FMO DATABASE

FMODB ID: K9RM3

Calculation Name: 1GME-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GME

Chain ID: B

ChEMBL ID:

UniProt ID: Q41560

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	109
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-751044.814249
FMO2-HF: Nuclear repulsion	708436.305435
FMO2-HF: Total energy	-42608.508814
FMO2-MP2: Total energy	-42735.057439

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(B:43:ASN)

Summations of interaction energy for fragment #1(B:43:ASN)

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.
-4.718	-1.208	0.033	-1.103	-2.44	0.006

Interaction energy analysis for fragmet #1(B:43:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.024

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	B	45	ARG	1	0.833	0.892	3.345	2.856	5.199	0.025	-0.788	-1.579	0.004
4	B	46	MET	0	0.018	0.002	4.796	-1.093	-1.018	-0.001	-0.013	-0.061	0.000
5	B	47	ASP	-1	-0.878	-0.909	7.776	0.703	0.703	0.000	0.000	0.000	0.000
6	B	48	TRP	0	-0.003	-0.017	11.071	0.146	0.146	0.000	0.000	0.000	0.000
7	B	49	LYS	1	0.840	0.920	13.789	-0.711	-0.711	0.000	0.000	0.000	0.000
8	B	50	GLU	-1	-0.805	-0.882	17.286	0.526	0.526	0.000	0.000	0.000	0.000
9	B	51	THR	0	-0.066	-0.034	20.672	-0.062	-0.062	0.000	0.000	0.000	0.000
10	B	52	PRO	0	-0.010	-0.029	23.770	0.014	0.014	0.000	0.000	0.000	0.000
11	B	53	GLU	-1	-0.818	-0.914	26.405	0.301	0.301	0.000	0.000	0.000	0.000
12	B	54	ALA	0	0.005	0.014	22.538	0.011	0.011	0.000	0.000	0.000	0.000
13	B	55	HIS	0	0.080	0.065	18.412	-0.021	-0.021	0.000	0.000	0.000	0.000
14	B	56	VAL	0	-0.050	-0.037	16.977	0.024	0.024	0.000	0.000	0.000	0.000
15	B	57	PHE	0	0.033	0.011	12.595	0.053	0.053	0.000	0.000	0.000	0.000
16	B	58	LYS	1	0.882	0.931	12.222	-0.718	-0.718	0.000	0.000	0.000	0.000
17	B	59	ALA	0	0.044	0.014	8.475	0.428	0.428	0.000	0.000	0.000	0.000
18	B	60	ASP	-1	-0.822	-0.867	7.483	-0.283	-0.283	0.000	0.000	0.000	0.000
19	B	61	LEU	0	-0.043	-0.039	6.853	0.161	0.161	0.000	0.000	0.000	0.000
20	B	62	PRO	0	0.045	0.011	7.959	-0.089	-0.089	0.000	0.000	0.000	0.000
21	B	63	GLY	0	-0.035	-0.024	9.670	-0.075	-0.075	0.000	0.000	0.000	0.000
22	B	64	VAL	0	-0.029	0.005	8.826	0.008	0.008	0.000	0.000	0.000	0.000
23	B	65	LYS	1	0.896	0.944	12.081	-0.211	-0.211	0.000	0.000	0.000	0.000
24	B	66	LYS	1	0.914	0.927	14.861	-0.245	-0.245	0.000	0.000	0.000	0.000
25	B	67	GLU	-1	-0.815	-0.893	16.853	0.410	0.410	0.000	0.000	0.000	0.000
26	B	68	GLU	-1	-0.845	-0.909	12.627	0.336	0.336	0.000	0.000	0.000	0.000
27	B	69	VAL	0	-0.050	-0.023	11.637	0.230	0.230	0.000	0.000	0.000	0.000
28	B	70	LYS	1	0.810	0.899	13.030	-1.087	-1.087	0.000	0.000	0.000	0.000
29	B	71	VAL	0	-0.018	-0.022	13.486	0.221	0.221	0.000	0.000	0.000	0.000
30	B	72	GLU	-1	-0.794	-0.884	15.456	0.763	0.763	0.000	0.000	0.000	0.000
31	B	73	VAL	0	0.034	0.008	16.725	0.125	0.125	0.000	0.000	0.000	0.000
32	B	74	GLU	-1	-0.787	-0.854	15.973	1.070	1.070	0.000	0.000	0.000	0.000
33	B	75	ASP	-1	-0.940	-0.987	19.477	0.752	0.752	0.000	0.000	0.000	0.000
34	B	76	GLY	0	0.008	0.017	22.118	-0.033	-0.033	0.000	0.000	0.000	0.000
35	B	77	ASN	0	0.027	0.012	21.301	0.060	0.060	0.000	0.000	0.000	0.000
36	B	78	VAL	0	0.006	-0.001	15.297	0.071	0.071	0.000	0.000	0.000	0.000
37	B	79	LEU	0	-0.011	0.019	13.772	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	80	VAL	0	-0.021	-0.024	12.077	0.288	0.288	0.000	0.000	0.000	0.000
39	B	81	VAL	0	0.003	0.004	9.397	-0.164	-0.164	0.000	0.000	0.000	0.000
40	B	82	SER	0	-0.038	-0.028	8.973	0.530	0.530	0.000	0.000	0.000	0.000
41	B	83	GLY	0	0.086	0.037	9.128	-0.391	-0.391	0.000	0.000	0.000	0.000
42	B	84	GLU	-1	-0.872	-0.928	8.475	1.119	1.119	0.000	0.000	0.000	0.000
43	B	85	ARG	1	0.822	0.899	6.584	0.698	0.698	0.000	0.000	0.000	0.000
44	B	86	THR	0	0.007	-0.017	8.560	-0.210	-0.210	0.000	0.000	0.000	0.000
45	B	87	LYS	1	0.884	0.948	11.345	0.392	0.392	0.000	0.000	0.000	0.000
46	B	88	GLU	-1	-0.894	-0.949	12.419	-0.055	-0.055	0.000	0.000	0.000	0.000
47	B	89	LYS	1	0.857	0.918	15.736	0.110	0.110	0.000	0.000	0.000	0.000
48	B	90	GLU	-1	-0.836	-0.907	17.583	-0.375	-0.375	0.000	0.000	0.000	0.000
49	B	91	ASP	-1	-0.825	-0.909	20.910	-0.153	-0.153	0.000	0.000	0.000	0.000
50	B	92	LYS	1	0.905	0.930	23.512	0.165	0.165	0.000	0.000	0.000	0.000
51	B	93	ASN	0	-0.063	-0.024	25.483	-0.007	-0.007	0.000	0.000	0.000	0.000
52	B	94	ASP	-1	-0.901	-0.929	22.445	-0.283	-0.283	0.000	0.000	0.000	0.000
53	B	95	LYS	1	0.920	0.951	23.622	0.328	0.328	0.000	0.000	0.000	0.000
54	B	96	TRP	0	-0.028	-0.012	15.884	-0.080	-0.080	0.000	0.000	0.000	0.000
55	B	97	HIS	0	0.008	0.002	20.545	-0.020	-0.020	0.000	0.000	0.000	0.000
56	B	98	ARG	1	0.840	0.895	15.591	1.015	1.015	0.000	0.000	0.000	0.000
57	B	99	VAL	0	0.001	-0.001	12.108	0.038	0.038	0.000	0.000	0.000	0.000
58	B	100	GLU	-1	-0.816	-0.884	11.076	-1.451	-1.451	0.000	0.000	0.000	0.000
59	B	101	ARG	1	0.918	0.964	8.688	0.366	0.366	0.000	0.000	0.000	0.000
60	B	102	SER	0	0.034	0.026	3.484	0.858	0.982	0.000	-0.029	-0.095	0.000
61	B	103	SER	0	0.002	-0.003	6.313	0.347	0.347	0.000	0.000	0.000	0.000
62	B	104	GLY	0	-0.005	0.008	6.324	-0.278	-0.278	0.000	0.000	0.000	0.000
63	B	105	LYS	1	0.871	0.928	6.976	-0.562	-0.562	0.000	0.000	0.000	0.000
64	B	106	PHE	0	-0.008	0.010	4.027	0.869	1.309	0.006	-0.120	-0.327	0.001
65	B	107	VAL	0	0.014	-0.012	5.162	-1.482	-1.482	0.000	0.000	0.000	0.000
66	B	108	ARG	1	0.871	0.939	3.501	-8.811	-8.283	0.003	-0.153	-0.378	0.001
67	B	109	ARG	1	0.823	0.883	7.918	-1.989	-1.989	0.000	0.000	0.000	0.000
68	B	110	PHE	0	-0.010	-0.004	9.179	0.177	0.177	0.000	0.000	0.000	0.000
69	B	111	ARG	1	0.885	0.942	13.668	-0.860	-0.860	0.000	0.000	0.000	0.000
70	B	112	LEU	0	-0.043	-0.021	17.281	-0.021	-0.021	0.000	0.000	0.000	0.000
71	B	113	LEU	0	0.007	-0.006	19.668	-0.016	-0.016	0.000	0.000	0.000	0.000
72	B	114	GLU	-1	-0.880	-0.931	23.182	0.508	0.508	0.000	0.000	0.000	0.000
73	B	115	ASP	-1	-0.933	-0.958	25.913	0.393	0.393	0.000	0.000	0.000	0.000
74	B	116	ALA	0	0.006	0.004	23.444	-0.004	-0.004	0.000	0.000	0.000	0.000
75	B	117	LYS	1	0.843	0.911	25.448	-0.357	-0.357	0.000	0.000	0.000	0.000
76	B	118	VAL	0	0.007	-0.001	22.785	0.031	0.031	0.000	0.000	0.000	0.000
77	B	119	GLU	-1	-0.904	-0.953	24.010	0.484	0.484	0.000	0.000	0.000	0.000
78	B	120	GLU	-1	-0.915	-0.947	25.905	0.342	0.342	0.000	0.000	0.000	0.000
79	B	121	VAL	0	-0.024	-0.010	19.246	0.009	0.009	0.000	0.000	0.000	0.000
80	B	122	LYS	1	0.914	0.971	21.761	-0.458	-0.458	0.000	0.000	0.000	0.000
81	B	123	ALA	0	0.040	-0.005	17.240	0.081	0.081	0.000	0.000	0.000	0.000
82	B	124	GLY	0	-0.005	0.015	18.271	-0.068	-0.068	0.000	0.000	0.000	0.000
83	B	125	LEU	0	-0.046	-0.030	13.639	0.102	0.102	0.000	0.000	0.000	0.000
84	B	126	GLU	-1	-0.912	-0.951	16.904	0.167	0.167	0.000	0.000	0.000	0.000
85	B	127	ASN	0	-0.011	-0.012	17.014	0.017	0.017	0.000	0.000	0.000	0.000
86	B	128	GLY	0	-0.007	0.001	13.220	-0.062	-0.062	0.000	0.000	0.000	0.000
87	B	129	VAL	0	0.003	0.014	11.946	0.066	0.066	0.000	0.000	0.000	0.000
88	B	130	LEU	0	0.011	0.005	11.864	-0.046	-0.046	0.000	0.000	0.000	0.000
89	B	131	THR	0	-0.026	-0.020	13.460	0.066	0.066	0.000	0.000	0.000	0.000
90	B	132	VAL	0	0.025	0.021	14.553	-0.062	-0.062	0.000	0.000	0.000	0.000
91	B	133	THR	0	-0.063	-0.032	17.007	-0.005	-0.005	0.000	0.000	0.000	0.000
92	B	134	VAL	0	0.066	0.026	18.523	-0.022	-0.022	0.000	0.000	0.000	0.000
93	B	135	PRO	0	-0.010	-0.006	21.228	-0.011	-0.011	0.000	0.000	0.000	0.000
94	B	136	LYS	1	0.789	0.885	23.952	-0.380	-0.380	0.000	0.000	0.000	0.000
95	B	137	ALA	0	0.011	0.016	26.214	-0.024	-0.024	0.000	0.000	0.000	0.000
96	B	138	GLU	-1	-0.950	-0.980	29.405	0.235	0.235	0.000	0.000	0.000	0.000
97	B	139	VAL	0	-0.049	-0.021	29.386	0.008	0.008	0.000	0.000	0.000	0.000
98	B	140	LYS	1	0.912	0.939	29.069	-0.272	-0.272	0.000	0.000	0.000	0.000
99	B	141	LYS	1	0.918	0.969	27.638	-0.187	-0.187	0.000	0.000	0.000	0.000
100	B	142	PRO	0	0.038	0.021	24.093	-0.020	-0.020	0.000	0.000	0.000	0.000
101	B	143	GLU	-1	-0.897	-0.941	27.245	0.201	0.201	0.000	0.000	0.000	0.000
102	B	144	VAL	0	0.000	-0.004	25.274	0.007	0.007	0.000	0.000	0.000	0.000
103	B	145	LYS	1	0.931	0.967	28.446	-0.158	-0.158	0.000	0.000	0.000	0.000
104	B	146	ALA	0	0.012	0.014	29.065	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	147	ILE	0	0.015	-0.001	29.696	-0.005	-0.005	0.000	0.000	0.000	0.000
106	B	148	GLN	0	-0.018	-0.008	30.699	-0.007	-0.007	0.000	0.000	0.000	0.000
107	B	149	ILE	0	0.011	0.005	27.340	-0.003	-0.003	0.000	0.000	0.000	0.000
108	B	150	SER	0	-0.008	-0.022	31.825	0.000	0.000	0.000	0.000	0.000	0.000
109	B	151	GLY	0	0.017	0.038	34.088	-0.011	-0.011	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:43:ASN)