FMO DATABASE

FMODB ID: JM8K9

Calculation Name: 1LDD-A-Xray315

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LDD

Chain ID: A

ChEMBL ID:

UniProt ID: Q12440

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	74
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-490949.007799
FMO2-HF: Nuclear repulsion	461288.584881
FMO2-HF: Total energy	-29660.422918
FMO2-MP2: Total energy	-29748.042511

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:773:LYS )

Summations of interaction energy for fragment #1(A:773: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.
55.188	36.534	58.261	-19.13	-20.476	-0.049

Interaction energy analysis for fragmet #1(A:773:LYS )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.913

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	775	GLU	-1	-0.791	-0.913	3.788	-28.789	-25.267	-0.036	-1.912	-1.574	-0.007
4	A	776	LEU	0	0.029	0.036	6.530	2.182	2.182	0.000	0.000	0.000	0.000
5	A	777	THR	0	-0.053	-0.019	3.553	0.779	1.029	0.004	-0.045	-0.209	0.000
6	A	778	LEU	0	0.017	0.007	4.336	1.257	1.388	0.000	-0.011	-0.120	0.000
7	A	779	GLN	0	0.012	0.023	6.509	1.515	1.515	0.000	0.000	0.000	0.000
8	A	780	ARG	1	0.928	0.950	8.906	21.791	21.791	0.000	0.000	0.000	0.000
9	A	781	SER	0	-0.056	-0.035	8.392	0.673	0.673	0.000	0.000	0.000	0.000
10	A	782	LEU	0	0.014	0.018	10.262	0.522	0.522	0.000	0.000	0.000	0.000
11	A	783	PRO	0	0.063	0.034	12.572	0.683	0.683	0.000	0.000	0.000	0.000
12	A	784	PHE	0	-0.019	-0.011	12.636	0.564	0.564	0.000	0.000	0.000	0.000
13	A	785	ILE	0	-0.006	-0.008	10.137	0.368	0.368	0.000	0.000	0.000	0.000
14	A	786	GLU	-1	-0.848	-0.943	14.437	-12.956	-12.956	0.000	0.000	0.000	0.000
15	A	787	GLY	0	0.038	0.026	17.647	0.619	0.619	0.000	0.000	0.000	0.000
16	A	788	MET	0	-0.098	-0.012	14.373	0.271	0.271	0.000	0.000	0.000	0.000
17	A	789	LEU	0	-0.018	-0.023	16.804	0.386	0.386	0.000	0.000	0.000	0.000
18	A	790	THR	0	-0.015	0.006	20.091	0.584	0.584	0.000	0.000	0.000	0.000
19	A	791	ASN	0	-0.078	-0.053	21.905	0.701	0.701	0.000	0.000	0.000	0.000
20	A	792	LEU	0	-0.073	-0.042	20.797	0.327	0.327	0.000	0.000	0.000	0.000
21	A	793	GLY	0	0.043	0.053	23.580	0.250	0.250	0.000	0.000	0.000	0.000
22	A	794	ALA	0	0.015	0.002	21.981	-0.489	-0.489	0.000	0.000	0.000	0.000
23	A	795	MET	0	-0.030	0.000	17.663	-0.036	-0.036	0.000	0.000	0.000	0.000
24	A	796	LYS	1	0.971	0.976	18.992	11.366	11.366	0.000	0.000	0.000	0.000
25	A	797	LEU	0	0.099	0.064	12.363	-0.197	-0.197	0.000	0.000	0.000	0.000
26	A	798	HIS	0	0.025	-0.011	14.134	-0.252	-0.252	0.000	0.000	0.000	0.000
27	A	799	LYS	1	0.913	0.962	14.961	12.640	12.640	0.000	0.000	0.000	0.000
28	A	800	ILE	0	0.104	0.057	12.170	-0.196	-0.196	0.000	0.000	0.000	0.000
29	A	801	HIS	0	0.017	0.020	6.845	0.418	0.418	0.000	0.000	0.000	0.000
30	A	802	SER	0	-0.080	-0.055	11.281	-0.741	-0.741	0.000	0.000	0.000	0.000
31	A	803	PHE	0	0.050	0.013	13.701	-0.067	-0.067	0.000	0.000	0.000	0.000
32	A	804	LEU	0	0.046	0.027	9.023	0.166	0.166	0.000	0.000	0.000	0.000
33	A	805	LYS	1	0.868	0.939	9.324	21.398	21.398	0.000	0.000	0.000	0.000
34	A	806	ILE	0	-0.061	-0.022	11.142	0.015	0.015	0.000	0.000	0.000	0.000
35	A	807	THR	0	-0.056	-0.027	14.152	0.371	0.371	0.000	0.000	0.000	0.000
36	A	808	VAL	0	-0.022	0.006	9.084	0.359	0.359	0.000	0.000	0.000	0.000
37	A	809	PRO	0	0.019	0.022	12.164	-0.346	-0.346	0.000	0.000	0.000	0.000
38	A	810	LYS	1	1.046	0.989	11.114	16.385	16.385	0.000	0.000	0.000	0.000
39	A	811	ASP	-1	-0.906	-0.932	10.598	-19.386	-19.386	0.000	0.000	0.000	0.000
40	A	812	TRP	0	-0.105	-0.054	9.458	-1.084	-1.084	0.000	0.000	0.000	0.000
41	A	813	GLY	0	-0.036	-0.011	6.663	-2.188	-2.188	0.000	0.000	0.000	0.000
42	A	814	TYR	0	0.091	0.017	4.857	0.766	0.766	0.000	0.000	0.000	0.000
43	A	815	ASN	0	0.000	-0.017	5.063	-2.598	-2.531	0.000	-0.003	-0.063	0.000
44	A	816	ARG	1	0.917	0.965	1.996	62.666	45.948	31.031	-5.321	-8.992	0.004
45	A	817	ILE	0	-0.022	0.002	1.688	-11.300	-12.903	11.415	-4.523	-5.290	-0.018
46	A	818	THR	0	-0.031	-0.004	2.902	7.512	6.927	0.159	0.739	-0.312	0.000
47	A	819	LEU	0	0.056	0.009	6.015	0.364	0.364	0.000	0.000	0.000	0.000
48	A	820	GLN	0	0.096	0.039	7.742	2.977	2.977	0.000	0.000	0.000	0.000
49	A	821	GLN	0	-0.016	0.015	1.703	-1.708	-5.426	15.688	-8.054	-3.916	-0.028
50	A	822	LEU	0	0.001	0.004	6.204	1.288	1.288	0.000	0.000	0.000	0.000
51	A	823	GLU	-1	-0.931	-0.967	8.194	-17.085	-17.085	0.000	0.000	0.000	0.000
52	A	824	GLY	0	0.010	0.011	9.877	1.194	1.194	0.000	0.000	0.000	0.000
53	A	825	TYR	0	0.030	0.000	8.188	0.831	0.831	0.000	0.000	0.000	0.000
54	A	826	LEU	0	0.005	-0.015	10.278	1.272	1.272	0.000	0.000	0.000	0.000
55	A	827	ASN	0	0.074	0.039	13.089	1.565	1.565	0.000	0.000	0.000	0.000
56	A	828	THR	0	0.025	0.033	13.116	0.676	0.676	0.000	0.000	0.000	0.000
57	A	829	LEU	0	-0.032	-0.023	12.862	0.809	0.809	0.000	0.000	0.000	0.000
58	A	830	ALA	0	-0.081	-0.052	15.996	0.783	0.783	0.000	0.000	0.000	0.000
59	A	831	ASP	-1	-0.964	-0.966	18.121	-13.277	-13.277	0.000	0.000	0.000	0.000
60	A	832	GLU	-1	-1.014	-0.989	16.613	-14.573	-14.573	0.000	0.000	0.000	0.000
61	A	833	GLY	0	0.041	0.007	20.423	0.264	0.264	0.000	0.000	0.000	0.000
62	A	834	ARG	1	0.888	0.955	16.586	14.229	14.229	0.000	0.000	0.000	0.000
63	A	835	LEU	0	-0.025	-0.012	15.507	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	836	LYS	1	1.016	1.011	19.868	10.134	10.134	0.000	0.000	0.000	0.000
65	A	837	TYR	0	-0.010	0.012	19.291	-0.120	-0.120	0.000	0.000	0.000	0.000
66	A	838	ILE	0	0.026	0.022	21.539	0.230	0.230	0.000	0.000	0.000	0.000
67	A	839	ALA	0	0.024	-0.011	24.089	-0.230	-0.230	0.000	0.000	0.000	0.000
68	A	840	ASN	0	-0.035	-0.030	25.523	0.122	0.122	0.000	0.000	0.000	0.000
69	A	841	GLY	0	-0.009	-0.006	21.119	-0.161	-0.161	0.000	0.000	0.000	0.000
70	A	842	SER	0	-0.121	-0.065	20.118	-0.351	-0.351	0.000	0.000	0.000	0.000
71	A	843	TYR	0	0.004	-0.014	16.150	0.033	0.033	0.000	0.000	0.000	0.000
72	A	844	GLU	-1	-0.919	-0.980	19.663	-10.306	-10.306	0.000	0.000	0.000	0.000
73	A	845	ILE	0	-0.040	-0.012	19.927	-0.388	-0.388	0.000	0.000	0.000	0.000
74	A	846	VAL	-1	-0.935	-0.951	21.619	-10.282	-10.282	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:773:LYS )