FMO DATABASE

FMODB ID: 7GYVK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-116482.700337
FMO2-HF: Nuclear repulsion	103283.867592
FMO2-HF: Total energy	-13198.832745
FMO2-MP2: Total energy	-13237.145778

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.
-177.649	-176.196	23.187	-12.151	-12.488	0.146

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 : -0.787 / q_NPA : -0.900

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	-0.031	-0.030	1.936	-34.742	-31.933	12.390	-7.543	-7.655	0.083
4	B	1203	ALA	0	0.007	0.005	1.800	-36.124	-38.119	10.775	-4.266	-4.514	0.060
5	B	1204	ALA	0	-0.010	0.004	3.818	-14.649	-14.010	0.022	-0.342	-0.319	0.003
6	B	1205	ARG	1	0.962	0.971	5.755	-42.656	-42.656	0.000	0.000	0.000	0.000
7	B	1206	LEU	0	-0.002	-0.009	5.884	-5.200	-5.200	0.000	0.000	0.000	0.000
8	B	1207	ARG	1	0.932	0.967	6.433	-36.330	-36.330	0.000	0.000	0.000	0.000
9	B	1208	ALA	0	-0.035	-0.007	9.690	-3.072	-3.072	0.000	0.000	0.000	0.000
10	B	1209	ALA	0	-0.036	-0.010	11.013	-2.025	-2.025	0.000	0.000	0.000	0.000
11	B	1210	GLY	0	-0.008	-0.001	12.804	-1.482	-1.482	0.000	0.000	0.000	0.000
12	B	1211	PHE	0	-0.041	-0.021	10.268	-0.686	-0.686	0.000	0.000	0.000	0.000
13	B	1212	GLY	0	0.017	0.000	12.232	0.345	0.345	0.000	0.000	0.000	0.000
14	B	1213	ALA	0	-0.049	-0.032	11.335	1.099	1.099	0.000	0.000	0.000	0.000
15	B	1214	VAL	0	0.039	0.001	12.629	-1.848	-1.848	0.000	0.000	0.000	0.000
16	B	1215	GLY	0	-0.001	-0.003	13.485	1.182	1.182	0.000	0.000	0.000	0.000
17	B	1216	ALA	0	0.010	-0.023	11.150	-0.434	-0.434	0.000	0.000	0.000	0.000
18	B	1217	GLY	0	-0.024	0.007	12.020	-1.119	-1.119	0.000	0.000	0.000	0.000
19	B	1218	ALA	0	-0.008	0.006	13.470	-0.112	-0.112	0.000	0.000	0.000	0.000
20	B	1219	THR	0	-0.018	-0.039	16.548	-0.508	-0.508	0.000	0.000	0.000	0.000
21	B	1220	ALA	0	0.035	-0.003	19.841	0.400	0.400	0.000	0.000	0.000	0.000
22	B	1221	GLU	-1	-0.751	-0.858	22.040	11.846	11.846	0.000	0.000	0.000	0.000
23	B	1222	GLU	-1	-0.817	-0.868	18.874	15.168	15.168	0.000	0.000	0.000	0.000
24	B	1223	THR	0	-0.028	0.000	17.268	0.462	0.462	0.000	0.000	0.000	0.000
25	B	1224	ARG	1	0.899	0.944	18.954	-11.432	-11.432	0.000	0.000	0.000	0.000
26	B	1225	ARG	1	0.847	0.904	22.057	-12.231	-12.231	0.000	0.000	0.000	0.000
27	B	1226	MET	0	-0.020	0.006	15.976	-0.204	-0.204	0.000	0.000	0.000	0.000
28	B	1227	LEU	0	0.011	0.006	17.790	0.268	0.268	0.000	0.000	0.000	0.000
29	B	1228	HIS	0	0.006	0.005	19.933	-0.082	-0.082	0.000	0.000	0.000	0.000
30	B	1229	ARG	1	0.987	0.998	19.723	-14.931	-14.931	0.000	0.000	0.000	0.000
31	B	1230	ALA	0	-0.012	0.006	17.531	-0.051	-0.051	0.000	0.000	0.000	0.000
32	B	1231	PHE	0	0.012	-0.006	19.288	-0.045	-0.045	0.000	0.000	0.000	0.000
33	B	1232	ASP	-1	-0.913	-0.940	22.357	11.975	11.975	0.000	0.000	0.000	0.000
34	B	1233	THR	0	-0.118	-0.079	19.927	0.080	0.080	0.000	0.000	0.000	0.000
35	B	1234	LEU	0	-0.058	-0.028	17.295	0.147	0.147	0.000	0.000	0.000	0.000
36	B	1235	ALA	0	-0.076	-0.010	21.392	-0.658	-0.658	0.000	0.000	0.000	0.000

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