FMO DATABASE

FMODB ID: VR3J1

Calculation Name: 3V67-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: 3V67

Chain ID: A

ChEMBL ID:
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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	OptHSide
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	-1215040.489187
FMO2-HF: Nuclear repulsion	1161061.777087
FMO2-HF: Total energy	-53978.7121
FMO2-MP2: Total energy	-54138.171624

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.
0.284	3.053	-0.036	-1.403	-1.329	0.002

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 : 0.060 / q_NPA : 0.008

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	0.997	0.995	3.795	-0.341	2.428	-0.036	-1.403	-1.329	0.002
4	A	44	ALA	0	0.012	0.031	7.052	0.063	0.063	0.000	0.000	0.000	0.000
5	A	45	ARG	1	0.945	0.974	10.198	0.245	0.245	0.000	0.000	0.000	0.000
6	A	46	ASP	-1	-0.748	-0.867	12.823	0.060	0.060	0.000	0.000	0.000	0.000
7	A	47	ILE	0	-0.043	-0.018	16.592	-0.025	-0.025	0.000	0.000	0.000	0.000
8	A	48	PRO	0	0.000	0.005	18.254	0.000	0.000	0.000	0.000	0.000	0.000
9	A	49	ASP	-1	-0.818	-0.906	21.326	0.007	0.007	0.000	0.000	0.000	0.000
10	A	50	GLU	-1	-0.898	-0.953	24.059	-0.021	-0.021	0.000	0.000	0.000	0.000
11	A	51	HIS	0	-0.022	-0.018	19.930	0.016	0.016	0.000	0.000	0.000	0.000
12	A	52	TYR	0	0.002	-0.008	22.108	0.021	0.021	0.000	0.000	0.000	0.000
13	A	53	GLN	0	0.024	0.007	23.507	0.013	0.013	0.000	0.000	0.000	0.000
14	A	54	ARG	1	0.856	0.920	25.820	-0.019	-0.019	0.000	0.000	0.000	0.000
15	A	55	ILE	0	-0.029	-0.029	20.870	0.007	0.007	0.000	0.000	0.000	0.000
16	A	56	ILE	0	0.036	0.017	25.231	0.010	0.010	0.000	0.000	0.000	0.000
17	A	57	GLU	-1	-0.768	-0.852	27.682	0.033	0.033	0.000	0.000	0.000	0.000
18	A	58	THR	0	-0.106	-0.063	27.202	0.003	0.003	0.000	0.000	0.000	0.000
19	A	59	ARG	1	0.819	0.888	26.921	-0.092	-0.092	0.000	0.000	0.000	0.000
20	A	60	ASP	-1	-0.772	-0.872	28.851	0.076	0.076	0.000	0.000	0.000	0.000
21	A	61	ALA	0	-0.027	0.004	32.204	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	62	ILE	0	-0.051	-0.037	28.435	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	63	GLN	0	0.050	0.022	31.336	0.007	0.007	0.000	0.000	0.000	0.000
24	A	64	ASN	0	-0.013	-0.016	33.707	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	65	LYS	1	0.859	0.951	35.374	-0.065	-0.065	0.000	0.000	0.000	0.000
26	A	66	TYR	0	-0.052	-0.049	33.074	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	67	SER	0	0.062	0.041	37.018	0.003	0.003	0.000	0.000	0.000	0.000
28	A	68	LYS	1	0.940	0.971	38.747	-0.055	-0.055	0.000	0.000	0.000	0.000
29	A	69	GLU	-1	-0.840	-0.887	37.446	0.072	0.072	0.000	0.000	0.000	0.000
30	A	70	THR	0	0.130	0.055	38.359	0.002	0.002	0.000	0.000	0.000	0.000
31	A	71	ASP	-1	-0.877	-0.917	36.559	0.099	0.099	0.000	0.000	0.000	0.000
32	A	72	LEU	0	0.088	0.029	29.543	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	73	GLY	0	0.058	0.027	32.303	0.004	0.004	0.000	0.000	0.000	0.000
34	A	74	ARG	1	0.814	0.888	33.271	-0.080	-0.080	0.000	0.000	0.000	0.000
35	A	75	ILE	0	0.002	0.004	31.629	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	76	LEU	0	-0.003	0.006	27.291	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	77	PHE	0	0.000	0.001	30.016	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	78	ARG	1	0.839	0.892	32.233	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	79	VAL	0	-0.045	-0.011	28.130	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	80	GLU	-1	-0.765	-0.842	25.095	0.155	0.155	0.000	0.000	0.000	0.000
41	A	81	GLY	0	0.065	0.026	28.843	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	82	ASN	0	-0.015	-0.003	31.163	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	83	ARG	1	0.799	0.912	23.693	-0.087	-0.087	0.000	0.000	0.000	0.000
44	A	84	ALA	0	0.043	0.018	29.333	0.002	0.002	0.000	0.000	0.000	0.000
45	A	85	GLY	0	0.009	-0.007	28.676	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	86	LYS	1	0.938	0.968	23.652	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	87	HIS	0	0.016	-0.005	23.575	0.011	0.011	0.000	0.000	0.000	0.000
48	A	88	ASP	-1	-0.770	-0.847	25.291	0.044	0.044	0.000	0.000	0.000	0.000
49	A	89	PRO	0	0.041	0.024	24.139	0.009	0.009	0.000	0.000	0.000	0.000
50	A	90	ARG	1	0.822	0.898	24.052	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	91	PRO	0	0.046	0.015	22.242	0.009	0.009	0.000	0.000	0.000	0.000
52	A	92	ARG	1	0.797	0.912	20.918	-0.181	-0.181	0.000	0.000	0.000	0.000
53	A	93	VAL	0	0.015	0.011	21.387	0.011	0.011	0.000	0.000	0.000	0.000
54	A	94	PHE	0	-0.050	-0.029	18.558	0.004	0.004	0.000	0.000	0.000	0.000
55	A	95	PHE	0	0.074	0.016	21.749	-0.012	-0.012	0.000	0.000	0.000	0.000
56	A	96	SER	0	0.016	0.028	20.175	0.027	0.027	0.000	0.000	0.000	0.000
57	A	97	ASP	-1	-0.727	-0.837	22.315	0.249	0.249	0.000	0.000	0.000	0.000
58	A	98	TYR	0	0.016	-0.006	22.536	0.026	0.026	0.000	0.000	0.000	0.000
59	A	99	ASN	0	-0.058	-0.041	23.253	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	100	GLY	0	0.013	0.026	19.181	0.019	0.019	0.000	0.000	0.000	0.000
61	A	101	ASN	0	-0.070	-0.041	19.143	0.052	0.052	0.000	0.000	0.000	0.000
62	A	102	VAL	0	0.001	-0.015	17.676	-0.022	-0.022	0.000	0.000	0.000	0.000
63	A	103	LEU	0	-0.037	-0.016	20.861	-0.016	-0.016	0.000	0.000	0.000	0.000
64	A	104	THR	0	-0.087	-0.090	22.141	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	105	THR	0	-0.003	0.008	25.194	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	106	ASP	-1	-0.908	-0.953	23.862	0.181	0.181	0.000	0.000	0.000	0.000
67	A	107	LYS	1	0.779	0.891	23.615	-0.146	-0.146	0.000	0.000	0.000	0.000
68	A	108	ARG	1	0.906	0.923	23.733	-0.076	-0.076	0.000	0.000	0.000	0.000
69	A	109	SER	0	-0.044	-0.011	20.056	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	110	ASN	0	0.129	0.063	19.177	0.039	0.039	0.000	0.000	0.000	0.000
71	A	111	PHE	0	-0.021	-0.004	12.063	0.037	0.037	0.000	0.000	0.000	0.000
72	A	112	GLN	0	0.018	0.003	14.843	0.054	0.054	0.000	0.000	0.000	0.000
73	A	113	LEU	0	0.053	0.041	16.090	0.031	0.031	0.000	0.000	0.000	0.000
74	A	114	ARG	1	0.932	0.955	12.992	-0.256	-0.256	0.000	0.000	0.000	0.000
75	A	115	ALA	0	-0.034	-0.012	11.239	0.112	0.112	0.000	0.000	0.000	0.000
76	A	116	MET	0	-0.017	0.007	12.012	0.097	0.097	0.000	0.000	0.000	0.000
77	A	117	GLN	0	0.073	0.036	14.452	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	118	ASN	0	0.020	0.017	7.848	0.210	0.210	0.000	0.000	0.000	0.000
79	A	119	PHE	0	-0.015	0.005	10.780	0.193	0.193	0.000	0.000	0.000	0.000
80	A	120	VAL	0	0.068	0.021	11.692	0.017	0.017	0.000	0.000	0.000	0.000
81	A	121	THR	0	-0.057	-0.032	11.836	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	122	SER	0	-0.098	-0.065	8.892	0.326	0.326	0.000	0.000	0.000	0.000
83	A	123	ILE	0	-0.084	-0.018	10.837	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	124	GLU	-1	-0.820	-0.889	11.036	0.605	0.605	0.000	0.000	0.000	0.000
85	A	125	ASP	-1	-0.795	-0.909	13.802	0.163	0.163	0.000	0.000	0.000	0.000
86	A	126	TYR	0	0.005	-0.003	16.926	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	127	ASN	0	-0.043	-0.016	19.712	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	128	LYS	1	0.857	0.920	17.633	-0.183	-0.183	0.000	0.000	0.000	0.000
89	A	129	PRO	0	0.000	0.024	17.538	0.032	0.032	0.000	0.000	0.000	0.000
90	A	130	LYS	1	0.828	0.911	13.542	-0.101	-0.101	0.000	0.000	0.000	0.000
91	A	131	GLN	0	-0.016	-0.029	13.513	0.036	0.036	0.000	0.000	0.000	0.000
92	A	132	ARG	1	0.807	0.896	7.623	-1.072	-1.072	0.000	0.000	0.000	0.000
93	A	133	LEU	0	0.013	0.008	8.720	0.021	0.021	0.000	0.000	0.000	0.000
94	A	134	TYR	0	-0.045	-0.052	7.605	-0.167	-0.167	0.000	0.000	0.000	0.000
95	A	135	GLY	0	0.021	0.008	8.716	0.009	0.009	0.000	0.000	0.000	0.000
96	A	136	ARG	1	0.877	0.917	10.648	0.138	0.138	0.000	0.000	0.000	0.000
97	A	137	TYR	0	-0.016	-0.004	12.718	0.002	0.002	0.000	0.000	0.000	0.000
98	A	138	MET	0	0.005	0.024	12.394	0.043	0.043	0.000	0.000	0.000	0.000
99	A	139	ILE	0	-0.031	-0.013	12.667	0.005	0.005	0.000	0.000	0.000	0.000
100	A	140	ALA	0	0.025	0.010	13.762	0.017	0.017	0.000	0.000	0.000	0.000
101	A	141	GLY	0	0.025	0.040	16.444	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	142	PRO	0	0.035	0.018	16.698	0.020	0.020	0.000	0.000	0.000	0.000
103	A	143	VAL	0	0.001	-0.024	19.654	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	144	PRO	0	0.043	0.032	23.251	0.007	0.007	0.000	0.000	0.000	0.000
105	A	145	ILE	0	-0.050	-0.032	26.137	-0.014	-0.014	0.000	0.000	0.000	0.000
106	A	146	VAL	0	0.050	0.032	28.567	0.008	0.008	0.000	0.000	0.000	0.000
107	A	147	LEU	0	-0.055	-0.033	29.127	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	148	ALA	0	-0.008	-0.013	32.812	0.006	0.006	0.000	0.000	0.000	0.000
109	A	149	ASP	-1	-0.906	-0.942	35.822	0.086	0.086	0.000	0.000	0.000	0.000
110	A	150	SER	0	-0.042	-0.009	31.665	0.004	0.004	0.000	0.000	0.000	0.000
111	A	151	GLU	-1	-0.939	-0.968	29.626	0.127	0.127	0.000	0.000	0.000	0.000
112	A	152	LEU	0	-0.059	-0.035	26.302	0.015	0.015	0.000	0.000	0.000	0.000
113	A	153	LEU	0	-0.009	0.005	20.942	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	154	MET	0	-0.039	-0.010	23.183	0.006	0.006	0.000	0.000	0.000	0.000
115	A	155	TYR	0	0.006	-0.024	17.001	0.019	0.019	0.000	0.000	0.000	0.000
116	A	156	VAL	0	0.004	-0.001	18.994	-0.018	-0.018	0.000	0.000	0.000	0.000
117	A	157	GLY	0	0.014	0.016	17.114	0.012	0.012	0.000	0.000	0.000	0.000
118	A	158	PHE	0	-0.010	-0.024	17.119	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	159	LYS	1	0.893	0.937	16.838	0.030	0.030	0.000	0.000	0.000	0.000
120	A	160	TRP	0	0.012	-0.006	13.770	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	161	ASN	0	-0.029	-0.035	16.415	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	162	GLU	-1	-0.847	-0.902	13.506	-0.326	-0.326	0.000	0.000	0.000	0.000
123	A	163	PRO	0	0.038	0.023	17.136	0.011	0.011	0.000	0.000	0.000	0.000
124	A	164	PRO	0	0.014	0.020	19.688	-0.017	-0.017	0.000	0.000	0.000	0.000
125	A	165	PRO	0	-0.002	0.001	19.990	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	166	LEU	0	0.017	0.010	20.372	0.018	0.018	0.000	0.000	0.000	0.000
127	A	167	LEU	0	-0.004	0.007	22.182	-0.019	-0.019	0.000	0.000	0.000	0.000
128	A	168	LEU	0	-0.021	-0.017	22.744	0.014	0.014	0.000	0.000	0.000	0.000
129	A	169	ARG	1	0.891	0.930	23.695	0.119	0.119	0.000	0.000	0.000	0.000
130	A	170	LEU	0	0.056	0.029	24.138	0.003	0.003	0.000	0.000	0.000	0.000
131	A	171	PHE	0	-0.003	0.003	26.340	0.005	0.005	0.000	0.000	0.000	0.000
132	A	172	ASP	-1	-0.918	-0.946	28.976	-0.115	-0.115	0.000	0.000	0.000	0.000

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