FMO DATABASE

FMODB ID: Z684N

Calculation Name: 1GD2-I-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GD2

Chain ID: I

ChEMBL ID:

UniProt ID: Q01663

Base Structure: X-ray

Registration Date: 2023-09-20

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	42
LigandCharge	DLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-160047.458345
FMO2-HF: Nuclear repulsion	142560.00747
FMO2-HF: Total energy	-17487.450875
FMO2-MP2: Total energy	-17539.637097

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(I:82:ARG)

Summations of interaction energy for fragment #1(I:82:ARG)

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.
12.975	15.651	-0.022	-1.344	-1.31	0.001

Interaction energy analysis for fragmet #1(I:82:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.989 / q_NPA : 0.986

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	I	84	ALA	0	0.023	0.015	3.825	1.166	3.757	-0.021	-1.328	-1.242	0.001
4	I	85	GLN	0	0.057	0.027	4.576	-0.253	-0.168	-0.001	-0.016	-0.068	0.000
5	I	86	ASN	0	-0.036	-0.012	5.850	-2.971	-2.971	0.000	0.000	0.000	0.000
6	I	87	ARG	1	0.970	0.996	8.528	22.600	22.600	0.000	0.000	0.000	0.000
7	I	105	GLU	-1	-0.941	-0.975	23.019	-11.251	-11.251	0.000	0.000	0.000	0.000
8	I	106	THR	0	0.051	0.006	25.413	0.348	0.348	0.000	0.000	0.000	0.000
9	I	107	GLN	0	-0.034	-0.014	27.669	0.099	0.099	0.000	0.000	0.000	0.000
10	I	108	VAL	0	0.017	0.003	29.578	0.292	0.292	0.000	0.000	0.000	0.000
11	I	109	VAL	0	0.019	-0.008	30.741	0.288	0.288	0.000	0.000	0.000	0.000
12	I	110	THR	0	0.032	0.024	31.122	0.214	0.214	0.000	0.000	0.000	0.000
13	I	111	LEU	0	0.026	0.006	32.850	0.196	0.196	0.000	0.000	0.000	0.000
14	I	112	LYS	1	0.931	0.971	35.224	8.349	8.349	0.000	0.000	0.000	0.000
15	I	113	GLU	-1	-0.896	-0.927	36.802	-7.245	-7.245	0.000	0.000	0.000	0.000
16	I	114	LEU	0	-0.017	-0.006	36.773	0.141	0.141	0.000	0.000	0.000	0.000
17	I	115	HIS	0	0.005	-0.012	39.413	0.120	0.120	0.000	0.000	0.000	0.000
18	I	116	SER	0	0.001	-0.014	41.299	0.223	0.223	0.000	0.000	0.000	0.000
19	I	117	SER	0	-0.028	0.000	41.582	0.176	0.176	0.000	0.000	0.000	0.000
20	I	118	THR	0	0.016	0.025	43.013	0.149	0.149	0.000	0.000	0.000	0.000
21	I	119	THR	0	-0.026	-0.028	45.163	0.144	0.144	0.000	0.000	0.000	0.000
22	I	120	LEU	0	0.000	0.012	47.313	0.155	0.155	0.000	0.000	0.000	0.000
23	I	121	GLU	-1	-0.903	-0.957	46.046	-6.305	-6.305	0.000	0.000	0.000	0.000
24	I	122	ASN	0	-0.062	-0.038	49.785	0.172	0.172	0.000	0.000	0.000	0.000
25	I	123	ASP	-1	-0.903	-0.951	51.567	-5.463	-5.463	0.000	0.000	0.000	0.000
26	I	124	GLN	0	-0.009	-0.021	51.706	0.080	0.080	0.000	0.000	0.000	0.000
27	I	125	LEU	0	-0.034	0.010	52.931	0.121	0.121	0.000	0.000	0.000	0.000
28	I	126	ARG	1	0.911	0.899	54.137	5.709	5.709	0.000	0.000	0.000	0.000
29	I	127	GLN	0	0.164	0.124	57.353	0.128	0.128	0.000	0.000	0.000	0.000
30	I	128	LYS	1	0.824	0.812	54.837	5.300	5.300	0.000	0.000	0.000	0.000
31	I	129	VAL	0	0.027	0.016	55.916	0.012	0.012	0.000	0.000	0.000	0.000
32	I	130	ARG	1	0.782	0.974	57.602	4.877	4.877	0.000	0.000	0.000	0.000
33	I	131	GLN	0	0.011	-0.008	59.957	0.012	0.012	0.000	0.000	0.000	0.000
34	I	132	LEU	0	0.005	0.017	56.653	0.046	0.046	0.000	0.000	0.000	0.000
35	I	133	GLU	-1	-0.840	-0.902	61.137	-4.795	-4.795	0.000	0.000	0.000	0.000
36	I	134	GLU	-1	-0.823	-0.891	63.086	-4.584	-4.584	0.000	0.000	0.000	0.000
37	I	135	GLU	-1	-0.888	-0.943	64.188	-4.545	-4.545	0.000	0.000	0.000	0.000
38	I	136	LEU	0	-0.016	-0.003	63.490	0.054	0.054	0.000	0.000	0.000	0.000
39	I	137	ARG	1	0.782	0.849	65.841	4.742	4.742	0.000	0.000	0.000	0.000
40	I	138	ILE	0	-0.029	-0.003	68.998	0.083	0.083	0.000	0.000	0.000	0.000
41	I	139	LEU	0	-0.015	0.026	67.115	0.066	0.066	0.000	0.000	0.000	0.000
42	I	140	DLY	1	0.858	0.925	70.051	4.325	4.325	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(I:82:ARG)