FMO DATABASE

FMODB ID: V58Z1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-435534.439748
FMO2-HF: Nuclear repulsion	401995.442064
FMO2-HF: Total energy	-33538.997683
FMO2-MP2: Total energy	-33638.274305

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.
0.411	4.267	0.388	-1.875	-2.369	0.004

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 : 0.022 / q_NPA : 0.018

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	0.898	0.941	3.370	0.108	3.081	0.032	-1.605	-1.400	0.004
4	D	217	GLN	0	0.030	0.010	2.689	-0.162	0.721	0.356	-0.270	-0.969	0.000
5	D	218	PRO	0	0.004	0.006	5.838	0.121	0.121	0.000	0.000	0.000	0.000
6	D	219	LYS	1	0.828	0.901	7.927	0.411	0.411	0.000	0.000	0.000	0.000
7	D	220	ILE	0	0.032	0.032	11.417	-0.017	-0.017	0.000	0.000	0.000	0.000
8	D	221	THR	0	-0.011	-0.036	13.775	0.025	0.025	0.000	0.000	0.000	0.000
9	D	222	LEU	0	-0.012	-0.008	16.289	0.019	0.019	0.000	0.000	0.000	0.000
10	D	223	GLU	-1	-0.825	-0.926	18.127	0.026	0.026	0.000	0.000	0.000	0.000
11	D	224	GLU	-1	-0.747	-0.839	16.342	-0.082	-0.082	0.000	0.000	0.000	0.000
12	D	225	PHE	0	-0.043	-0.010	13.131	0.023	0.023	0.000	0.000	0.000	0.000
13	D	226	ILE	0	-0.053	-0.038	16.006	0.025	0.025	0.000	0.000	0.000	0.000
14	D	227	GLU	-1	-0.942	-0.967	19.391	0.023	0.023	0.000	0.000	0.000	0.000
15	D	228	THR	0	-0.049	-0.028	17.800	-0.010	-0.010	0.000	0.000	0.000	0.000
16	D	229	GLU	-1	-0.853	-0.914	12.947	-0.013	-0.013	0.000	0.000	0.000	0.000
17	D	230	ARG	1	0.922	0.958	14.759	-0.131	-0.131	0.000	0.000	0.000	0.000
18	D	231	GLY	0	-0.039	-0.020	16.469	0.020	0.020	0.000	0.000	0.000	0.000
19	D	232	LYS	1	0.820	0.889	14.453	0.044	0.044	0.000	0.000	0.000	0.000
20	D	233	LEU	0	-0.039	0.000	11.719	0.030	0.030	0.000	0.000	0.000	0.000
21	D	234	ASP	-1	-0.715	-0.825	14.666	0.234	0.234	0.000	0.000	0.000	0.000
22	D	235	LYS	1	0.963	0.962	16.652	-0.119	-0.119	0.000	0.000	0.000	0.000
23	D	236	SER	0	-0.076	-0.046	19.203	-0.006	-0.006	0.000	0.000	0.000	0.000
24	D	237	LYS	1	0.797	0.879	16.117	-0.271	-0.271	0.000	0.000	0.000	0.000
25	D	238	LEU	0	0.008	0.024	14.968	0.066	0.066	0.000	0.000	0.000	0.000
26	D	239	THR	0	0.008	-0.009	14.916	-0.037	-0.037	0.000	0.000	0.000	0.000
27	D	240	PRO	0	0.006	0.008	16.924	0.004	0.004	0.000	0.000	0.000	0.000
28	D	241	ILE	0	0.036	0.028	16.141	0.020	0.020	0.000	0.000	0.000	0.000
29	D	242	THR	0	0.007	-0.013	18.517	-0.035	-0.035	0.000	0.000	0.000	0.000
30	D	243	ILE	0	0.055	0.017	19.038	0.031	0.031	0.000	0.000	0.000	0.000
31	D	244	ALA	0	0.028	0.025	19.506	0.018	0.018	0.000	0.000	0.000	0.000
32	D	245	ASN	0	0.018	0.007	15.646	0.029	0.029	0.000	0.000	0.000	0.000
33	D	246	PHE	0	0.050	0.027	14.575	0.076	0.076	0.000	0.000	0.000	0.000
34	D	247	ALA	0	0.035	0.014	14.785	0.037	0.037	0.000	0.000	0.000	0.000
35	D	248	GLN	0	-0.039	-0.024	14.063	0.033	0.033	0.000	0.000	0.000	0.000
36	D	249	TRP	0	0.043	0.022	8.187	0.008	0.008	0.000	0.000	0.000	0.000
37	D	250	LYS	1	0.881	0.935	10.434	-0.345	-0.345	0.000	0.000	0.000	0.000
38	D	251	LYS	1	0.834	0.899	12.173	-0.772	-0.772	0.000	0.000	0.000	0.000
39	D	252	ASP	-1	-0.784	-0.873	7.961	0.932	0.932	0.000	0.000	0.000	0.000
40	D	253	HIS	0	0.010	0.020	7.487	0.034	0.034	0.000	0.000	0.000	0.000
41	D	254	VAL	0	0.009	0.000	8.970	-0.045	-0.045	0.000	0.000	0.000	0.000
42	D	255	ILE	0	0.028	0.016	9.513	-0.064	-0.064	0.000	0.000	0.000	0.000
43	D	256	ALA	0	0.003	0.003	4.829	-0.087	-0.087	0.000	0.000	0.000	0.000
44	D	257	LYS	1	0.930	0.979	6.863	-0.380	-0.380	0.000	0.000	0.000	0.000
45	D	258	ILE	0	-0.011	-0.013	8.983	-0.139	-0.139	0.000	0.000	0.000	0.000
46	D	259	ASN	0	0.040	0.004	8.258	-0.159	-0.159	0.000	0.000	0.000	0.000
47	D	260	ALA	0	-0.050	-0.014	6.773	-0.159	-0.159	0.000	0.000	0.000	0.000
48	D	261	GLU	-1	-0.835	-0.929	8.742	0.014	0.014	0.000	0.000	0.000	0.000
49	D	262	LYS	1	0.851	0.914	12.272	-0.139	-0.139	0.000	0.000	0.000	0.000
50	D	263	LYS	1	0.950	0.998	8.829	0.682	0.682	0.000	0.000	0.000	0.000
51	D	264	LEU	0	-0.005	-0.006	12.879	-0.033	-0.033	0.000	0.000	0.000	0.000
52	D	265	SER	0	-0.025	-0.021	15.908	0.021	0.021	0.000	0.000	0.000	0.000
53	D	266	SER	0	0.016	0.010	17.877	0.006	0.006	0.000	0.000	0.000	0.000
54	D	267	LYS	1	0.893	0.951	19.400	0.176	0.176	0.000	0.000	0.000	0.000
55	D	268	ARG	1	0.839	0.910	22.065	0.017	0.017	0.000	0.000	0.000	0.000
56	D	269	LYS	1	0.963	0.972	24.281	0.068	0.068	0.000	0.000	0.000	0.000
57	D	270	PRO	0	0.023	0.004	27.555	0.004	0.004	0.000	0.000	0.000	0.000
58	D	271	THR	0	0.001	-0.022	28.292	-0.002	-0.002	0.000	0.000	0.000	0.000
59	D	272	GLY	0	0.061	0.016	30.966	0.001	0.001	0.000	0.000	0.000	0.000
60	D	273	ARG	1	1.010	1.007	29.560	-0.026	-0.026	0.000	0.000	0.000	0.000
61	D	274	GLU	-1	-0.754	-0.820	27.576	-0.003	-0.003	0.000	0.000	0.000	0.000
62	D	275	ILE	0	-0.002	0.004	32.282	0.000	0.000	0.000	0.000	0.000	0.000
63	D	276	ILE	0	0.032	0.011	35.223	0.000	0.000	0.000	0.000	0.000	0.000
64	D	277	LEU	0	-0.015	-0.009	33.008	0.002	0.002	0.000	0.000	0.000	0.000
65	D	278	LYS	1	0.755	0.860	34.233	0.005	0.005	0.000	0.000	0.000	0.000
66	D	279	MET	0	-0.012	-0.025	36.151	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	280	SER	0	-0.039	-0.015	39.338	0.001	0.001	0.000	0.000	0.000	0.000
68	D	281	ALA	0	-0.030	0.002	38.089	0.002	0.002	0.000	0.000	0.000	0.000
69	D	282	GLU	-1	-0.832	-0.878	40.108	-0.002	-0.002	0.000	0.000	0.000	0.000
70	D	320	ASP	-1	-0.825	-0.920	37.229	0.058	0.058	0.000	0.000	0.000	0.000
71	D	321	GLY	0	-0.104	-0.043	38.599	-0.003	-0.003	0.000	0.000	0.000	0.000
72	D	322	GLY	0	-0.060	-0.027	40.444	-0.003	-0.003	0.000	0.000	0.000	0.000
73	D	323	ILE	0	-0.021	-0.023	34.957	0.001	0.001	0.000	0.000	0.000	0.000
74	D	324	LYS	1	0.868	0.932	29.976	-0.099	-0.099	0.000	0.000	0.000	0.000
75	D	325	ASP	-1	-0.835	-0.909	31.889	0.064	0.064	0.000	0.000	0.000	0.000
76	D	326	TYR	0	-0.057	-0.044	26.893	0.009	0.009	0.000	0.000	0.000	0.000
77	D	327	GLY	0	0.021	0.019	27.625	0.007	0.007	0.000	0.000	0.000	0.000
78	D	328	ASP	-1	-0.934	-0.948	25.304	0.091	0.091	0.000	0.000	0.000	0.000
79	D	329	GLY	0	-0.007	0.003	23.660	0.001	0.001	0.000	0.000	0.000	0.000
80	D	330	SER	0	-0.115	-0.084	22.042	0.020	0.020	0.000	0.000	0.000	0.000
81	D	331	ASN	0	-0.068	-0.050	22.082	0.000	0.000	0.000	0.000	0.000	0.000
82	D	332	PRO	0	0.030	0.045	22.035	-0.006	-0.006	0.000	0.000	0.000	0.000
83	D	333	THR	0	-0.011	-0.024	24.690	0.012	0.012	0.000	0.000	0.000	0.000
84	D	334	PHE	0	-0.025	-0.028	23.111	-0.007	-0.007	0.000	0.000	0.000	0.000
85	D	335	ASP	-1	-0.846	-0.899	28.287	0.115	0.115	0.000	0.000	0.000	0.000
86	D	336	ILE	0	-0.009	0.001	31.595	-0.006	-0.006	0.000	0.000	0.000	0.000

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