FMO DATABASE

FMODB ID: LN9R9

Calculation Name: 3GGM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGM

Chain ID: A

ChEMBL ID:

UniProt ID: Q6HGT3

Base Structure: X-ray

Registration Date: 2023-09-23

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-400491.176412
FMO2-HF: Nuclear repulsion	372130.037095
FMO2-HF: Total energy	-28361.139317
FMO2-MP2: Total energy	-28444.017345

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(A:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

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.
-1.914	0.991	0.197	-1.035	-2.067	-0.002

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.020

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	A	2	VAL	0	0.004	0.007	2.956	-1.540	1.109	0.197	-0.999	-1.847	-0.002
4	A	3	PRO	0	0.014	0.031	4.663	0.186	0.272	-0.001	-0.011	-0.073	0.000
5	A	4	ASP	-1	-0.799	-0.910	8.374	-0.557	-0.557	0.000	0.000	0.000	0.000
6	A	5	MET	0	-0.097	-0.044	11.245	0.134	0.134	0.000	0.000	0.000	0.000
7	A	6	ILE	0	0.020	0.022	9.779	-0.039	-0.039	0.000	0.000	0.000	0.000
8	A	7	LEU	0	-0.024	0.004	14.033	0.046	0.046	0.000	0.000	0.000	0.000
9	A	8	TYR	0	0.072	0.025	16.797	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	9	ASN	0	-0.001	-0.002	18.748	0.020	0.020	0.000	0.000	0.000	0.000
11	A	10	GLY	0	-0.013	-0.007	21.948	0.016	0.016	0.000	0.000	0.000	0.000
12	A	11	LYS	1	0.849	0.934	23.891	0.093	0.093	0.000	0.000	0.000	0.000
13	A	12	ILE	0	0.015	0.004	20.132	0.006	0.006	0.000	0.000	0.000	0.000
14	A	13	THR	0	-0.003	-0.001	23.963	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	14	THR	0	-0.076	-0.038	21.307	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	15	LEU	0	-0.004	-0.020	24.288	0.009	0.009	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.809	-0.859	22.012	-0.104	-0.104	0.000	0.000	0.000	0.000
18	A	17	PRO	0	-0.023	-0.035	24.745	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.086	-0.057	23.720	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	GLN	0	-0.019	-0.022	19.162	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	20	PRO	0	0.029	0.034	23.633	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.845	-0.922	25.176	-0.105	-0.105	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.007	0.025	19.788	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	23	SER	0	-0.042	-0.035	20.632	0.005	0.005	0.000	0.000	0.000	0.000
25	A	24	ALA	0	-0.003	-0.019	16.392	0.007	0.007	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.000	0.008	15.953	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	26	ALA	0	0.015	0.007	10.736	0.001	0.001	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.021	-0.022	12.755	0.029	0.029	0.000	0.000	0.000	0.000
29	A	28	THR	0	0.031	-0.049	8.709	-0.135	-0.135	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.776	-0.860	11.406	-0.439	-0.439	0.000	0.000	0.000	0.000
31	A	30	GLY	0	-0.043	-0.044	13.913	0.020	0.020	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.159	-0.064	14.622	0.054	0.054	0.000	0.000	0.000	0.000
33	A	32	ILE	0	-0.041	-0.027	14.088	-0.063	-0.063	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.011	0.035	8.662	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	34	ALA	0	0.030	0.010	11.154	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.029	-0.012	13.022	0.012	0.012	0.000	0.000	0.000	0.000
37	A	36	GLY	0	0.064	0.036	15.893	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	37	GLY	0	0.015	-0.006	16.451	0.026	0.026	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.946	-0.990	15.574	-0.235	-0.235	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.758	-0.866	12.524	-0.303	-0.303	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.013	-0.010	10.918	-0.077	-0.077	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.065	-0.027	10.123	-0.067	-0.067	0.000	0.000	0.000	0.000
43	A	42	ASN	0	-0.040	-0.018	8.176	0.102	0.102	0.000	0.000	0.000	0.000
44	A	43	SER	0	-0.074	-0.036	5.444	-0.063	-0.063	0.000	0.000	0.000	0.000
45	A	44	ALA	0	-0.004	-0.007	5.681	0.118	0.118	0.000	0.000	0.000	0.000
46	A	45	THR	0	-0.014	-0.013	4.797	0.017	0.187	0.001	-0.025	-0.147	0.000
47	A	46	GLU	-1	-0.930	-0.969	8.017	-0.106	-0.106	0.000	0.000	0.000	0.000
48	A	47	LYS	1	0.940	0.969	9.253	0.232	0.232	0.000	0.000	0.000	0.000
49	A	48	THR	0	-0.066	-0.009	8.007	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	49	LYS	1	0.918	0.955	11.000	0.405	0.405	0.000	0.000	0.000	0.000
51	A	50	LYS	1	1.011	1.006	12.460	0.118	0.118	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.024	-0.030	15.833	0.027	0.027	0.000	0.000	0.000	0.000
53	A	52	ASP	-1	-0.803	-0.881	19.267	-0.138	-0.138	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.004	-0.023	21.330	0.015	0.015	0.000	0.000	0.000	0.000
55	A	54	LYS	1	0.889	0.946	23.623	0.105	0.105	0.000	0.000	0.000	0.000
56	A	55	ARG	1	0.932	0.962	25.492	0.114	0.114	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.938	0.979	26.681	0.107	0.107	0.000	0.000	0.000	0.000
58	A	57	ARG	1	0.919	0.961	26.244	0.091	0.091	0.000	0.000	0.000	0.000
59	A	58	ALA	0	-0.007	-0.007	23.032	0.003	0.003	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.017	-0.016	25.012	0.001	0.001	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.011	0.014	23.432	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.013	0.014	25.080	0.011	0.011	0.000	0.000	0.000	0.000
63	A	62	LEU	0	-0.012	-0.019	27.235	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	63	ASN	0	-0.014	-0.011	24.559	0.002	0.002	0.000	0.000	0.000	0.000
65	A	64	ASP	-1	-0.752	-0.869	28.257	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	65	SER	0	-0.025	-0.005	30.995	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	HIS	1	0.828	0.895	32.460	0.052	0.052	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.016	0.003	33.431	0.003	0.003	0.000	0.000	0.000	0.000
69	A	68	HIS	0	0.041	0.031	33.630	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.030	-0.018	30.853	0.002	0.002	0.000	0.000	0.000	0.000
71	A	70	ILE	0	0.027	0.000	33.835	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.892	0.938	27.835	0.094	0.094	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.019	-0.003	33.947	0.003	0.003	0.000	0.000	0.000	0.000
74	A	73	LEU	0	0.008	0.034	35.575	0.003	0.003	0.000	0.000	0.000	0.000
75	A	74	GLU	-1	-0.965	-0.976	37.426	-0.055	-0.055	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)