FMO DATABASE

FMODB ID: 52ZQZ

Calculation Name: 4A9A-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A9A

Chain ID: D

ChEMBL ID:

UniProt ID: P39729

Base Structure: X-ray

Registration Date: 2023-06-21

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-434680.369074
FMO2-HF: Nuclear repulsion	401142.42757
FMO2-HF: Total energy	-33537.941504
FMO2-MP2: Total energy	-33637.232657

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(D:214:LEU)

Summations of interaction energy for fragment #1(D:214:LEU)

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.
-1.095	3.028	0.377	-1.998	-2.501	-0.002

Interaction energy analysis for fragmet #1(D:214:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.008

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	D	216	LYS	1	0.887	0.932	2.912	-0.252	3.288	0.321	-1.882	-1.978	-0.002
4	D	217	GLN	0	0.066	0.023	3.249	-1.015	-0.432	0.056	-0.116	-0.523	0.000
5	D	218	PRO	0	-0.018	0.010	6.062	0.104	0.104	0.000	0.000	0.000	0.000
6	D	219	LYS	1	0.914	0.944	9.448	0.194	0.194	0.000	0.000	0.000	0.000
7	D	220	ILE	0	0.038	0.037	11.115	-0.015	-0.015	0.000	0.000	0.000	0.000
8	D	221	THR	0	-0.038	-0.052	13.298	0.028	0.028	0.000	0.000	0.000	0.000
9	D	222	LEU	0	-0.026	-0.035	16.344	0.019	0.019	0.000	0.000	0.000	0.000
10	D	223	GLU	-1	-0.839	-0.926	18.007	0.046	0.046	0.000	0.000	0.000	0.000
11	D	224	GLU	-1	-0.769	-0.845	16.263	-0.061	-0.061	0.000	0.000	0.000	0.000
12	D	225	PHE	0	-0.026	-0.028	13.605	0.019	0.019	0.000	0.000	0.000	0.000
13	D	226	ILE	0	-0.041	-0.024	16.158	0.023	0.023	0.000	0.000	0.000	0.000
14	D	227	GLU	-1	-0.938	-0.964	19.607	0.032	0.032	0.000	0.000	0.000	0.000
15	D	228	THR	0	-0.055	-0.027	18.096	-0.019	-0.019	0.000	0.000	0.000	0.000
16	D	229	GLU	-1	-0.927	-0.959	12.792	0.004	0.004	0.000	0.000	0.000	0.000
17	D	230	ARG	1	0.952	0.977	14.732	-0.169	-0.169	0.000	0.000	0.000	0.000
18	D	231	GLY	0	-0.067	-0.039	16.272	0.024	0.024	0.000	0.000	0.000	0.000
19	D	232	LYS	1	0.908	0.963	14.247	0.065	0.065	0.000	0.000	0.000	0.000
20	D	233	LEU	0	-0.054	-0.009	11.172	0.017	0.017	0.000	0.000	0.000	0.000
21	D	234	ASP	-1	-0.830	-0.921	14.723	0.205	0.205	0.000	0.000	0.000	0.000
22	D	235	LYS	1	0.962	0.963	16.759	-0.137	-0.137	0.000	0.000	0.000	0.000
23	D	236	SER	0	-0.049	-0.019	19.220	0.005	0.005	0.000	0.000	0.000	0.000
24	D	237	LYS	1	0.924	0.961	15.956	-0.262	-0.262	0.000	0.000	0.000	0.000
25	D	238	LEU	0	-0.006	0.020	15.289	0.069	0.069	0.000	0.000	0.000	0.000
26	D	239	THR	0	-0.003	-0.017	14.874	-0.048	-0.048	0.000	0.000	0.000	0.000
27	D	240	PRO	0	-0.005	0.007	16.851	0.019	0.019	0.000	0.000	0.000	0.000
28	D	241	ILE	0	0.020	0.015	16.100	0.021	0.021	0.000	0.000	0.000	0.000
29	D	242	THR	0	0.009	0.002	18.686	-0.044	-0.044	0.000	0.000	0.000	0.000
30	D	243	ILE	0	0.057	0.012	19.330	0.037	0.037	0.000	0.000	0.000	0.000
31	D	244	ALA	0	0.021	0.021	19.885	0.021	0.021	0.000	0.000	0.000	0.000
32	D	245	ASN	0	0.047	0.011	15.703	0.022	0.022	0.000	0.000	0.000	0.000
33	D	246	PHE	0	0.056	0.029	14.807	0.091	0.091	0.000	0.000	0.000	0.000
34	D	247	ALA	0	0.023	0.013	14.968	0.048	0.048	0.000	0.000	0.000	0.000
35	D	248	GLN	0	-0.018	-0.018	13.993	0.029	0.029	0.000	0.000	0.000	0.000
36	D	249	TRP	0	0.026	0.024	8.663	0.033	0.033	0.000	0.000	0.000	0.000
37	D	250	LYS	1	0.952	0.974	10.536	-0.372	-0.372	0.000	0.000	0.000	0.000
38	D	251	LYS	1	0.937	0.975	12.248	-0.814	-0.814	0.000	0.000	0.000	0.000
39	D	252	ASP	-1	-0.872	-0.941	7.915	1.304	1.304	0.000	0.000	0.000	0.000
40	D	253	HIS	0	-0.056	-0.017	7.940	0.061	0.061	0.000	0.000	0.000	0.000
41	D	254	VAL	0	0.002	-0.014	9.004	-0.029	-0.029	0.000	0.000	0.000	0.000
42	D	255	ILE	0	0.021	0.009	9.773	-0.073	-0.073	0.000	0.000	0.000	0.000
43	D	256	ALA	0	0.008	0.009	5.186	-0.085	-0.085	0.000	0.000	0.000	0.000
44	D	257	LYS	1	0.917	0.972	7.195	-0.574	-0.574	0.000	0.000	0.000	0.000
45	D	258	ILE	0	0.008	-0.001	9.426	-0.134	-0.134	0.000	0.000	0.000	0.000
46	D	259	ASN	0	0.013	-0.010	8.354	-0.211	-0.211	0.000	0.000	0.000	0.000
47	D	260	ALA	0	-0.042	-0.012	6.627	-0.171	-0.171	0.000	0.000	0.000	0.000
48	D	261	GLU	-1	-0.863	-0.952	8.682	0.157	0.157	0.000	0.000	0.000	0.000
49	D	262	LYS	1	0.863	0.945	12.107	-0.219	-0.219	0.000	0.000	0.000	0.000
50	D	263	LYS	1	0.983	1.005	8.605	0.485	0.485	0.000	0.000	0.000	0.000
51	D	264	LEU	0	-0.018	-0.016	12.227	-0.039	-0.039	0.000	0.000	0.000	0.000
52	D	265	SER	0	0.006	0.001	15.624	0.009	0.009	0.000	0.000	0.000	0.000
53	D	266	SER	0	-0.033	0.006	17.658	-0.006	-0.006	0.000	0.000	0.000	0.000
54	D	267	LYS	1	0.894	0.942	19.181	0.112	0.112	0.000	0.000	0.000	0.000
55	D	268	ARG	1	0.977	0.981	21.908	-0.017	-0.017	0.000	0.000	0.000	0.000
56	D	269	LYS	1	0.973	0.970	24.403	0.040	0.040	0.000	0.000	0.000	0.000
57	D	270	PRO	0	-0.010	0.009	27.537	0.005	0.005	0.000	0.000	0.000	0.000
58	D	271	THR	0	0.025	0.021	28.199	-0.003	-0.003	0.000	0.000	0.000	0.000
59	D	272	GLY	0	0.074	0.026	30.879	0.000	0.000	0.000	0.000	0.000	0.000
60	D	273	ARG	1	1.001	1.000	30.119	-0.062	-0.062	0.000	0.000	0.000	0.000
61	D	274	GLU	-1	-0.871	-0.939	27.330	0.035	0.035	0.000	0.000	0.000	0.000
62	D	275	ILE	0	-0.036	-0.012	32.247	-0.001	-0.001	0.000	0.000	0.000	0.000
63	D	276	ILE	0	0.049	0.017	35.176	0.000	0.000	0.000	0.000	0.000	0.000
64	D	277	LEU	0	-0.013	-0.007	33.108	0.001	0.001	0.000	0.000	0.000	0.000
65	D	278	LYS	1	0.945	0.962	32.857	-0.011	-0.011	0.000	0.000	0.000	0.000
66	D	279	MET	0	-0.004	0.002	36.353	-0.002	-0.002	0.000	0.000	0.000	0.000
67	D	280	SER	0	-0.070	-0.033	39.320	0.000	0.000	0.000	0.000	0.000	0.000
68	D	281	ALA	0	-0.037	-0.001	38.191	0.002	0.002	0.000	0.000	0.000	0.000
69	D	282	GLU	-1	-0.985	-0.978	39.543	0.017	0.017	0.000	0.000	0.000	0.000
70	D	320	ASP	-1	-0.899	-0.957	37.778	0.082	0.082	0.000	0.000	0.000	0.000
71	D	321	GLY	0	-0.049	-0.019	38.839	-0.003	-0.003	0.000	0.000	0.000	0.000
72	D	322	GLY	0	-0.040	-0.009	40.525	-0.004	-0.004	0.000	0.000	0.000	0.000
73	D	323	ILE	0	-0.050	-0.033	35.019	0.003	0.003	0.000	0.000	0.000	0.000
74	D	324	LYS	1	0.913	0.938	29.361	-0.139	-0.139	0.000	0.000	0.000	0.000
75	D	325	ASP	-1	-0.878	-0.944	32.453	0.093	0.093	0.000	0.000	0.000	0.000
76	D	326	TYR	0	-0.034	-0.030	26.733	0.010	0.010	0.000	0.000	0.000	0.000
77	D	327	GLY	0	0.034	0.032	27.839	0.010	0.010	0.000	0.000	0.000	0.000
78	D	328	ASP	-1	-0.904	-0.939	25.928	0.141	0.141	0.000	0.000	0.000	0.000
79	D	329	GLY	0	-0.040	-0.015	23.592	0.005	0.005	0.000	0.000	0.000	0.000
80	D	330	SER	0	-0.096	-0.067	21.997	0.025	0.025	0.000	0.000	0.000	0.000
81	D	331	ASN	0	-0.072	-0.053	22.123	-0.014	-0.014	0.000	0.000	0.000	0.000
82	D	332	PRO	0	0.033	0.043	22.184	-0.011	-0.011	0.000	0.000	0.000	0.000
83	D	333	THR	0	0.035	0.018	25.073	0.013	0.013	0.000	0.000	0.000	0.000
84	D	334	PHE	0	-0.049	-0.040	23.425	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	335	ASP	-1	-0.880	-0.916	28.782	0.151	0.151	0.000	0.000	0.000	0.000
86	D	336	ILE	0	-0.026	-0.007	32.091	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:214:LEU)