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.041	-0.009	32.223	0.003	0.003	0.000	0.000	0.000	0.000
111	A	151	GLU	-1	-0.937	-0.967	30.271	0.134	0.134	0.000	0.000	0.000	0.000
112	A	152	LEU	0	-0.072	-0.042	26.838	0.011	0.011	0.000	0.000	0.000	0.000
113	A	153	LEU	0	-0.002	0.010	21.205	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	154	MET	0	-0.053	-0.017	23.595	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	155	TYR	0	0.013	-0.016	17.673	0.026	0.026	0.000	0.000	0.000	0.000
116	A	156	VAL	0	0.006	-0.006	19.448	-0.025	-0.025	0.000	0.000	0.000	0.000
117	A	157	GLY	0	0.027	0.025	17.426	0.022	0.022	0.000	0.000	0.000	0.000
118	A	158	PHE	0	-0.013	-0.021	17.431	-0.028	-0.028	0.000	0.000	0.000	0.000
119	A	159	LYS	1	0.903	0.944	17.180	0.005	0.005	0.000	0.000	0.000	0.000
120	A	160	TRP	0	0.030	0.009	13.455	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	161	ASN	0	-0.018	-0.018	16.740	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	162	GLU	-1	-0.834	-0.907	12.962	-0.248	-0.248	0.000	0.000	0.000	0.000
123	A	163	PRO	0	0.017	0.013	16.718	0.002	0.002	0.000	0.000	0.000	0.000
124	A	164	PRO	0	0.006	0.020	19.143	-0.016	-0.016	0.000	0.000	0.000	0.000
125	A	165	PRO	0	-0.001	0.001	19.493	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	166	LEU	0	0.002	0.001	20.469	0.013	0.013	0.000	0.000	0.000	0.000
127	A	167	LEU	0	0.016	0.004	22.060	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	168	LEU	0	-0.020	-0.009	22.556	0.010	0.010	0.000	0.000	0.000	0.000
129	A	169	ARG	1	0.865	0.916	23.861	0.088	0.088	0.000	0.000	0.000	0.000
130	A	170	LEU	0	0.038	0.023	24.122	0.005	0.005	0.000	0.000	0.000	0.000
131	A	171	PHE	0	0.020	0.014	26.219	0.004	0.004	0.000	0.000	0.000	0.000
132	A	172	ASP	-1	-0.912	-0.941	28.998	-0.079	-0.079	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)