FMO DATABASE

FMODB ID: J3V49

Calculation Name: 3DLV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DLV

Chain ID: B

ChEMBL ID:

UniProt ID: Q8TZT9

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:

Apendix: None

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	104
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-801053.291767
FMO2-HF: Nuclear repulsion	759984.378539
FMO2-HF: Total energy	-41068.913228
FMO2-MP2: Total energy	-41191.688176

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:2:GLY)

Summations of interaction energy for fragment #1(B:2: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.
-5.039	-7.978	15.441	-7.393	-5.108	-0.036

Interaction energy analysis for fragmet #1(B:2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.026

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	4	PHE	0	-0.030	-0.020	2.656	0.067	2.590	0.114	-1.256	-1.381	0.006
4	B	5	VAL	0	0.038	0.019	6.481	-0.039	-0.039	0.000	0.000	0.000	0.000
5	B	6	VAL	0	-0.035	-0.018	9.060	0.041	0.041	0.000	0.000	0.000	0.000
6	B	7	TRP	0	0.106	0.044	11.392	0.068	0.068	0.000	0.000	0.000	0.000
7	B	8	PRO	0	0.060	0.018	14.965	0.013	0.013	0.000	0.000	0.000	0.000
8	B	9	SER	0	0.029	0.018	17.285	0.020	0.020	0.000	0.000	0.000	0.000
9	B	10	GLU	-1	-0.793	-0.876	12.402	-0.671	-0.671	0.000	0.000	0.000	0.000
10	B	11	LEU	0	-0.030	-0.030	13.968	0.038	0.038	0.000	0.000	0.000	0.000
11	B	12	ASP	-1	-0.690	-0.843	16.848	-0.230	-0.230	0.000	0.000	0.000	0.000
12	B	13	SER	0	-0.050	-0.047	20.530	0.018	0.018	0.000	0.000	0.000	0.000
13	B	14	ARG	1	0.865	0.931	22.979	0.224	0.224	0.000	0.000	0.000	0.000
14	B	15	LEU	0	-0.008	0.032	21.295	0.016	0.016	0.000	0.000	0.000	0.000
15	B	16	SER	0	0.030	0.010	23.775	0.006	0.006	0.000	0.000	0.000	0.000
16	B	17	ARG	1	0.888	0.915	16.832	0.097	0.097	0.000	0.000	0.000	0.000
17	B	18	LYS	1	0.945	0.980	21.247	0.055	0.055	0.000	0.000	0.000	0.000
18	B	19	TYR	0	-0.057	-0.060	23.348	-0.004	-0.004	0.000	0.000	0.000	0.000
19	B	20	GLY	0	0.068	0.042	19.311	-0.019	-0.019	0.000	0.000	0.000	0.000
20	B	21	ARG	1	0.780	0.914	17.644	0.139	0.139	0.000	0.000	0.000	0.000
21	B	22	ILE	0	-0.020	-0.017	12.724	0.047	0.047	0.000	0.000	0.000	0.000
22	B	23	VAL	0	-0.003	0.006	13.918	0.060	0.060	0.000	0.000	0.000	0.000
23	B	24	PRO	0	0.005	-0.011	16.208	0.020	0.020	0.000	0.000	0.000	0.000
24	B	25	ARG	1	1.024	0.994	19.285	0.046	0.046	0.000	0.000	0.000	0.000
25	B	26	SER	0	0.028	0.022	22.413	-0.013	-0.013	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.023	-0.005	16.625	-0.002	-0.002	0.000	0.000	0.000	0.000
27	B	28	ALA	0	-0.027	0.009	18.770	-0.030	-0.030	0.000	0.000	0.000	0.000
28	B	29	VAL	0	0.035	0.021	19.306	0.029	0.029	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.874	-0.916	21.676	-0.182	-0.182	0.000	0.000	0.000	0.000
30	B	31	SER	0	0.029	0.009	23.584	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	32	PRO	0	-0.063	-0.008	18.623	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	33	ARG	1	0.882	0.930	20.670	0.291	0.291	0.000	0.000	0.000	0.000
33	B	34	VAL	0	0.065	0.022	17.587	-0.043	-0.043	0.000	0.000	0.000	0.000
34	B	35	GLU	-1	-0.754	-0.867	17.958	-0.403	-0.403	0.000	0.000	0.000	0.000
35	B	36	GLU	-1	-0.763	-0.847	19.527	-0.333	-0.333	0.000	0.000	0.000	0.000
36	B	37	ILE	0	-0.011	-0.010	13.514	-0.027	-0.027	0.000	0.000	0.000	0.000
37	B	38	VAL	0	-0.005	0.006	14.473	-0.113	-0.113	0.000	0.000	0.000	0.000
38	B	39	ARG	1	0.954	0.980	15.182	0.312	0.312	0.000	0.000	0.000	0.000
39	B	40	ALA	0	-0.025	-0.018	15.185	0.004	0.004	0.000	0.000	0.000	0.000
40	B	41	ALA	0	-0.032	-0.021	10.872	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	42	GLU	-1	-0.846	-0.924	11.777	-0.671	-0.671	0.000	0.000	0.000	0.000
42	B	43	GLU	-1	-0.885	-0.934	14.137	-0.311	-0.311	0.000	0.000	0.000	0.000
43	B	44	LEU	0	-0.081	-0.042	10.956	0.080	0.080	0.000	0.000	0.000	0.000
44	B	45	LYS	1	0.823	0.916	10.824	0.472	0.472	0.000	0.000	0.000	0.000
45	B	46	PHE	0	-0.015	-0.008	7.653	-0.223	-0.223	0.000	0.000	0.000	0.000
46	B	47	LYS	1	0.905	0.951	7.554	1.487	1.487	0.000	0.000	0.000	0.000
47	B	48	VAL	0	0.032	-0.002	8.853	-0.425	-0.425	0.000	0.000	0.000	0.000
48	B	49	ILE	0	-0.094	-0.038	8.209	0.181	0.181	0.000	0.000	0.000	0.000
49	B	50	ARG	1	0.879	0.901	11.680	0.651	0.651	0.000	0.000	0.000	0.000
50	B	51	VAL	0	0.002	0.006	13.933	-0.124	-0.124	0.000	0.000	0.000	0.000
51	B	52	GLU	-1	-0.817	-0.869	16.668	-0.381	-0.381	0.000	0.000	0.000	0.000
52	B	53	GLU	-1	-0.873	-0.955	19.238	-0.362	-0.362	0.000	0.000	0.000	0.000
53	B	54	ASP	-1	-0.911	-0.941	22.037	-0.222	-0.222	0.000	0.000	0.000	0.000
54	B	55	LYS	1	0.778	0.872	25.161	0.275	0.275	0.000	0.000	0.000	0.000
55	B	56	LEU	0	0.085	0.042	28.114	0.010	0.010	0.000	0.000	0.000	0.000
56	B	57	ASN	0	0.008	-0.004	30.997	0.002	0.002	0.000	0.000	0.000	0.000
57	B	58	PRO	0	-0.134	-0.046	32.484	0.006	0.006	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.955	0.923	30.948	0.133	0.133	0.000	0.000	0.000	0.000
59	B	60	LEU	0	0.009	0.012	35.603	0.005	0.005	0.000	0.000	0.000	0.000
60	B	61	SER	0	0.015	0.010	37.479	0.004	0.004	0.000	0.000	0.000	0.000
61	B	62	GLY	0	0.001	0.011	38.185	0.004	0.004	0.000	0.000	0.000	0.000
62	B	63	ILE	0	-0.043	-0.025	35.827	0.001	0.001	0.000	0.000	0.000	0.000
63	B	64	ASP	-1	-0.846	-0.915	31.717	-0.139	-0.139	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.853	-0.933	31.791	-0.117	-0.117	0.000	0.000	0.000	0.000
65	B	66	GLU	-1	-0.937	-0.942	27.429	-0.162	-0.162	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.009	0.007	25.915	-0.020	-0.020	0.000	0.000	0.000	0.000
67	B	68	ARG	1	0.929	0.998	27.931	0.181	0.181	0.000	0.000	0.000	0.000
68	B	69	THR	0	-0.067	-0.054	23.876	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	70	PHE	0	0.056	0.043	19.433	-0.012	-0.012	0.000	0.000	0.000	0.000
70	B	71	GLY	0	0.037	0.004	19.626	0.001	0.001	0.000	0.000	0.000	0.000
71	B	72	MET	0	-0.062	-0.022	14.708	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	73	ILE	0	0.017	0.012	11.979	0.024	0.024	0.000	0.000	0.000	0.000
73	B	74	VAL	0	-0.026	-0.003	8.980	-0.163	-0.163	0.000	0.000	0.000	0.000
74	B	75	LEU	0	0.016	0.013	7.279	0.192	0.192	0.000	0.000	0.000	0.000
75	B	76	GLU	-1	-0.742	-0.852	4.275	-2.766	-2.490	0.000	-0.093	-0.183	0.000
76	B	77	SER	0	-0.017	-0.011	2.876	1.707	2.808	0.038	-0.503	-0.636	0.001
77	B	78	PRO	0	0.052	0.031	1.737	-5.110	-12.868	15.198	-5.136	-2.304	-0.040
78	B	79	TYR	0	-0.032	-0.010	4.113	1.935	2.182	0.001	-0.038	-0.210	0.000
79	B	80	GLY	0	0.069	0.027	3.119	-1.968	-1.334	0.091	-0.365	-0.360	-0.003
80	B	81	LYS	1	0.867	0.910	4.738	0.175	0.213	-0.001	-0.002	-0.034	0.000
81	B	82	SER	0	-0.009	-0.011	6.074	0.027	0.027	0.000	0.000	0.000	0.000
82	B	83	LYS	1	0.969	0.972	8.107	-0.301	-0.301	0.000	0.000	0.000	0.000
83	B	84	SER	0	0.070	0.043	6.271	-0.165	-0.165	0.000	0.000	0.000	0.000
84	B	85	LEU	0	0.005	0.006	8.108	0.072	0.072	0.000	0.000	0.000	0.000
85	B	86	LYS	1	0.905	0.957	10.870	0.167	0.167	0.000	0.000	0.000	0.000
86	B	87	LEU	0	0.027	0.023	9.832	0.047	0.047	0.000	0.000	0.000	0.000
87	B	88	ILE	0	0.036	0.021	9.820	0.043	0.043	0.000	0.000	0.000	0.000
88	B	89	ALA	0	-0.008	-0.008	13.492	0.065	0.065	0.000	0.000	0.000	0.000
89	B	90	GLN	0	-0.039	-0.030	16.004	0.023	0.023	0.000	0.000	0.000	0.000
90	B	91	LYS	1	0.836	0.904	16.014	0.382	0.382	0.000	0.000	0.000	0.000
91	B	92	ILE	0	0.051	0.026	16.703	0.033	0.033	0.000	0.000	0.000	0.000
92	B	93	ARG	1	0.829	0.894	19.607	0.251	0.251	0.000	0.000	0.000	0.000
93	B	94	GLU	-1	-0.841	-0.884	20.629	-0.241	-0.241	0.000	0.000	0.000	0.000
94	B	95	PHE	0	-0.010	-0.009	18.623	0.025	0.025	0.000	0.000	0.000	0.000
95	B	96	ARG	1	0.765	0.839	23.134	0.294	0.294	0.000	0.000	0.000	0.000
96	B	97	ARG	1	0.966	0.983	25.710	0.164	0.164	0.000	0.000	0.000	0.000
97	B	98	ARG	1	0.857	0.924	22.550	0.242	0.242	0.000	0.000	0.000	0.000
98	B	99	SER	0	-0.050	-0.028	26.880	0.007	0.007	0.000	0.000	0.000	0.000
99	B	100	ALA	0	-0.010	0.002	29.460	0.009	0.009	0.000	0.000	0.000	0.000
100	B	101	GLY	0	0.032	0.025	31.222	0.009	0.009	0.000	0.000	0.000	0.000
101	B	102	THR	0	-0.015	-0.016	32.717	0.012	0.012	0.000	0.000	0.000	0.000
102	B	103	LEU	0	-0.071	-0.024	32.213	-0.009	-0.009	0.000	0.000	0.000	0.000
103	B	104	VAL	0	0.001	-0.012	33.035	-0.005	-0.005	0.000	0.000	0.000	0.000
104	B	105	PRO	0	0.022	0.027	34.379	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:GLY)