FMO DATABASE

FMODB ID: 987N2

Calculation Name: 3D6R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D6R

Chain ID: B

ChEMBL ID:

UniProt ID: P69270

Base Structure: X-ray

Registration Date: 2023-09-22

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1082148.872625
FMO2-HF: Nuclear repulsion	1030668.092359
FMO2-HF: Total energy	-51480.780266
FMO2-MP2: Total energy	-51626.986825

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:83:SER)

Summations of interaction energy for fragment #1(B:83:SER)

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.
0.701	1.657	4.445	-2.356	-3.046	0.006

Interaction energy analysis for fragmet #1(B:83:SER)

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 : 0.014

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	85	PRO	0	0.037	0.015	3.521	-1.515	1.114	0.001	-1.350	-1.280	0.005
4	B	86	ALA	0	-0.032	-0.009	5.914	0.918	0.918	0.000	0.000	0.000	0.000
5	B	87	PRO	0	0.039	0.009	7.321	0.115	0.115	0.000	0.000	0.000	0.000
6	B	88	ARG	1	0.936	0.979	6.387	-1.311	-1.311	0.000	0.000	0.000	0.000
7	B	89	TYR	0	-0.008	-0.015	9.290	0.119	0.119	0.000	0.000	0.000	0.000
8	B	90	ILE	0	-0.028	-0.003	9.429	0.143	0.143	0.000	0.000	0.000	0.000
9	B	91	THR	0	-0.015	-0.014	13.342	-0.087	-0.087	0.000	0.000	0.000	0.000
10	B	92	ASP	-1	-0.763	-0.843	16.999	0.516	0.516	0.000	0.000	0.000	0.000
11	B	93	MET	0	-0.076	-0.028	19.612	-0.018	-0.018	0.000	0.000	0.000	0.000
12	B	94	SER	0	0.004	0.006	21.611	-0.009	-0.009	0.000	0.000	0.000	0.000
13	B	95	ILE	0	0.053	-0.002	23.921	-0.007	-0.007	0.000	0.000	0.000	0.000
14	B	96	GLU	-1	-0.838	-0.915	25.296	0.109	0.109	0.000	0.000	0.000	0.000
15	B	97	GLU	-1	-0.850	-0.926	25.438	0.211	0.211	0.000	0.000	0.000	0.000
16	B	98	ILE	0	-0.037	-0.026	22.081	-0.007	-0.007	0.000	0.000	0.000	0.000
17	B	99	SER	0	-0.046	-0.026	25.993	-0.018	-0.018	0.000	0.000	0.000	0.000
18	B	100	ARG	1	0.784	0.911	28.846	-0.137	-0.137	0.000	0.000	0.000	0.000
19	B	101	GLU	-1	-0.907	-0.949	31.680	0.044	0.044	0.000	0.000	0.000	0.000
20	B	102	TRP	0	-0.082	-0.039	31.147	0.007	0.007	0.000	0.000	0.000	0.000
21	B	103	TYR	0	0.001	-0.011	35.137	-0.006	-0.006	0.000	0.000	0.000	0.000
22	B	104	MET	0	-0.057	0.006	36.079	0.005	0.005	0.000	0.000	0.000	0.000
23	B	105	LEU	0	0.005	0.005	39.072	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	106	MET	0	-0.075	-0.042	41.417	-0.005	-0.005	0.000	0.000	0.000	0.000
25	B	107	PRO	0	0.030	0.000	39.033	0.004	0.004	0.000	0.000	0.000	0.000
26	B	108	ARG	1	0.877	0.953	37.575	-0.057	-0.057	0.000	0.000	0.000	0.000
27	B	109	GLN	0	0.024	-0.009	34.857	0.005	0.005	0.000	0.000	0.000	0.000
28	B	110	LYS	1	0.942	0.969	33.062	-0.065	-0.065	0.000	0.000	0.000	0.000
29	B	111	ILE	0	0.027	0.022	31.132	0.005	0.005	0.000	0.000	0.000	0.000
30	B	112	THR	0	-0.034	-0.017	27.230	0.002	0.002	0.000	0.000	0.000	0.000
31	B	113	GLY	0	0.059	0.042	27.335	0.003	0.003	0.000	0.000	0.000	0.000
32	B	114	GLY	0	-0.006	-0.001	26.176	-0.001	-0.001	0.000	0.000	0.000	0.000
33	B	115	LEU	0	-0.057	-0.017	22.732	0.003	0.003	0.000	0.000	0.000	0.000
34	B	116	MET	0	-0.013	-0.003	26.914	0.000	0.000	0.000	0.000	0.000	0.000
35	B	117	VAL	0	0.006	0.004	28.261	0.011	0.011	0.000	0.000	0.000	0.000
36	B	118	LYS	1	0.919	0.954	30.361	-0.047	-0.047	0.000	0.000	0.000	0.000
37	B	119	MET	0	0.032	0.013	32.116	0.012	0.012	0.000	0.000	0.000	0.000
38	B	120	ASP	-1	-0.738	-0.874	34.511	0.068	0.068	0.000	0.000	0.000	0.000
39	B	121	GLN	0	-0.036	-0.034	37.609	0.009	0.009	0.000	0.000	0.000	0.000
40	B	122	ALA	0	0.006	-0.001	39.819	0.000	0.000	0.000	0.000	0.000	0.000
41	B	123	ILE	0	-0.073	-0.020	36.337	0.002	0.002	0.000	0.000	0.000	0.000
42	B	124	MET	0	0.036	0.038	39.075	-0.002	-0.002	0.000	0.000	0.000	0.000
43	B	125	ASP	-1	-0.863	-0.912	39.720	0.101	0.101	0.000	0.000	0.000	0.000
44	B	126	LYS	1	0.902	0.955	36.258	-0.111	-0.111	0.000	0.000	0.000	0.000
45	B	127	ARG	1	0.876	0.939	31.190	-0.201	-0.201	0.000	0.000	0.000	0.000
46	B	128	ILE	0	-0.009	-0.010	29.545	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	129	THR	0	-0.033	-0.007	25.327	0.021	0.021	0.000	0.000	0.000	0.000
48	B	130	LEU	0	-0.001	0.008	23.827	-0.014	-0.014	0.000	0.000	0.000	0.000
49	B	131	LYS	1	0.957	0.977	21.778	-0.232	-0.232	0.000	0.000	0.000	0.000
50	B	132	ALA	0	0.021	-0.004	18.887	-0.040	-0.040	0.000	0.000	0.000	0.000
51	B	133	ASN	0	0.030	0.036	17.666	0.078	0.078	0.000	0.000	0.000	0.000
52	B	134	PHE	0	-0.006	-0.012	12.657	-0.042	-0.042	0.000	0.000	0.000	0.000
53	B	135	SER	0	0.027	0.019	12.291	0.073	0.073	0.000	0.000	0.000	0.000
54	B	136	VAL	0	-0.015	0.003	7.459	0.025	0.025	0.000	0.000	0.000	0.000
55	B	137	LEU	0	0.051	0.025	7.492	-0.210	-0.210	0.000	0.000	0.000	0.000
56	B	138	PHE	0	-0.006	-0.009	1.867	0.671	-1.060	4.445	-1.006	-1.709	0.001
57	B	139	ASP	-1	-0.905	-0.971	5.352	3.752	3.810	-0.001	0.000	-0.057	0.000
58	B	140	GLN	0	-0.019	-0.005	7.639	-0.175	-0.175	0.000	0.000	0.000	0.000
59	B	141	LEU	0	-0.053	-0.028	10.615	-0.133	-0.133	0.000	0.000	0.000	0.000
60	B	142	GLU	-1	-0.931	-0.975	12.508	-0.271	-0.271	0.000	0.000	0.000	0.000
61	B	143	THR	0	-0.017	0.001	14.003	-0.025	-0.025	0.000	0.000	0.000	0.000
62	B	144	LEU	0	-0.043	-0.025	16.306	0.047	0.047	0.000	0.000	0.000	0.000
63	B	145	VAL	0	-0.043	-0.029	18.183	-0.032	-0.032	0.000	0.000	0.000	0.000
64	B	146	SER	0	-0.026	-0.041	20.690	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	147	LEU	0	0.005	0.017	21.358	0.031	0.031	0.000	0.000	0.000	0.000
66	B	148	ARG	1	0.804	0.890	23.300	-0.124	-0.124	0.000	0.000	0.000	0.000
67	B	149	ALA	0	0.006	-0.001	25.948	0.024	0.024	0.000	0.000	0.000	0.000
68	B	150	PHE	0	-0.008	-0.008	25.930	-0.013	-0.013	0.000	0.000	0.000	0.000
69	B	151	THR	0	0.007	-0.017	30.200	0.009	0.009	0.000	0.000	0.000	0.000
70	B	152	ASP	-1	-0.841	-0.925	32.572	0.193	0.193	0.000	0.000	0.000	0.000
71	B	153	ASP	-1	-0.913	-0.928	33.678	0.133	0.133	0.000	0.000	0.000	0.000
72	B	154	GLY	0	-0.002	0.004	31.612	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	155	ALA	0	0.001	0.009	32.372	-0.004	-0.004	0.000	0.000	0.000	0.000
74	B	156	ILE	0	-0.021	-0.008	29.779	0.010	0.010	0.000	0.000	0.000	0.000
75	B	157	VAL	0	0.000	-0.004	32.049	-0.010	-0.010	0.000	0.000	0.000	0.000
76	B	158	ALA	0	-0.017	-0.029	30.521	-0.008	-0.008	0.000	0.000	0.000	0.000
77	B	159	GLU	-1	-0.777	-0.870	27.040	0.094	0.094	0.000	0.000	0.000	0.000
78	B	160	ILE	0	-0.024	0.001	24.465	-0.012	-0.012	0.000	0.000	0.000	0.000
79	B	161	SER	0	0.006	-0.003	24.906	0.006	0.006	0.000	0.000	0.000	0.000
80	B	162	PRO	0	0.046	0.021	22.857	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	163	ILE	0	-0.014	-0.002	25.622	0.003	0.003	0.000	0.000	0.000	0.000
82	B	164	PRO	0	0.004	-0.006	28.127	-0.011	-0.011	0.000	0.000	0.000	0.000
83	B	165	SER	0	-0.029	-0.013	29.123	-0.009	-0.009	0.000	0.000	0.000	0.000
84	B	166	MET	0	-0.052	-0.013	28.364	-0.005	-0.005	0.000	0.000	0.000	0.000
85	B	167	PRO	0	0.010	0.001	26.305	-0.007	-0.007	0.000	0.000	0.000	0.000
86	B	168	GLY	0	-0.002	0.005	22.095	0.014	0.014	0.000	0.000	0.000	0.000
87	B	169	HIS	0	0.013	0.018	19.983	0.004	0.004	0.000	0.000	0.000	0.000
88	B	170	SER	0	0.064	0.048	20.457	-0.009	-0.009	0.000	0.000	0.000	0.000
89	B	171	THR	0	0.062	0.000	16.686	0.011	0.011	0.000	0.000	0.000	0.000
90	B	172	GLU	-1	-0.948	-0.974	19.321	0.032	0.032	0.000	0.000	0.000	0.000
91	B	173	ASP	-1	-0.767	-0.895	22.823	-0.001	-0.001	0.000	0.000	0.000	0.000
92	B	174	VAL	0	0.008	0.003	19.051	0.017	0.017	0.000	0.000	0.000	0.000
93	B	175	LYS	1	0.904	0.954	17.217	-0.210	-0.210	0.000	0.000	0.000	0.000
94	B	176	ASN	0	0.038	0.025	22.760	0.020	0.020	0.000	0.000	0.000	0.000
95	B	177	ALA	0	-0.028	-0.019	24.798	0.003	0.003	0.000	0.000	0.000	0.000
96	B	178	ILE	0	0.002	-0.009	20.962	0.004	0.004	0.000	0.000	0.000	0.000
97	B	179	GLY	0	0.033	0.026	25.375	0.005	0.005	0.000	0.000	0.000	0.000
98	B	180	ILE	0	-0.041	-0.036	27.778	-0.005	-0.005	0.000	0.000	0.000	0.000
99	B	181	LEU	0	-0.030	0.006	27.050	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	182	ILE	0	0.002	-0.004	25.891	0.000	0.000	0.000	0.000	0.000	0.000
101	B	183	GLY	0	0.045	0.027	30.141	-0.003	-0.003	0.000	0.000	0.000	0.000
102	B	184	GLY	0	-0.034	-0.028	33.017	-0.006	-0.006	0.000	0.000	0.000	0.000
103	B	185	LEU	0	-0.019	-0.029	30.770	-0.004	-0.004	0.000	0.000	0.000	0.000
104	B	186	GLU	-1	-0.902	-0.950	32.010	0.156	0.156	0.000	0.000	0.000	0.000
105	B	187	TRP	0	-0.052	-0.007	35.582	-0.005	-0.005	0.000	0.000	0.000	0.000
106	B	188	ASN	0	-0.064	-0.025	38.046	-0.009	-0.009	0.000	0.000	0.000	0.000
107	B	189	ASP	-1	-0.823	-0.898	38.610	0.102	0.102	0.000	0.000	0.000	0.000
108	B	190	ASN	0	-0.096	-0.054	34.687	0.005	0.005	0.000	0.000	0.000	0.000
109	B	191	SER	0	0.005	0.009	33.252	0.001	0.001	0.000	0.000	0.000	0.000
110	B	192	ILE	0	0.034	0.005	27.375	0.005	0.005	0.000	0.000	0.000	0.000
111	B	193	ARG	1	0.901	0.938	26.394	-0.257	-0.257	0.000	0.000	0.000	0.000
112	B	194	ALA	0	0.029	0.007	21.715	-0.016	-0.016	0.000	0.000	0.000	0.000
113	B	195	SER	0	-0.039	-0.041	19.260	0.032	0.032	0.000	0.000	0.000	0.000
114	B	196	GLU	-1	-0.850	-0.938	17.151	0.590	0.590	0.000	0.000	0.000	0.000
115	B	197	ASN	0	-0.022	-0.022	14.155	0.215	0.215	0.000	0.000	0.000	0.000
116	B	198	ILE	0	-0.033	-0.017	14.930	0.027	0.027	0.000	0.000	0.000	0.000
117	B	199	GLN	0	-0.065	-0.039	16.994	0.005	0.005	0.000	0.000	0.000	0.000
118	B	200	ARG	1	0.881	0.962	7.309	-2.387	-2.387	0.000	0.000	0.000	0.000
119	B	201	PHE	0	-0.034	-0.004	8.136	0.142	0.142	0.000	0.000	0.000	0.000
120	B	202	ALA	0	-0.016	0.007	12.857	-0.108	-0.108	0.000	0.000	0.000	0.000
121	B	218	GLN	0	0.024	0.015	48.896	-0.001	-0.001	0.000	0.000	0.000	0.000
122	B	219	LYS	1	0.802	0.859	42.159	-0.093	-0.093	0.000	0.000	0.000	0.000
123	B	220	ARG	1	0.931	0.963	45.147	-0.088	-0.088	0.000	0.000	0.000	0.000
124	B	221	TYR	0	-0.003	-0.016	48.735	0.002	0.002	0.000	0.000	0.000	0.000
125	B	222	MET	0	-0.050	-0.012	51.780	0.000	0.000	0.000	0.000	0.000	0.000
126	B	223	ALA	0	0.047	0.025	52.783	-0.002	-0.002	0.000	0.000	0.000	0.000
127	B	224	ARG	1	0.979	0.990	55.180	-0.058	-0.058	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:83:SER)