FMO DATABASE

FMODB ID: LZ8K9

Calculation Name: 2GMY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GMY

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D1C9

Base Structure: X-ray

Registration Date: 2023-09-20

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1379553.647553
FMO2-HF: Nuclear repulsion	1321428.441683
FMO2-HF: Total energy	-58125.20587
FMO2-MP2: Total energy	-58295.108825

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:2:LYS)

Summations of interaction energy for fragment #1(A:2:LYS)

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.
7.468	11.64	0.467	-1.878	-2.762	-0.01

Interaction energy analysis for fragmet #1(A:2:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.971 / q_NPA : 0.974

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	4	ARG	1	0.836	0.925	2.801	17.618	20.646	0.386	-1.560	-1.854	-0.010
4	A	5	ILE	0	0.050	0.019	5.373	-1.917	-1.811	-0.001	-0.005	-0.100	0.000
5	A	6	ASN	0	-0.002	0.005	7.836	3.093	3.093	0.000	0.000	0.000	0.000
6	A	7	TYR	0	0.062	0.014	9.490	1.541	1.541	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.030	0.024	12.550	1.187	1.187	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.900	0.945	12.086	21.659	21.659	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.004	0.002	11.892	0.723	0.723	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.007	0.001	13.876	1.153	1.153	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.027	0.014	17.301	0.382	0.382	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.909	-0.953	19.279	-12.108	-12.108	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.011	0.012	18.885	0.453	0.453	0.000	0.000	0.000	0.000
14	A	15	PHE	0	0.003	-0.009	16.834	0.171	0.171	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.967	0.975	19.279	13.089	13.089	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.018	0.023	22.784	0.480	0.480	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.005	0.002	19.981	0.392	0.392	0.000	0.000	0.000	0.000
18	A	19	MET	0	-0.027	-0.014	20.690	0.141	0.141	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.004	0.005	23.170	0.428	0.428	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.010	0.012	25.188	0.393	0.393	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.837	-0.914	22.537	-11.686	-11.686	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.020	-0.017	25.240	0.369	0.369	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.017	0.018	27.882	0.318	0.318	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.020	0.001	27.050	0.284	0.284	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.010	0.000	26.426	0.080	0.080	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.045	-0.017	29.372	0.291	0.291	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.020	-0.004	32.343	0.359	0.359	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.013	0.001	34.346	0.260	0.260	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.039	-0.008	31.777	0.163	0.163	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.815	-0.895	33.959	-7.836	-7.836	0.000	0.000	0.000	0.000
31	A	32	HIS	0	0.076	0.021	30.660	-0.311	-0.311	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.866	0.943	30.038	7.670	7.670	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.028	-0.001	30.230	-0.239	-0.239	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.009	0.013	26.862	-0.287	-0.287	0.000	0.000	0.000	0.000
35	A	36	HIS	0	-0.061	-0.060	25.788	-0.610	-0.610	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.008	0.000	25.266	-0.377	-0.377	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.014	0.002	25.598	-0.273	-0.273	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.851	0.917	21.963	11.195	11.195	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.014	0.017	20.532	-0.629	-0.629	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.813	0.890	21.276	9.886	9.886	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.039	0.015	22.154	-0.214	-0.214	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.005	-0.021	17.287	-0.687	-0.687	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.036	-0.016	17.276	-0.597	-0.597	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.077	-0.017	18.577	-0.263	-0.263	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.074	-0.058	16.903	-0.119	-0.119	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.004	0.021	14.727	-0.779	-0.779	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.118	-0.031	12.458	-1.261	-1.261	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.085	0.035	10.359	0.548	0.548	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.019	-0.016	10.048	0.338	0.338	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.009	-0.016	12.031	0.519	0.519	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.031	0.020	15.327	0.658	0.658	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.817	-0.899	14.130	-14.637	-14.637	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.026	-0.012	15.561	0.595	0.595	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.854	0.890	17.757	13.389	13.389	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.024	0.034	19.591	0.588	0.588	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.787	0.886	15.940	14.936	14.936	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.860	-0.917	21.768	-11.833	-11.833	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.021	-0.001	23.920	0.466	0.466	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.821	0.883	21.793	11.143	11.143	0.000	0.000	0.000	0.000
60	A	61	HIS	0	-0.058	-0.021	25.770	0.210	0.210	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.852	-0.895	27.577	-9.150	-9.150	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.041	-0.013	30.087	0.280	0.280	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.057	-0.012	28.919	0.244	0.244	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.035	0.013	29.770	-0.207	-0.207	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.725	-0.868	25.883	-10.245	-10.245	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.027	0.000	27.623	-0.152	-0.152	0.000	0.000	0.000	0.000
67	A	68	TRP	0	0.008	-0.004	26.804	-0.257	-0.257	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.014	0.025	23.649	-0.197	-0.197	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.067	-0.055	23.742	-0.593	-0.593	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.016	-0.003	25.219	-0.124	-0.124	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.022	0.050	24.416	0.160	0.160	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.039	-0.031	22.364	0.051	0.051	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.019	-0.018	24.087	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.009	0.002	27.481	0.426	0.426	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.917	0.965	29.906	8.804	8.804	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.864	-0.931	31.857	-7.508	-7.508	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.045	-0.003	31.672	0.196	0.196	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.016	-0.007	33.716	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.069	-0.023	31.784	0.088	0.088	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.060	-0.047	28.582	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.045	0.021	34.935	0.198	0.198	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.873	-0.959	37.069	-7.199	-7.199	0.000	0.000	0.000	0.000
83	A	84	GLN	0	0.035	0.036	37.258	-0.092	-0.092	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.816	-0.918	33.260	-8.349	-8.349	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.856	0.920	33.332	7.458	7.458	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.004	0.016	34.414	-0.132	-0.132	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.011	0.002	31.096	-0.153	-0.153	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.003	-0.017	28.371	-0.277	-0.277	0.000	0.000	0.000	0.000
89	A	90	GLY	0	-0.012	0.001	29.959	-0.229	-0.229	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.027	0.015	31.674	-0.122	-0.122	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.016	-0.001	25.959	-0.256	-0.256	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.782	-0.874	26.724	-10.171	-10.171	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.004	-0.003	27.462	-0.254	-0.254	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.047	0.022	27.930	-0.121	-0.121	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.053	-0.037	22.456	-0.392	-0.392	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.832	0.936	24.157	9.856	9.856	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.040	0.026	25.999	0.224	0.224	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.048	-0.030	26.394	0.249	0.249	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.960	-0.975	25.413	-10.395	-10.395	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.063	-0.040	29.263	0.371	0.371	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.004	0.005	31.457	0.262	0.262	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.076	-0.037	32.538	0.147	0.147	0.000	0.000	0.000	0.000
103	A	104	PRO	0	0.004	0.000	33.729	0.167	0.167	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.833	-0.920	37.005	-7.098	-7.098	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.881	-0.928	39.218	-6.962	-6.962	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.064	-0.042	34.798	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.021	0.000	36.922	-0.019	-0.019	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.964	-0.979	38.327	-6.486	-6.486	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.012	-0.015	38.523	0.109	0.109	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.031	-0.019	34.831	0.010	0.010	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.956	0.965	38.345	6.688	6.688	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.060	-0.005	41.559	0.121	0.121	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.046	-0.029	39.554	0.101	0.101	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.034	-0.006	35.979	-0.111	-0.111	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.013	0.011	40.567	0.073	0.073	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.843	-0.942	40.366	-7.108	-7.108	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.969	-0.981	39.605	-7.480	-7.480	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.865	-0.942	37.605	-7.521	-7.521	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.037	0.023	35.872	-0.311	-0.311	0.000	0.000	0.000	0.000
120	A	121	VAL	0	0.001	0.012	34.819	-0.316	-0.316	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.853	0.929	33.678	7.549	7.549	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.021	0.010	31.319	-0.385	-0.385	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.005	-0.015	30.101	-0.362	-0.362	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.004	0.005	29.359	-0.370	-0.370	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.011	0.012	27.486	-0.462	-0.462	0.000	0.000	0.000	0.000
126	A	127	ILE	0	0.005	0.004	25.665	-0.533	-0.533	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.020	0.019	24.531	-0.489	-0.489	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.012	-0.003	23.643	-0.578	-0.578	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.047	-0.009	19.236	-0.773	-0.773	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.044	0.015	19.589	-1.060	-1.060	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.014	0.011	19.311	-0.708	-0.708	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.009	-0.024	16.699	-1.527	-1.527	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.011	-0.016	15.278	-0.653	-0.653	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.886	0.935	14.116	12.549	12.549	0.000	0.000	0.000	0.000
135	A	136	ILE	0	0.011	0.018	13.564	-1.338	-1.338	0.000	0.000	0.000	0.000
136	A	137	ALA	0	0.008	0.000	11.306	-1.857	-1.857	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.035	0.017	9.480	-2.345	-2.345	0.000	0.000	0.000	0.000
138	A	139	GLY	0	0.003	0.013	9.205	-2.054	-2.054	0.000	0.000	0.000	0.000
139	A	140	PHE	0	-0.019	-0.023	8.915	-2.298	-2.298	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.891	0.945	4.126	22.695	22.823	-0.001	-0.027	-0.101	0.000
141	A	142	SER	0	0.006	0.001	5.239	-2.044	-2.044	0.000	0.000	0.000	0.000
142	A	143	GLN	0	-0.027	-0.017	3.475	2.159	3.069	0.083	-0.286	-0.707	0.000
143	A	144	HIS	0	-0.031	-0.013	6.798	-0.256	-0.256	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.007	0.001	9.621	-0.798	-0.798	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.023	0.013	10.211	0.530	0.530	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.873	-0.935	13.088	-14.264	-14.264	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.019	0.000	16.811	0.376	0.376	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:LYS)