FMO DATABASE

FMODB ID: 59LYZ

Calculation Name: 3VX7-B-Xray313

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX7

Chain ID: B

ChEMBL ID:

UniProt ID: W0TH64

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	152
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1544968.380962
FMO2-HF: Nuclear repulsion	1483209.214212
FMO2-HF: Total energy	-61759.166749
FMO2-MP2: Total energy	-61940.952875

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(B:-4:ACE )

Summations of interaction energy for fragment #1(B:-4:ACE )

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.
0.652	1.408	0	-0.254	-0.502	0

Interaction energy analysis for fragmet #1(B:-4:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : -0.007

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].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].
3	B	-2	LEU	0	0.012	-0.005	3.869	0.944	1.700	-0.254	-0.502
4	B	-1	GLY	0	0.044	0.014	5.725	0.183	0.183	0.000	0.000
5	B	0	SER	0	-0.064	-0.040	8.574	0.086	0.086	0.000	0.000
6	B	1	MET	0	-0.048	-0.031	6.092	0.063	0.063	0.000	0.000
7	B	2	LEU	0	0.018	0.029	11.096	0.058	0.058	0.000	0.000
8	B	3	THR	0	0.005	0.067	14.809	-0.013	-0.013	0.000	0.000
9	B	4	LEU	0	0.033	0.020	16.819	0.002	0.002	0.000	0.000
10	B	5	PRO	0	-0.039	-0.033	19.623	0.003	0.003	0.000	0.000
11	B	6	GLU	-1	-0.725	-0.873	15.627	-0.026	-0.026	0.000	0.000
12	B	7	TYR	0	-0.050	-0.044	19.914	-0.006	-0.006	0.000	0.000
13	B	8	ASN	0	-0.033	-0.045	21.148	-0.002	-0.002	0.000	0.000
14	B	9	GLU	-1	-0.994	-0.982	22.227	0.008	0.008	0.000	0.000
15	B	10	GLN	0	0.006	-0.001	18.922	-0.005	-0.005	0.000	0.000
16	B	11	ILE	0	0.014	0.021	24.379	-0.002	-0.002	0.000	0.000
17	B	12	PRO	0	0.028	0.013	26.865	-0.001	-0.001	0.000	0.000
18	B	13	ASN	0	0.024	0.009	26.829	0.003	0.003	0.000	0.000
19	B	14	VAL	0	0.045	0.031	25.557	0.000	0.000	0.000	0.000
20	B	15	ARG	1	0.900	0.960	28.467	0.031	0.031	0.000	0.000
21	B	16	SER	0	-0.078	-0.038	31.212	0.002	0.002	0.000	0.000
22	B	17	LEU	0	-0.020	-0.015	27.994	0.002	0.002	0.000	0.000
23	B	18	LEU	0	0.012	0.003	30.001	-0.001	-0.001	0.000	0.000
24	B	19	THR	0	-0.042	-0.029	33.112	0.001	0.001	0.000	0.000
25	B	20	LYS	1	0.899	0.953	34.236	0.030	0.030	0.000	0.000
26	B	21	TRP	0	0.001	-0.002	33.999	0.000	0.000	0.000	0.000
27	B	22	ALA	0	0.015	-0.002	36.901	0.000	0.000	0.000	0.000
28	B	23	LYS	1	0.811	0.921	38.388	0.050	0.050	0.000	0.000
29	B	24	VAL	0	-0.047	-0.021	36.384	-0.001	-0.001	0.000	0.000
30	B	25	GLU	-1	-0.901	-0.946	39.501	-0.033	-0.033	0.000	0.000
31	B	26	ARG	1	0.889	0.943	40.188	0.035	0.035	0.000	0.000
32	B	27	ILE	0	0.041	0.010	34.628	-0.003	-0.003	0.000	0.000
33	B	28	GLN	0	-0.066	-0.024	36.844	0.002	0.002	0.000	0.000
34	B	29	ASP	-1	-0.855	-0.920	33.575	-0.034	-0.034	0.000	0.000
35	B	30	VAL	0	-0.022	-0.018	31.411	0.002	0.002	0.000	0.000
36	B	31	GLN	0	-0.043	-0.026	29.960	0.001	0.001	0.000	0.000
37	B	32	ASP	-1	-0.830	-0.923	25.909	-0.054	-0.054	0.000	0.000
38	B	33	GLY	0	0.028	-0.004	26.982	-0.010	-0.010	0.000	0.000
39	B	34	LEU	0	-0.071	-0.016	28.680	0.007	0.007	0.000	0.000
40	B	35	GLN	0	0.027	0.017	31.519	-0.005	-0.005	0.000	0.000
41	B	36	LEU	0	-0.050	-0.034	32.914	0.004	0.004	0.000	0.000
42	B	37	ASP	-1	-0.844	-0.891	35.988	-0.042	-0.042	0.000	0.000
43	B	38	VAL	0	-0.036	-0.031	36.154	0.001	0.001	0.000	0.000
44	B	39	ARG	1	1.005	1.033	39.487	0.033	0.033	0.000	0.000
45	B	40	LEU	0	-0.036	-0.020	37.105	0.000	0.000	0.000	0.000
46	B	41	LYS	1	0.929	0.963	39.882	0.052	0.052	0.000	0.000
47	B	42	THR	0	-0.048	-0.052	43.844	0.001	0.001	0.000	0.000
48	B	43	ASP	-1	-0.856	-0.934	46.366	-0.038	-0.038	0.000	0.000
49	B	44	THR	0	-0.031	-0.007	41.346	-0.002	-0.002	0.000	0.000
50	B	45	LEU	0	0.021	0.017	41.024	-0.001	-0.001	0.000	0.000
51	B	46	LEU	0	-0.066	-0.043	34.655	-0.002	-0.002	0.000	0.000
52	B	47	GLU	-1	-0.776	-0.864	36.380	-0.050	-0.050	0.000	0.000
53	B	48	LEU	0	-0.022	-0.025	30.963	-0.005	-0.005	0.000	0.000
54	B	49	HIS	0	-0.047	-0.039	30.803	0.002	0.002	0.000	0.000
55	B	50	ILE	0	-0.016	-0.008	25.850	-0.008	-0.008	0.000	0.000
56	B	51	TYR	0	0.020	0.007	24.175	0.010	0.010	0.000	0.000
57	B	52	TYR	0	-0.040	-0.093	16.435	-0.008	-0.008	0.000	0.000
58	B	53	ASP	-1	-0.827	-0.925	19.691	-0.174	-0.174	0.000	0.000
59	B	54	HIS	0	0.012	-0.007	18.828	-0.017	-0.017	0.000	0.000
60	B	55	VAL	0	-0.072	-0.016	17.427	-0.006	-0.006	0.000	0.000
61	B	56	TYR	0	0.005	0.012	14.840	-0.029	-0.029	0.000	0.000
62	B	57	HIS	1	0.925	0.962	12.339	0.245	0.245	0.000	0.000
63	B	58	VAL	0	0.042	0.058	15.162	0.002	0.002	0.000	0.000
64	B	59	PRO	0	0.014	0.014	17.388	0.015	0.015	0.000	0.000
65	B	60	SER	0	-0.024	-0.021	21.003	-0.018	-0.018	0.000	0.000
66	B	61	ILE	0	0.018	0.004	23.499	0.013	0.013	0.000	0.000
67	B	62	LYS	1	0.877	0.980	27.031	0.075	0.075	0.000	0.000
68	B	63	PHE	0	0.020	-0.005	29.740	0.006	0.006	0.000	0.000
69	B	64	ARG	1	0.920	0.972	33.267	0.054	0.054	0.000	0.000
70	B	65	LEU	0	0.000	0.012	36.616	0.002	0.002	0.000	0.000
71	B	66	TRP	0	0.012	-0.017	39.654	0.001	0.001	0.000	0.000
72	B	67	SER	0	-0.028	-0.001	43.239	0.000	0.000	0.000	0.000
73	B	68	LEU	0	-0.034	-0.013	46.443	0.001	0.001	0.000	0.000
74	B	69	ASP	-1	-0.810	-0.881	49.138	-0.035	-0.035	0.000	0.000
75	B	70	THR	0	-0.024	-0.048	52.243	0.001	0.001	0.000	0.000
76	B	71	GLU	-1	-0.984	-0.956	55.627	-0.027	-0.027	0.000	0.000
77	B	72	GLU	-1	-0.959	-0.979	57.812	-0.021	-0.021	0.000	0.000
78	B	73	ASP	-1	-0.915	-0.956	61.218	-0.019	-0.019	0.000	0.000
79	B	74	ILE	0	-0.079	-0.029	55.245	0.000	0.000	0.000	0.000
80	B	75	SER	0	-0.050	-0.046	53.334	-0.001	-0.001	0.000	0.000
81	B	76	SER	0	0.003	-0.002	52.052	0.000	0.000	0.000	0.000
82	B	77	LEU	0	0.025	0.012	45.211	-0.001	-0.001	0.000	0.000
83	B	78	ARG	1	0.866	0.927	47.196	0.039	0.039	0.000	0.000
84	B	79	LEU	0	-0.020	-0.014	39.925	-0.002	-0.002	0.000	0.000
85	B	80	LEU	0	-0.029	-0.005	42.053	0.001	0.001	0.000	0.000
86	B	81	THR	0	-0.023	-0.029	40.011	-0.002	-0.002	0.000	0.000
87	B	82	LEU	0	-0.007	0.008	39.654	0.002	0.002	0.000	0.000
88	B	83	SER	0	0.007	0.005	39.057	-0.005	-0.005	0.000	0.000
89	B	84	ASP	-1	-0.847	-0.947	33.437	-0.094	-0.094	0.000	0.000
90	B	85	SER	0	-0.030	-0.021	36.499	-0.002	-0.002	0.000	0.000
91	B	86	GLU	-1	-0.861	-0.940	39.033	-0.053	-0.053	0.000	0.000
92	B	87	LEU	0	-0.004	-0.010	34.056	0.001	0.001	0.000	0.000
93	B	88	ARG	1	0.803	0.894	29.477	0.105	0.105	0.000	0.000
94	B	89	SER	0	-0.046	0.008	36.504	0.001	0.001	0.000	0.000
95	B	90	ILE	0	-0.014	-0.014	39.051	0.002	0.002	0.000	0.000
96	B	91	LEU	0	-0.028	-0.007	33.472	0.000	0.000	0.000	0.000
97	B	92	ASN	0	-0.049	-0.011	32.802	0.003	0.003	0.000	0.000
98	B	93	LEU	0	0.026	0.015	30.127	-0.005	-0.005	0.000	0.000
99	B	94	GLY	0	0.037	0.024	28.833	-0.008	-0.008	0.000	0.000
100	B	95	THR	0	-0.004	-0.022	24.343	-0.001	-0.001	0.000	0.000
101	B	96	PHE	0	-0.004	0.013	23.533	-0.012	-0.012	0.000	0.000
102	B	97	SER	0	-0.018	-0.027	25.233	0.008	0.008	0.000	0.000
103	B	98	VAL	0	0.044	0.032	26.830	-0.006	-0.006	0.000	0.000
104	B	99	THR	0	-0.047	-0.007	27.929	0.006	0.006	0.000	0.000
105	B	100	LEU	0	0.004	0.000	30.636	0.001	0.001	0.000	0.000
106	B	101	SER	0	0.019	0.022	31.361	0.002	0.002	0.000	0.000
107	B	102	THR	0	0.064	0.007	33.382	0.004	0.004	0.000	0.000
108	B	103	ASP	-1	-0.826	-0.903	32.920	-0.062	-0.062	0.000	0.000
109	B	104	MET	0	-0.013	-0.011	29.075	0.001	0.001	0.000	0.000
110	B	105	GLU	-1	-0.851	-0.924	33.150	-0.043	-0.043	0.000	0.000
111	B	106	MET	0	-0.047	-0.014	34.592	0.003	0.003	0.000	0.000
112	B	107	LYS	1	0.780	0.897	37.856	0.047	0.047	0.000	0.000
113	B	108	SER	0	-0.067	-0.047	38.793	0.001	0.001	0.000	0.000
114	B	109	VAL	0	0.004	-0.011	36.269	-0.003	-0.003	0.000	0.000
115	B	110	TYR	0	-0.020	-0.019	32.289	0.003	0.003	0.000	0.000
116	B	111	TYR	0	-0.007	0.015	32.518	-0.001	-0.001	0.000	0.000
117	B	112	TYR	0	-0.021	-0.022	27.209	0.001	0.001	0.000	0.000
118	B	113	ILE	0	-0.010	0.018	24.911	-0.002	-0.002	0.000	0.000
119	B	114	ASN	0	0.007	-0.022	22.992	0.003	0.003	0.000	0.000
120	B	115	ASN	0	-0.012	-0.023	19.948	-0.008	-0.008	0.000	0.000
121	B	116	CYS	0	-0.031	-0.012	17.703	-0.010	-0.010	0.000	0.000
122	B	117	ASP	-1	-0.890	-0.945	15.875	-0.315	-0.315	0.000	0.000
123	B	118	THR	0	-0.011	-0.002	16.690	0.005	0.005	0.000	0.000
124	B	119	ASP	-1	-0.855	-0.943	11.655	-0.443	-0.443	0.000	0.000
125	B	120	ALA	0	-0.028	-0.010	13.221	-0.002	-0.002	0.000	0.000
126	B	121	ASN	0	-0.055	-0.015	14.082	0.035	0.035	0.000	0.000
127	B	122	VAL	0	-0.052	-0.001	15.758	0.030	0.030	0.000	0.000
128	B	123	GLY	0	-0.010	-0.024	14.378	0.035	0.035	0.000	0.000
129	B	124	SER	0	0.004	-0.020	10.446	-0.036	-0.036	0.000	0.000
130	B	125	ASP	-1	-0.939	-0.949	11.791	-0.013	-0.013	0.000	0.000
131	B	126	VAL	0	0.055	0.021	12.278	-0.029	-0.029	0.000	0.000
132	B	127	GLU	-1	-0.903	-0.956	14.933	0.017	0.017	0.000	0.000
133	B	128	HIS	0	0.007	-0.006	18.222	-0.016	-0.016	0.000	0.000
134	B	129	TYR	0	-0.023	-0.007	13.782	0.011	0.011	0.000	0.000
135	B	130	LEU	0	0.025	-0.016	18.528	-0.012	-0.012	0.000	0.000
136	B	131	THR	0	-0.003	0.007	21.702	0.000	0.000	0.000	0.000
137	B	132	ARG	1	0.878	0.959	15.698	0.123	0.123	0.000	0.000
138	B	133	TRP	0	0.041	0.022	20.318	0.002	0.002	0.000	0.000
139	B	134	ILE	0	-0.007	0.012	21.833	0.000	0.000	0.000	0.000
140	B	135	SER	0	-0.027	-0.025	24.939	0.006	0.006	0.000	0.000
141	B	136	LEU	0	-0.021	-0.006	21.718	0.005	0.005	0.000	0.000
142	B	137	TYR	0	0.029	-0.007	20.963	-0.001	-0.001	0.000	0.000
143	B	138	ILE	0	0.001	0.021	25.859	0.004	0.004	0.000	0.000
144	B	139	ARG	1	0.973	0.982	28.631	0.081	0.081	0.000	0.000
145	B	140	ILE	0	-0.038	-0.005	26.609	0.004	0.004	0.000	0.000
146	B	141	PHE	0	-0.014	-0.027	30.217	0.004	0.004	0.000	0.000
147	B	142	ASP	-1	-0.834	-0.935	33.506	-0.045	-0.045	0.000	0.000
148	B	143	LEU	0	-0.014	-0.004	32.886	-0.002	-0.002	0.000	0.000
149	B	144	ASN	0	-0.049	-0.030	34.465	0.000	0.000	0.000	0.000
150	B	145	PHE	0	-0.016	0.017	30.710	0.004	0.004	0.000	0.000
151	B	146	VAL	0	-0.035	-0.020	33.215	-0.004	-0.004	0.000	0.000
152	B	147	PRO	-1	-0.962	-0.963	29.244	-0.042	-0.042	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:-4:ACE )