FMO DATABASE

FMODB ID: 52MZZ

Calculation Name: 1BV4-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-531664.383063
FMO2-HF: Nuclear repulsion	499151.791074
FMO2-HF: Total energy	-32512.591989
FMO2-MP2: Total energy	-32603.776648

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(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.
-157.232	-139.701	9.21	-12.151	-14.586	-0.136

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 : 0.859 / q_NPA : 0.932

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	0.028	-0.002	2.332	-4.468	-1.481	1.551	-1.418	-3.119	-0.005
4	C	118	MET	0	-0.013	-0.008	5.799	4.121	4.121	0.000	0.000	0.000	0.000
5	C	119	SER	0	-0.001	0.016	9.533	-0.841	-0.841	0.000	0.000	0.000	0.000
6	C	120	SER	0	-0.044	-0.020	12.256	0.783	0.783	0.000	0.000	0.000	0.000
7	C	121	VAL	0	0.045	0.016	15.534	0.346	0.346	0.000	0.000	0.000	0.000
8	C	122	ARG	1	0.928	0.957	18.867	13.928	13.928	0.000	0.000	0.000	0.000
9	C	123	ARG	1	0.940	0.984	18.635	13.091	13.091	0.000	0.000	0.000	0.000
10	C	124	MET	0	-0.068	0.017	17.406	0.696	0.696	0.000	0.000	0.000	0.000
11	C	125	PRO	0	0.090	0.045	19.183	-0.577	-0.577	0.000	0.000	0.000	0.000
12	C	126	LEU	0	0.121	0.062	13.525	-0.284	-0.284	0.000	0.000	0.000	0.000
13	C	127	ASN	0	0.049	0.002	16.471	-1.454	-1.454	0.000	0.000	0.000	0.000
14	C	128	ARG	1	0.897	0.914	18.144	14.580	14.580	0.000	0.000	0.000	0.000
15	C	129	ALA	0	0.048	0.020	14.231	-0.108	-0.108	0.000	0.000	0.000	0.000
16	C	130	LYS	1	0.919	0.978	13.298	16.265	16.265	0.000	0.000	0.000	0.000
17	C	131	ALA	0	-0.035	-0.012	14.261	-0.515	-0.515	0.000	0.000	0.000	0.000
18	C	132	LEU	0	-0.001	-0.006	14.044	0.151	0.151	0.000	0.000	0.000	0.000
19	C	133	CYS	0	-0.091	-0.022	8.237	-0.976	-0.976	0.000	0.000	0.000	0.000
20	C	134	SER	0	-0.011	0.009	11.159	-0.467	-0.467	0.000	0.000	0.000	0.000
21	C	135	GLU	-1	-0.951	-0.965	12.959	-15.778	-15.778	0.000	0.000	0.000	0.000
22	C	136	LEU	0	-0.055	-0.031	11.929	0.696	0.696	0.000	0.000	0.000	0.000
23	C	137	GLN	0	-0.052	-0.030	10.929	-1.203	-1.203	0.000	0.000	0.000	0.000
24	C	138	GLY	0	0.030	0.014	7.447	-1.980	-1.980	0.000	0.000	0.000	0.000
25	C	139	THR	0	-0.021	-0.019	6.064	4.100	4.100	0.000	0.000	0.000	0.000
26	C	140	VAL	0	-0.006	-0.005	7.358	-2.061	-2.061	0.000	0.000	0.000	0.000
27	C	141	ALA	0	-0.010	-0.024	5.292	-2.757	-2.757	0.000	0.000	0.000	0.000
28	C	142	THR	0	-0.007	-0.015	4.468	9.885	9.983	-0.001	-0.002	-0.094	0.000
29	C	143	PRO	0	-0.043	-0.018	3.981	-13.846	-13.656	-0.001	-0.046	-0.143	0.000
30	C	144	ARG	1	0.879	0.945	2.892	59.415	60.073	0.103	-0.163	-0.598	-0.001
31	C	145	ASN	0	0.064	0.042	5.351	8.035	8.081	-0.001	0.000	-0.045	0.000
32	C	146	ALA	0	0.019	-0.005	7.846	-1.340	-1.340	0.000	0.000	0.000	0.000
33	C	147	GLU	-1	-0.955	-0.987	7.977	-28.202	-28.202	0.000	0.000	0.000	0.000
34	C	148	GLU	-1	-0.807	-0.927	2.162	-105.803	-99.962	2.612	-4.338	-4.114	-0.062
35	C	149	ASN	0	-0.003	0.027	5.640	0.824	0.824	0.000	0.000	0.000	0.000
36	C	150	ARG	1	0.945	0.978	8.383	26.289	26.289	0.000	0.000	0.000	0.000
37	C	151	ALA	0	-0.007	-0.004	6.044	2.160	2.160	0.000	0.000	0.000	0.000
38	C	152	ILE	0	0.039	0.006	5.214	2.116	2.116	0.000	0.000	0.000	0.000
39	C	153	GLN	0	-0.013	-0.024	7.952	2.978	2.978	0.000	0.000	0.000	0.000
40	C	154	ASN	0	-0.064	-0.016	10.295	2.887	2.887	0.000	0.000	0.000	0.000
41	C	155	VAL	0	-0.054	-0.016	7.783	1.664	1.664	0.000	0.000	0.000	0.000
42	C	156	ALA	0	-0.020	-0.004	10.782	1.467	1.467	0.000	0.000	0.000	0.000
43	C	157	LYS	1	0.918	0.957	13.080	17.268	17.268	0.000	0.000	0.000	0.000
44	C	158	ASP	-1	-0.858	-0.944	16.192	-13.823	-13.823	0.000	0.000	0.000	0.000
45	C	159	VAL	0	-0.030	-0.005	16.213	-1.191	-1.191	0.000	0.000	0.000	0.000
46	C	160	ALA	0	-0.009	-0.010	13.152	0.398	0.398	0.000	0.000	0.000	0.000
47	C	161	PHE	0	-0.039	-0.015	13.788	-0.296	-0.296	0.000	0.000	0.000	0.000
48	C	162	LEU	0	-0.015	0.005	9.217	-2.037	-2.037	0.000	0.000	0.000	0.000
49	C	163	GLY	0	-0.032	-0.021	8.793	2.720	2.720	0.000	0.000	0.000	0.000
50	C	164	ILE	0	-0.015	0.007	9.780	-0.283	-0.283	0.000	0.000	0.000	0.000
51	C	174	GLU	-1	-0.952	-0.996	12.954	-19.891	-19.891	0.000	0.000	0.000	0.000
52	C	175	ASP	-1	-0.781	-0.884	8.264	-33.869	-33.869	0.000	0.000	0.000	0.000
53	C	176	LEU	0	-0.080	-0.066	10.063	2.136	2.136	0.000	0.000	0.000	0.000
54	C	177	THR	0	-0.130	-0.054	9.649	0.708	0.708	0.000	0.000	0.000	0.000
55	C	178	GLY	0	0.021	0.037	11.011	-0.235	-0.235	0.000	0.000	0.000	0.000
56	C	200	CYS	0	-0.002	-0.019	16.496	-0.443	-0.443	0.000	0.000	0.000	0.000
57	C	201	VAL	0	0.031	0.012	13.560	0.589	0.589	0.000	0.000	0.000	0.000
58	C	202	VAL	0	-0.018	-0.004	14.478	-0.995	-0.995	0.000	0.000	0.000	0.000
59	C	203	LEU	0	-0.022	0.011	10.543	0.489	0.489	0.000	0.000	0.000	0.000
60	C	204	LEU	0	0.003	-0.014	14.369	0.823	0.823	0.000	0.000	0.000	0.000
61	C	205	THR	0	0.081	0.036	16.030	-0.817	-0.817	0.000	0.000	0.000	0.000
62	C	206	ASN	0	-0.024	0.002	17.707	-0.873	-0.873	0.000	0.000	0.000	0.000
63	C	207	GLY	0	-0.005	-0.019	14.385	-0.085	-0.085	0.000	0.000	0.000	0.000
64	C	208	LYS	1	0.921	0.954	14.414	16.355	16.355	0.000	0.000	0.000	0.000
65	C	209	TRP	0	-0.020	-0.037	9.817	-0.218	-0.218	0.000	0.000	0.000	0.000
66	C	210	ASN	0	0.004	0.008	16.169	0.623	0.623	0.000	0.000	0.000	0.000
67	C	211	ASP	-1	-0.922	-0.950	18.106	-16.358	-16.358	0.000	0.000	0.000	0.000
68	C	212	VAL	0	-0.021	-0.012	18.960	0.884	0.884	0.000	0.000	0.000	0.000
69	C	213	PRO	0	0.041	0.033	20.382	-0.591	-0.591	0.000	0.000	0.000	0.000
70	C	215	SER	0	-0.014	-0.020	20.284	-0.228	-0.228	0.000	0.000	0.000	0.000
71	C	216	ASP	-1	-0.880	-0.922	22.549	-12.301	-12.301	0.000	0.000	0.000	0.000
72	C	217	SER	0	-0.058	-0.054	20.988	-0.689	-0.689	0.000	0.000	0.000	0.000
73	C	218	PHE	0	0.031	0.008	17.618	0.472	0.472	0.000	0.000	0.000	0.000
74	C	219	LEU	0	-0.014	0.009	15.561	0.150	0.150	0.000	0.000	0.000	0.000
75	C	220	VAL	0	0.027	0.005	11.858	-0.601	-0.601	0.000	0.000	0.000	0.000
76	C	221	VAL	0	0.068	0.030	7.555	0.912	0.912	0.000	0.000	0.000	0.000
77	C	223	GLU	-1	-0.806	-0.901	2.595	-95.403	-89.797	0.674	-3.124	-3.156	-0.039
78	C	224	PHE	0	0.021	0.016	3.645	1.313	1.827	0.007	-0.153	-0.367	-0.001
79	C	225	SER	0	0.019	0.008	2.372	-5.662	-4.071	4.266	-2.907	-2.950	-0.028

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