FMO DATABASE

FMODB ID: ZY1JN

Calculation Name: 2GMQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GMQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KUD5

Base Structure: X-ray

Registration Date: 2023-06-19

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-817187.844887
FMO2-HF: Nuclear repulsion	776095.868414
FMO2-HF: Total energy	-41091.976473
FMO2-MP2: Total energy	-41212.858922

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-0.223	1.119	-0.007	-0.757	-0.579	0.003

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.023

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

Sort

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	14	LYS	1	0.853	0.920	3.851	1.531	2.873	-0.007	-0.757	-0.579	0.003
4	A	15	GLU	-1	-0.872	-0.930	6.728	-0.693	-0.693	0.000	0.000	0.000	0.000
5	A	16	ILE	0	-0.006	-0.003	10.323	0.120	0.120	0.000	0.000	0.000	0.000
6	A	17	ALA	0	0.011	0.012	13.766	0.024	0.024	0.000	0.000	0.000	0.000
7	A	18	ILE	0	-0.025	-0.015	17.092	0.026	0.026	0.000	0.000	0.000	0.000
8	A	19	GLN	0	0.022	0.020	20.041	0.029	0.029	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.771	-0.899	23.621	-0.257	-0.257	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.914	0.956	25.053	0.228	0.228	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.759	-0.861	23.871	-0.301	-0.301	0.000	0.000	0.000	0.000
12	A	23	LEU	0	-0.039	-0.009	20.746	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.025	-0.007	24.833	0.044	0.044	0.000	0.000	0.000	0.000
14	A	25	LEU	0	0.030	0.014	23.890	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	26	GLN	0	0.020	0.020	24.940	0.008	0.008	0.000	0.000	0.000	0.000
16	A	27	TRP	0	0.069	0.036	24.852	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.955	0.971	25.022	0.252	0.252	0.000	0.000	0.000	0.000
18	A	29	GLY	0	0.038	0.016	28.821	0.008	0.008	0.000	0.000	0.000	0.000
19	A	30	ASN	0	-0.034	-0.020	31.341	0.003	0.003	0.000	0.000	0.000	0.000
20	A	31	THR	0	0.026	0.004	31.892	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.054	0.034	29.509	0.000	0.000	0.000	0.000	0.000	0.000
22	A	33	LYS	1	0.865	0.917	19.544	0.396	0.396	0.000	0.000	0.000	0.000
23	A	34	LEU	0	0.006	0.016	21.257	0.011	0.011	0.000	0.000	0.000	0.000
24	A	35	VAL	0	-0.074	-0.031	21.852	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.898	0.944	20.329	0.297	0.297	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.024	0.023	19.362	0.046	0.046	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.861	0.926	21.134	0.244	0.244	0.000	0.000	0.000	0.000
28	A	39	LEU	0	0.031	0.017	19.818	0.027	0.027	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.845	0.913	23.665	0.281	0.281	0.000	0.000	0.000	0.000
30	A	41	ASN	0	0.022	-0.009	26.601	0.004	0.004	0.000	0.000	0.000	0.000
31	A	42	THR	0	0.031	0.015	28.003	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.785	0.865	21.504	0.361	0.361	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.020	0.012	23.209	-0.017	-0.017	0.000	0.000	0.000	0.000
34	A	45	MET	0	0.015	0.011	24.000	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	46	GLU	-1	-0.814	-0.863	23.851	-0.306	-0.306	0.000	0.000	0.000	0.000
36	A	47	MET	0	0.004	-0.006	19.808	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	48	TRP	0	0.028	0.028	21.159	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.014	-0.018	23.007	0.014	0.014	0.000	0.000	0.000	0.000
39	A	50	ASN	0	-0.032	-0.033	21.784	0.027	0.027	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.834	0.920	18.792	0.258	0.258	0.000	0.000	0.000	0.000
41	A	52	GLN	0	0.022	0.022	17.250	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	53	ILE	0	-0.026	-0.022	15.075	-0.086	-0.086	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.026	-0.024	15.740	0.095	0.095	0.000	0.000	0.000	0.000
44	A	55	GLU	-1	-0.896	-0.969	15.537	-0.467	-0.467	0.000	0.000	0.000	0.000
45	A	56	GLU	-1	-0.916	-0.946	13.739	-0.458	-0.458	0.000	0.000	0.000	0.000
46	A	57	ASN	0	-0.001	0.013	11.307	-0.096	-0.096	0.000	0.000	0.000	0.000
47	A	58	ILE	0	-0.064	-0.029	10.857	-0.236	-0.236	0.000	0.000	0.000	0.000
48	A	59	GLN	0	-0.045	-0.042	10.572	-0.110	-0.110	0.000	0.000	0.000	0.000
49	A	60	GLU	-1	-0.776	-0.875	6.542	-1.786	-1.786	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.090	-0.028	6.396	-0.921	-0.921	0.000	0.000	0.000	0.000
51	A	62	THR	0	0.057	0.029	5.184	-0.070	-0.070	0.000	0.000	0.000	0.000
52	A	63	THR	0	-0.047	-0.028	8.336	0.295	0.295	0.000	0.000	0.000	0.000
53	A	64	LEU	0	-0.004	0.007	11.022	0.012	0.012	0.000	0.000	0.000	0.000
54	A	65	ASN	0	-0.008	-0.031	14.465	0.107	0.107	0.000	0.000	0.000	0.000
55	A	66	ILE	0	0.005	0.006	16.689	0.038	0.038	0.000	0.000	0.000	0.000
56	A	67	ILE	0	0.005	0.001	19.306	0.031	0.031	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.830	0.896	22.801	0.235	0.235	0.000	0.000	0.000	0.000
58	A	69	ASN	0	-0.040	-0.035	26.543	0.000	0.000	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.024	0.021	28.033	0.010	0.010	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.888	0.959	25.251	0.183	0.183	0.000	0.000	0.000	0.000
61	A	72	SER	0	0.013	-0.006	19.866	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.009	-0.002	19.772	0.023	0.023	0.000	0.000	0.000	0.000
63	A	74	ALA	0	0.038	0.033	14.116	-0.033	-0.033	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.037	-0.029	15.257	0.070	0.070	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.757	-0.861	10.618	-1.024	-1.024	0.000	0.000	0.000	0.000
66	A	77	VAL	0	-0.032	-0.015	11.405	0.226	0.226	0.000	0.000	0.000	0.000
67	A	78	TYR	0	-0.012	-0.029	11.532	-0.054	-0.054	0.000	0.000	0.000	0.000
68	A	79	PRO	0	0.095	0.057	7.553	0.227	0.227	0.000	0.000	0.000	0.000
69	A	80	GLU	-1	-0.849	-0.926	9.167	-1.071	-1.071	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.808	0.917	12.376	0.661	0.661	0.000	0.000	0.000	0.000
71	A	82	SER	0	-0.038	-0.010	12.467	0.133	0.133	0.000	0.000	0.000	0.000
72	A	83	ILE	0	0.012	0.019	15.155	0.013	0.013	0.000	0.000	0.000	0.000
73	A	84	TYR	0	0.074	0.026	17.223	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	85	VAL	0	-0.040	-0.018	20.886	0.030	0.030	0.000	0.000	0.000	0.000
75	A	86	LYS	1	1.035	1.018	24.518	0.171	0.171	0.000	0.000	0.000	0.000
76	A	87	PRO	0	-0.006	0.012	28.075	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	88	ASN	0	-0.001	0.001	29.349	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	89	LEU	0	0.025	0.000	32.555	0.000	0.000	0.000	0.000	0.000	0.000
79	A	90	GLY	0	0.022	0.009	33.176	0.001	0.001	0.000	0.000	0.000	0.000
80	A	91	ARG	1	0.931	0.971	31.443	0.158	0.158	0.000	0.000	0.000	0.000
81	A	92	ILE	0	0.023	0.012	24.399	0.006	0.006	0.000	0.000	0.000	0.000
82	A	93	ASN	0	0.013	0.009	24.026	0.014	0.014	0.000	0.000	0.000	0.000
83	A	94	VAL	0	-0.008	-0.010	23.572	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	95	PRO	0	0.040	0.036	18.408	0.007	0.007	0.000	0.000	0.000	0.000
85	A	96	VAL	0	-0.068	-0.046	19.108	0.039	0.039	0.000	0.000	0.000	0.000
86	A	97	PHE	0	0.101	0.048	13.378	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	98	PHE	0	-0.003	-0.015	16.614	0.095	0.095	0.000	0.000	0.000	0.000
88	A	99	ILE	0	0.024	0.014	15.804	-0.083	-0.083	0.000	0.000	0.000	0.000
89	A	100	LYS	1	0.804	0.888	10.658	1.015	1.015	0.000	0.000	0.000	0.000
90	A	101	THR	0	0.049	0.026	15.150	0.040	0.040	0.000	0.000	0.000	0.000
91	A	102	PRO	0	-0.030	-0.029	17.117	0.019	0.019	0.000	0.000	0.000	0.000
92	A	103	ILE	0	0.065	0.044	20.834	0.012	0.012	0.000	0.000	0.000	0.000
93	A	104	ASN	0	0.008	-0.007	23.026	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.805	0.900	26.681	0.196	0.196	0.000	0.000	0.000	0.000
95	A	106	GLY	0	0.028	0.014	28.749	0.000	0.000	0.000	0.000	0.000	0.000
96	A	107	VAL	0	0.054	0.026	25.706	0.004	0.004	0.000	0.000	0.000	0.000
97	A	108	PHE	0	0.009	-0.001	23.122	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.828	-0.914	26.740	-0.201	-0.201	0.000	0.000	0.000	0.000
99	A	110	GLU	-1	-0.928	-0.946	30.074	-0.132	-0.132	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.047	-0.009	23.747	0.003	0.003	0.000	0.000	0.000	0.000
101	A	112	PHE	0	-0.053	-0.033	22.759	0.005	0.005	0.000	0.000	0.000	0.000
102	A	113	GLY	0	0.002	0.016	28.788	0.003	0.003	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)