FMO DATABASE

FMODB ID: M3R1Z

Calculation Name: 1DML-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DML

Chain ID: B

ChEMBL ID:

UniProt ID: P07917

Base Structure: X-ray

Registration Date: 2023-03-13

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	36
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-116812.385907
FMO2-HF: Nuclear repulsion	103613.775019
FMO2-HF: Total energy	-13198.610888
FMO2-MP2: Total energy	-13236.963881

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(B:1200:ASP)

Summations of interaction energy for fragment #1(B:1200:ASP)

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.
-147.206	-141.612	10.924	-7.792	-8.725	0.097

Interaction energy analysis for fragmet #1(B:1200:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.806 / q_NPA : -0.909

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	B	1202	VAL	0	-0.019	-0.014	1.952	-36.485	-33.213	10.723	-6.938	-7.056	0.085
4	B	1203	ALA	0	0.014	0.010	2.787	-20.062	-17.918	0.202	-0.810	-1.536	0.012
5	B	1204	ALA	0	0.004	0.008	4.189	-8.324	-8.146	-0.001	-0.044	-0.133	0.000
6	B	1205	ARG	1	0.949	0.968	5.922	-40.404	-40.404	0.000	0.000	0.000	0.000
7	B	1206	LEU	0	-0.005	-0.012	7.000	-4.022	-4.022	0.000	0.000	0.000	0.000
8	B	1207	ARG	1	0.925	0.966	6.092	-31.801	-31.801	0.000	0.000	0.000	0.000
9	B	1208	ALA	0	-0.027	-0.002	9.856	-2.434	-2.434	0.000	0.000	0.000	0.000
10	B	1209	ALA	0	-0.032	-0.009	11.839	-1.643	-1.643	0.000	0.000	0.000	0.000
11	B	1210	GLY	0	-0.005	-0.001	13.409	-1.268	-1.268	0.000	0.000	0.000	0.000
12	B	1211	PHE	0	-0.044	-0.022	11.177	-0.606	-0.606	0.000	0.000	0.000	0.000
13	B	1212	GLY	0	0.015	-0.001	12.516	0.236	0.236	0.000	0.000	0.000	0.000
14	B	1213	ALA	0	-0.043	-0.031	11.334	0.926	0.926	0.000	0.000	0.000	0.000
15	B	1214	VAL	0	0.042	0.007	12.656	-1.527	-1.527	0.000	0.000	0.000	0.000
16	B	1215	GLY	0	-0.016	-0.010	13.609	1.026	1.026	0.000	0.000	0.000	0.000
17	B	1216	ALA	0	0.013	-0.021	11.305	-0.390	-0.390	0.000	0.000	0.000	0.000
18	B	1217	GLY	0	-0.028	0.003	12.095	-0.961	-0.961	0.000	0.000	0.000	0.000
19	B	1218	ALA	0	-0.001	0.008	13.510	-0.120	-0.120	0.000	0.000	0.000	0.000
20	B	1219	THR	0	-0.015	-0.027	16.579	-0.445	-0.445	0.000	0.000	0.000	0.000
21	B	1220	ALA	0	0.043	0.002	19.903	0.355	0.355	0.000	0.000	0.000	0.000
22	B	1221	GLU	-1	-0.809	-0.921	22.125	11.362	11.362	0.000	0.000	0.000	0.000
23	B	1222	GLU	-1	-0.842	-0.896	18.904	14.420	14.420	0.000	0.000	0.000	0.000
24	B	1223	THR	0	-0.021	0.003	17.321	0.309	0.309	0.000	0.000	0.000	0.000
25	B	1224	ARG	1	0.932	0.979	19.023	-10.934	-10.934	0.000	0.000	0.000	0.000
26	B	1225	ARG	1	0.884	0.938	21.974	-11.787	-11.787	0.000	0.000	0.000	0.000
27	B	1226	MET	0	-0.004	0.019	16.250	-0.249	-0.249	0.000	0.000	0.000	0.000
28	B	1227	LEU	0	0.010	0.003	18.106	0.229	0.229	0.000	0.000	0.000	0.000
29	B	1228	HIS	0	-0.001	0.002	20.517	-0.087	-0.087	0.000	0.000	0.000	0.000
30	B	1229	ARG	1	0.971	0.992	20.492	-13.887	-13.887	0.000	0.000	0.000	0.000
31	B	1230	ALA	0	-0.011	0.001	18.352	-0.027	-0.027	0.000	0.000	0.000	0.000
32	B	1231	PHE	0	0.006	-0.010	20.160	0.011	0.011	0.000	0.000	0.000	0.000
33	B	1232	ASP	-1	-0.916	-0.947	23.253	11.476	11.476	0.000	0.000	0.000	0.000
34	B	1233	THR	0	-0.146	-0.077	20.777	0.087	0.087	0.000	0.000	0.000	0.000
35	B	1234	LEU	0	-0.039	-0.023	18.411	0.187	0.187	0.000	0.000	0.000	0.000
36	B	1235	ALA	0	-0.054	0.001	22.225	-0.367	-0.367	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1200:ASP)