FMO DATABASE

FMODB ID: YZ322

Calculation Name: 1BV4-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1BV4

Chain ID: C

ChEMBL ID:

UniProt ID: P08661

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-531191.349892
FMO2-HF: Nuclear repulsion	498678.23686
FMO2-HF: Total energy	-32513.113032
FMO2-MP2: Total energy	-32604.200269

3D Structure Molmil

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(C:115:LYS)

Summations of interaction energy for fragment #1(C:115:LYS)

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.
-195.408	-192.983	38.194	-19.254	-21.365	-0.21

Interaction energy analysis for fragmet #1(C:115:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.818 / q_NPA : 0.910

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

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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	C	117	PHE	0	0.029	-0.003	2.466	-3.831	-0.453	2.750	-2.175	-3.953	0.002
4	C	118	MET	0	-0.012	-0.003	6.127	4.431	4.431	0.000	0.000	0.000	0.000
5	C	119	SER	0	0.035	0.031	9.554	-1.389	-1.389	0.000	0.000	0.000	0.000
6	C	120	SER	0	-0.072	-0.040	12.108	0.965	0.965	0.000	0.000	0.000	0.000
7	C	121	VAL	0	0.032	0.007	15.262	0.334	0.334	0.000	0.000	0.000	0.000
8	C	122	ARG	1	0.946	0.968	18.703	14.295	14.295	0.000	0.000	0.000	0.000
9	C	123	ARG	1	0.885	0.940	18.313	13.960	13.960	0.000	0.000	0.000	0.000
10	C	124	MET	0	-0.052	0.010	16.799	0.811	0.811	0.000	0.000	0.000	0.000
11	C	125	PRO	0	0.079	0.039	18.271	-0.668	-0.668	0.000	0.000	0.000	0.000
12	C	126	LEU	0	0.104	0.054	12.420	-0.313	-0.313	0.000	0.000	0.000	0.000
13	C	127	ASN	0	0.014	-0.002	15.684	-1.200	-1.200	0.000	0.000	0.000	0.000
14	C	128	ARG	1	0.910	0.933	17.539	15.336	15.336	0.000	0.000	0.000	0.000
15	C	129	ALA	0	0.045	0.022	13.570	-0.125	-0.125	0.000	0.000	0.000	0.000
16	C	130	LYS	1	0.924	0.966	12.762	16.874	16.874	0.000	0.000	0.000	0.000
17	C	131	ALA	0	-0.025	-0.003	13.828	-0.490	-0.490	0.000	0.000	0.000	0.000
18	C	132	LEU	0	-0.015	-0.014	14.198	0.254	0.254	0.000	0.000	0.000	0.000
19	C	133	CYS	0	-0.094	-0.022	8.162	-1.520	-1.520	0.000	0.000	0.000	0.000
20	C	134	SER	0	0.051	0.031	11.281	-0.596	-0.596	0.000	0.000	0.000	0.000
21	C	135	GLU	-1	-0.980	-0.974	13.059	-15.856	-15.856	0.000	0.000	0.000	0.000
22	C	136	LEU	0	-0.077	-0.039	12.028	0.813	0.813	0.000	0.000	0.000	0.000
23	C	137	GLN	0	-0.052	-0.029	11.058	-1.149	-1.149	0.000	0.000	0.000	0.000
24	C	138	GLY	0	0.034	0.023	7.637	-1.716	-1.716	0.000	0.000	0.000	0.000
25	C	139	THR	0	-0.020	-0.019	5.893	3.968	3.968	0.000	0.000	0.000	0.000
26	C	140	VAL	0	0.004	-0.004	7.135	-2.826	-2.826	0.000	0.000	0.000	0.000
27	C	141	ALA	0	-0.003	-0.013	4.301	-3.509	-3.420	-0.001	-0.013	-0.075	0.000
28	C	142	THR	0	0.001	-0.004	3.325	13.396	13.744	0.001	-0.117	-0.231	0.000
29	C	143	PRO	0	-0.029	-0.017	3.315	-20.090	-19.178	0.078	-0.450	-0.541	-0.004
30	C	144	ARG	1	0.849	0.923	2.729	63.862	64.625	0.122	-0.198	-0.688	-0.001
31	C	145	ASN	0	0.006	0.002	5.159	9.123	9.182	-0.001	-0.001	-0.057	0.000
32	C	146	ALA	0	0.025	-0.001	7.370	-2.132	-2.132	0.000	0.000	0.000	0.000
33	C	147	GLU	-1	-0.856	-0.913	7.625	-25.314	-25.314	0.000	0.000	0.000	0.000
34	C	148	GLU	-1	-0.762	-0.882	1.705	-109.018	-112.718	14.003	-5.490	-4.814	-0.073
35	C	149	ASN	0	-0.011	0.016	5.392	-0.631	-0.593	-0.001	0.000	-0.036	0.000
36	C	150	ARG	1	0.883	0.923	7.941	26.991	26.991	0.000	0.000	0.000	0.000
37	C	151	ALA	0	-0.011	-0.005	5.817	2.233	2.233	0.000	0.000	0.000	0.000
38	C	152	ILE	0	0.023	0.000	3.874	2.153	2.289	-0.001	-0.013	-0.123	0.000
39	C	153	GLN	0	-0.013	-0.012	7.770	3.520	3.520	0.000	0.000	0.000	0.000
40	C	154	ASN	0	-0.058	-0.017	10.745	3.238	3.238	0.000	0.000	0.000	0.000
41	C	155	VAL	0	-0.057	-0.026	8.495	1.873	1.873	0.000	0.000	0.000	0.000
42	C	156	ALA	0	-0.011	0.011	11.023	1.586	1.586	0.000	0.000	0.000	0.000
43	C	157	LYS	1	0.922	0.955	12.892	18.959	18.959	0.000	0.000	0.000	0.000
44	C	158	ASP	-1	-0.821	-0.903	15.894	-14.622	-14.622	0.000	0.000	0.000	0.000
45	C	159	VAL	0	-0.030	-0.011	15.522	-1.337	-1.337	0.000	0.000	0.000	0.000
46	C	160	ALA	0	-0.010	-0.007	12.224	0.434	0.434	0.000	0.000	0.000	0.000
47	C	161	PHE	0	-0.032	-0.014	12.519	-0.327	-0.327	0.000	0.000	0.000	0.000
48	C	162	LEU	0	-0.020	0.004	7.683	-2.539	-2.539	0.000	0.000	0.000	0.000
49	C	163	GLY	0	-0.027	-0.017	7.760	3.319	3.319	0.000	0.000	0.000	0.000
50	C	164	ILE	0	-0.040	-0.006	8.919	0.424	0.424	0.000	0.000	0.000	0.000
51	C	174	GLU	-1	-0.952	-0.984	12.382	-20.085	-20.085	0.000	0.000	0.000	0.000
52	C	175	ASP	-1	-0.757	-0.868	7.645	-36.479	-36.479	0.000	0.000	0.000	0.000
53	C	176	LEU	0	-0.074	-0.059	9.494	2.468	2.468	0.000	0.000	0.000	0.000
54	C	177	THR	0	-0.110	-0.051	9.128	1.213	1.213	0.000	0.000	0.000	0.000
55	C	178	GLY	0	0.018	0.034	10.688	-0.187	-0.187	0.000	0.000	0.000	0.000
56	C	200	CYS	0	-0.004	-0.017	15.504	-0.380	-0.380	0.000	0.000	0.000	0.000
57	C	201	VAL	0	0.026	0.009	12.510	0.607	0.607	0.000	0.000	0.000	0.000
58	C	202	VAL	0	-0.012	-0.001	13.224	-1.210	-1.210	0.000	0.000	0.000	0.000
59	C	203	LEU	0	-0.030	-0.001	9.586	0.599	0.599	0.000	0.000	0.000	0.000
60	C	204	LEU	0	0.026	-0.001	13.256	0.829	0.829	0.000	0.000	0.000	0.000
61	C	205	THR	0	0.077	0.032	15.490	-0.883	-0.883	0.000	0.000	0.000	0.000
62	C	206	ASN	0	-0.037	-0.013	17.602	-0.882	-0.882	0.000	0.000	0.000	0.000
63	C	207	GLY	0	-0.002	-0.009	14.000	-0.009	-0.009	0.000	0.000	0.000	0.000
64	C	208	LYS	1	0.904	0.951	13.669	16.605	16.605	0.000	0.000	0.000	0.000
65	C	209	TRP	0	-0.001	-0.020	9.093	-0.111	-0.111	0.000	0.000	0.000	0.000
66	C	210	ASN	0	-0.014	-0.005	15.298	0.903	0.903	0.000	0.000	0.000	0.000
67	C	211	ASP	-1	-0.917	-0.950	16.922	-17.309	-17.309	0.000	0.000	0.000	0.000
68	C	212	VAL	0	-0.020	-0.009	17.671	0.988	0.988	0.000	0.000	0.000	0.000
69	C	213	PRO	0	0.057	0.033	19.355	-0.602	-0.602	0.000	0.000	0.000	0.000
70	C	215	SER	0	-0.016	-0.020	19.370	-0.246	-0.246	0.000	0.000	0.000	0.000
71	C	216	ASP	-1	-0.884	-0.925	21.425	-12.767	-12.767	0.000	0.000	0.000	0.000
72	C	217	SER	0	-0.058	-0.049	19.970	-0.777	-0.777	0.000	0.000	0.000	0.000
73	C	218	PHE	0	0.041	0.010	16.544	0.499	0.499	0.000	0.000	0.000	0.000
74	C	219	LEU	0	-0.003	0.013	15.213	0.151	0.151	0.000	0.000	0.000	0.000
75	C	220	VAL	0	0.021	0.006	11.631	-0.755	-0.755	0.000	0.000	0.000	0.000
76	C	221	VAL	0	0.069	0.031	7.289	1.149	1.149	0.000	0.000	0.000	0.000
77	C	223	GLU	-1	-0.775	-0.896	1.858	-138.019	-139.948	17.377	-7.784	-7.663	-0.108
78	C	224	PHE	0	0.022	0.010	3.667	2.106	2.594	0.005	-0.133	-0.359	0.000
79	C	225	SER	0	0.014	0.009	2.385	-4.778	-2.935	3.862	-2.880	-2.825	-0.026

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Interactive mode: IFIE and PIEDA for fragment #1(C:115:LYS)