FMO DATABASE

FMODB ID: 89MRY

Calculation Name: 3VVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VVV

Chain ID: A

ChEMBL ID:

UniProt ID: Q13137

Base Structure: X-ray

Registration Date: 2023-09-23

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1005498.16197
FMO2-HF: Nuclear repulsion	958005.115012
FMO2-HF: Total energy	-47493.046957
FMO2-MP2: Total energy	-47632.955477

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:19:GLY)

Summations of interaction energy for fragment #1(A:19:GLY)

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.
-1.035	0.319	-0.006	-0.735	-0.613	0.004

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.016

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	21	SER	0	0.006	0.003	3.815	-0.942	0.412	-0.006	-0.735	-0.613	0.004
4	A	22	GLN	0	-0.013	-0.006	5.846	0.727	0.727	0.000	0.000	0.000	0.000
5	A	23	VAL	0	0.004	0.015	8.270	0.430	0.430	0.000	0.000	0.000	0.000
6	A	24	ILE	0	-0.005	-0.005	10.526	-0.255	-0.255	0.000	0.000	0.000	0.000
7	A	25	PHE	0	-0.004	-0.007	12.426	0.141	0.141	0.000	0.000	0.000	0.000
8	A	26	ASN	0	-0.068	-0.049	15.711	0.013	0.013	0.000	0.000	0.000	0.000
9	A	27	SER	0	0.035	-0.003	18.920	0.028	0.028	0.000	0.000	0.000	0.000
10	A	28	VAL	0	-0.049	0.000	17.812	0.016	0.016	0.000	0.000	0.000	0.000
11	A	29	GLU	-1	-0.884	-0.938	21.026	-0.285	-0.285	0.000	0.000	0.000	0.000
12	A	30	LYS	1	0.943	0.948	22.354	0.342	0.342	0.000	0.000	0.000	0.000
13	A	31	PHE	0	-0.024	-0.004	24.188	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	32	TYR	0	0.066	0.046	21.953	0.000	0.000	0.000	0.000	0.000	0.000
15	A	33	ILE	0	0.040	0.007	27.964	0.010	0.010	0.000	0.000	0.000	0.000
16	A	34	PRO	0	0.004	0.005	31.344	0.000	0.000	0.000	0.000	0.000	0.000
17	A	35	GLY	0	-0.019	-0.012	32.273	0.009	0.009	0.000	0.000	0.000	0.000
18	A	36	GLY	0	-0.006	0.009	32.268	0.010	0.010	0.000	0.000	0.000	0.000
19	A	37	ASP	-1	-0.807	-0.901	29.893	-0.175	-0.175	0.000	0.000	0.000	0.000
20	A	38	VAL	0	0.026	0.010	24.031	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	39	THR	0	-0.042	-0.012	24.568	0.006	0.006	0.000	0.000	0.000	0.000
22	A	40	CYS	0	-0.034	0.004	18.841	-0.032	-0.032	0.000	0.000	0.000	0.000
23	A	41	HIS	0	0.086	0.041	20.740	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	42	TYR	0	-0.013	-0.023	15.678	-0.067	-0.067	0.000	0.000	0.000	0.000
25	A	43	THR	0	-0.053	-0.016	15.931	0.073	0.073	0.000	0.000	0.000	0.000
26	A	44	PHE	0	0.056	0.028	13.629	-0.129	-0.129	0.000	0.000	0.000	0.000
27	A	45	THR	0	0.005	-0.016	9.950	0.085	0.085	0.000	0.000	0.000	0.000
28	A	46	GLN	0	-0.028	-0.025	12.536	0.048	0.048	0.000	0.000	0.000	0.000
29	A	47	HIS	0	0.003	-0.007	10.855	0.071	0.071	0.000	0.000	0.000	0.000
30	A	48	PHE	0	-0.033	0.005	9.732	0.043	0.043	0.000	0.000	0.000	0.000
31	A	49	ILE	0	-0.019	-0.014	11.811	0.035	0.035	0.000	0.000	0.000	0.000
32	A	50	PRO	0	0.006	0.021	14.145	0.017	0.017	0.000	0.000	0.000	0.000
33	A	51	ARG	1	0.798	0.901	12.372	0.027	0.027	0.000	0.000	0.000	0.000
34	A	52	ARG	1	0.924	0.950	17.691	0.050	0.050	0.000	0.000	0.000	0.000
35	A	53	LYS	1	0.931	0.966	19.422	0.024	0.024	0.000	0.000	0.000	0.000
36	A	54	ASP	-1	-0.690	-0.818	14.635	-0.271	-0.271	0.000	0.000	0.000	0.000
37	A	55	TRP	0	-0.050	-0.030	15.459	0.000	0.000	0.000	0.000	0.000	0.000
38	A	56	ILE	0	0.003	0.008	15.194	-0.086	-0.086	0.000	0.000	0.000	0.000
39	A	57	GLY	0	0.011	0.005	15.912	0.070	0.070	0.000	0.000	0.000	0.000
40	A	58	ILE	0	-0.012	0.006	16.991	-0.071	-0.071	0.000	0.000	0.000	0.000
41	A	59	PHE	0	0.005	0.007	15.142	0.051	0.051	0.000	0.000	0.000	0.000
42	A	60	ARG	1	1.013	1.017	18.146	0.195	0.195	0.000	0.000	0.000	0.000
43	A	61	VAL	0	0.003	-0.018	16.720	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	62	GLY	0	-0.028	-0.020	16.035	0.051	0.051	0.000	0.000	0.000	0.000
45	A	63	TRP	0	-0.084	-0.026	10.686	0.078	0.078	0.000	0.000	0.000	0.000
46	A	64	LYS	1	0.952	0.965	14.709	0.072	0.072	0.000	0.000	0.000	0.000
47	A	65	THR	0	-0.012	0.005	14.180	0.032	0.032	0.000	0.000	0.000	0.000
48	A	66	THR	0	0.037	0.003	12.342	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	67	ARG	1	0.929	0.945	15.073	0.027	0.027	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.854	-0.926	17.970	-0.172	-0.172	0.000	0.000	0.000	0.000
51	A	69	TYR	0	-0.073	-0.005	18.205	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	70	TYR	0	0.008	0.006	19.589	0.031	0.031	0.000	0.000	0.000	0.000
53	A	71	THR	0	-0.007	-0.020	21.762	0.027	0.027	0.000	0.000	0.000	0.000
54	A	72	PHE	0	-0.034	-0.029	19.825	-0.036	-0.036	0.000	0.000	0.000	0.000
55	A	73	MET	0	-0.009	0.015	20.431	0.037	0.037	0.000	0.000	0.000	0.000
56	A	74	TRP	0	-0.026	-0.012	19.970	-0.029	-0.029	0.000	0.000	0.000	0.000
57	A	75	VAL	0	-0.016	0.000	17.519	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	76	THR	0	-0.007	-0.032	19.679	0.039	0.039	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.068	-0.011	21.717	0.004	0.004	0.000	0.000	0.000	0.000
60	A	78	PRO	0	-0.005	-0.020	24.539	0.005	0.005	0.000	0.000	0.000	0.000
61	A	79	ILE	0	0.038	0.009	19.136	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	80	ASP	-1	-0.884	-0.934	23.064	-0.149	-0.149	0.000	0.000	0.000	0.000
63	A	81	LEU	0	0.024	0.012	22.317	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	82	ASN	0	-0.065	-0.052	21.659	0.011	0.011	0.000	0.000	0.000	0.000
65	A	83	ASN	0	-0.009	-0.003	16.971	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	84	LYS	1	0.936	0.981	16.236	0.119	0.119	0.000	0.000	0.000	0.000
67	A	85	SER	0	0.021	0.005	15.193	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	86	ALA	0	-0.070	-0.044	17.089	0.030	0.030	0.000	0.000	0.000	0.000
69	A	87	LYS	1	0.926	0.978	20.228	0.259	0.259	0.000	0.000	0.000	0.000
70	A	88	GLN	0	0.054	0.024	20.573	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	89	GLN	0	-0.058	-0.012	19.100	0.064	0.064	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.883	-0.949	21.393	-0.286	-0.286	0.000	0.000	0.000	0.000
73	A	91	VAL	0	-0.009	0.021	20.389	0.026	0.026	0.000	0.000	0.000	0.000
74	A	92	GLN	0	0.011	0.015	23.265	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	93	PHE	0	0.025	0.007	20.003	0.011	0.011	0.000	0.000	0.000	0.000
76	A	94	LYS	1	0.859	0.915	25.934	0.160	0.160	0.000	0.000	0.000	0.000
77	A	95	ALA	0	0.093	0.036	29.140	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	96	TYR	0	-0.080	-0.036	30.950	0.000	0.000	0.000	0.000	0.000	0.000
79	A	97	TYR	0	-0.039	-0.033	27.079	0.006	0.006	0.000	0.000	0.000	0.000
80	A	98	LEU	0	-0.008	0.016	25.398	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	99	PRO	0	-0.016	-0.010	24.400	0.020	0.020	0.000	0.000	0.000	0.000
82	A	100	LYS	1	0.849	0.926	27.620	0.158	0.158	0.000	0.000	0.000	0.000
83	A	101	ASP	-1	-0.850	-0.884	27.519	-0.191	-0.191	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-0.886	-0.945	29.056	-0.181	-0.181	0.000	0.000	0.000	0.000
85	A	103	GLU	-1	-0.937	-0.952	24.421	-0.217	-0.217	0.000	0.000	0.000	0.000
86	A	104	TYR	0	-0.029	-0.017	21.093	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	105	TYR	0	-0.055	-0.068	19.835	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	106	GLN	0	0.003	0.005	12.749	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	107	PHE	0	0.039	0.011	15.962	0.047	0.047	0.000	0.000	0.000	0.000
90	A	108	CYS	0	-0.040	-0.019	11.665	-0.168	-0.168	0.000	0.000	0.000	0.000
91	A	109	TYR	0	-0.033	-0.044	11.146	0.134	0.134	0.000	0.000	0.000	0.000
92	A	110	VAL	0	-0.012	-0.004	10.466	-0.206	-0.206	0.000	0.000	0.000	0.000
93	A	111	ASP	-1	-0.785	-0.899	10.041	-0.047	-0.047	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.855	-0.951	12.579	0.019	0.019	0.000	0.000	0.000	0.000
95	A	113	ASP	-1	-0.899	-0.932	11.731	0.285	0.285	0.000	0.000	0.000	0.000
96	A	114	GLY	0	-0.066	-0.025	12.553	0.079	0.079	0.000	0.000	0.000	0.000
97	A	115	VAL	0	-0.052	-0.022	6.250	0.007	0.007	0.000	0.000	0.000	0.000
98	A	116	VAL	0	0.033	0.010	7.248	-0.107	-0.107	0.000	0.000	0.000	0.000
99	A	117	ARG	1	0.830	0.917	5.179	-0.338	-0.338	0.000	0.000	0.000	0.000
100	A	118	GLY	0	0.057	0.016	7.459	-0.343	-0.343	0.000	0.000	0.000	0.000
101	A	119	ALA	0	0.012	0.003	9.076	0.228	0.228	0.000	0.000	0.000	0.000
102	A	120	SER	0	-0.043	-0.018	11.102	-0.075	-0.075	0.000	0.000	0.000	0.000
103	A	121	ILE	0	-0.014	-0.002	14.359	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	122	PRO	0	0.014	0.009	16.582	0.015	0.015	0.000	0.000	0.000	0.000
105	A	123	PHE	0	-0.014	0.006	18.745	0.014	0.014	0.000	0.000	0.000	0.000
106	A	124	GLN	0	0.006	0.001	22.291	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	125	PHE	0	0.007	0.001	23.704	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	126	ARG	1	0.802	0.868	27.825	0.246	0.246	0.000	0.000	0.000	0.000
109	A	127	PRO	0	-0.025	-0.017	31.140	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	128	GLU	-1	-0.917	-0.946	32.454	-0.194	-0.194	0.000	0.000	0.000	0.000
111	A	129	ASN	0	-0.065	-0.037	31.721	0.009	0.009	0.000	0.000	0.000	0.000
112	A	130	GLU	-1	-0.909	-0.969	34.565	-0.138	-0.138	0.000	0.000	0.000	0.000
113	A	131	GLU	-1	-0.980	-0.989	31.922	-0.171	-0.171	0.000	0.000	0.000	0.000
114	A	132	ASP	-1	-0.862	-0.902	29.612	-0.242	-0.242	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)