FMO DATABASE

FMODB ID: 7G5NK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-491118.750126
FMO2-HF: Nuclear repulsion	461457.695648
FMO2-HF: Total energy	-29661.054478
FMO2-MP2: Total energy	-29748.667919

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.
67.09	48.223	58.509	-19.158	-20.483	-0.045

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 : 0.915 / q_NPA : 0.914

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	-0.796	-0.914	3.788	-28.928	-25.412	-0.052	-1.898	-1.566	-0.006
4	A	776	LEU	0	0.030	0.036	6.538	2.140	2.140	0.000	0.000	0.000	0.000
5	A	777	THR	0	-0.049	-0.018	3.561	0.803	1.051	0.003	-0.044	-0.208	0.000
6	A	778	LEU	0	0.014	0.007	4.338	1.281	1.412	-0.001	-0.009	-0.120	0.000
7	A	779	GLN	0	0.008	0.021	6.512	1.450	1.450	0.000	0.000	0.000	0.000
8	A	780	ARG	1	0.934	0.952	8.913	21.758	21.758	0.000	0.000	0.000	0.000
9	A	781	SER	0	-0.052	-0.032	8.392	0.667	0.667	0.000	0.000	0.000	0.000
10	A	782	LEU	0	0.011	0.015	10.264	0.529	0.529	0.000	0.000	0.000	0.000
11	A	783	PRO	0	0.061	0.032	12.573	0.656	0.656	0.000	0.000	0.000	0.000
12	A	784	PHE	0	-0.011	-0.006	12.636	0.568	0.568	0.000	0.000	0.000	0.000
13	A	785	ILE	0	-0.001	-0.004	10.135	0.400	0.400	0.000	0.000	0.000	0.000
14	A	786	GLU	-1	-0.867	-0.953	14.434	-12.937	-12.937	0.000	0.000	0.000	0.000
15	A	787	GLY	0	0.038	0.025	17.646	0.606	0.606	0.000	0.000	0.000	0.000
16	A	788	MET	0	-0.088	-0.006	14.369	0.284	0.284	0.000	0.000	0.000	0.000
17	A	789	LEU	0	-0.016	-0.023	16.800	0.394	0.394	0.000	0.000	0.000	0.000
18	A	790	THR	0	-0.037	-0.007	20.087	0.565	0.565	0.000	0.000	0.000	0.000
19	A	791	ASN	0	-0.070	-0.049	21.903	0.685	0.685	0.000	0.000	0.000	0.000
20	A	792	LEU	0	-0.062	-0.035	20.791	0.320	0.320	0.000	0.000	0.000	0.000
21	A	793	GLY	0	0.040	0.052	23.578	0.245	0.245	0.000	0.000	0.000	0.000
22	A	794	ALA	0	0.008	-0.003	21.976	-0.477	-0.477	0.000	0.000	0.000	0.000
23	A	795	MET	0	-0.023	0.005	17.655	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	796	LYS	1	0.976	0.979	18.983	11.380	11.380	0.000	0.000	0.000	0.000
25	A	797	LEU	0	0.100	0.063	12.355	-0.158	-0.158	0.000	0.000	0.000	0.000
26	A	798	HIS	0	0.026	-0.010	14.125	-0.235	-0.235	0.000	0.000	0.000	0.000
27	A	799	LYS	1	0.914	0.963	14.970	12.623	12.623	0.000	0.000	0.000	0.000
28	A	800	ILE	0	0.098	0.054	12.163	-0.164	-0.164	0.000	0.000	0.000	0.000
29	A	801	HIS	0	0.022	0.021	6.854	0.474	0.474	0.000	0.000	0.000	0.000
30	A	802	SER	0	-0.079	-0.054	11.289	-0.752	-0.752	0.000	0.000	0.000	0.000
31	A	803	PHE	0	0.052	0.014	13.708	-0.080	-0.080	0.000	0.000	0.000	0.000
32	A	804	LEU	0	0.043	0.025	9.018	0.208	0.208	0.000	0.000	0.000	0.000
33	A	805	LYS	1	0.870	0.940	9.329	21.406	21.406	0.000	0.000	0.000	0.000
34	A	806	ILE	0	-0.059	-0.021	11.147	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	807	THR	0	-0.056	-0.026	14.147	0.356	0.356	0.000	0.000	0.000	0.000
36	A	808	VAL	0	-0.021	0.007	9.085	0.380	0.380	0.000	0.000	0.000	0.000
37	A	809	PRO	0	0.017	0.022	12.163	-0.350	-0.350	0.000	0.000	0.000	0.000
38	A	810	LYS	1	1.046	0.989	11.113	16.419	16.419	0.000	0.000	0.000	0.000
39	A	811	ASP	-1	-0.904	-0.931	10.595	-19.361	-19.361	0.000	0.000	0.000	0.000
40	A	812	TRP	0	-0.104	-0.053	9.464	-1.040	-1.040	0.000	0.000	0.000	0.000
41	A	813	GLY	0	-0.035	-0.011	6.663	-2.113	-2.113	0.000	0.000	0.000	0.000
42	A	814	TYR	0	0.088	0.016	4.854	0.825	0.825	0.000	0.000	0.000	0.000
43	A	815	ASN	0	0.002	-0.017	5.067	-2.539	-2.473	-0.001	-0.002	-0.062	0.000
44	A	816	ARG	1	0.919	0.966	1.996	62.866	46.160	31.012	-5.301	-9.005	0.004
45	A	817	ILE	0	-0.020	0.004	1.681	-10.881	-12.592	11.471	-4.474	-5.286	-0.017
46	A	818	THR	0	-0.032	-0.004	2.910	7.274	6.698	0.157	0.729	-0.310	0.000
47	A	819	LEU	0	0.059	0.010	6.021	0.265	0.265	0.000	0.000	0.000	0.000
48	A	820	GLN	0	0.095	0.039	7.743	2.990	2.990	0.000	0.000	0.000	0.000
49	A	821	GLN	0	-0.014	0.016	1.700	-1.484	-5.319	15.920	-8.159	-3.926	-0.026
50	A	822	LEU	0	-0.002	0.003	6.204	1.252	1.252	0.000	0.000	0.000	0.000
51	A	823	GLU	-1	-0.933	-0.968	8.186	-17.131	-17.131	0.000	0.000	0.000	0.000
52	A	824	GLY	0	0.015	0.013	9.877	1.206	1.206	0.000	0.000	0.000	0.000
53	A	825	TYR	0	0.030	0.001	8.186	0.880	0.880	0.000	0.000	0.000	0.000
54	A	826	LEU	0	0.003	-0.016	10.276	1.259	1.259	0.000	0.000	0.000	0.000
55	A	827	ASN	0	0.074	0.039	13.086	1.556	1.556	0.000	0.000	0.000	0.000
56	A	828	THR	0	0.034	0.038	13.116	0.683	0.683	0.000	0.000	0.000	0.000
57	A	829	LEU	0	-0.029	-0.022	12.861	0.832	0.832	0.000	0.000	0.000	0.000
58	A	830	ALA	0	-0.092	-0.059	15.996	0.776	0.776	0.000	0.000	0.000	0.000
59	A	831	ASP	-1	-0.955	-0.960	18.121	-13.281	-13.281	0.000	0.000	0.000	0.000
60	A	832	GLU	-1	-1.002	-0.982	16.616	-14.569	-14.569	0.000	0.000	0.000	0.000
61	A	833	GLY	0	0.047	0.012	20.424	0.259	0.259	0.000	0.000	0.000	0.000
62	A	834	ARG	1	0.875	0.946	16.587	14.301	14.301	0.000	0.000	0.000	0.000
63	A	835	LEU	0	-0.035	-0.021	15.503	0.076	0.076	0.000	0.000	0.000	0.000
64	A	836	LYS	1	1.011	1.008	19.866	10.118	10.118	0.000	0.000	0.000	0.000
65	A	837	TYR	0	0.001	0.020	19.284	-0.109	-0.109	0.000	0.000	0.000	0.000
66	A	838	ILE	0	0.019	0.018	21.534	0.206	0.206	0.000	0.000	0.000	0.000
67	A	839	ALA	0	0.032	-0.007	24.082	-0.235	-0.235	0.000	0.000	0.000	0.000
68	A	840	ASN	0	-0.029	-0.028	25.514	0.124	0.124	0.000	0.000	0.000	0.000
69	A	841	GLY	0	-0.001	-0.002	21.111	-0.144	-0.144	0.000	0.000	0.000	0.000
70	A	842	SER	0	-0.122	-0.064	20.110	-0.342	-0.342	0.000	0.000	0.000	0.000
71	A	843	TYR	0	0.007	-0.011	16.144	0.060	0.060	0.000	0.000	0.000	0.000
72	A	844	GLU	-1	-0.909	-0.971	19.657	-10.306	-10.306	0.000	0.000	0.000	0.000
73	A	845	ILE	0	-0.017	0.004	19.926	-0.318	-0.318	0.000	0.000	0.000	0.000
74	A	846	VAL	0	-0.017	0.007	21.617	0.665	0.665	0.000	0.000	0.000	0.000

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