FMO DATABASE

FMODB ID: KR613

Calculation Name: 2ZV3-A-Xray311

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZV3

Chain ID: A

ChEMBL ID:

UniProt ID: Q60363

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	110
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-849584.098568
FMO2-HF: Nuclear repulsion	807347.874577
FMO2-HF: Total energy	-42236.22399
FMO2-MP2: Total energy	-42358.309911

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:1:MET )

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

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.
-114.481	-104.649	22.743	-8.685	-23.895	-0.151

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.788 / q_NPA : 0.923

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	3	MET	0	0.031	0.032	3.762	2.507	4.859	-0.030	-1.236	-1.087	-0.002
4	A	4	VAL	0	-0.046	-0.014	6.606	0.323	0.323	0.000	0.000	0.000	0.000
5	A	5	VAL	0	0.000	-0.011	9.934	1.399	1.399	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.001	-0.008	13.140	0.420	0.420	0.000	0.000	0.000	0.000
7	A	7	ILE	0	0.019	-0.002	16.287	0.802	0.802	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.779	0.868	19.566	11.999	11.999	0.000	0.000	0.000	0.000
9	A	9	ASN	0	-0.002	-0.016	23.038	0.059	0.059	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.795	-0.875	25.109	-11.230	-11.230	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.047	-0.025	25.518	0.374	0.374	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.023	0.030	28.823	0.306	0.306	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.063	-0.023	23.056	0.268	0.268	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.084	0.041	27.541	-0.086	-0.086	0.000	0.000	0.000	0.000
15	A	15	LYS	1	1.002	0.976	25.173	11.274	11.274	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.036	0.020	24.239	-0.473	-0.473	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.897	0.949	24.662	10.717	10.717	0.000	0.000	0.000	0.000
18	A	18	MET	0	0.037	0.023	21.594	-0.380	-0.380	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.001	0.009	19.742	-0.753	-0.753	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.004	0.006	19.750	-0.584	-0.584	0.000	0.000	0.000	0.000
21	A	21	GLN	0	0.020	0.040	20.650	-0.442	-0.442	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.074	0.026	17.389	-0.496	-0.496	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.017	0.004	16.009	-1.136	-1.136	0.000	0.000	0.000	0.000
24	A	24	HIS	0	0.011	-0.004	16.558	-0.798	-0.798	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.014	0.005	15.132	-0.356	-0.356	0.000	0.000	0.000	0.000
26	A	26	ILE	0	0.008	-0.016	11.296	-1.231	-1.231	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.009	0.005	11.757	-1.252	-1.252	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.874	-0.951	13.229	-15.843	-15.843	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.041	0.003	9.593	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.029	0.006	8.203	-1.052	-1.052	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.030	-0.018	9.043	-0.224	-0.224	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.805	-0.908	10.533	-18.750	-18.750	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.024	-0.007	5.299	0.168	0.168	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.923	0.961	7.437	19.740	19.740	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.915	0.950	8.688	16.809	16.809	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.866	0.954	8.578	20.250	20.250	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.014	0.002	5.475	0.859	0.859	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.048	0.018	5.870	-2.543	-2.543	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.998	0.998	7.549	20.675	20.675	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.018	0.014	2.215	-1.917	-1.660	1.430	-0.390	-1.297	0.001
41	A	41	VAL	0	-0.018	-0.004	3.415	-5.353	-3.864	0.952	-0.811	-1.631	-0.013
42	A	42	ASP	-1	-0.898	-0.955	4.784	-24.574	-24.566	0.000	-0.007	-0.001	0.000
43	A	43	GLU	-1	-0.989	-1.011	3.312	-52.908	-50.345	0.317	-1.099	-1.781	-0.009
44	A	44	TRP	0	-0.038	-0.007	2.736	-2.607	-0.245	0.879	-0.846	-2.396	0.000
45	A	45	LEU	0	-0.038	-0.027	3.568	0.489	0.525	0.031	0.082	-0.150	0.001
46	A	46	ARG	1	0.906	0.975	6.955	33.398	33.398	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.956	-0.970	2.831	-82.756	-79.500	0.185	-1.838	-1.602	-0.018
48	A	48	GLY	0	0.019	0.016	6.437	-0.730	-0.730	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.020	-0.013	5.773	2.916	2.916	0.000	0.000	0.000	0.000
50	A	50	LYS	1	1.013	1.009	5.048	47.770	47.770	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.872	0.924	6.494	26.159	26.159	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.010	-0.002	8.772	1.111	1.111	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.000	0.005	11.021	0.107	0.107	0.000	0.000	0.000	0.000
54	A	54	VAL	0	0.024	0.025	13.449	0.722	0.722	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.939	0.978	16.097	14.184	14.184	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.007	-0.002	19.103	-0.215	-0.215	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.046	-0.050	21.550	0.313	0.313	0.000	0.000	0.000	0.000
58	A	58	SER	0	0.050	0.027	24.774	0.591	0.591	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.839	-0.930	24.648	-11.407	-11.407	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.986	0.992	24.472	10.850	10.850	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.854	-0.923	21.426	-14.117	-14.117	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.025	-0.003	19.037	-0.701	-0.701	0.000	0.000	0.000	0.000
63	A	63	ILE	0	0.015	-0.007	19.594	-0.742	-0.742	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.921	-0.951	20.590	-12.930	-12.930	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.040	-0.016	15.572	-0.554	-0.554	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.037	0.024	15.812	-1.074	-1.074	0.000	0.000	0.000	0.000
67	A	67	ASN	0	0.027	0.006	16.434	-0.585	-0.585	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.949	0.985	16.376	14.949	14.949	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.042	0.023	12.154	-0.560	-0.560	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.873	0.923	13.034	16.661	16.661	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.086	-0.040	15.253	0.251	0.251	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.858	-0.924	12.055	-18.841	-18.841	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.031	0.001	12.052	-0.730	-0.730	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.059	-0.029	7.476	-1.422	-1.422	0.000	0.000	0.000	0.000
75	A	75	PRO	0	-0.042	-0.011	5.868	1.830	1.830	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.046	-0.022	9.000	-0.958	-0.958	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.032	-0.008	11.562	1.089	1.089	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.050	0.008	14.765	-0.344	-0.344	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.016	0.010	17.482	0.491	0.491	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.969	0.977	20.414	10.520	10.520	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.875	-0.941	24.213	-10.915	-10.915	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.035	-0.012	26.444	0.266	0.266	0.000	0.000	0.000	0.000
83	A	83	NME	0	0.025	0.014	29.663	0.205	0.205	0.000	0.000	0.000	0.000
84	A	89	ACE	0	0.008	-0.007	34.256	0.049	0.049	0.000	0.000	0.000	0.000
85	A	90	GLY	0	0.027	0.016	30.461	0.007	0.007	0.000	0.000	0.000	0.000
86	A	91	THR	0	-0.067	-0.024	27.106	-0.062	-0.062	0.000	0.000	0.000	0.000
87	A	92	LEU	0	0.021	0.020	22.827	-0.232	-0.232	0.000	0.000	0.000	0.000
88	A	93	THR	0	-0.013	-0.056	22.455	-0.147	-0.147	0.000	0.000	0.000	0.000
89	A	94	ALA	0	0.021	0.001	17.984	-0.216	-0.216	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.005	0.015	14.236	0.396	0.396	0.000	0.000	0.000	0.000
91	A	96	ALA	0	-0.022	0.012	11.274	-0.600	-0.600	0.000	0.000	0.000	0.000
92	A	97	ILE	0	0.006	-0.001	8.341	0.942	0.942	0.000	0.000	0.000	0.000
93	A	98	GLY	0	0.017	0.035	5.504	-3.254	-3.254	0.000	0.000	0.000	0.000
94	A	99	PRO	0	-0.054	-0.052	2.470	2.695	3.409	0.469	-0.226	-0.958	0.000
95	A	100	GLU	-1	-0.845	-0.959	2.051	-32.409	-35.365	8.020	-1.585	-3.479	-0.011
96	A	101	LYS	1	0.924	0.954	2.334	25.536	22.796	4.175	3.283	-4.719	-0.033
97	A	102	ASP	-1	-0.848	-0.934	2.153	-98.978	-96.652	6.313	-3.970	-4.669	-0.067
98	A	103	GLU	-1	-0.789	-0.905	4.184	-36.992	-36.827	0.002	-0.042	-0.125	0.000
99	A	104	LYS	1	0.909	0.957	6.381	31.695	31.695	0.000	0.000	0.000	0.000
100	A	105	ILE	0	-0.011	0.001	5.167	3.662	3.662	0.000	0.000	0.000	0.000
101	A	106	ASP	-1	-0.811	-0.891	7.983	-31.607	-31.607	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.837	0.929	9.953	22.213	22.213	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.078	-0.041	11.703	2.061	2.061	0.000	0.000	0.000	0.000
104	A	109	THR	0	-0.011	-0.032	11.054	0.998	0.998	0.000	0.000	0.000	0.000
105	A	110	GLY	0	0.036	0.034	12.659	0.225	0.225	0.000	0.000	0.000	0.000
106	A	111	HIS	0	-0.030	-0.008	13.387	0.019	0.019	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.053	-0.016	15.415	1.044	1.044	0.000	0.000	0.000	0.000
108	A	113	LYS	1	0.932	0.962	16.749	14.056	14.056	0.000	0.000	0.000	0.000
109	A	114	LEU	0	0.019	-0.005	14.355	-0.385	-0.385	0.000	0.000	0.000	0.000
110	A	115	LEU	-1	-0.937	-0.969	17.840	-14.403	-14.403	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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