FMO DATABASE

FMODB ID: MNYGZ

Calculation Name: 4GQM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GQM

Chain ID: A

ChEMBL ID:

UniProt ID: A0A654

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	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	105
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-719463.063822
FMO2-HF: Nuclear repulsion	677020.128384
FMO2-HF: Total energy	-42442.935438
FMO2-MP2: Total energy	-42565.156385

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:GLY)

Summations of interaction energy for fragment #1(A:-1: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.
-11.618	-6.775	10.775	-7.665	-7.954	-0.07

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / q_NPA : 0.040

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	1	MET	0	-0.013	-0.005	3.877	-0.481	1.622	-0.005	-1.174	-0.924	0.005
4	A	2	SER	0	0.028	-0.013	2.275	-3.714	-2.761	2.083	-1.426	-1.610	-0.016
5	A	3	GLU	-1	-0.919	-0.969	2.380	-1.727	-0.416	3.116	-2.033	-2.394	-0.022
6	A	4	HIS	0	-0.049	-0.029	5.171	1.103	1.190	-0.001	-0.007	-0.079	0.000
7	A	5	VAL	0	0.045	0.032	7.527	0.452	0.452	0.000	0.000	0.000	0.000
8	A	6	HIS	0	-0.042	-0.047	5.370	0.700	0.700	0.000	0.000	0.000	0.000
9	A	7	LYS	1	0.935	0.975	8.980	0.912	0.912	0.000	0.000	0.000	0.000
10	A	8	GLU	-1	-0.967	-0.988	10.995	-0.733	-0.733	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.014	-0.001	11.215	0.163	0.163	0.000	0.000	0.000	0.000
12	A	10	LEU	0	-0.020	-0.011	11.709	0.115	0.115	0.000	0.000	0.000	0.000
13	A	11	HIS	0	-0.024	-0.002	14.854	0.070	0.070	0.000	0.000	0.000	0.000
14	A	12	LEU	0	-0.013	-0.014	16.701	0.056	0.056	0.000	0.000	0.000	0.000
15	A	13	GLY	0	0.028	0.013	17.597	0.042	0.042	0.000	0.000	0.000	0.000
16	A	14	GLU	-1	-0.810	-0.907	19.164	-0.136	-0.136	0.000	0.000	0.000	0.000
17	A	15	VAL	0	-0.043	0.003	20.985	0.029	0.029	0.000	0.000	0.000	0.000
18	A	16	PHE	0	-0.040	-0.029	21.326	0.025	0.025	0.000	0.000	0.000	0.000
19	A	17	ARG	1	0.802	0.898	20.837	0.183	0.183	0.000	0.000	0.000	0.000
20	A	18	SER	0	-0.006	-0.018	24.748	0.021	0.021	0.000	0.000	0.000	0.000
21	A	19	GLN	0	-0.055	-0.035	27.014	0.010	0.010	0.000	0.000	0.000	0.000
22	A	20	ARG	1	0.624	0.766	26.183	0.135	0.135	0.000	0.000	0.000	0.000
23	A	21	GLU	-1	-0.854	-0.926	28.289	-0.095	-0.095	0.000	0.000	0.000	0.000
24	A	22	GLU	-1	-0.905	-0.940	30.939	-0.115	-0.115	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.881	0.938	32.806	0.119	0.119	0.000	0.000	0.000	0.000
26	A	24	ALA	0	-0.027	-0.010	34.240	0.004	0.004	0.000	0.000	0.000	0.000
27	A	25	LEU	0	-0.027	0.007	32.648	0.005	0.005	0.000	0.000	0.000	0.000
28	A	26	SER	0	-0.012	-0.040	31.702	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	27	LEU	0	0.036	-0.005	25.806	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	28	LYS	1	0.970	0.976	29.698	0.058	0.058	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.810	-0.854	32.750	-0.076	-0.076	0.000	0.000	0.000	0.000
32	A	30	VAL	0	0.018	0.013	28.906	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	31	GLU	-1	-0.810	-0.883	30.781	-0.099	-0.099	0.000	0.000	0.000	0.000
34	A	32	ALA	0	-0.052	-0.033	32.134	0.001	0.001	0.000	0.000	0.000	0.000
35	A	33	ALA	0	-0.023	-0.003	34.448	0.002	0.002	0.000	0.000	0.000	0.000
36	A	34	THR	0	-0.041	-0.045	31.167	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	35	SER	0	-0.050	-0.021	32.693	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	36	ILE	0	-0.024	-0.005	26.375	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.882	0.930	27.230	0.102	0.102	0.000	0.000	0.000	0.000
40	A	38	LEU	0	0.074	0.035	26.620	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	39	SER	0	-0.013	-0.006	24.070	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	40	ALA	0	-0.011	-0.005	22.198	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	41	LEU	0	0.005	0.004	22.079	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	42	GLU	-1	-0.881	-0.959	22.174	-0.114	-0.114	0.000	0.000	0.000	0.000
45	A	43	ALA	0	-0.046	-0.020	18.436	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	44	ILE	0	0.004	0.008	17.760	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	45	GLU	-1	-0.751	-0.845	18.650	-0.181	-0.181	0.000	0.000	0.000	0.000
48	A	46	ALA	0	-0.066	-0.020	17.536	0.012	0.012	0.000	0.000	0.000	0.000
49	A	47	GLY	0	0.044	0.025	14.654	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	48	HIS	0	-0.017	-0.005	13.130	-0.119	-0.119	0.000	0.000	0.000	0.000
51	A	49	LEU	0	0.089	0.033	9.161	0.073	0.073	0.000	0.000	0.000	0.000
52	A	50	GLY	0	0.049	0.030	12.741	0.032	0.032	0.000	0.000	0.000	0.000
53	A	51	LYS	1	0.869	0.935	13.848	0.161	0.161	0.000	0.000	0.000	0.000
54	A	52	LEU	0	-0.009	0.002	15.217	0.028	0.028	0.000	0.000	0.000	0.000
55	A	53	ILE	0	0.005	0.015	13.717	0.024	0.024	0.000	0.000	0.000	0.000
56	A	54	SER	0	0.018	-0.003	15.964	0.026	0.026	0.000	0.000	0.000	0.000
57	A	55	PRO	0	-0.054	-0.012	17.566	0.031	0.031	0.000	0.000	0.000	0.000
58	A	56	VAL	0	0.048	0.044	21.350	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	57	TYR	0	-0.042	-0.051	20.110	0.040	0.040	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.020	0.014	25.695	0.013	0.013	0.000	0.000	0.000	0.000
61	A	59	GLN	0	0.075	0.051	26.594	0.020	0.020	0.000	0.000	0.000	0.000
62	A	60	GLY	0	-0.008	-0.005	28.134	0.011	0.011	0.000	0.000	0.000	0.000
63	A	61	PHE	0	-0.024	-0.027	27.864	0.008	0.008	0.000	0.000	0.000	0.000
64	A	62	MET	0	0.016	0.013	31.776	0.008	0.008	0.000	0.000	0.000	0.000
65	A	63	LYS	1	0.914	0.957	29.715	0.058	0.058	0.000	0.000	0.000	0.000
66	A	64	LYS	1	0.929	0.964	30.093	0.080	0.080	0.000	0.000	0.000	0.000
67	A	65	TYR	0	0.001	0.005	34.970	0.003	0.003	0.000	0.000	0.000	0.000
68	A	66	ALA	0	0.017	0.006	37.299	0.003	0.003	0.000	0.000	0.000	0.000
69	A	67	ALA	0	0.011	0.001	37.507	0.003	0.003	0.000	0.000	0.000	0.000
70	A	68	PHE	0	-0.074	-0.034	39.165	0.002	0.002	0.000	0.000	0.000	0.000
71	A	69	LEU	0	-0.038	-0.015	40.930	0.001	0.001	0.000	0.000	0.000	0.000
72	A	70	ASP	-1	-0.908	-0.942	43.450	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	71	MET	0	-0.066	-0.021	41.730	0.003	0.003	0.000	0.000	0.000	0.000
74	A	72	ASP	-1	-0.800	-0.904	39.279	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	73	GLY	0	0.056	0.003	36.898	0.000	0.000	0.000	0.000	0.000	0.000
76	A	74	ASP	-1	-0.910	-0.940	34.163	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	75	ARG	1	0.790	0.852	35.919	0.028	0.028	0.000	0.000	0.000	0.000
78	A	76	LEU	0	0.021	0.023	38.584	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	77	LEU	0	-0.010	-0.012	32.168	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	78	LYS	1	0.819	0.895	34.219	0.019	0.019	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.814	-0.871	36.915	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	80	HIS	0	-0.077	-0.032	36.840	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	81	PRO	0	0.032	0.016	35.260	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	82	TYR	0	0.020	-0.004	33.509	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	83	VAL	0	0.017	0.012	31.968	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	84	LEU	0	-0.006	0.001	30.154	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	85	LYS	1	0.819	0.918	27.082	0.043	0.043	0.000	0.000	0.000	0.000
88	A	86	ILE	0	0.068	0.025	27.266	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	87	PHE	0	-0.040	-0.034	25.870	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	88	GLN	0	-0.049	-0.020	24.948	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	89	GLU	-1	-0.766	-0.875	22.928	-0.070	-0.070	0.000	0.000	0.000	0.000
92	A	90	PHE	0	-0.031	-0.022	21.395	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	91	SER	0	-0.007	-0.008	20.074	-0.025	-0.025	0.000	0.000	0.000	0.000
94	A	92	ASP	-1	-0.930	-0.967	18.682	-0.065	-0.065	0.000	0.000	0.000	0.000
95	A	93	GLN	0	0.005	-0.001	15.706	0.007	0.007	0.000	0.000	0.000	0.000
96	A	94	ASN	0	-0.056	-0.034	15.681	-0.069	-0.069	0.000	0.000	0.000	0.000
97	A	95	MET	0	-0.045	-0.023	14.149	-0.069	-0.069	0.000	0.000	0.000	0.000
98	A	96	ASP	-1	-0.883	-0.936	12.505	-0.100	-0.100	0.000	0.000	0.000	0.000
99	A	97	MET	0	-0.039	-0.019	11.257	-0.048	-0.048	0.000	0.000	0.000	0.000
100	A	98	LEU	0	-0.069	-0.039	9.889	-0.201	-0.201	0.000	0.000	0.000	0.000
101	A	99	LEU	0	-0.002	0.001	7.938	-0.192	-0.192	0.000	0.000	0.000	0.000
102	A	100	ASP	-1	-0.890	-0.954	6.819	-0.391	-0.391	0.000	0.000	0.000	0.000
103	A	101	LEU	0	-0.085	-0.038	5.811	-0.244	-0.244	0.000	0.000	0.000	0.000
104	A	102	GLU	-1	-0.813	-0.871	2.685	-4.579	-3.896	0.275	-0.435	-0.523	-0.001
105	A	103	SER	0	-0.102	-0.037	2.055	-2.714	-3.008	5.307	-2.590	-2.424	-0.036

Top

Graph

Manual

About

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