FMO DATABASE

FMODB ID: J3Y59

Calculation Name: 2GN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GN5

Chain ID: A

ChEMBL ID:

UniProt ID: P69542

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-546040.749878
FMO2-HF: Nuclear repulsion	512161.132245
FMO2-HF: Total energy	-33879.617632
FMO2-MP2: Total energy	-33978.401844

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-1.421	-2.535	1.051	2.706	-2.643	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : 0.004

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	3	LYN	0	-0.053	-0.027	3.206	-0.783	-2.650	0.113	3.151	-1.397	0.005
4	A	4	VAL	0	-0.017	-0.014	6.875	0.284	0.284	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.878	-0.927	6.285	0.786	0.786	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.045	0.033	7.861	0.174	0.174	0.000	0.000	0.000	0.000
7	A	7	LYN	0	0.012	-0.015	7.581	-0.122	-0.122	0.000	0.000	0.000	0.000
8	A	8	PRO	0	-0.053	-0.016	9.025	-0.039	-0.039	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.046	0.030	12.443	0.021	0.021	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.024	-0.017	15.042	0.003	0.003	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.012	0.003	17.019	-0.013	-0.013	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.036	-0.025	19.878	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.073	-0.035	17.105	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.014	0.015	19.868	-0.025	-0.025	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.027	-0.017	21.374	-0.010	-0.010	0.000	0.000	0.000	0.000
16	A	16	ARG	1	1.002	1.010	24.406	0.136	0.136	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.063	-0.040	25.863	0.008	0.008	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.007	-0.015	28.641	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.039	0.034	30.080	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.019	-0.004	32.673	0.006	0.006	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.918	0.962	35.755	0.076	0.076	0.000	0.000	0.000	0.000
22	A	22	GLN	0	0.038	0.015	37.020	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.019	-0.010	39.002	0.005	0.005	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.919	0.941	40.676	0.072	0.072	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.005	0.002	41.400	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.070	0.049	39.055	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.054	-0.030	36.383	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.007	-0.002	32.899	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.064	-0.028	29.769	0.013	0.013	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.810	-0.891	28.042	-0.146	-0.146	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.102	-0.044	25.446	0.015	0.015	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.009	0.009	24.667	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.021	-0.024	19.234	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	TYR	0	0.009	0.007	20.584	0.005	0.005	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.009	0.004	14.577	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.820	-0.910	14.132	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.007	-0.012	12.299	-0.064	-0.064	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.030	0.029	10.857	0.057	0.057	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.095	-0.038	11.864	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.896	-0.958	13.671	0.140	0.140	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.054	-0.030	15.692	0.041	0.041	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.008	0.013	12.994	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.014	-0.019	14.767	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.025	-0.014	17.235	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.013	0.000	17.434	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	LYN	0	-0.015	-0.019	19.971	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.015	0.001	15.983	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.044	-0.049	20.676	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.002	-0.006	19.864	-0.022	-0.022	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.742	-0.841	22.005	-0.288	-0.288	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.853	-0.918	24.918	-0.183	-0.183	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.017	0.003	27.740	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.058	-0.043	22.009	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.032	-0.019	22.450	0.011	0.011	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.015	0.013	21.024	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	56	TYR	0	0.029	0.018	15.407	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.025	0.006	16.072	0.035	0.035	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.012	-0.029	15.091	-0.040	-0.040	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.016	-0.008	12.082	0.048	0.048	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.050	-0.010	6.165	-0.079	-0.079	0.000	0.000	0.000	0.000
61	A	61	TYR	0	-0.004	0.002	8.373	-0.189	-0.189	0.000	0.000	0.000	0.000
62	A	62	THR	-1	-0.783	-0.895	6.425	-1.484	-1.484	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.036	-0.032	8.824	0.148	0.148	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.013	0.007	11.509	-0.091	-0.091	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.005	-0.013	14.320	0.045	0.045	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.014	0.002	16.811	0.060	0.060	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.003	-0.007	16.838	-0.064	-0.064	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.023	-0.023	14.113	0.032	0.032	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.791	0.888	19.426	0.220	0.220	0.000	0.000	0.000	0.000
70	A	70	VAL	0	0.032	0.010	23.291	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.002	0.023	26.268	0.010	0.010	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.062	-0.057	29.304	0.019	0.019	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.024	0.008	28.701	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	74	GLY	0	-0.001	-0.005	25.313	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.015	0.005	19.587	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.007	-0.010	22.800	0.019	0.019	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.046	0.022	16.812	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.013	0.000	21.060	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.824	-0.890	23.340	-0.237	-0.237	0.000	0.000	0.000	0.000
80	A	80	ARG	0	0.036	0.018	20.558	0.006	0.006	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.030	0.030	14.710	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.777	0.866	16.742	0.344	0.344	0.000	0.000	0.000	0.000
83	A	83	LEU	0	0.006	0.017	12.321	-0.049	-0.049	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.032	-0.017	9.691	0.040	0.040	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.049	0.027	9.477	-0.091	-0.091	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.051	0.022	3.796	-0.254	-0.161	0.000	-0.015	-0.078	0.000
87	A	87	LYS	1	0.823	0.919	2.770	0.250	0.910	0.938	-0.430	-1.168	-0.006

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