FMO DATABASE

FMODB ID: 89M5Y

Calculation Name: 3GMG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GMG

Chain ID: A

ChEMBL ID:

UniProt ID: P9WFG3

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	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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1115445.398284
FMO2-HF: Nuclear repulsion	1064083.299408
FMO2-HF: Total energy	-51362.098876
FMO2-MP2: Total energy	-51512.096953

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:149:ALA)

Summations of interaction energy for fragment #1(A:149:ALA)

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.
-4.824	-1.837	0.045	-1.341	-1.691	0.005

Interaction energy analysis for fragmet #1(A:149:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.054 / 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	A	151	LEU	0	0.056	0.022	3.357	-4.059	-1.716	0.029	-1.192	-1.181	0.005
4	A	152	ALA	0	0.053	0.034	3.310	-0.960	-0.478	0.017	-0.111	-0.387	0.000
5	A	153	ALA	0	0.048	0.029	4.530	0.334	0.496	-0.001	-0.038	-0.123	0.000
6	A	154	LEU	0	-0.031	-0.020	6.501	0.230	0.230	0.000	0.000	0.000	0.000
7	A	155	SER	0	0.008	-0.013	7.627	0.040	0.040	0.000	0.000	0.000	0.000
8	A	156	ILE	0	0.011	0.007	8.092	0.033	0.033	0.000	0.000	0.000	0.000
9	A	157	LEU	0	-0.017	0.002	10.549	0.070	0.070	0.000	0.000	0.000	0.000
10	A	158	VAL	0	-0.056	-0.032	12.530	0.032	0.032	0.000	0.000	0.000	0.000
11	A	159	GLY	0	0.006	0.005	13.926	0.022	0.022	0.000	0.000	0.000	0.000
12	A	160	ALA	0	-0.028	-0.012	11.790	0.015	0.015	0.000	0.000	0.000	0.000
13	A	161	VAL	0	-0.016	-0.013	9.253	0.009	0.009	0.000	0.000	0.000	0.000
14	A	162	GLY	0	0.022	0.014	12.592	0.003	0.003	0.000	0.000	0.000	0.000
15	A	163	ALA	0	-0.029	-0.020	11.748	-0.083	-0.083	0.000	0.000	0.000	0.000
16	A	164	THR	0	-0.018	-0.030	12.507	0.056	0.056	0.000	0.000	0.000	0.000
17	A	165	GLY	0	0.033	0.019	13.165	-0.074	-0.074	0.000	0.000	0.000	0.000
18	A	166	PRO	0	0.054	0.039	15.561	0.031	0.031	0.000	0.000	0.000	0.000
19	A	167	GLY	0	0.059	0.016	18.539	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	168	VAL	0	-0.037	-0.016	21.137	0.012	0.012	0.000	0.000	0.000	0.000
21	A	169	MET	0	-0.010	0.000	23.878	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	170	ILE	0	0.000	0.001	26.458	0.006	0.006	0.000	0.000	0.000	0.000
23	A	171	THR	0	-0.027	-0.011	29.297	0.001	0.001	0.000	0.000	0.000	0.000
24	A	172	ILE	0	-0.003	-0.004	32.282	0.002	0.002	0.000	0.000	0.000	0.000
25	A	173	ASP	-1	-0.924	-0.965	34.858	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	174	ASP	-1	-0.753	-0.900	38.217	-0.036	-0.036	0.000	0.000	0.000	0.000
27	A	175	PRO	0	0.017	0.006	40.387	0.002	0.002	0.000	0.000	0.000	0.000
28	A	176	GLY	0	-0.035	0.026	43.766	0.002	0.002	0.000	0.000	0.000	0.000
29	A	177	PRO	0	-0.028	-0.017	41.883	0.001	0.001	0.000	0.000	0.000	0.000
30	A	178	GLY	0	-0.012	-0.051	42.352	0.002	0.002	0.000	0.000	0.000	0.000
31	A	179	VAL	0	-0.063	-0.034	36.236	0.001	0.001	0.000	0.000	0.000	0.000
32	A	180	ALA	0	0.016	0.007	38.807	0.000	0.000	0.000	0.000	0.000	0.000
33	A	181	PRO	0	0.017	-0.009	35.373	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	182	GLU	-1	-0.882	-0.945	34.409	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	183	VAL	0	0.029	0.030	34.802	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	184	MET	0	0.005	0.005	30.303	-0.007	-0.007	0.000	0.000	0.000	0.000
37	A	185	ILE	0	-0.046	-0.028	30.285	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	186	ASP	-1	-0.898	-0.945	29.991	-0.041	-0.041	0.000	0.000	0.000	0.000
39	A	187	VAL	0	-0.011	-0.006	28.084	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	188	ILE	0	-0.034	-0.016	24.702	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	189	ASN	0	0.001	-0.017	25.605	-0.009	-0.009	0.000	0.000	0.000	0.000
42	A	190	GLU	-1	-0.806	-0.893	27.046	-0.062	-0.062	0.000	0.000	0.000	0.000
43	A	191	LEU	0	-0.026	-0.020	23.679	-0.008	-0.008	0.000	0.000	0.000	0.000
44	A	192	ARG	1	0.894	0.945	22.016	0.049	0.049	0.000	0.000	0.000	0.000
45	A	193	ALA	0	-0.034	0.000	22.682	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	194	ALA	0	-0.043	-0.018	24.134	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	195	GLY	0	-0.001	0.001	20.265	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	196	ALA	0	-0.051	-0.018	18.671	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	197	GLU	-1	-0.963	-0.983	13.647	-0.356	-0.356	0.000	0.000	0.000	0.000
50	A	198	ALA	0	-0.082	-0.044	15.022	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	199	ILE	0	0.026	0.013	17.013	0.005	0.005	0.000	0.000	0.000	0.000
52	A	200	GLN	0	-0.018	-0.021	20.613	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	201	ILE	0	0.020	0.010	22.430	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	202	ASN	0	0.038	0.026	25.034	0.004	0.004	0.000	0.000	0.000	0.000
55	A	203	ASP	-1	-0.679	-0.834	28.090	-0.048	-0.048	0.000	0.000	0.000	0.000
56	A	204	ALA	0	-0.019	-0.009	30.899	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	205	HIS	0	-0.032	-0.020	32.338	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	206	ARG	1	0.800	0.890	29.264	0.041	0.041	0.000	0.000	0.000	0.000
59	A	207	SER	0	0.036	0.009	24.371	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	208	VAL	0	-0.035	-0.017	24.571	0.007	0.007	0.000	0.000	0.000	0.000
61	A	209	ARG	1	0.852	0.932	13.806	0.190	0.190	0.000	0.000	0.000	0.000
62	A	210	VAL	0	0.003	-0.003	21.248	0.016	0.016	0.000	0.000	0.000	0.000
63	A	211	GLY	0	0.013	-0.013	19.806	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	212	VAL	0	-0.031	-0.021	20.537	0.001	0.001	0.000	0.000	0.000	0.000
65	A	213	ASP	-1	-0.829	-0.890	22.246	0.012	0.012	0.000	0.000	0.000	0.000
66	A	214	THR	0	-0.057	-0.040	24.269	0.000	0.000	0.000	0.000	0.000	0.000
67	A	215	TRP	0	-0.013	0.005	26.049	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	216	VAL	0	0.017	-0.009	29.833	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	217	VAL	0	-0.003	0.006	32.300	0.003	0.003	0.000	0.000	0.000	0.000
70	A	218	GLY	0	0.001	0.003	35.899	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	219	VAL	0	0.002	-0.007	38.750	0.001	0.001	0.000	0.000	0.000	0.000
72	A	220	PRO	0	0.052	0.032	39.794	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	221	GLY	0	0.025	0.010	39.851	0.002	0.002	0.000	0.000	0.000	0.000
74	A	222	SER	0	-0.058	-0.023	38.228	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	223	LEU	0	0.033	0.034	34.315	0.003	0.003	0.000	0.000	0.000	0.000
76	A	224	THR	0	-0.040	-0.020	32.961	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	225	VAL	0	0.043	0.011	27.647	0.002	0.002	0.000	0.000	0.000	0.000
78	A	226	ASP	-1	-0.761	-0.854	25.406	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	227	THR	0	-0.095	-0.060	28.399	0.002	0.002	0.000	0.000	0.000	0.000
80	A	228	LYS	1	0.883	0.942	25.370	0.048	0.048	0.000	0.000	0.000	0.000
81	A	229	VAL	0	0.010	0.016	31.148	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	230	LEU	0	-0.068	-0.013	29.485	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	231	SER	0	-0.017	-0.025	34.018	0.004	0.004	0.000	0.000	0.000	0.000
84	A	232	PRO	0	-0.050	0.016	35.702	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	233	PRO	0	0.014	-0.010	35.388	0.002	0.002	0.000	0.000	0.000	0.000
86	A	234	TYR	0	0.018	0.000	31.477	0.000	0.000	0.000	0.000	0.000	0.000
87	A	235	SER	0	-0.016	-0.012	28.546	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	236	ILE	0	-0.006	-0.007	25.225	0.001	0.001	0.000	0.000	0.000	0.000
89	A	237	LEU	0	-0.022	0.001	21.930	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	238	ALA	0	0.032	-0.002	20.678	0.003	0.003	0.000	0.000	0.000	0.000
91	A	239	ILE	0	-0.018	0.014	14.909	0.001	0.001	0.000	0.000	0.000	0.000
92	A	240	GLY	0	0.057	0.010	17.959	0.004	0.004	0.000	0.000	0.000	0.000
93	A	241	ASP	-1	-0.797	-0.885	18.873	-0.169	-0.169	0.000	0.000	0.000	0.000
94	A	242	PRO	0	-0.013	-0.002	21.019	0.018	0.018	0.000	0.000	0.000	0.000
95	A	243	PRO	0	0.019	0.005	23.891	0.014	0.014	0.000	0.000	0.000	0.000
96	A	244	THR	0	-0.028	-0.031	23.804	0.015	0.015	0.000	0.000	0.000	0.000
97	A	245	LEU	0	-0.029	-0.007	21.155	0.011	0.011	0.000	0.000	0.000	0.000
98	A	246	ALA	0	-0.009	-0.018	25.601	0.010	0.010	0.000	0.000	0.000	0.000
99	A	247	ALA	0	-0.039	-0.014	28.831	0.009	0.009	0.000	0.000	0.000	0.000
100	A	248	ALA	0	-0.003	-0.004	27.986	0.007	0.007	0.000	0.000	0.000	0.000
101	A	249	MET	0	-0.009	-0.001	28.217	0.007	0.007	0.000	0.000	0.000	0.000
102	A	250	ASN	0	-0.057	-0.026	31.525	0.008	0.008	0.000	0.000	0.000	0.000
103	A	251	ILE	0	-0.031	0.011	31.419	0.004	0.004	0.000	0.000	0.000	0.000
104	A	252	PRO	0	-0.024	-0.016	35.344	0.001	0.001	0.000	0.000	0.000	0.000
105	A	253	GLY	0	-0.051	-0.036	38.190	0.001	0.001	0.000	0.000	0.000	0.000
106	A	254	GLY	0	0.038	0.039	35.395	0.002	0.002	0.000	0.000	0.000	0.000
107	A	255	ALA	0	0.016	-0.009	33.134	0.002	0.002	0.000	0.000	0.000	0.000
108	A	256	GLN	0	-0.021	-0.028	34.935	0.003	0.003	0.000	0.000	0.000	0.000
109	A	257	ASP	-1	-0.829	-0.922	36.379	-0.041	-0.041	0.000	0.000	0.000	0.000
110	A	258	GLY	0	-0.050	-0.029	38.571	0.003	0.003	0.000	0.000	0.000	0.000
111	A	259	VAL	0	-0.001	-0.003	35.908	0.002	0.002	0.000	0.000	0.000	0.000
112	A	260	LYS	1	0.911	0.963	39.229	0.051	0.051	0.000	0.000	0.000	0.000
113	A	261	ARG	1	0.910	0.968	41.295	0.034	0.034	0.000	0.000	0.000	0.000
114	A	262	VAL	0	-0.058	-0.016	41.610	0.002	0.002	0.000	0.000	0.000	0.000
115	A	263	GLY	0	-0.015	0.003	44.503	0.001	0.001	0.000	0.000	0.000	0.000
116	A	264	GLY	0	0.024	0.020	40.693	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	265	ARG	1	0.902	0.937	39.039	0.055	0.055	0.000	0.000	0.000	0.000
118	A	266	MET	0	0.011	0.013	32.720	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	267	VAL	0	-0.043	-0.017	33.052	0.002	0.002	0.000	0.000	0.000	0.000
120	A	268	VAL	0	0.025	0.012	29.101	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	269	GLN	0	-0.058	-0.031	27.911	0.008	0.008	0.000	0.000	0.000	0.000
122	A	270	GLN	0	0.036	0.013	26.017	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	271	ALA	0	0.000	-0.002	23.497	0.007	0.007	0.000	0.000	0.000	0.000
124	A	272	ASP	-1	-0.849	-0.926	21.558	-0.193	-0.193	0.000	0.000	0.000	0.000
125	A	273	ARG	1	0.739	0.843	17.908	0.235	0.235	0.000	0.000	0.000	0.000
126	A	274	VAL	0	-0.017	0.010	18.821	0.025	0.025	0.000	0.000	0.000	0.000
127	A	275	ASP	-1	-0.786	-0.866	17.427	-0.299	-0.299	0.000	0.000	0.000	0.000
128	A	276	VAL	0	-0.018	-0.003	16.622	0.031	0.031	0.000	0.000	0.000	0.000
129	A	277	THR	0	0.008	-0.014	16.367	-0.023	-0.023	0.000	0.000	0.000	0.000
130	A	278	ALA	0	-0.014	0.009	18.192	0.013	0.013	0.000	0.000	0.000	0.000
131	A	279	LEU	0	-0.006	0.006	15.358	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	280	ARG	1	0.815	0.890	17.844	0.033	0.033	0.000	0.000	0.000	0.000
133	A	281	GLN	0	-0.023	-0.010	19.091	0.020	0.020	0.000	0.000	0.000	0.000
134	A	282	PRO	0	-0.034	0.008	19.061	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	283	LYS	1	0.942	0.954	21.781	-0.030	-0.030	0.000	0.000	0.000	0.000
136	A	284	GLN	0	0.000	-0.003	23.592	0.003	0.003	0.000	0.000	0.000	0.000
137	A	285	HIS	0	-0.011	-0.009	21.071	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	286	GLN	0	-0.002	-0.008	25.278	0.003	0.003	0.000	0.000	0.000	0.000
139	A	287	TYR	0	0.006	-0.002	27.584	0.001	0.001	0.000	0.000	0.000	0.000
140	A	288	ALA	0	-0.006	0.014	23.520	0.006	0.006	0.000	0.000	0.000	0.000
141	A	289	GLN	0	0.002	-0.006	21.888	0.010	0.010	0.000	0.000	0.000	0.000
142	A	290	PRO	0	-0.017	-0.005	16.997	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	291	VAL	0	0.026	0.017	17.149	0.019	0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:149:ALA)