FMO DATABASE

FMODB ID: MVGQZ

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1385506.471898
FMO2-HF: Nuclear repulsion	1327380.638204
FMO2-HF: Total energy	-58125.833694
FMO2-MP2: Total energy	-58295.635288

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.
-0.71099999999997	5.295	2.716	-3.577	-5.144	-0.027

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 : 1.006 / q_NPA : 1.008

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	0.832	0.915	2.512	18.151	22.243	1.494	-2.569	-3.017	-0.015
4	A	5	ILE	0	0.052	0.016	4.551	-1.879	-1.714	-0.001	-0.008	-0.156	0.000
5	A	6	ASN	0	0.005	0.006	7.168	3.605	3.605	0.000	0.000	0.000	0.000
6	A	7	TYR	0	0.069	0.025	9.423	2.246	2.246	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.019	0.015	12.356	1.230	1.230	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.910	0.951	12.384	21.676	21.676	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.006	0.001	11.537	0.552	0.552	0.000	0.000	0.000	0.000
10	A	11	SER	0	0.004	-0.004	13.642	1.196	1.196	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.020	0.015	16.985	0.253	0.253	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.806	-0.881	18.955	-12.940	-12.940	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.029	0.020	18.495	0.494	0.494	0.000	0.000	0.000	0.000
14	A	15	PHE	0	-0.001	-0.007	17.037	0.077	0.077	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.857	0.897	19.054	13.426	13.426	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.013	0.017	22.716	0.468	0.468	0.000	0.000	0.000	0.000
17	A	18	VAL	0	0.003	-0.001	19.658	0.401	0.401	0.000	0.000	0.000	0.000
18	A	19	MET	0	-0.006	-0.003	20.408	0.109	0.109	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.008	0.003	22.845	0.455	0.455	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.004	0.011	24.170	0.423	0.423	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.811	-0.899	21.946	-12.138	-12.138	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.023	-0.014	24.537	0.317	0.317	0.000	0.000	0.000	0.000
23	A	24	TYR	0	0.011	0.023	27.421	0.348	0.348	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.025	0.004	26.044	0.308	0.308	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.004	0.006	25.679	0.181	0.181	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.058	-0.039	28.584	0.280	0.280	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.035	-0.018	31.169	0.367	0.367	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.007	-0.005	33.460	0.249	0.249	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.033	-0.003	30.997	0.188	0.188	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.791	-0.866	33.142	-8.102	-8.102	0.000	0.000	0.000	0.000
31	A	32	HIS	0	0.062	0.019	29.246	-0.214	-0.214	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.805	0.893	28.641	7.931	7.931	0.000	0.000	0.000	0.000
33	A	34	PHE	0	0.049	0.009	28.918	-0.244	-0.244	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.005	0.012	25.742	-0.293	-0.293	0.000	0.000	0.000	0.000
35	A	36	HIS	0	-0.033	-0.041	24.423	-0.676	-0.676	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.004	0.009	24.063	-0.397	-0.397	0.000	0.000	0.000	0.000
37	A	38	ILE	0	-0.007	-0.004	24.696	-0.300	-0.300	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.790	0.888	21.121	11.436	11.436	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.007	0.015	19.524	-0.747	-0.747	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.813	0.884	20.247	10.187	10.187	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.044	0.017	21.307	-0.229	-0.229	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.004	-0.029	16.230	-0.758	-0.758	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.038	-0.016	16.363	-0.720	-0.720	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.028	0.006	18.021	-0.294	-0.294	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.074	-0.052	16.458	-0.208	-0.208	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.018	0.013	14.484	-0.936	-0.936	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.109	-0.018	12.003	-1.466	-1.466	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.059	0.019	9.544	0.376	0.376	0.000	0.000	0.000	0.000
49	A	50	PHE	0	0.002	-0.009	8.986	0.451	0.451	0.000	0.000	0.000	0.000
50	A	51	CYS	0	-0.021	0.005	10.811	0.619	0.619	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.026	0.018	14.159	0.836	0.836	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.810	-0.896	12.942	-15.368	-15.368	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.019	-0.004	14.272	0.796	0.796	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.865	0.913	16.356	14.309	14.309	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.022	0.030	18.173	0.692	0.692	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.742	0.854	14.618	15.788	15.788	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.827	-0.912	20.298	-12.368	-12.368	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.013	-0.015	22.639	0.517	0.517	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.835	0.881	20.676	11.454	11.454	0.000	0.000	0.000	0.000
60	A	61	HIS	0	-0.063	-0.009	24.618	0.140	0.140	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.847	-0.921	26.316	-9.413	-9.413	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.028	-0.007	28.598	0.286	0.286	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.046	-0.012	27.146	0.252	0.252	0.000	0.000	0.000	0.000
64	A	65	SER	0	0.038	0.009	27.986	-0.254	-0.254	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.748	-0.861	24.621	-10.563	-10.563	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.017	0.003	26.581	-0.146	-0.146	0.000	0.000	0.000	0.000
67	A	68	TRP	0	0.029	0.001	25.670	-0.223	-0.223	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.016	0.022	22.497	-0.233	-0.233	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.071	-0.054	22.328	-0.614	-0.614	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.019	-0.006	23.669	-0.184	-0.184	0.000	0.000	0.000	0.000
71	A	72	MET	0	0.035	0.054	23.138	0.130	0.130	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.025	-0.016	21.568	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.021	-0.020	23.216	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.009	0.001	26.726	0.412	0.412	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.865	0.938	28.990	9.120	9.120	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.857	-0.931	31.496	-7.813	-7.813	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.054	-0.018	30.614	0.214	0.214	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.016	-0.007	32.738	0.006	0.006	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.079	-0.028	30.615	0.106	0.106	0.000	0.000	0.000	0.000
80	A	81	TYR	0	-0.061	-0.038	27.358	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.033	-0.019	33.809	0.194	0.194	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.850	-0.953	35.860	-7.503	-7.503	0.000	0.000	0.000	0.000
83	A	84	GLN	0	0.003	0.024	36.279	-0.085	-0.085	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.766	-0.869	32.079	-8.519	-8.519	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.816	0.910	32.183	7.539	7.539	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.026	0.019	33.369	-0.147	-0.147	0.000	0.000	0.000	0.000
87	A	88	LEU	0	-0.019	-0.003	30.217	-0.171	-0.171	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.012	-0.020	27.170	-0.318	-0.318	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.005	0.009	29.178	-0.236	-0.236	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.018	0.006	31.213	-0.112	-0.112	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.008	-0.008	24.973	-0.265	-0.265	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.753	-0.854	26.325	-10.344	-10.344	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.008	0.014	27.184	-0.226	-0.226	0.000	0.000	0.000	0.000
94	A	95	VAL	0	0.049	0.015	27.381	-0.205	-0.205	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.088	-0.059	21.901	-0.404	-0.404	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.824	0.920	23.548	10.056	10.056	0.000	0.000	0.000	0.000
97	A	98	ILE	0	0.046	0.032	25.789	0.270	0.270	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.044	-0.029	26.243	0.283	0.283	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.926	-0.964	24.861	-10.742	-10.742	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.058	-0.030	29.083	0.365	0.365	0.000	0.000	0.000	0.000
101	A	102	GLY	0	0.003	0.002	31.606	0.260	0.260	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.082	-0.039	32.267	0.126	0.126	0.000	0.000	0.000	0.000
103	A	104	PRO	0	0.035	0.017	33.682	0.139	0.139	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.849	-0.927	36.948	-7.314	-7.314	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.886	-0.930	38.478	-7.203	-7.203	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.049	-0.018	34.458	0.004	0.004	0.000	0.000	0.000	0.000
107	A	108	PHE	0	-0.004	-0.005	36.600	-0.033	-0.033	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.954	-0.979	38.026	-6.560	-6.560	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.015	-0.028	37.694	0.092	0.092	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.036	-0.020	34.120	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.828	0.871	37.659	6.966	6.966	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.052	0.001	40.917	0.147	0.147	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.039	-0.024	38.662	0.126	0.126	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.035	-0.009	34.750	-0.123	-0.123	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.005	-0.028	39.556	0.076	0.076	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.769	-0.883	39.376	-7.241	-7.241	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.909	-0.944	38.840	-7.654	-7.654	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.807	-0.881	36.428	-7.752	-7.752	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.047	0.028	34.805	-0.325	-0.325	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.004	0.015	34.070	-0.309	-0.309	0.000	0.000	0.000	0.000
121	A	122	LYS	1	0.833	0.923	32.726	7.686	7.686	0.000	0.000	0.000	0.000
122	A	123	ILE	0	0.025	0.014	30.588	-0.413	-0.413	0.000	0.000	0.000	0.000
123	A	124	THR	0	-0.003	-0.013	29.232	-0.388	-0.388	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.020	-0.007	28.628	-0.396	-0.396	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.005	0.001	26.555	-0.483	-0.483	0.000	0.000	0.000	0.000
126	A	127	ILE	0	0.025	0.012	24.781	-0.574	-0.574	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.030	0.022	23.769	-0.532	-0.532	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.013	0.012	23.017	-0.633	-0.633	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.033	-0.003	18.350	-0.851	-0.851	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.036	0.018	18.858	-1.188	-1.188	0.000	0.000	0.000	0.000
131	A	132	THR	0	-0.024	-0.006	18.869	-0.729	-0.729	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.026	-0.038	16.529	-1.687	-1.687	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.001	-0.044	14.636	-0.839	-0.839	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.887	0.935	13.583	13.030	13.030	0.000	0.000	0.000	0.000
135	A	136	ILE	0	0.007	0.016	13.262	-1.476	-1.476	0.000	0.000	0.000	0.000
136	A	137	ALA	0	-0.009	-0.002	10.572	-2.084	-2.084	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.044	0.019	8.928	-2.783	-2.783	0.000	0.000	0.000	0.000
138	A	139	GLY	0	-0.002	0.013	9.111	-2.137	-2.137	0.000	0.000	0.000	0.000
139	A	140	PHE	0	-0.005	-0.014	8.160	-2.341	-2.341	0.000	0.000	0.000	0.000
140	A	141	ARG	1	0.918	0.953	4.197	22.299	22.462	-0.001	-0.037	-0.125	0.000
141	A	142	SER	0	0.018	0.024	4.651	-5.615	-5.611	-0.001	-0.017	0.015	0.000
142	A	143	GLN	0	-0.021	-0.011	2.635	0.036	1.618	1.225	-0.946	-1.861	-0.012
143	A	144	HIS	0	-0.022	-0.009	5.817	0.311	0.311	0.000	0.000	0.000	0.000
144	A	145	PRO	0	-0.019	-0.004	9.005	-0.834	-0.834	0.000	0.000	0.000	0.000
145	A	146	VAL	0	0.020	0.006	9.761	0.336	0.336	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.842	-0.915	12.603	-15.091	-15.091	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.016	0.006	16.372	0.581	0.581	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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