FMO DATABASE

FMODB ID: N1L4Q

Calculation Name: 3VX7-B-Xray372

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: 2023-03-14

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1540060.960756
FMO2-HF: Nuclear repulsion	1478451.419123
FMO2-HF: Total energy	-61609.541633
FMO2-MP2: Total energy	-61790.713341

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:-3:PRO)

Summations of interaction energy for fragment #1(B:-3: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.
-3.642	-1.732	-0.015	-0.842	-1.053	0.005

Interaction energy analysis for fragmet #1(B:-3:PRO)

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 : -0.008

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	B	-1	GLY	0	0.061	0.030	3.746	-1.904	-0.059	-0.014	-0.833	-0.998	0.005
4	B	0	SER	0	-0.048	-0.016	6.102	0.110	0.110	0.000	0.000	0.000	0.000
5	B	1	MET	0	-0.028	-0.022	4.465	-0.061	0.004	-0.001	-0.009	-0.055	0.000
6	B	2	LEU	0	-0.032	0.008	9.813	0.181	0.181	0.000	0.000	0.000	0.000
7	B	3	THR	0	-0.007	-0.014	13.473	-0.029	-0.029	0.000	0.000	0.000	0.000
8	B	4	LEU	0	0.022	0.021	15.199	0.048	0.048	0.000	0.000	0.000	0.000
9	B	5	PRO	0	-0.004	-0.024	17.779	0.033	0.033	0.000	0.000	0.000	0.000
10	B	6	GLU	-1	-0.709	-0.830	14.716	-0.661	-0.661	0.000	0.000	0.000	0.000
11	B	7	TYR	0	-0.083	-0.063	18.454	0.028	0.028	0.000	0.000	0.000	0.000
12	B	8	ASN	0	-0.067	-0.066	19.829	0.052	0.052	0.000	0.000	0.000	0.000
13	B	9	GLU	-1	-0.971	-0.974	21.142	-0.312	-0.312	0.000	0.000	0.000	0.000
14	B	10	GLN	0	-0.006	-0.011	18.349	0.039	0.039	0.000	0.000	0.000	0.000
15	B	11	ILE	0	0.022	0.024	23.589	0.019	0.019	0.000	0.000	0.000	0.000
16	B	12	PRO	0	0.046	0.018	25.751	0.019	0.019	0.000	0.000	0.000	0.000
17	B	13	ASN	0	0.009	0.010	25.917	0.024	0.024	0.000	0.000	0.000	0.000
18	B	14	VAL	0	0.031	0.027	24.467	0.016	0.016	0.000	0.000	0.000	0.000
19	B	15	ARG	1	0.859	0.915	27.631	0.165	0.165	0.000	0.000	0.000	0.000
20	B	16	SER	0	-0.064	-0.035	30.670	0.016	0.016	0.000	0.000	0.000	0.000
21	B	17	LEU	0	-0.048	-0.032	27.225	0.013	0.013	0.000	0.000	0.000	0.000
22	B	18	LEU	0	0.030	0.003	28.861	0.008	0.008	0.000	0.000	0.000	0.000
23	B	19	THR	0	-0.035	-0.023	32.132	0.009	0.009	0.000	0.000	0.000	0.000
24	B	20	LYS	1	0.885	0.949	33.755	0.127	0.127	0.000	0.000	0.000	0.000
25	B	21	TRP	0	-0.003	-0.005	32.113	0.006	0.006	0.000	0.000	0.000	0.000
26	B	22	ALA	0	0.016	-0.004	35.816	0.000	0.000	0.000	0.000	0.000	0.000
27	B	23	LYS	1	0.834	0.925	36.706	0.100	0.100	0.000	0.000	0.000	0.000
28	B	24	VAL	0	-0.053	-0.030	34.705	0.000	0.000	0.000	0.000	0.000	0.000
29	B	25	GLU	-1	-0.885	-0.938	37.743	-0.087	-0.087	0.000	0.000	0.000	0.000
30	B	26	ARG	1	0.803	0.884	38.178	0.118	0.118	0.000	0.000	0.000	0.000
31	B	27	ILE	0	0.023	0.001	32.990	-0.006	-0.006	0.000	0.000	0.000	0.000
32	B	28	GLN	0	0.000	0.024	34.550	0.008	0.008	0.000	0.000	0.000	0.000
33	B	29	ASP	-1	-0.802	-0.886	31.864	-0.175	-0.175	0.000	0.000	0.000	0.000
34	B	30	VAL	0	-0.042	-0.026	28.952	0.012	0.012	0.000	0.000	0.000	0.000
35	B	31	GLN	0	-0.069	-0.041	26.638	0.009	0.009	0.000	0.000	0.000	0.000
36	B	32	ASP	-1	-0.781	-0.886	23.477	-0.304	-0.304	0.000	0.000	0.000	0.000
37	B	33	GLY	0	0.055	0.015	24.570	-0.021	-0.021	0.000	0.000	0.000	0.000
38	B	34	LEU	0	-0.068	-0.012	26.509	0.015	0.015	0.000	0.000	0.000	0.000
39	B	35	GLN	0	-0.002	-0.001	29.095	-0.011	-0.011	0.000	0.000	0.000	0.000
40	B	36	LEU	0	-0.014	-0.015	30.288	0.009	0.009	0.000	0.000	0.000	0.000
41	B	37	ASP	-1	-0.823	-0.876	33.694	-0.121	-0.121	0.000	0.000	0.000	0.000
42	B	38	VAL	0	-0.022	-0.022	33.780	0.001	0.001	0.000	0.000	0.000	0.000
43	B	39	ARG	1	0.982	1.024	37.118	0.078	0.078	0.000	0.000	0.000	0.000
44	B	40	LEU	0	-0.038	-0.019	34.657	0.001	0.001	0.000	0.000	0.000	0.000
45	B	41	LYS	1	0.904	0.957	36.862	0.089	0.089	0.000	0.000	0.000	0.000
46	B	42	THR	0	-0.030	-0.033	41.209	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	43	ASP	-1	-0.845	-0.918	43.475	-0.067	-0.067	0.000	0.000	0.000	0.000
48	B	44	THR	0	-0.044	-0.023	38.157	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	45	LEU	0	0.005	0.008	38.549	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	46	LEU	0	-0.062	-0.046	31.706	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	47	GLU	-1	-0.694	-0.783	33.473	-0.140	-0.140	0.000	0.000	0.000	0.000
52	B	48	LEU	0	-0.019	-0.022	27.787	-0.007	-0.007	0.000	0.000	0.000	0.000
53	B	49	HIS	0	-0.048	-0.047	27.701	-0.012	-0.012	0.000	0.000	0.000	0.000
54	B	50	ILE	0	-0.015	-0.004	23.678	-0.010	-0.010	0.000	0.000	0.000	0.000
55	B	51	TYR	0	0.008	-0.002	20.615	0.020	0.020	0.000	0.000	0.000	0.000
56	B	52	TYR	0	0.004	-0.028	14.413	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	53	ASP	-1	-0.833	-0.917	15.500	-0.517	-0.517	0.000	0.000	0.000	0.000
58	B	54	HIS	0	0.031	0.003	15.481	-0.096	-0.096	0.000	0.000	0.000	0.000
59	B	55	VAL	0	-0.075	-0.027	12.490	-0.079	-0.079	0.000	0.000	0.000	0.000
60	B	56	TYR	0	0.019	0.020	10.247	-0.135	-0.135	0.000	0.000	0.000	0.000
61	B	57	HIS	1	0.868	0.941	9.863	1.203	1.203	0.000	0.000	0.000	0.000
62	B	58	VAL	0	0.056	0.040	12.326	-0.034	-0.034	0.000	0.000	0.000	0.000
63	B	59	PRO	0	0.028	0.019	14.853	0.045	0.045	0.000	0.000	0.000	0.000
64	B	60	SER	0	-0.018	-0.021	18.273	-0.007	-0.007	0.000	0.000	0.000	0.000
65	B	61	ILE	0	0.009	-0.001	20.444	0.021	0.021	0.000	0.000	0.000	0.000
66	B	62	LYS	1	0.885	0.979	23.910	0.220	0.220	0.000	0.000	0.000	0.000
67	B	63	PHE	0	0.016	-0.009	26.130	0.005	0.005	0.000	0.000	0.000	0.000
68	B	64	ARG	1	0.807	0.870	29.750	0.135	0.135	0.000	0.000	0.000	0.000
69	B	65	LEU	0	-0.003	0.006	32.881	0.000	0.000	0.000	0.000	0.000	0.000
70	B	66	TRP	0	0.015	-0.012	36.059	0.004	0.004	0.000	0.000	0.000	0.000
71	B	67	SER	0	-0.045	-0.030	39.667	0.000	0.000	0.000	0.000	0.000	0.000
72	B	68	LEU	0	-0.012	-0.012	42.916	0.000	0.000	0.000	0.000	0.000	0.000
73	B	69	ASP	-1	-0.777	-0.839	45.825	-0.062	-0.062	0.000	0.000	0.000	0.000
74	B	70	THR	0	0.007	-0.012	48.720	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	71	GLU	-1	-0.921	-0.940	51.013	-0.056	-0.056	0.000	0.000	0.000	0.000
76	B	72	GLU	-1	-0.972	-0.984	54.092	-0.042	-0.042	0.000	0.000	0.000	0.000
77	B	73	ASP	-1	-0.931	-0.964	57.609	-0.044	-0.044	0.000	0.000	0.000	0.000
78	B	74	ILE	0	-0.072	-0.025	51.854	-0.001	-0.001	0.000	0.000	0.000	0.000
79	B	75	SER	0	-0.042	-0.027	49.923	0.000	0.000	0.000	0.000	0.000	0.000
80	B	76	SER	0	-0.026	-0.038	48.597	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	77	LEU	0	-0.014	-0.004	41.365	-0.001	-0.001	0.000	0.000	0.000	0.000
82	B	78	ARG	1	0.836	0.906	43.289	0.065	0.065	0.000	0.000	0.000	0.000
83	B	79	LEU	0	-0.017	-0.005	35.738	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	80	LEU	0	-0.026	-0.002	37.861	0.005	0.005	0.000	0.000	0.000	0.000
85	B	81	THR	0	-0.033	-0.022	35.521	-0.006	-0.006	0.000	0.000	0.000	0.000
86	B	82	LEU	0	-0.011	0.001	35.414	0.006	0.006	0.000	0.000	0.000	0.000
87	B	83	SER	0	0.020	-0.034	34.685	-0.005	-0.005	0.000	0.000	0.000	0.000
88	B	84	ASP	-1	-0.818	-0.919	29.534	-0.106	-0.106	0.000	0.000	0.000	0.000
89	B	85	SER	0	-0.015	-0.014	32.414	0.001	0.001	0.000	0.000	0.000	0.000
90	B	86	GLU	-1	-0.843	-0.898	35.140	-0.067	-0.067	0.000	0.000	0.000	0.000
91	B	87	LEU	0	-0.012	-0.001	30.206	0.000	0.000	0.000	0.000	0.000	0.000
92	B	88	ARG	1	0.777	0.871	26.243	0.101	0.101	0.000	0.000	0.000	0.000
93	B	89	SER	0	-0.060	0.001	33.028	0.003	0.003	0.000	0.000	0.000	0.000
94	B	90	ILE	0	-0.015	-0.016	35.818	0.001	0.001	0.000	0.000	0.000	0.000
95	B	91	LEU	0	0.002	0.005	30.087	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	92	ASN	0	-0.062	-0.032	30.199	0.016	0.016	0.000	0.000	0.000	0.000
97	B	93	LEU	0	0.024	0.008	26.422	-0.008	-0.008	0.000	0.000	0.000	0.000
98	B	94	GLY	0	0.027	0.023	25.768	-0.009	-0.009	0.000	0.000	0.000	0.000
99	B	95	THR	0	0.001	-0.016	21.170	0.010	0.010	0.000	0.000	0.000	0.000
100	B	96	PHE	0	-0.011	0.011	19.756	-0.004	-0.004	0.000	0.000	0.000	0.000
101	B	97	SER	0	-0.001	-0.012	21.460	0.017	0.017	0.000	0.000	0.000	0.000
102	B	98	VAL	0	0.014	0.018	22.895	-0.022	-0.022	0.000	0.000	0.000	0.000
103	B	99	THR	0	-0.019	0.000	23.320	0.016	0.016	0.000	0.000	0.000	0.000
104	B	100	LEU	0	-0.013	-0.002	26.058	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	101	SER	0	0.016	0.013	26.127	0.010	0.010	0.000	0.000	0.000	0.000
106	B	102	THR	0	0.069	0.018	28.510	0.006	0.006	0.000	0.000	0.000	0.000
107	B	103	ASP	-1	-0.836	-0.903	28.165	-0.158	-0.158	0.000	0.000	0.000	0.000
108	B	104	MET	0	-0.004	-0.003	24.216	0.006	0.006	0.000	0.000	0.000	0.000
109	B	105	GLU	-1	-0.857	-0.923	28.579	-0.115	-0.115	0.000	0.000	0.000	0.000
110	B	106	MET	0	-0.061	-0.019	29.867	0.013	0.013	0.000	0.000	0.000	0.000
111	B	107	LYS	1	0.793	0.888	32.972	0.121	0.121	0.000	0.000	0.000	0.000
112	B	108	SER	0	-0.034	-0.033	34.125	0.007	0.007	0.000	0.000	0.000	0.000
113	B	109	VAL	0	-0.011	-0.002	31.706	-0.005	-0.005	0.000	0.000	0.000	0.000
114	B	110	TYR	0	0.003	-0.002	28.227	-0.002	-0.002	0.000	0.000	0.000	0.000
115	B	111	TYR	0	0.011	0.022	28.424	0.004	0.004	0.000	0.000	0.000	0.000
116	B	112	TYR	0	-0.020	-0.028	22.921	-0.013	-0.013	0.000	0.000	0.000	0.000
117	B	113	ILE	0	-0.020	0.009	21.441	0.016	0.016	0.000	0.000	0.000	0.000
118	B	114	ASN	0	-0.032	-0.045	18.803	-0.030	-0.030	0.000	0.000	0.000	0.000
119	B	115	ASN	0	-0.006	-0.026	16.157	0.019	0.019	0.000	0.000	0.000	0.000
120	B	116	CYS	0	-0.008	0.016	13.284	-0.040	-0.040	0.000	0.000	0.000	0.000
121	B	117	ASP	-1	-0.870	-0.923	12.056	-0.458	-0.458	0.000	0.000	0.000	0.000
122	B	118	THR	0	-0.030	-0.036	13.488	0.030	0.030	0.000	0.000	0.000	0.000
123	B	119	ASP	-1	-0.830	-0.903	9.175	-1.371	-1.371	0.000	0.000	0.000	0.000
124	B	120	ALA	0	-0.062	-0.022	10.337	0.024	0.024	0.000	0.000	0.000	0.000
125	B	121	ASN	0	-0.073	-0.037	11.694	0.130	0.130	0.000	0.000	0.000	0.000
126	B	122	VAL	0	-0.030	0.001	14.748	0.056	0.056	0.000	0.000	0.000	0.000
127	B	123	GLY	0	0.000	-0.009	13.561	0.082	0.082	0.000	0.000	0.000	0.000
128	B	124	SER	0	-0.007	-0.020	10.516	-0.110	-0.110	0.000	0.000	0.000	0.000
129	B	125	ASP	-1	-0.912	-0.937	11.461	-0.476	-0.476	0.000	0.000	0.000	0.000
130	B	126	VAL	0	0.067	0.030	12.219	-0.004	-0.004	0.000	0.000	0.000	0.000
131	B	127	GLU	-1	-0.880	-0.934	14.838	-0.229	-0.229	0.000	0.000	0.000	0.000
132	B	128	HIS	0	-0.040	-0.036	18.296	0.018	0.018	0.000	0.000	0.000	0.000
133	B	129	TYR	0	-0.033	-0.040	12.585	0.104	0.104	0.000	0.000	0.000	0.000
134	B	130	LEU	0	0.014	-0.014	17.990	0.016	0.016	0.000	0.000	0.000	0.000
135	B	131	THR	0	-0.001	0.003	20.956	0.024	0.024	0.000	0.000	0.000	0.000
136	B	132	ARG	1	0.846	0.933	15.082	0.476	0.476	0.000	0.000	0.000	0.000
137	B	133	TRP	0	0.040	0.027	18.875	0.025	0.025	0.000	0.000	0.000	0.000
138	B	134	ILE	0	-0.011	0.011	20.684	0.030	0.030	0.000	0.000	0.000	0.000
139	B	135	SER	0	-0.058	-0.044	24.184	0.031	0.031	0.000	0.000	0.000	0.000
140	B	136	LEU	0	-0.021	-0.004	19.866	0.026	0.026	0.000	0.000	0.000	0.000
141	B	137	TYR	0	0.066	0.008	18.362	0.011	0.011	0.000	0.000	0.000	0.000
142	B	138	ILE	0	0.001	0.019	23.940	0.016	0.016	0.000	0.000	0.000	0.000
143	B	139	ARG	1	0.953	0.978	26.982	0.143	0.143	0.000	0.000	0.000	0.000
144	B	140	ILE	0	-0.029	0.001	23.949	0.015	0.015	0.000	0.000	0.000	0.000
145	B	141	PHE	0	-0.012	-0.024	27.324	0.010	0.010	0.000	0.000	0.000	0.000
146	B	142	ASP	-1	-0.808	-0.901	31.459	-0.089	-0.089	0.000	0.000	0.000	0.000
147	B	143	LEU	0	0.001	0.006	30.623	-0.006	-0.006	0.000	0.000	0.000	0.000
148	B	144	ASN	0	-0.068	-0.045	32.758	0.004	0.004	0.000	0.000	0.000	0.000
149	B	145	PHE	0	-0.011	0.016	30.249	0.003	0.003	0.000	0.000	0.000	0.000
150	B	146	VAL	0	0.002	0.000	32.040	-0.005	-0.005	0.000	0.000	0.000	0.000
151	B	147	PRO	0	-0.039	-0.002	28.353	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:-3:PRO)