FMO DATABASE

FMODB ID: JQM79

Calculation Name: 3VPR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VPR

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WD9

Base Structure: X-ray

Registration Date: 2023-09-20

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	189
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2041791.232199
FMO2-HF: Nuclear repulsion	1966877.006041
FMO2-HF: Total energy	-74914.226158
FMO2-MP2: Total energy	-75134.851269

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:1:VAL)

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

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.
-1.435	0.647	0.502	-0.753	-1.83	0

Interaction energy analysis for fragmet #1(A:1:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.022

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].
3	A	3	THR	0	-0.039	-0.027	2.711	0.557	2.532	0.502	-0.715	-1.762
4	A	4	THR	0	-0.012	-0.041	4.179	0.119	0.187	0.001	-0.022	-0.046
5	A	5	ARG	1	0.848	0.914	7.347	0.977	0.977	0.000	0.000	0.000
6	A	6	ASP	-1	-0.781	-0.892	4.632	-3.951	-3.912	-0.001	-0.016	-0.022
7	A	7	ARG	1	0.946	0.984	6.829	0.786	0.786	0.000	0.000	0.000
8	A	8	ILE	0	-0.005	-0.005	9.322	0.181	0.181	0.000	0.000	0.000
9	A	9	LEU	0	-0.018	-0.001	11.149	0.120	0.120	0.000	0.000	0.000
10	A	10	GLU	-1	-0.934	-0.960	9.570	-0.172	-0.172	0.000	0.000	0.000
11	A	11	GLU	-1	-0.923	-0.977	12.263	-0.066	-0.066	0.000	0.000	0.000
12	A	12	ALA	0	-0.015	-0.006	14.841	0.064	0.064	0.000	0.000	0.000
13	A	13	ALA	0	-0.003	0.000	15.202	0.052	0.052	0.000	0.000	0.000
14	A	14	LYS	1	0.942	0.972	13.811	0.093	0.093	0.000	0.000	0.000
15	A	15	LEU	0	0.070	0.044	18.134	0.026	0.026	0.000	0.000	0.000
16	A	16	PHE	0	-0.032	-0.036	19.699	0.019	0.019	0.000	0.000	0.000
17	A	17	THR	0	-0.059	-0.026	19.989	0.019	0.019	0.000	0.000	0.000
18	A	18	GLU	-1	-0.956	-0.973	21.171	-0.055	-0.055	0.000	0.000	0.000
19	A	19	LYS	1	0.866	0.941	24.280	0.112	0.112	0.000	0.000	0.000
20	A	20	GLY	0	0.013	0.015	25.169	0.006	0.006	0.000	0.000	0.000
21	A	21	TYR	0	-0.030	-0.021	22.735	-0.011	-0.011	0.000	0.000	0.000
22	A	22	GLU	-1	-0.883	-0.969	25.408	-0.141	-0.141	0.000	0.000	0.000
23	A	23	ALA	0	-0.031	0.002	28.804	0.001	0.001	0.000	0.000	0.000
24	A	24	THR	0	-0.006	0.006	22.575	0.008	0.008	0.000	0.000	0.000
25	A	25	SER	0	-0.030	-0.014	25.494	-0.016	-0.016	0.000	0.000	0.000
26	A	26	VAL	0	0.062	0.009	21.623	-0.007	-0.007	0.000	0.000	0.000
27	A	27	GLN	0	-0.026	-0.023	22.209	-0.013	-0.013	0.000	0.000	0.000
28	A	28	ASP	-1	-0.795	-0.910	23.509	-0.114	-0.114	0.000	0.000	0.000
29	A	29	LEU	0	0.008	0.015	18.235	0.003	0.003	0.000	0.000	0.000
30	A	30	ALA	0	-0.024	-0.016	18.765	-0.011	-0.011	0.000	0.000	0.000
31	A	31	GLN	0	-0.044	-0.021	19.324	0.003	0.003	0.000	0.000	0.000
32	A	32	ALA	0	-0.001	0.016	19.572	0.011	0.011	0.000	0.000	0.000
33	A	33	LEU	0	-0.009	-0.003	13.530	-0.001	-0.001	0.000	0.000	0.000
34	A	34	GLY	0	-0.007	0.018	15.534	-0.009	-0.009	0.000	0.000	0.000
35	A	35	LEU	0	-0.061	-0.031	13.176	-0.012	-0.012	0.000	0.000	0.000
36	A	36	SER	0	0.044	0.016	17.687	0.009	0.009	0.000	0.000	0.000
37	A	37	LYS	1	0.998	0.970	19.308	0.116	0.116	0.000	0.000	0.000
38	A	38	ALA	0	-0.011	0.004	20.782	-0.016	-0.016	0.000	0.000	0.000
39	A	39	ALA	0	0.051	0.035	15.749	-0.017	-0.017	0.000	0.000	0.000
40	A	40	LEU	0	0.021	0.034	15.626	-0.048	-0.048	0.000	0.000	0.000
41	A	41	TYR	0	-0.005	-0.017	17.362	-0.020	-0.020	0.000	0.000	0.000
42	A	42	HIS	0	0.007	0.014	17.009	-0.013	-0.013	0.000	0.000	0.000
43	A	43	HIS	0	-0.093	-0.041	11.284	-0.064	-0.064	0.000	0.000	0.000
44	A	44	PHE	0	0.041	0.014	12.088	-0.050	-0.050	0.000	0.000	0.000
45	A	45	GLY	0	0.030	0.038	17.163	0.021	0.021	0.000	0.000	0.000
46	A	46	SER	0	-0.054	-0.049	20.409	0.037	0.037	0.000	0.000	0.000
47	A	47	LYS	1	0.916	0.958	20.479	0.147	0.147	0.000	0.000	0.000
48	A	48	GLU	-1	-0.780	-0.883	21.390	-0.267	-0.267	0.000	0.000	0.000
49	A	49	GLU	-1	-0.820	-0.914	17.911	-0.411	-0.411	0.000	0.000	0.000
50	A	50	ILE	0	-0.024	0.001	16.266	-0.033	-0.033	0.000	0.000	0.000
51	A	51	LEU	0	-0.021	-0.005	17.675	-0.027	-0.027	0.000	0.000	0.000
52	A	52	TYR	0	-0.002	-0.008	19.647	0.012	0.012	0.000	0.000	0.000
53	A	53	GLU	-1	-0.798	-0.921	13.930	-0.697	-0.697	0.000	0.000	0.000
54	A	54	ILE	0	-0.027	0.007	14.849	-0.041	-0.041	0.000	0.000	0.000
55	A	55	SER	0	-0.019	-0.025	15.921	0.026	0.026	0.000	0.000	0.000
56	A	56	LEU	0	-0.035	-0.017	15.923	0.015	0.015	0.000	0.000	0.000
57	A	57	LEU	0	-0.018	0.013	9.817	0.018	0.018	0.000	0.000	0.000
58	A	58	ALA	0	0.025	0.015	13.769	0.028	0.028	0.000	0.000	0.000
59	A	59	LEU	0	0.017	-0.014	15.930	0.041	0.041	0.000	0.000	0.000
60	A	60	LYS	1	0.922	0.961	14.881	0.538	0.538	0.000	0.000	0.000
61	A	61	GLY	0	0.028	0.017	14.102	0.018	0.018	0.000	0.000	0.000
62	A	62	LEU	0	-0.009	-0.006	14.779	0.051	0.051	0.000	0.000	0.000
63	A	63	VAL	0	-0.021	-0.022	18.305	0.028	0.028	0.000	0.000	0.000
64	A	64	ALA	0	0.002	0.008	15.891	0.023	0.023	0.000	0.000	0.000
65	A	65	ALA	0	-0.041	-0.027	17.702	0.035	0.035	0.000	0.000	0.000
66	A	66	GLY	0	-0.005	-0.011	18.822	0.026	0.026	0.000	0.000	0.000
67	A	67	GLU	-1	-0.912	-0.967	19.877	-0.173	-0.173	0.000	0.000	0.000
68	A	68	LYS	1	0.911	0.955	15.665	0.115	0.115	0.000	0.000	0.000
69	A	69	ALA	0	-0.021	-0.007	21.953	0.012	0.012	0.000	0.000	0.000
70	A	70	LEU	0	-0.040	-0.009	25.206	0.008	0.008	0.000	0.000	0.000
71	A	71	GLU	-1	-0.923	-0.956	24.297	-0.051	-0.051	0.000	0.000	0.000
72	A	72	VAL	0	-0.088	-0.026	26.406	0.011	0.011	0.000	0.000	0.000
73	A	73	ALA	0	0.014	0.003	28.853	-0.004	-0.004	0.000	0.000	0.000
74	A	74	ASP	-1	-0.840	-0.941	32.541	0.002	0.002	0.000	0.000	0.000
75	A	75	PRO	0	0.059	0.028	32.582	0.001	0.001	0.000	0.000	0.000
76	A	76	LYS	1	0.961	0.983	32.992	-0.011	-0.011	0.000	0.000	0.000
77	A	77	GLU	-1	-0.824	-0.889	29.299	0.031	0.031	0.000	0.000	0.000
78	A	78	ALA	0	-0.002	-0.007	28.442	0.002	0.002	0.000	0.000	0.000
79	A	79	LEU	0	-0.003	0.002	28.012	-0.005	-0.005	0.000	0.000	0.000
80	A	80	ARG	1	0.813	0.871	27.388	-0.042	-0.042	0.000	0.000	0.000
81	A	81	ARG	1	0.947	0.973	21.925	-0.034	-0.034	0.000	0.000	0.000
82	A	82	PHE	0	0.021	0.026	23.906	-0.002	-0.002	0.000	0.000	0.000
83	A	83	MET	0	-0.057	-0.025	24.013	-0.006	-0.006	0.000	0.000	0.000
84	A	84	GLU	-1	-0.773	-0.835	23.740	0.048	0.048	0.000	0.000	0.000
85	A	85	ALA	0	-0.005	0.007	19.739	0.008	0.008	0.000	0.000	0.000
86	A	86	HIS	0	0.011	0.014	19.514	-0.012	-0.012	0.000	0.000	0.000
87	A	87	ALA	0	0.007	-0.006	20.576	-0.011	-0.011	0.000	0.000	0.000
88	A	88	ARG	1	0.890	0.966	16.912	-0.132	-0.132	0.000	0.000	0.000
89	A	89	TYR	0	-0.010	0.011	12.743	-0.002	-0.002	0.000	0.000	0.000
90	A	90	PHE	0	-0.036	-0.031	16.407	-0.018	-0.018	0.000	0.000	0.000
91	A	91	GLU	-1	-0.894	-0.963	18.415	0.067	0.067	0.000	0.000	0.000
92	A	92	GLU	-1	-0.952	-0.974	13.497	0.154	0.154	0.000	0.000	0.000
93	A	93	ASN	0	-0.051	-0.023	11.967	-0.053	-0.053	0.000	0.000	0.000
94	A	94	TYR	0	0.055	0.030	14.767	-0.045	-0.045	0.000	0.000	0.000
95	A	95	PRO	0	0.050	0.009	15.275	-0.016	-0.016	0.000	0.000	0.000
96	A	96	PHE	0	0.041	0.020	11.149	-0.012	-0.012	0.000	0.000	0.000
97	A	97	PHE	0	-0.005	-0.005	16.813	-0.006	-0.006	0.000	0.000	0.000
98	A	98	VAL	0	0.005	0.018	19.909	0.004	0.004	0.000	0.000	0.000
99	A	99	THR	0	-0.050	-0.019	19.206	0.004	0.004	0.000	0.000	0.000
100	A	100	MET	0	-0.014	-0.007	19.896	0.005	0.005	0.000	0.000	0.000
101	A	101	LEU	0	-0.053	-0.021	21.757	0.010	0.010	0.000	0.000	0.000
102	A	102	GLN	0	-0.039	-0.028	23.891	0.013	0.013	0.000	0.000	0.000
103	A	103	GLY	0	0.032	0.011	24.725	0.007	0.007	0.000	0.000	0.000
104	A	104	ILE	0	0.038	0.040	25.743	-0.002	-0.002	0.000	0.000	0.000
105	A	105	LYS	1	0.909	0.924	27.152	0.106	0.106	0.000	0.000	0.000
106	A	106	SER	0	-0.035	-0.024	26.753	0.007	0.007	0.000	0.000	0.000
107	A	107	LEU	0	-0.031	0.019	22.713	-0.005	-0.005	0.000	0.000	0.000
108	A	108	SER	0	-0.015	-0.002	26.176	0.021	0.021	0.000	0.000	0.000
109	A	109	PRO	0	-0.012	-0.033	27.978	-0.006	-0.006	0.000	0.000	0.000
110	A	110	GLU	-1	-0.896	-0.945	26.446	-0.200	-0.200	0.000	0.000	0.000
111	A	111	ASN	0	0.008	0.001	23.539	-0.010	-0.010	0.000	0.000	0.000
112	A	112	ARG	1	0.883	0.940	24.534	0.144	0.144	0.000	0.000	0.000
113	A	113	LEU	0	0.005	0.011	26.750	0.004	0.004	0.000	0.000	0.000
114	A	114	LYS	1	0.971	0.975	22.336	0.266	0.266	0.000	0.000	0.000
115	A	115	THR	0	0.030	0.024	22.344	-0.014	-0.014	0.000	0.000	0.000
116	A	116	ILE	0	-0.050	-0.029	23.391	0.007	0.007	0.000	0.000	0.000
117	A	117	ALA	0	0.022	0.025	25.487	0.010	0.010	0.000	0.000	0.000
118	A	118	LEU	0	-0.013	-0.006	19.224	0.004	0.004	0.000	0.000	0.000
119	A	119	ARG	1	0.865	0.930	23.295	0.132	0.132	0.000	0.000	0.000
120	A	120	ASP	-1	-0.829	-0.923	25.085	-0.107	-0.107	0.000	0.000	0.000
121	A	121	ARG	1	0.924	0.972	22.744	0.179	0.179	0.000	0.000	0.000
122	A	122	HIS	0	0.004	-0.004	22.390	0.000	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.866	-0.947	25.123	-0.069	-0.069	0.000	0.000	0.000
124	A	124	GLU	-1	-0.929	-0.979	28.730	-0.069	-0.069	0.000	0.000	0.000
125	A	125	ASN	0	0.047	0.018	24.201	0.011	0.011	0.000	0.000	0.000
126	A	126	LEU	0	-0.012	0.012	28.051	0.010	0.010	0.000	0.000	0.000
127	A	127	ARG	1	0.900	0.943	29.488	0.081	0.081	0.000	0.000	0.000
128	A	128	ALA	0	-0.001	0.015	30.616	0.006	0.006	0.000	0.000	0.000
129	A	129	ILE	0	-0.007	0.000	27.573	0.006	0.006	0.000	0.000	0.000
130	A	130	LEU	0	-0.028	-0.022	32.103	0.006	0.006	0.000	0.000	0.000
131	A	131	ARG	1	0.936	0.970	34.574	0.060	0.060	0.000	0.000	0.000
132	A	132	ARG	1	0.886	0.964	30.561	0.035	0.035	0.000	0.000	0.000
133	A	133	GLY	0	0.038	0.012	36.329	0.004	0.004	0.000	0.000	0.000
134	A	134	VAL	0	-0.036	-0.008	37.853	0.003	0.003	0.000	0.000	0.000
135	A	135	GLU	-1	-0.925	-0.966	38.848	-0.036	-0.036	0.000	0.000	0.000
136	A	136	GLN	0	-0.085	-0.056	36.760	0.000	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.015	0.015	41.497	0.003	0.003	0.000	0.000	0.000
138	A	138	VAL	0	-0.081	-0.031	38.279	0.003	0.003	0.000	0.000	0.000
139	A	139	PHE	0	-0.076	-0.027	34.961	0.003	0.003	0.000	0.000	0.000
140	A	140	ARG	1	0.992	0.993	40.977	0.014	0.014	0.000	0.000	0.000
141	A	141	GLU	-1	-0.896	-0.955	42.701	-0.028	-0.028	0.000	0.000	0.000
142	A	142	VAL	0	-0.053	-0.029	39.891	0.001	0.001	0.000	0.000	0.000
143	A	143	ASP	-1	-0.814	-0.894	40.600	-0.044	-0.044	0.000	0.000	0.000
144	A	144	VAL	0	0.057	0.014	36.122	-0.001	-0.001	0.000	0.000	0.000
145	A	145	ALA	0	-0.025	-0.003	36.165	-0.003	-0.003	0.000	0.000	0.000
146	A	146	LEU	0	-0.015	-0.017	36.190	-0.002	-0.002	0.000	0.000	0.000
147	A	147	ALA	0	0.013	0.006	36.890	0.000	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.045	0.008	33.081	0.001	0.001	0.000	0.000	0.000
149	A	149	ARG	1	0.888	0.945	32.028	0.070	0.070	0.000	0.000	0.000
150	A	150	ALA	0	0.003	0.019	33.599	-0.001	-0.001	0.000	0.000	0.000
151	A	151	VAL	0	0.047	0.016	29.581	0.002	0.002	0.000	0.000	0.000
152	A	152	LEU	0	0.012	0.001	27.079	0.000	0.000	0.000	0.000	0.000
153	A	153	SER	0	-0.091	-0.045	29.209	-0.004	-0.004	0.000	0.000	0.000
154	A	154	MET	0	-0.040	-0.015	31.119	0.002	0.002	0.000	0.000	0.000
155	A	155	LEU	0	0.008	0.011	25.800	0.005	0.005	0.000	0.000	0.000
156	A	156	ASN	0	0.010	-0.020	25.523	-0.003	-0.003	0.000	0.000	0.000
157	A	157	TRP	0	0.011	0.013	27.126	-0.006	-0.006	0.000	0.000	0.000
158	A	158	MET	0	-0.014	0.001	25.686	0.002	0.002	0.000	0.000	0.000
159	A	159	ILE	0	-0.024	-0.011	23.522	0.005	0.005	0.000	0.000	0.000
160	A	160	ARG	1	0.859	0.924	25.829	0.058	0.058	0.000	0.000	0.000
161	A	161	TRP	0	-0.021	-0.001	29.093	0.005	0.005	0.000	0.000	0.000
162	A	162	PHE	0	-0.046	-0.006	22.365	0.001	0.001	0.000	0.000	0.000
163	A	163	ARG	1	0.934	0.963	25.936	-0.022	-0.022	0.000	0.000	0.000
164	A	164	PRO	0	0.018	0.002	21.010	0.009	0.009	0.000	0.000	0.000
165	A	165	ASP	-1	-0.976	-0.967	23.045	0.071	0.071	0.000	0.000	0.000
166	A	166	GLY	0	0.005	0.003	25.353	0.009	0.009	0.000	0.000	0.000
167	A	167	PRO	0	0.017	0.002	25.683	0.006	0.006	0.000	0.000	0.000
168	A	168	MET	0	-0.048	-0.026	26.211	0.007	0.007	0.000	0.000	0.000
169	A	169	ARG	1	1.012	1.001	19.783	-0.151	-0.151	0.000	0.000	0.000
170	A	170	ALA	0	0.063	0.035	22.330	-0.009	-0.009	0.000	0.000	0.000
171	A	171	GLU	-1	-0.801	-0.929	21.845	0.086	0.086	0.000	0.000	0.000
172	A	172	GLU	-1	-0.942	-0.975	24.287	0.072	0.072	0.000	0.000	0.000
173	A	173	VAL	0	-0.029	-0.008	27.483	-0.007	-0.007	0.000	0.000	0.000
174	A	174	ALA	0	0.006	-0.002	26.116	-0.006	-0.006	0.000	0.000	0.000
175	A	175	ARG	1	0.853	0.894	26.241	-0.070	-0.070	0.000	0.000	0.000
176	A	176	ALA	0	-0.001	0.000	29.809	-0.003	-0.003	0.000	0.000	0.000
177	A	177	TYR	0	0.007	-0.009	29.872	-0.004	-0.004	0.000	0.000	0.000
178	A	178	HIS	0	-0.034	-0.013	30.699	-0.001	-0.001	0.000	0.000	0.000
179	A	179	ASP	-1	-0.848	-0.934	32.694	0.015	0.015	0.000	0.000	0.000
180	A	180	LEU	0	-0.014	-0.005	35.685	-0.002	-0.002	0.000	0.000	0.000
181	A	181	ILE	0	-0.064	-0.038	33.787	-0.002	-0.002	0.000	0.000	0.000
182	A	182	LEU	0	-0.049	-0.020	35.786	-0.002	-0.002	0.000	0.000	0.000
183	A	183	ARG	1	0.846	0.923	37.679	-0.017	-0.017	0.000	0.000	0.000
184	A	184	GLY	0	0.021	0.034	40.232	-0.001	-0.001	0.000	0.000	0.000
185	A	185	LEU	0	-0.021	-0.031	42.068	0.002	0.002	0.000	0.000	0.000
186	A	186	GLU	-1	-0.982	-0.970	43.947	-0.001	-0.001	0.000	0.000	0.000
187	A	187	ARG	1	0.952	0.973	46.542	-0.011	-0.011	0.000	0.000	0.000
188	A	188	GLY	0	0.054	0.019	47.938	-0.001	-0.001	0.000	0.000	0.000
189	A	189	SER	0	-0.047	-0.013	45.872	0.001	0.001	0.000	0.000	0.000

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