FMO DATABASE

FMODB ID: YZ152

Calculation Name: 3LH2-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LH2

Chain ID: S

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-287151.977771
FMO2-HF: Nuclear repulsion	262734.087664
FMO2-HF: Total energy	-24417.890107
FMO2-MP2: Total energy	-24491.303907

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(S:6:HIS)

Summations of interaction energy for fragment #1(S:6:HIS)

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.
-18.071	-16.865	7.808	-4.596	-4.418	-0.04

Interaction energy analysis for fragmet #1(S:6:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.019

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	S	8	THR	0	-0.008	-0.005	1.908	-15.597	-14.667	7.809	-4.570	-4.170	-0.040
4	S	9	GLU	-1	-0.911	-0.950	4.257	-3.151	-2.875	-0.001	-0.026	-0.248	0.000
5	S	10	TYR	0	-0.010	-0.009	6.730	0.799	0.799	0.000	0.000	0.000	0.000
6	S	11	THR	0	-0.005	-0.001	10.333	0.003	0.003	0.000	0.000	0.000	0.000
7	S	12	LEU	0	0.012	-0.007	13.633	0.039	0.039	0.000	0.000	0.000	0.000
8	S	13	GLN	0	-0.020	0.001	16.761	0.058	0.058	0.000	0.000	0.000	0.000
9	S	14	ALA	0	0.007	0.003	20.438	0.015	0.015	0.000	0.000	0.000	0.000
10	S	15	ASN	0	-0.007	-0.009	22.844	0.038	0.038	0.000	0.000	0.000	0.000
11	S	16	TRP	0	0.048	0.015	25.205	-0.025	-0.025	0.000	0.000	0.000	0.000
12	S	17	PHE	0	-0.041	-0.037	26.016	-0.017	-0.017	0.000	0.000	0.000	0.000
13	S	18	ASP	-1	-0.836	-0.898	24.152	-0.501	-0.501	0.000	0.000	0.000	0.000
14	S	19	ILE	0	-0.024	-0.004	20.396	-0.056	-0.056	0.000	0.000	0.000	0.000
15	S	20	THR	0	0.032	0.000	21.102	-0.067	-0.067	0.000	0.000	0.000	0.000
16	S	21	GLY	0	0.030	0.022	22.401	-0.018	-0.018	0.000	0.000	0.000	0.000
17	S	22	ILE	0	0.011	0.001	17.365	-0.045	-0.045	0.000	0.000	0.000	0.000
18	S	23	LEU	0	-0.015	-0.011	16.967	-0.106	-0.106	0.000	0.000	0.000	0.000
19	S	24	TRP	0	-0.018	-0.003	18.197	-0.068	-0.068	0.000	0.000	0.000	0.000
20	S	25	LEU	0	-0.010	-0.019	18.640	-0.009	-0.009	0.000	0.000	0.000	0.000
21	S	26	LEU	0	-0.025	0.000	11.855	-0.070	-0.070	0.000	0.000	0.000	0.000
22	S	27	GLY	0	0.011	0.010	14.476	-0.158	-0.158	0.000	0.000	0.000	0.000
23	S	28	GLN	0	-0.084	-0.039	15.704	0.041	0.041	0.000	0.000	0.000	0.000
24	S	29	VAL	0	-0.052	-0.017	13.153	0.073	0.073	0.000	0.000	0.000	0.000
25	S	30	ASP	-1	-0.942	-0.952	10.220	-1.597	-1.597	0.000	0.000	0.000	0.000
26	S	31	GLY	0	-0.011	-0.006	9.832	-0.489	-0.489	0.000	0.000	0.000	0.000
27	S	32	LYS	1	0.911	0.943	6.726	2.991	2.991	0.000	0.000	0.000	0.000
28	S	33	ILE	0	0.001	0.001	10.759	-0.231	-0.231	0.000	0.000	0.000	0.000
29	S	34	ILE	0	-0.024	-0.007	7.656	0.170	0.170	0.000	0.000	0.000	0.000
30	S	35	ASN	0	0.008	-0.019	11.317	0.345	0.345	0.000	0.000	0.000	0.000
31	S	36	SER	0	-0.035	-0.004	14.471	-0.068	-0.068	0.000	0.000	0.000	0.000
32	S	37	ASP	-1	-0.840	-0.909	17.748	-0.516	-0.516	0.000	0.000	0.000	0.000
33	S	38	VAL	0	-0.069	-0.036	20.706	-0.015	-0.015	0.000	0.000	0.000	0.000
34	S	39	GLN	0	-0.024	-0.023	22.686	0.059	0.059	0.000	0.000	0.000	0.000
35	S	40	ALA	0	-0.032	0.001	25.633	-0.003	-0.003	0.000	0.000	0.000	0.000
36	S	41	PHE	0	0.031	0.001	23.086	0.003	0.003	0.000	0.000	0.000	0.000
37	S	42	VAL	0	-0.005	-0.003	29.245	0.012	0.012	0.000	0.000	0.000	0.000
38	S	43	LEU	0	0.006	0.007	29.006	-0.005	-0.005	0.000	0.000	0.000	0.000
39	S	44	LEU	0	0.019	0.005	32.421	0.018	0.018	0.000	0.000	0.000	0.000
40	S	45	ARG	1	0.950	0.980	33.772	0.193	0.193	0.000	0.000	0.000	0.000
41	S	46	VAL	0	0.008	0.000	34.731	0.011	0.011	0.000	0.000	0.000	0.000
42	S	47	ALA	0	0.002	-0.006	37.504	-0.003	-0.003	0.000	0.000	0.000	0.000
43	S	48	LEU	0	0.002	0.013	35.896	0.008	0.008	0.000	0.000	0.000	0.000
44	S	49	PRO	0	0.026	0.014	40.225	-0.003	-0.003	0.000	0.000	0.000	0.000
45	S	50	ALA	0	0.099	0.039	38.667	-0.002	-0.002	0.000	0.000	0.000	0.000
46	S	51	ALA	0	0.009	-0.028	39.399	0.003	0.003	0.000	0.000	0.000	0.000
47	S	52	LYS	1	0.878	0.939	39.506	0.078	0.078	0.000	0.000	0.000	0.000
48	S	53	VAL	0	0.026	0.039	33.997	-0.002	-0.002	0.000	0.000	0.000	0.000
49	S	54	ALA	0	-0.004	-0.003	33.863	-0.007	-0.007	0.000	0.000	0.000	0.000
50	S	55	GLU	-1	-0.829	-0.882	33.779	-0.071	-0.071	0.000	0.000	0.000	0.000
51	S	56	PHE	0	0.003	-0.018	33.080	0.000	0.000	0.000	0.000	0.000	0.000
52	S	57	SER	0	0.028	0.002	29.756	-0.011	-0.011	0.000	0.000	0.000	0.000
53	S	58	ALA	0	0.005	0.017	29.543	-0.008	-0.008	0.000	0.000	0.000	0.000
54	S	59	LYS	1	0.915	0.933	30.285	0.078	0.078	0.000	0.000	0.000	0.000
55	S	60	LEU	0	-0.021	-0.001	28.983	-0.001	-0.001	0.000	0.000	0.000	0.000
56	S	61	ALA	0	0.004	0.017	26.043	-0.015	-0.015	0.000	0.000	0.000	0.000
57	S	62	ASP	-1	-0.901	-0.953	26.494	-0.081	-0.081	0.000	0.000	0.000	0.000
58	S	63	PHE	0	-0.107	-0.055	28.315	-0.002	-0.002	0.000	0.000	0.000	0.000
59	S	64	SER	0	-0.031	-0.025	25.398	-0.010	-0.010	0.000	0.000	0.000	0.000
60	S	65	GLY	0	0.029	0.025	23.714	-0.021	-0.021	0.000	0.000	0.000	0.000
61	S	66	GLY	0	-0.041	-0.021	21.680	-0.015	-0.015	0.000	0.000	0.000	0.000
62	S	67	SER	0	-0.033	-0.021	20.958	-0.032	-0.032	0.000	0.000	0.000	0.000
63	S	68	LEU	0	-0.005	-0.005	21.927	-0.031	-0.031	0.000	0.000	0.000	0.000
64	S	69	GLN	0	-0.022	-0.009	22.201	0.019	0.019	0.000	0.000	0.000	0.000
65	S	70	LEU	0	-0.024	-0.006	25.539	-0.001	-0.001	0.000	0.000	0.000	0.000
66	S	71	LEU	0	-0.008	0.000	25.250	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(S:6:HIS)