FMO DATABASE

FMODB ID: 6687Z

Calculation Name: 1LDD-A-Xray372

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: 2023-06-19

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	74
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-490071.969011
FMO2-HF: Nuclear repulsion	460409.937755
FMO2-HF: Total energy	-29662.031256
FMO2-MP2: Total energy	-29749.490064

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.
38.642	45.091	15.807	-9.794	-12.462	-0.068

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 : 0.943 / q_NPA : 0.952

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	A	775	GLU	-1	-0.806	-0.918	3.877	-25.167	-22.721	-0.032	-1.310	-1.103	-0.002
4	A	776	LEU	0	0.018	0.023	7.210	2.010	2.010	0.000	0.000	0.000	0.000
5	A	777	THR	0	-0.050	-0.020	4.180	0.961	1.111	-0.001	-0.015	-0.135	0.000
6	A	778	LEU	0	0.007	0.009	5.027	0.976	0.976	0.000	0.000	0.000	0.000
7	A	779	GLN	0	0.023	0.032	7.272	1.306	1.306	0.000	0.000	0.000	0.000
8	A	780	ARG	1	0.897	0.948	9.354	19.778	19.778	0.000	0.000	0.000	0.000
9	A	781	SER	0	-0.049	-0.038	8.567	0.612	0.612	0.000	0.000	0.000	0.000
10	A	782	LEU	0	0.008	0.020	10.525	0.530	0.530	0.000	0.000	0.000	0.000
11	A	783	PRO	0	0.067	0.028	13.147	0.551	0.551	0.000	0.000	0.000	0.000
12	A	784	PHE	0	-0.017	-0.005	13.118	0.512	0.512	0.000	0.000	0.000	0.000
13	A	785	ILE	0	-0.002	0.001	10.762	0.368	0.368	0.000	0.000	0.000	0.000
14	A	786	GLU	-1	-0.789	-0.895	15.015	-12.761	-12.761	0.000	0.000	0.000	0.000
15	A	787	GLY	0	0.033	0.030	18.216	0.615	0.615	0.000	0.000	0.000	0.000
16	A	788	MET	0	-0.056	-0.016	15.936	0.243	0.243	0.000	0.000	0.000	0.000
17	A	789	LEU	0	-0.001	-0.012	17.731	0.367	0.367	0.000	0.000	0.000	0.000
18	A	790	THR	0	-0.032	-0.026	20.613	0.550	0.550	0.000	0.000	0.000	0.000
19	A	791	ASN	0	-0.106	-0.061	22.480	0.689	0.689	0.000	0.000	0.000	0.000
20	A	792	LEU	0	-0.050	-0.023	20.412	0.242	0.242	0.000	0.000	0.000	0.000
21	A	793	GLY	0	0.024	0.031	23.977	0.197	0.197	0.000	0.000	0.000	0.000
22	A	794	ALA	0	-0.004	-0.006	22.385	-0.460	-0.460	0.000	0.000	0.000	0.000
23	A	795	MET	0	-0.017	0.001	17.991	0.030	0.030	0.000	0.000	0.000	0.000
24	A	796	LYS	1	0.924	0.943	19.059	11.473	11.473	0.000	0.000	0.000	0.000
25	A	797	LEU	0	0.051	0.041	12.215	-0.089	-0.089	0.000	0.000	0.000	0.000
26	A	798	HIS	0	0.067	0.020	13.986	-0.236	-0.236	0.000	0.000	0.000	0.000
27	A	799	LYS	1	0.891	0.957	14.962	12.855	12.855	0.000	0.000	0.000	0.000
28	A	800	ILE	0	0.090	0.054	12.476	-0.092	-0.092	0.000	0.000	0.000	0.000
29	A	801	HIS	0	0.009	0.016	6.729	0.909	0.909	0.000	0.000	0.000	0.000
30	A	802	SER	0	-0.090	-0.062	11.191	-0.773	-0.773	0.000	0.000	0.000	0.000
31	A	803	PHE	0	0.064	0.023	13.963	-0.052	-0.052	0.000	0.000	0.000	0.000
32	A	804	LEU	0	0.057	0.035	9.525	0.160	0.160	0.000	0.000	0.000	0.000
33	A	805	LYS	1	0.868	0.940	8.696	22.665	22.665	0.000	0.000	0.000	0.000
34	A	806	ILE	0	-0.064	-0.024	11.164	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	807	THR	0	-0.029	-0.018	13.582	0.691	0.691	0.000	0.000	0.000	0.000
36	A	808	VAL	0	-0.018	0.005	9.112	0.326	0.326	0.000	0.000	0.000	0.000
37	A	809	PRO	0	-0.003	0.014	12.131	-0.298	-0.298	0.000	0.000	0.000	0.000
38	A	810	LYS	1	1.027	0.995	10.544	16.085	16.085	0.000	0.000	0.000	0.000
39	A	811	ASP	-1	-0.893	-0.931	10.182	-17.939	-17.939	0.000	0.000	0.000	0.000
40	A	812	TRP	0	-0.038	-0.032	9.822	-0.574	-0.574	0.000	0.000	0.000	0.000
41	A	813	GLY	0	-0.006	0.001	6.170	-1.459	-1.459	0.000	0.000	0.000	0.000
42	A	814	TYR	0	0.079	0.009	4.851	0.494	0.494	0.000	0.000	0.000	0.000
43	A	815	ASN	0	-0.045	-0.044	5.434	-1.756	-1.756	0.000	0.000	0.000	0.000
44	A	816	ARG	1	0.941	0.977	2.375	40.708	43.071	1.341	-1.334	-2.371	0.002
45	A	817	ILE	0	0.026	0.028	1.847	-18.333	-19.157	12.394	-5.190	-6.379	-0.049
46	A	818	THR	0	-0.017	-0.006	3.445	6.103	6.294	0.044	0.023	-0.257	0.000
47	A	819	LEU	0	0.050	0.010	6.139	0.170	0.170	0.000	0.000	0.000	0.000
48	A	820	GLN	0	0.082	0.034	7.861	1.985	1.985	0.000	0.000	0.000	0.000
49	A	821	GLN	0	-0.040	-0.030	2.420	-4.628	-2.505	2.061	-1.968	-2.217	-0.019
50	A	822	LEU	0	0.005	0.013	6.816	1.275	1.275	0.000	0.000	0.000	0.000
51	A	823	GLU	-1	-0.930	-0.967	8.743	-17.497	-17.497	0.000	0.000	0.000	0.000
52	A	824	GLY	0	0.020	0.014	10.524	1.168	1.168	0.000	0.000	0.000	0.000
53	A	825	TYR	0	-0.003	-0.001	9.013	1.055	1.055	0.000	0.000	0.000	0.000
54	A	826	LEU	0	0.010	-0.011	11.114	1.176	1.176	0.000	0.000	0.000	0.000
55	A	827	ASN	0	0.027	0.029	13.825	1.664	1.664	0.000	0.000	0.000	0.000
56	A	828	THR	0	0.057	0.022	13.505	0.643	0.643	0.000	0.000	0.000	0.000
57	A	829	LEU	0	-0.043	-0.033	13.141	0.730	0.730	0.000	0.000	0.000	0.000
58	A	830	ALA	0	-0.052	-0.034	16.589	0.654	0.654	0.000	0.000	0.000	0.000
59	A	831	ASP	-1	-0.932	-0.944	18.958	-13.482	-13.482	0.000	0.000	0.000	0.000
60	A	832	GLU	-1	-0.879	-0.918	17.370	-13.867	-13.867	0.000	0.000	0.000	0.000
61	A	833	GLY	0	-0.010	-0.005	20.884	0.051	0.051	0.000	0.000	0.000	0.000
62	A	834	ARG	1	0.734	0.849	17.476	14.042	14.042	0.000	0.000	0.000	0.000
63	A	835	LEU	0	-0.040	-0.024	15.974	0.152	0.152	0.000	0.000	0.000	0.000
64	A	836	LYS	1	0.858	0.922	20.476	10.217	10.217	0.000	0.000	0.000	0.000
65	A	837	TYR	0	0.032	0.011	19.696	0.178	0.178	0.000	0.000	0.000	0.000
66	A	838	ILE	0	-0.041	-0.014	21.950	0.548	0.548	0.000	0.000	0.000	0.000
67	A	839	ALA	0	0.045	0.016	24.028	-0.335	-0.335	0.000	0.000	0.000	0.000
68	A	840	ASN	0	0.001	-0.007	25.702	0.238	0.238	0.000	0.000	0.000	0.000
69	A	841	GLY	0	-0.003	0.017	21.397	-0.125	-0.125	0.000	0.000	0.000	0.000
70	A	842	SER	0	-0.059	-0.041	20.429	-0.303	-0.303	0.000	0.000	0.000	0.000
71	A	843	TYR	0	-0.003	-0.025	16.150	-0.120	-0.120	0.000	0.000	0.000	0.000
72	A	844	GLU	-1	-0.791	-0.889	20.170	-10.064	-10.064	0.000	0.000	0.000	0.000
73	A	845	ILE	0	0.008	0.008	20.639	-0.439	-0.439	0.000	0.000	0.000	0.000
74	A	846	VAL	0	-0.020	0.001	22.206	0.605	0.605	0.000	0.000	0.000	0.000

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