FMO DATABASE

FMODB ID: V5M41

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	OptAll
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	-531028.499484
FMO2-HF: Nuclear repulsion	498515.040148
FMO2-HF: Total energy	-32513.459337
FMO2-MP2: Total energy	-32604.52579

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.
-196.457	-195.274	44.636	-21.568	-24.248	-0.222

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 : 0.814 / q_NPA : 0.897

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	C	117	PHE	0	0.023	-0.006	2.292	-5.190	-1.912	3.431	-2.392	-4.317	0.000
4	C	118	MET	0	-0.013	-0.006	6.081	4.007	4.007	0.000	0.000	0.000	0.000
5	C	119	SER	0	0.032	0.029	9.638	-1.039	-1.039	0.000	0.000	0.000	0.000
6	C	120	SER	0	-0.052	-0.037	12.135	0.851	0.851	0.000	0.000	0.000	0.000
7	C	121	VAL	0	0.023	0.001	15.143	0.346	0.346	0.000	0.000	0.000	0.000
8	C	122	ARG	1	0.928	0.958	18.345	14.353	14.353	0.000	0.000	0.000	0.000
9	C	123	ARG	1	0.878	0.943	18.218	13.985	13.985	0.000	0.000	0.000	0.000
10	C	124	MET	0	-0.051	0.007	16.619	0.822	0.822	0.000	0.000	0.000	0.000
11	C	125	PRO	0	0.080	0.043	17.859	-0.750	-0.750	0.000	0.000	0.000	0.000
12	C	126	LEU	0	0.074	0.042	11.963	-0.169	-0.169	0.000	0.000	0.000	0.000
13	C	127	ASN	0	0.030	0.002	15.412	-1.121	-1.121	0.000	0.000	0.000	0.000
14	C	128	ARG	1	0.897	0.942	17.939	15.916	15.916	0.000	0.000	0.000	0.000
15	C	129	ALA	0	0.023	0.012	13.019	-0.177	-0.177	0.000	0.000	0.000	0.000
16	C	130	LYS	1	0.916	0.948	12.374	17.009	17.009	0.000	0.000	0.000	0.000
17	C	131	ALA	0	0.001	0.016	13.445	-0.509	-0.509	0.000	0.000	0.000	0.000
18	C	132	LEU	0	-0.032	-0.021	14.188	0.410	0.410	0.000	0.000	0.000	0.000
19	C	133	CYS	0	-0.060	0.003	8.142	-1.232	-1.232	0.000	0.000	0.000	0.000
20	C	134	SER	0	0.062	0.031	11.350	-0.464	-0.464	0.000	0.000	0.000	0.000
21	C	135	GLU	-1	-0.966	-0.969	13.273	-15.777	-15.777	0.000	0.000	0.000	0.000
22	C	136	LEU	0	-0.085	-0.042	11.956	0.736	0.736	0.000	0.000	0.000	0.000
23	C	137	GLN	0	-0.041	-0.018	11.090	-1.185	-1.185	0.000	0.000	0.000	0.000
24	C	138	GLY	0	0.018	0.010	7.896	-1.568	-1.568	0.000	0.000	0.000	0.000
25	C	139	THR	0	-0.014	-0.013	5.804	3.686	3.686	0.000	0.000	0.000	0.000
26	C	140	VAL	0	0.020	0.002	7.378	-1.689	-1.689	0.000	0.000	0.000	0.000
27	C	141	ALA	0	-0.009	-0.011	4.222	-4.280	-4.175	-0.001	-0.018	-0.085	0.000
28	C	142	THR	0	-0.010	-0.020	3.018	14.033	14.705	0.009	-0.292	-0.390	0.000
29	C	143	PRO	0	-0.035	-0.018	2.921	-22.934	-21.235	0.376	-0.976	-1.098	-0.010
30	C	144	ARG	1	0.842	0.909	2.476	70.109	71.467	0.348	-0.549	-1.156	-0.002
31	C	145	ASN	0	-0.022	-0.018	4.760	9.580	9.668	-0.001	-0.004	-0.083	0.000
32	C	146	ALA	0	0.040	0.008	6.934	-2.397	-2.397	0.000	0.000	0.000	0.000
33	C	147	GLU	-1	-0.801	-0.865	7.161	-24.675	-24.675	0.000	0.000	0.000	0.000
34	C	148	GLU	-1	-0.744	-0.857	1.704	-110.731	-114.792	15.561	-5.729	-5.771	-0.071
35	C	149	ASN	0	-0.010	0.006	4.848	-0.228	-0.167	-0.001	-0.002	-0.058	0.000
36	C	150	ARG	1	0.810	0.872	7.831	27.172	27.172	0.000	0.000	0.000	0.000
37	C	151	ALA	0	-0.017	-0.011	5.653	2.243	2.243	0.000	0.000	0.000	0.000
38	C	152	ILE	0	0.034	0.015	3.634	1.966	2.176	0.001	-0.032	-0.179	0.000
39	C	153	GLN	0	0.024	0.012	7.618	3.507	3.507	0.000	0.000	0.000	0.000
40	C	154	ASN	0	-0.066	-0.020	10.417	3.215	3.215	0.000	0.000	0.000	0.000
41	C	155	VAL	0	-0.044	-0.022	8.461	1.753	1.753	0.000	0.000	0.000	0.000
42	C	156	ALA	0	0.006	-0.002	10.974	1.594	1.594	0.000	0.000	0.000	0.000
43	C	157	LYS	1	0.889	0.955	12.631	19.625	19.625	0.000	0.000	0.000	0.000
44	C	158	ASP	-1	-0.808	-0.898	15.833	-14.623	-14.623	0.000	0.000	0.000	0.000
45	C	159	VAL	0	-0.013	0.001	15.530	-1.316	-1.316	0.000	0.000	0.000	0.000
46	C	160	ALA	0	-0.005	0.003	12.120	0.611	0.611	0.000	0.000	0.000	0.000
47	C	161	PHE	0	-0.026	-0.015	12.263	-0.246	-0.246	0.000	0.000	0.000	0.000
48	C	162	LEU	0	-0.022	-0.004	7.300	-2.487	-2.487	0.000	0.000	0.000	0.000
49	C	163	GLY	0	-0.022	-0.009	7.482	3.545	3.545	0.000	0.000	0.000	0.000
50	C	164	ILE	0	-0.042	-0.028	8.014	1.401	1.401	0.000	0.000	0.000	0.000
51	C	174	GLU	-1	-0.871	-0.899	12.331	-20.282	-20.282	0.000	0.000	0.000	0.000
52	C	175	ASP	-1	-0.758	-0.848	7.334	-37.740	-37.740	0.000	0.000	0.000	0.000
53	C	176	LEU	0	-0.057	-0.043	9.426	2.591	2.591	0.000	0.000	0.000	0.000
54	C	177	THR	0	-0.117	-0.064	8.700	1.090	1.090	0.000	0.000	0.000	0.000
55	C	178	GLY	0	-0.065	-0.054	10.533	-1.110	-1.110	0.000	0.000	0.000	0.000
56	C	200	CYS	0	-0.002	-0.017	15.469	-0.015	-0.015	0.000	0.000	0.000	0.000
57	C	201	VAL	0	-0.003	-0.003	11.987	0.694	0.694	0.000	0.000	0.000	0.000
58	C	202	VAL	0	-0.010	-0.005	12.908	-1.253	-1.253	0.000	0.000	0.000	0.000
59	C	203	LEU	0	-0.016	-0.003	9.572	0.304	0.304	0.000	0.000	0.000	0.000
60	C	204	LEU	0	0.023	0.000	13.046	1.043	1.043	0.000	0.000	0.000	0.000
61	C	205	THR	0	0.062	0.015	15.198	-0.887	-0.887	0.000	0.000	0.000	0.000
62	C	206	ASN	0	-0.036	-0.010	16.747	-1.003	-1.003	0.000	0.000	0.000	0.000
63	C	207	GLY	0	0.012	0.005	13.605	0.162	0.162	0.000	0.000	0.000	0.000
64	C	208	LYS	1	0.894	0.951	13.350	16.722	16.722	0.000	0.000	0.000	0.000
65	C	209	TRP	0	0.008	-0.009	8.246	-0.020	-0.020	0.000	0.000	0.000	0.000
66	C	210	ASN	0	-0.010	-0.011	14.705	0.929	0.929	0.000	0.000	0.000	0.000
67	C	211	ASP	-1	-0.864	-0.924	16.351	-17.888	-17.888	0.000	0.000	0.000	0.000
68	C	212	VAL	0	-0.030	-0.018	17.392	1.030	1.030	0.000	0.000	0.000	0.000
69	C	213	PRO	0	0.038	0.033	19.156	-0.574	-0.574	0.000	0.000	0.000	0.000
70	C	215	SER	0	-0.023	-0.010	19.250	-0.293	-0.293	0.000	0.000	0.000	0.000
71	C	216	ASP	-1	-0.885	-0.939	21.546	-12.904	-12.904	0.000	0.000	0.000	0.000
72	C	217	SER	0	-0.047	-0.038	19.843	-0.785	-0.785	0.000	0.000	0.000	0.000
73	C	218	PHE	0	0.049	0.020	16.366	0.576	0.576	0.000	0.000	0.000	0.000
74	C	219	LEU	0	-0.016	-0.011	14.805	0.125	0.125	0.000	0.000	0.000	0.000
75	C	220	VAL	0	0.018	0.009	11.463	-0.779	-0.779	0.000	0.000	0.000	0.000
76	C	221	VAL	0	0.034	0.016	7.006	1.154	1.154	0.000	0.000	0.000	0.000
77	C	223	GLU	-1	-0.774	-0.891	1.763	-141.730	-146.521	21.880	-9.059	-8.030	-0.115
78	C	224	PHE	0	0.034	0.021	3.418	3.005	3.474	0.008	-0.122	-0.354	0.000
79	C	225	SER	0	0.018	0.010	2.460	-6.307	-4.212	3.025	-2.393	-2.727	-0.024

Top

Graph

Manual

About

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