FMO DATABASE

FMODB ID: 2243R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-116459.175345
FMO2-HF: Nuclear repulsion	103260.236769
FMO2-HF: Total energy	-13198.938576
FMO2-MP2: Total energy	-13237.233721

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.
-171.575	-171.848	27.262	-13.603	-13.385	0.155

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 : -0.764 / q_NPA : -0.884

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	-0.046	-0.028	1.829	-31.529	-30.445	13.624	-7.658	-7.050	0.077
4	B	1203	ALA	0	0.001	-0.008	1.807	-33.913	-36.162	13.586	-5.633	-5.704	0.073
5	B	1204	ALA	0	-0.030	-0.008	3.599	-15.467	-14.678	0.053	-0.305	-0.537	0.005
6	B	1205	ARG	1	0.959	0.967	5.361	-41.648	-41.545	-0.001	-0.007	-0.094	0.000
7	B	1206	LEU	0	-0.004	0.006	5.696	-5.081	-5.081	0.000	0.000	0.000	0.000
8	B	1207	ARG	1	0.941	0.968	6.058	-38.228	-38.228	0.000	0.000	0.000	0.000
9	B	1208	ALA	0	-0.024	-0.006	9.409	-2.992	-2.992	0.000	0.000	0.000	0.000
10	B	1209	ALA	0	-0.048	-0.012	11.045	-2.216	-2.216	0.000	0.000	0.000	0.000
11	B	1210	GLY	0	0.002	0.003	12.779	-1.337	-1.337	0.000	0.000	0.000	0.000
12	B	1211	PHE	0	-0.044	-0.026	10.140	-0.802	-0.802	0.000	0.000	0.000	0.000
13	B	1212	GLY	0	0.009	-0.002	11.597	0.988	0.988	0.000	0.000	0.000	0.000
14	B	1213	ALA	0	-0.046	-0.028	11.603	1.103	1.103	0.000	0.000	0.000	0.000
15	B	1214	VAL	0	0.040	0.007	12.398	-1.952	-1.952	0.000	0.000	0.000	0.000
16	B	1215	GLY	0	0.006	0.003	12.882	1.344	1.344	0.000	0.000	0.000	0.000
17	B	1216	ALA	0	-0.023	-0.030	11.331	0.471	0.471	0.000	0.000	0.000	0.000
18	B	1217	GLY	0	-0.004	0.012	12.339	-0.770	-0.770	0.000	0.000	0.000	0.000
19	B	1218	ALA	0	0.010	0.006	13.298	-0.070	-0.070	0.000	0.000	0.000	0.000
20	B	1219	THR	0	-0.030	-0.046	16.484	-0.407	-0.407	0.000	0.000	0.000	0.000
21	B	1220	ALA	0	0.037	0.008	19.843	0.304	0.304	0.000	0.000	0.000	0.000
22	B	1221	GLU	-1	-0.720	-0.824	21.604	12.094	12.094	0.000	0.000	0.000	0.000
23	B	1222	GLU	-1	-0.826	-0.873	18.850	15.336	15.336	0.000	0.000	0.000	0.000
24	B	1223	THR	0	-0.053	-0.024	16.370	0.415	0.415	0.000	0.000	0.000	0.000
25	B	1224	ARG	1	0.908	0.939	18.658	-11.417	-11.417	0.000	0.000	0.000	0.000
26	B	1225	ARG	1	0.836	0.892	21.731	-12.186	-12.186	0.000	0.000	0.000	0.000
27	B	1226	MET	0	-0.010	0.009	15.834	-0.299	-0.299	0.000	0.000	0.000	0.000
28	B	1227	LEU	0	0.006	-0.002	17.789	0.332	0.332	0.000	0.000	0.000	0.000
29	B	1228	HIS	0	-0.009	0.001	19.747	-0.073	-0.073	0.000	0.000	0.000	0.000
30	B	1229	ARG	1	0.998	1.001	19.331	-15.079	-15.079	0.000	0.000	0.000	0.000
31	B	1230	ALA	0	-0.017	0.011	17.445	0.123	0.123	0.000	0.000	0.000	0.000
32	B	1231	PHE	0	-0.012	-0.013	19.196	-0.081	-0.081	0.000	0.000	0.000	0.000
33	B	1232	ASP	-1	-0.914	-0.958	22.434	12.273	12.273	0.000	0.000	0.000	0.000
34	B	1233	THR	0	-0.088	-0.057	19.911	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	1234	LEU	0	-0.045	-0.028	17.308	-0.016	-0.016	0.000	0.000	0.000	0.000
36	B	1235	ALA	0	-0.085	-0.013	21.433	-0.787	-0.787	0.000	0.000	0.000	0.000

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