FMO DATABASE

FMODB ID: RYYY8

Calculation Name: 3V30-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3V30

Chain ID: A

ChEMBL ID:

UniProt ID: P48382

Base Structure: X-ray

Registration Date: 2023-09-27

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1530156.168211
FMO2-HF: Nuclear repulsion	1468589.300042
FMO2-HF: Total energy	-61566.868169
FMO2-MP2: Total energy	-61750.073277

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:92:LEU)

Summations of interaction energy for fragment #1(A:92:LEU)

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.
-10.858	-2.53	5.048	-4.352	-9.027	-0.009

Interaction energy analysis for fragmet #1(A:92:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.020

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	94	ILE	0	0.076	0.017	3.209	-3.050	0.142	0.079	-1.713	-1.559	0.006
4	A	95	HIS	0	-0.045	-0.020	5.904	0.061	0.061	0.000	0.000	0.000	0.000
5	A	96	GLN	0	0.016	0.011	2.358	-1.129	-0.007	1.758	-0.712	-2.168	-0.001
6	A	97	LEU	0	-0.002	0.009	2.456	-2.067	-0.430	2.068	-0.898	-2.807	-0.005
7	A	98	ALA	0	-0.015	-0.008	4.379	0.159	0.304	0.001	-0.026	-0.120	0.000
8	A	99	ALA	0	-0.047	-0.027	5.945	0.124	0.124	0.000	0.000	0.000	0.000
9	A	100	GLN	0	-0.045	-0.034	2.748	-2.484	-0.709	1.130	-0.930	-1.975	-0.009
10	A	101	GLY	0	0.059	0.051	5.884	0.050	0.050	0.000	0.000	0.000	0.000
11	A	102	GLU	-1	-0.886	-0.916	3.353	-1.199	-0.899	0.013	-0.057	-0.257	0.000
12	A	103	LEU	0	-0.004	-0.013	6.481	-0.240	-0.240	0.000	0.000	0.000	0.000
13	A	104	ASP	-1	-0.855	-0.928	9.753	-0.582	-0.582	0.000	0.000	0.000	0.000
14	A	105	GLN	0	-0.051	-0.042	3.999	-0.632	-0.475	-0.001	-0.016	-0.141	0.000
15	A	106	LEU	0	-0.003	0.002	7.536	-0.176	-0.176	0.000	0.000	0.000	0.000
16	A	107	LYS	1	0.871	0.924	8.246	0.628	0.628	0.000	0.000	0.000	0.000
17	A	108	GLU	-1	-0.872	-0.913	9.492	-0.611	-0.611	0.000	0.000	0.000	0.000
18	A	109	HIS	0	-0.067	-0.043	4.802	-0.364	-0.364	0.000	0.000	0.000	0.000
19	A	110	LEU	0	-0.028	-0.016	9.658	0.141	0.141	0.000	0.000	0.000	0.000
20	A	111	ARG	1	0.854	0.927	12.854	0.737	0.737	0.000	0.000	0.000	0.000
21	A	112	LYS	1	0.826	0.888	14.828	0.638	0.638	0.000	0.000	0.000	0.000
22	A	113	GLY	0	-0.018	0.009	16.679	0.052	0.052	0.000	0.000	0.000	0.000
23	A	114	ASP	-1	-0.825	-0.895	16.823	-0.463	-0.463	0.000	0.000	0.000	0.000
24	A	115	ASN	0	0.042	0.003	18.371	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	116	LEU	0	-0.039	-0.011	11.284	0.015	0.015	0.000	0.000	0.000	0.000
26	A	117	VAL	0	0.034	0.019	13.267	-0.070	-0.070	0.000	0.000	0.000	0.000
27	A	118	ASN	0	0.024	0.009	14.043	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	119	LYS	1	0.884	0.947	10.784	0.504	0.504	0.000	0.000	0.000	0.000
29	A	120	PRO	0	0.041	0.035	12.838	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	121	ASP	-1	-0.757	-0.884	10.451	-0.121	-0.121	0.000	0.000	0.000	0.000
31	A	122	GLU	-1	-0.904	-0.965	10.939	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	123	ARG	1	0.918	0.962	11.222	-0.097	-0.097	0.000	0.000	0.000	0.000
33	A	124	GLY	0	-0.001	0.009	15.304	0.002	0.002	0.000	0.000	0.000	0.000
34	A	125	PHE	0	0.010	0.009	12.388	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	126	THR	0	0.049	0.023	12.727	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	127	PRO	0	0.023	-0.006	9.565	0.025	0.025	0.000	0.000	0.000	0.000
37	A	128	LEU	0	0.030	0.028	10.733	0.010	0.010	0.000	0.000	0.000	0.000
38	A	129	ILE	0	-0.007	0.015	13.855	0.031	0.031	0.000	0.000	0.000	0.000
39	A	130	TRP	0	-0.046	-0.032	8.705	0.097	0.097	0.000	0.000	0.000	0.000
40	A	131	ALA	0	0.022	0.009	10.720	0.030	0.030	0.000	0.000	0.000	0.000
41	A	132	SER	0	-0.022	-0.034	11.540	0.043	0.043	0.000	0.000	0.000	0.000
42	A	133	ALA	0	-0.047	-0.019	13.037	0.028	0.028	0.000	0.000	0.000	0.000
43	A	134	PHE	0	-0.038	-0.025	9.799	0.060	0.060	0.000	0.000	0.000	0.000
44	A	135	GLY	0	0.007	0.012	12.515	0.000	0.000	0.000	0.000	0.000	0.000
45	A	136	GLU	-1	-0.885	-0.945	9.582	-0.381	-0.381	0.000	0.000	0.000	0.000
46	A	137	ILE	0	-0.009	-0.019	13.042	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	138	GLU	-1	-0.940	-0.966	14.519	-0.359	-0.359	0.000	0.000	0.000	0.000
48	A	139	THR	0	0.044	0.012	10.023	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	140	VAL	0	-0.010	-0.006	13.131	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	141	ARG	1	0.858	0.901	15.648	0.256	0.256	0.000	0.000	0.000	0.000
51	A	142	PHE	0	-0.014	0.003	12.743	0.007	0.007	0.000	0.000	0.000	0.000
52	A	143	LEU	0	0.002	-0.001	11.687	0.000	0.000	0.000	0.000	0.000	0.000
53	A	144	LEU	0	0.038	0.016	16.016	0.020	0.020	0.000	0.000	0.000	0.000
54	A	145	GLU	-1	-0.935	-0.935	19.577	-0.235	-0.235	0.000	0.000	0.000	0.000
55	A	146	TRP	0	-0.033	-0.015	16.809	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	147	GLY	0	-0.014	-0.004	19.394	0.009	0.009	0.000	0.000	0.000	0.000
57	A	148	ALA	0	-0.082	-0.038	16.461	0.005	0.005	0.000	0.000	0.000	0.000
58	A	149	ASP	-1	-0.860	-0.941	18.364	-0.173	-0.173	0.000	0.000	0.000	0.000
59	A	150	PRO	0	-0.053	-0.039	19.277	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	151	HIS	0	-0.012	-0.010	20.754	0.018	0.018	0.000	0.000	0.000	0.000
61	A	152	ILE	0	-0.073	-0.020	18.375	0.013	0.013	0.000	0.000	0.000	0.000
62	A	153	LEU	0	-0.026	-0.008	20.104	0.002	0.002	0.000	0.000	0.000	0.000
63	A	154	ALA	0	-0.028	-0.009	17.219	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	155	LYS	1	0.840	0.894	17.947	0.044	0.044	0.000	0.000	0.000	0.000
65	A	156	GLU	-1	-0.979	-0.984	20.725	0.041	0.041	0.000	0.000	0.000	0.000
66	A	157	ARG	1	0.810	0.900	22.422	0.061	0.061	0.000	0.000	0.000	0.000
67	A	158	GLU	-1	-0.814	-0.901	18.415	-0.036	-0.036	0.000	0.000	0.000	0.000
68	A	159	SER	0	0.077	0.035	20.054	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	160	ALA	0	0.041	0.007	17.755	0.007	0.007	0.000	0.000	0.000	0.000
70	A	161	LEU	0	0.042	0.038	18.730	0.005	0.005	0.000	0.000	0.000	0.000
71	A	162	SER	0	0.052	0.022	21.989	0.005	0.005	0.000	0.000	0.000	0.000
72	A	163	LEU	0	-0.002	0.014	16.031	0.014	0.014	0.000	0.000	0.000	0.000
73	A	164	ALA	0	0.025	0.019	18.375	0.007	0.007	0.000	0.000	0.000	0.000
74	A	165	SER	0	-0.028	-0.045	19.258	0.010	0.010	0.000	0.000	0.000	0.000
75	A	166	THR	0	-0.047	-0.033	20.183	0.013	0.013	0.000	0.000	0.000	0.000
76	A	167	GLY	0	-0.022	-0.002	18.832	0.014	0.014	0.000	0.000	0.000	0.000
77	A	168	GLY	0	-0.002	0.003	19.862	0.000	0.000	0.000	0.000	0.000	0.000
78	A	169	TYR	0	-0.012	0.002	15.642	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	170	THR	0	-0.015	-0.027	20.772	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	171	ASP	-1	-0.914	-0.955	21.444	-0.119	-0.119	0.000	0.000	0.000	0.000
81	A	172	ILE	0	0.015	0.020	16.194	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	173	VAL	0	0.001	-0.004	20.425	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	174	GLY	0	-0.011	-0.005	23.245	0.001	0.001	0.000	0.000	0.000	0.000
84	A	175	LEU	0	-0.026	-0.020	20.131	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	176	LEU	0	0.001	-0.009	19.339	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	177	LEU	0	0.004	-0.006	23.204	0.004	0.004	0.000	0.000	0.000	0.000
87	A	178	GLU	-1	-0.872	-0.904	26.403	-0.108	-0.108	0.000	0.000	0.000	0.000
88	A	179	ARG	1	0.779	0.882	22.797	0.213	0.213	0.000	0.000	0.000	0.000
89	A	180	ASP	-1	-0.927	-0.957	26.368	-0.110	-0.110	0.000	0.000	0.000	0.000
90	A	181	VAL	0	-0.035	-0.009	23.327	0.002	0.002	0.000	0.000	0.000	0.000
91	A	182	ASP	-1	-0.843	-0.926	26.747	-0.068	-0.068	0.000	0.000	0.000	0.000
92	A	183	ILE	0	-0.023	-0.026	27.829	0.000	0.000	0.000	0.000	0.000	0.000
93	A	184	ASN	0	-0.027	-0.024	29.502	0.007	0.007	0.000	0.000	0.000	0.000
94	A	185	ILE	0	-0.020	0.010	25.134	0.006	0.006	0.000	0.000	0.000	0.000
95	A	186	TYR	0	-0.015	-0.037	27.968	0.001	0.001	0.000	0.000	0.000	0.000
96	A	187	ASP	-1	-0.812	-0.886	24.539	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	188	TRP	0	0.036	0.003	25.657	0.002	0.002	0.000	0.000	0.000	0.000
98	A	189	ASN	0	-0.083	-0.030	24.530	0.016	0.016	0.000	0.000	0.000	0.000
99	A	190	GLY	0	0.003	0.010	26.595	0.005	0.005	0.000	0.000	0.000	0.000
100	A	191	GLY	0	-0.037	-0.012	27.950	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	192	THR	0	0.096	0.030	28.232	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	193	PRO	0	0.017	0.008	25.553	0.006	0.006	0.000	0.000	0.000	0.000
103	A	194	LEU	0	0.018	0.007	26.800	0.003	0.003	0.000	0.000	0.000	0.000
104	A	195	LEU	0	0.005	0.016	29.755	0.004	0.004	0.000	0.000	0.000	0.000
105	A	196	TYR	0	-0.041	-0.042	24.435	0.011	0.011	0.000	0.000	0.000	0.000
106	A	197	ALA	0	-0.011	-0.001	26.101	0.004	0.004	0.000	0.000	0.000	0.000
107	A	198	VAL	0	-0.029	-0.019	27.036	0.004	0.004	0.000	0.000	0.000	0.000
108	A	199	ARG	1	0.914	0.961	27.548	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	200	GLY	0	0.019	0.004	25.521	0.008	0.008	0.000	0.000	0.000	0.000
110	A	201	ASN	0	-0.062	-0.029	26.485	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	202	HIS	0	0.033	0.036	22.952	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	203	VAL	0	-0.027	-0.024	27.438	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	204	LYS	1	0.984	0.993	27.480	0.059	0.059	0.000	0.000	0.000	0.000
114	A	205	CYS	0	0.028	0.035	25.390	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	206	VAL	0	0.015	0.007	27.331	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	207	GLU	-1	-0.904	-0.972	30.514	-0.046	-0.046	0.000	0.000	0.000	0.000
117	A	208	ALA	0	-0.034	-0.015	28.305	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	209	LEU	0	0.015	-0.002	26.868	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	210	LEU	0	0.017	0.006	30.530	0.000	0.000	0.000	0.000	0.000	0.000
120	A	211	ALA	0	-0.088	-0.036	33.270	0.001	0.001	0.000	0.000	0.000	0.000
121	A	212	ARG	1	0.821	0.889	28.906	0.101	0.101	0.000	0.000	0.000	0.000
122	A	213	GLY	0	-0.018	0.001	33.589	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	214	ALA	0	-0.028	-0.004	31.832	0.001	0.001	0.000	0.000	0.000	0.000
124	A	215	ASP	-1	-0.796	-0.861	33.811	-0.033	-0.033	0.000	0.000	0.000	0.000
125	A	216	LEU	0	-0.035	-0.037	35.537	0.002	0.002	0.000	0.000	0.000	0.000
126	A	217	THR	0	-0.123	-0.083	37.495	0.004	0.004	0.000	0.000	0.000	0.000
127	A	218	THR	0	-0.013	-0.020	34.261	0.002	0.002	0.000	0.000	0.000	0.000
128	A	219	GLU	-1	-0.964	-0.986	35.746	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	220	ALA	0	-0.017	-0.020	32.405	-0.002	-0.002	0.000	0.000	0.000	0.000
130	A	221	ASP	-1	-0.772	-0.865	32.199	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	222	SER	0	-0.129	-0.068	33.597	0.001	0.001	0.000	0.000	0.000	0.000
132	A	223	GLY	0	0.019	0.006	35.329	0.002	0.002	0.000	0.000	0.000	0.000
133	A	224	TYR	0	-0.082	-0.026	35.388	0.000	0.000	0.000	0.000	0.000	0.000
134	A	225	THR	0	0.059	0.005	35.929	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	226	PRO	0	0.017	-0.005	33.706	0.003	0.003	0.000	0.000	0.000	0.000
136	A	227	MET	0	-0.016	-0.007	35.204	0.001	0.001	0.000	0.000	0.000	0.000
137	A	228	ASP	-1	-0.788	-0.851	38.291	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	229	LEU	0	-0.033	-0.010	31.890	0.004	0.004	0.000	0.000	0.000	0.000
139	A	230	ALA	0	-0.021	-0.013	35.179	0.003	0.003	0.000	0.000	0.000	0.000
140	A	231	VAL	0	-0.031	-0.022	36.057	0.002	0.002	0.000	0.000	0.000	0.000
141	A	232	ALA	0	-0.024	-0.007	37.552	0.002	0.002	0.000	0.000	0.000	0.000
142	A	233	LEU	0	-0.057	-0.026	32.053	0.004	0.004	0.000	0.000	0.000	0.000
143	A	234	GLY	0	0.001	0.017	36.012	0.002	0.002	0.000	0.000	0.000	0.000
144	A	235	TYR	0	-0.043	-0.016	29.649	0.002	0.002	0.000	0.000	0.000	0.000
145	A	236	ARG	1	0.914	0.935	35.532	0.004	0.004	0.000	0.000	0.000	0.000
146	A	237	LYS	1	0.899	0.970	34.695	0.029	0.029	0.000	0.000	0.000	0.000
147	A	238	VAL	0	0.062	0.029	31.966	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	239	GLN	0	0.028	0.009	34.876	0.000	0.000	0.000	0.000	0.000	0.000
149	A	240	GLN	0	0.009	0.005	38.375	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	241	VAL	0	-0.059	-0.026	34.053	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	242	ILE	0	0.045	0.017	35.069	-0.002	-0.002	0.000	0.000	0.000	0.000
152	A	243	GLU	-1	-0.847	-0.921	38.276	-0.017	-0.017	0.000	0.000	0.000	0.000
153	A	244	ASN	0	-0.021	-0.027	40.052	0.001	0.001	0.000	0.000	0.000	0.000
154	A	245	HIS	0	0.024	0.000	38.236	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	246	ILE	0	0.043	0.013	40.371	-0.001	-0.001	0.000	0.000	0.000	0.000
156	A	247	LEU	0	-0.029	-0.013	42.978	0.000	0.000	0.000	0.000	0.000	0.000
157	A	248	LYS	1	0.861	0.944	38.655	0.044	0.044	0.000	0.000	0.000	0.000
158	A	249	LEU	0	-0.033	0.004	40.908	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	250	PHE	0	-0.035	-0.012	44.709	0.000	0.000	0.000	0.000	0.000	0.000
160	A	251	GLN	0	-0.053	-0.018	47.873	0.002	0.002	0.000	0.000	0.000	0.000
161	A	252	SER	0	-0.002	0.010	47.741	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:92:LEU)