FMO DATABASE

FMODB ID: 7JRMK

Calculation Name: 1DML-B-Xray309

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: 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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	36
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-116734.697588
FMO2-HF: Nuclear repulsion	103536.759366
FMO2-HF: Total energy	-13197.938222
FMO2-MP2: Total energy	-13236.306053

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.
-135.152	-129.741	10.946	-7.703	-8.654	0.095

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 : -0.808 / q_NPA : -0.911

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	-0.018	-0.014	1.952	-35.992	-32.862	10.747	-6.880	-6.996	0.084
4	B	1203	ALA	0	0.016	0.012	2.793	-20.298	-18.194	0.199	-0.777	-1.527	0.011
5	B	1204	ALA	0	0.002	0.008	4.133	-8.560	-8.383	0.000	-0.046	-0.131	0.000
6	B	1205	ARG	1	0.947	0.966	5.851	-40.452	-40.452	0.000	0.000	0.000	0.000
7	B	1206	LEU	0	-0.002	-0.010	7.000	-4.021	-4.021	0.000	0.000	0.000	0.000
8	B	1207	ARG	1	0.925	0.967	6.083	-31.923	-31.923	0.000	0.000	0.000	0.000
9	B	1208	ALA	0	-0.029	-0.004	9.823	-2.496	-2.496	0.000	0.000	0.000	0.000
10	B	1209	ALA	0	-0.032	-0.009	11.801	-1.677	-1.677	0.000	0.000	0.000	0.000
11	B	1210	GLY	0	-0.005	0.000	13.375	-1.298	-1.298	0.000	0.000	0.000	0.000
12	B	1211	PHE	0	-0.037	-0.019	11.176	-0.547	-0.547	0.000	0.000	0.000	0.000
13	B	1212	GLY	0	0.017	-0.001	12.516	0.227	0.227	0.000	0.000	0.000	0.000
14	B	1213	ALA	0	-0.048	-0.033	11.358	0.956	0.956	0.000	0.000	0.000	0.000
15	B	1214	VAL	0	0.046	0.010	12.692	-1.558	-1.558	0.000	0.000	0.000	0.000
16	B	1215	GLY	0	-0.017	-0.011	13.609	1.033	1.033	0.000	0.000	0.000	0.000
17	B	1216	ALA	0	0.011	-0.023	11.371	-0.376	-0.376	0.000	0.000	0.000	0.000
18	B	1217	GLY	0	-0.031	0.003	12.145	-0.991	-0.991	0.000	0.000	0.000	0.000
19	B	1218	ALA	0	0.001	0.008	13.547	-0.156	-0.156	0.000	0.000	0.000	0.000
20	B	1219	THR	0	-0.019	-0.030	16.615	-0.481	-0.481	0.000	0.000	0.000	0.000
21	B	1220	ALA	0	0.042	0.002	19.949	0.347	0.347	0.000	0.000	0.000	0.000
22	B	1221	GLU	-1	-0.812	-0.922	22.180	11.360	11.360	0.000	0.000	0.000	0.000
23	B	1222	GLU	-1	-0.845	-0.897	18.932	14.443	14.443	0.000	0.000	0.000	0.000
24	B	1223	THR	0	-0.022	0.002	17.382	0.328	0.328	0.000	0.000	0.000	0.000
25	B	1224	ARG	1	0.933	0.980	19.073	-10.967	-10.967	0.000	0.000	0.000	0.000
26	B	1225	ARG	1	0.885	0.938	22.004	-11.806	-11.806	0.000	0.000	0.000	0.000
27	B	1226	MET	0	-0.005	0.018	16.283	-0.224	-0.224	0.000	0.000	0.000	0.000
28	B	1227	LEU	0	0.009	0.001	18.105	0.234	0.234	0.000	0.000	0.000	0.000
29	B	1228	HIS	0	-0.009	-0.001	20.517	-0.116	-0.116	0.000	0.000	0.000	0.000
30	B	1229	ARG	1	0.968	0.989	20.501	-13.891	-13.891	0.000	0.000	0.000	0.000
31	B	1230	ALA	0	-0.015	-0.001	18.352	-0.004	-0.004	0.000	0.000	0.000	0.000
32	B	1231	PHE	0	-0.005	-0.017	20.160	0.016	0.016	0.000	0.000	0.000	0.000
33	B	1232	ASP	-1	-0.919	-0.948	23.253	11.481	11.481	0.000	0.000	0.000	0.000
34	B	1233	THR	0	-0.159	-0.084	20.777	0.137	0.137	0.000	0.000	0.000	0.000
35	B	1234	LEU	0	-0.073	-0.044	18.411	0.311	0.311	0.000	0.000	0.000	0.000
36	B	1235	ALA	-1	-0.966	-0.949	22.225	11.809	11.809	0.000	0.000	0.000	0.000

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