FMO DATABASE

FMODB ID: GN821

Calculation Name: 1DVK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DVK

Chain ID: A

ChEMBL ID:

UniProt ID: P33411

Base Structure: X-ray

Registration Date: 2023-03-13

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	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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1514009.573051
FMO2-HF: Nuclear repulsion	1454149.871743
FMO2-HF: Total energy	-59859.701307
FMO2-MP2: Total energy	-60035.469296

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:79:MET)

Summations of interaction energy for fragment #1(A:79:MET)

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.
-4.744	-3.712	5.342	-0.883	-5.493	0.004

Interaction energy analysis for fragmet #1(A:79:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.015

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	81	ILE	0	0.096	0.016	2.826	-2.197	-0.696	5.257	-1.773	-4.986	0.003
4	A	82	GLN	0	-0.004	0.000	3.942	-1.341	-2.034	0.079	0.937	-0.324	0.001
5	A	83	GLU	-1	-0.796	-0.860	6.396	2.089	2.089	0.000	0.000	0.000	0.000
6	A	84	ALA	0	0.021	0.026	3.439	-0.720	-0.496	0.006	-0.047	-0.183	0.000
7	A	85	ILE	0	0.002	-0.002	5.588	-0.296	-0.296	0.000	0.000	0.000	0.000
8	A	86	ALA	0	-0.007	-0.019	8.542	-0.138	-0.138	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.067	-0.041	8.112	-0.195	-0.195	0.000	0.000	0.000	0.000
10	A	88	ASP	-1	-0.752	-0.849	9.345	-0.240	-0.240	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.766	0.862	10.937	-0.067	-0.067	0.000	0.000	0.000	0.000
12	A	90	THR	0	0.007	0.007	12.897	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	91	ILE	0	-0.074	-0.031	11.227	0.005	0.005	0.000	0.000	0.000	0.000
14	A	92	SER	0	0.026	0.021	15.389	0.033	0.033	0.000	0.000	0.000	0.000
15	A	93	VAL	0	0.040	0.002	18.901	0.010	0.010	0.000	0.000	0.000	0.000
16	A	94	ILE	0	0.017	0.032	21.184	0.008	0.008	0.000	0.000	0.000	0.000
17	A	95	ILE	0	-0.003	-0.003	21.308	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	96	ASP	-1	-0.780	-0.857	21.596	-0.086	-0.086	0.000	0.000	0.000	0.000
19	A	97	PRO	0	0.026	-0.003	23.026	0.004	0.004	0.000	0.000	0.000	0.000
20	A	98	SER	0	-0.058	-0.046	23.782	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	99	GLN	0	-0.029	-0.036	19.130	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	100	ILE	0	-0.060	-0.012	20.253	0.010	0.010	0.000	0.000	0.000	0.000
23	A	101	GLY	0	0.022	0.002	21.671	0.016	0.016	0.000	0.000	0.000	0.000
24	A	102	SER	0	-0.016	0.017	18.186	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	103	THR	0	-0.010	-0.025	16.046	0.018	0.018	0.000	0.000	0.000	0.000
26	A	104	GLU	-1	-0.939	-0.957	13.042	-0.364	-0.364	0.000	0.000	0.000	0.000
27	A	105	GLY	0	0.046	0.013	13.160	0.015	0.015	0.000	0.000	0.000	0.000
28	A	106	LYS	1	0.866	0.948	13.673	-0.159	-0.159	0.000	0.000	0.000	0.000
29	A	107	PRO	0	0.015	-0.005	10.083	0.074	0.074	0.000	0.000	0.000	0.000
30	A	108	LEU	0	0.033	0.020	12.284	0.065	0.065	0.000	0.000	0.000	0.000
31	A	109	LEU	0	0.033	0.025	13.723	0.022	0.022	0.000	0.000	0.000	0.000
32	A	110	SER	0	-0.004	-0.016	14.438	0.001	0.001	0.000	0.000	0.000	0.000
33	A	111	MET	0	-0.018	0.005	12.452	0.050	0.050	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.869	0.911	14.931	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	113	CYS	0	-0.019	-0.002	17.858	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	114	ASN	0	0.009	0.003	16.482	0.023	0.023	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.023	-0.006	15.556	0.001	0.001	0.000	0.000	0.000	0.000
38	A	116	TYR	0	-0.009	-0.016	19.564	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	117	ILE	0	0.019	0.010	22.676	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	118	HIS	0	0.001	-0.009	20.195	0.028	0.028	0.000	0.000	0.000	0.000
41	A	119	GLU	-1	-0.849	-0.891	23.541	0.065	0.065	0.000	0.000	0.000	0.000
42	A	120	ILE	0	0.058	0.037	25.295	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	121	LEU	0	-0.049	-0.027	25.743	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	122	SER	0	-0.051	-0.015	26.356	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	123	ARG	1	0.770	0.823	28.417	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	124	TRP	0	-0.022	-0.009	31.251	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	125	LYS	1	0.906	0.939	30.839	-0.106	-0.106	0.000	0.000	0.000	0.000
48	A	126	ALA	0	-0.032	-0.024	32.405	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	127	SER	0	0.018	-0.001	34.159	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	128	LEU	0	-0.036	-0.008	35.272	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	129	GLU	-1	-0.964	-0.987	37.555	0.063	0.063	0.000	0.000	0.000	0.000
52	A	130	ALA	0	-0.002	0.008	40.580	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	131	TYR	0	-0.009	-0.012	37.457	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	132	HIS	1	0.831	0.894	38.734	-0.067	-0.067	0.000	0.000	0.000	0.000
55	A	133	PRO	0	0.090	0.037	38.344	0.007	0.007	0.000	0.000	0.000	0.000
56	A	134	GLU	-1	-0.800	-0.880	38.373	0.088	0.088	0.000	0.000	0.000	0.000
57	A	135	LEU	0	-0.023	0.000	37.436	0.007	0.007	0.000	0.000	0.000	0.000
58	A	136	PHE	0	0.037	0.043	30.744	0.012	0.012	0.000	0.000	0.000	0.000
59	A	137	LEU	0	0.005	-0.001	32.647	0.012	0.012	0.000	0.000	0.000	0.000
60	A	138	ASP	-1	-0.778	-0.902	32.350	0.153	0.153	0.000	0.000	0.000	0.000
61	A	139	THR	0	-0.035	-0.028	30.576	0.004	0.004	0.000	0.000	0.000	0.000
62	A	140	LYS	1	0.945	0.976	28.246	-0.161	-0.161	0.000	0.000	0.000	0.000
63	A	141	LYS	1	0.792	0.886	27.640	-0.134	-0.134	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.010	0.009	28.053	0.017	0.017	0.000	0.000	0.000	0.000
65	A	143	LEU	0	0.030	0.010	25.646	0.010	0.010	0.000	0.000	0.000	0.000
66	A	144	PHE	0	-0.009	0.013	21.800	0.023	0.023	0.000	0.000	0.000	0.000
67	A	145	PRO	0	-0.003	-0.005	21.970	0.039	0.039	0.000	0.000	0.000	0.000
68	A	146	LEU	0	0.042	0.029	20.801	0.037	0.037	0.000	0.000	0.000	0.000
69	A	147	LEU	0	0.005	0.001	20.019	0.024	0.024	0.000	0.000	0.000	0.000
70	A	148	LEU	0	-0.025	-0.007	16.423	0.055	0.055	0.000	0.000	0.000	0.000
71	A	149	GLN	0	-0.003	-0.015	16.100	0.063	0.063	0.000	0.000	0.000	0.000
72	A	150	LEU	0	-0.029	0.000	15.798	0.041	0.041	0.000	0.000	0.000	0.000
73	A	151	ARG	1	0.865	0.933	13.234	-0.435	-0.435	0.000	0.000	0.000	0.000
74	A	152	ARG	1	0.912	0.966	11.582	-0.680	-0.680	0.000	0.000	0.000	0.000
75	A	153	ASN	0	0.010	-0.005	9.787	-0.037	-0.037	0.000	0.000	0.000	0.000
76	A	154	GLN	0	-0.020	-0.026	13.003	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	155	LEU	0	-0.019	0.013	14.704	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	156	ALA	0	0.060	0.026	17.025	-0.009	-0.009	0.000	0.000	0.000	0.000
79	A	157	PRO	0	0.046	0.009	17.535	0.006	0.006	0.000	0.000	0.000	0.000
80	A	158	ASP	-1	-0.821	-0.905	19.588	0.048	0.048	0.000	0.000	0.000	0.000
81	A	159	LEU	0	-0.016	0.005	21.981	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	160	LEU	0	-0.026	-0.016	17.201	0.007	0.007	0.000	0.000	0.000	0.000
83	A	161	ILE	0	0.016	0.012	21.253	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	162	SER	0	-0.004	-0.014	23.319	-0.009	-0.009	0.000	0.000	0.000	0.000
85	A	163	LEU	0	-0.021	-0.012	22.373	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	164	ALA	0	0.029	0.003	22.126	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	165	THR	0	-0.013	-0.012	24.212	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	166	VAL	0	-0.051	-0.013	27.612	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	167	LEU	0	-0.016	-0.017	23.603	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	168	TYR	0	-0.001	-0.013	26.200	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	169	HIS	0	-0.009	-0.024	27.546	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	170	LEU	0	-0.045	-0.014	29.313	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	171	GLN	0	-0.025	-0.014	23.957	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	172	GLN	0	-0.015	0.011	29.100	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	173	PRO	0	0.055	0.026	32.962	0.001	0.001	0.000	0.000	0.000	0.000
96	A	174	LYS	1	0.937	0.956	36.064	0.003	0.003	0.000	0.000	0.000	0.000
97	A	175	GLU	-1	-0.806	-0.887	33.188	0.000	0.000	0.000	0.000	0.000	0.000
98	A	176	ILE	0	0.073	0.045	35.341	0.003	0.003	0.000	0.000	0.000	0.000
99	A	177	ASN	0	0.008	-0.011	36.649	0.005	0.005	0.000	0.000	0.000	0.000
100	A	178	LEU	0	0.016	0.018	35.384	0.003	0.003	0.000	0.000	0.000	0.000
101	A	179	ALA	0	0.029	0.021	32.671	0.002	0.002	0.000	0.000	0.000	0.000
102	A	180	VAL	0	0.014	0.005	33.883	0.007	0.007	0.000	0.000	0.000	0.000
103	A	181	GLN	0	0.020	-0.001	36.392	0.002	0.002	0.000	0.000	0.000	0.000
104	A	182	SER	0	-0.018	-0.028	31.486	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	183	TYR	0	-0.043	-0.048	31.525	0.003	0.003	0.000	0.000	0.000	0.000
106	A	184	MET	0	-0.014	0.002	33.036	0.005	0.005	0.000	0.000	0.000	0.000
107	A	185	LYS	1	0.874	0.964	32.622	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	186	LEU	0	0.043	0.030	27.626	0.003	0.003	0.000	0.000	0.000	0.000
109	A	187	SER	0	-0.086	-0.050	31.092	0.006	0.006	0.000	0.000	0.000	0.000
110	A	188	ILE	0	-0.014	-0.014	33.494	0.004	0.004	0.000	0.000	0.000	0.000
111	A	189	GLY	0	0.001	0.017	31.183	0.002	0.002	0.000	0.000	0.000	0.000
112	A	190	ASN	0	-0.021	-0.021	31.584	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	191	VAL	0	-0.017	-0.010	26.787	0.005	0.005	0.000	0.000	0.000	0.000
114	A	192	ALA	0	-0.036	-0.014	28.722	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	193	TRP	0	0.060	0.035	24.109	0.002	0.002	0.000	0.000	0.000	0.000
116	A	194	PRO	0	-0.009	-0.026	27.961	0.004	0.004	0.000	0.000	0.000	0.000
117	A	195	ILE	0	-0.041	-0.021	30.956	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	196	GLY	0	0.031	0.023	34.421	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	197	VAL	0	-0.034	-0.002	29.911	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	218	ALA	0	0.055	0.040	28.648	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	219	ASN	0	-0.063	-0.056	29.603	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	220	ILE	0	-0.003	0.003	25.680	0.003	0.003	0.000	0.000	0.000	0.000
123	A	221	MET	0	-0.031	-0.010	25.661	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	222	ILE	0	-0.012	-0.010	26.756	0.011	0.011	0.000	0.000	0.000	0.000
125	A	223	ASP	-1	-0.790	-0.872	25.876	0.207	0.207	0.000	0.000	0.000	0.000
126	A	224	GLU	-1	-0.868	-0.932	28.198	0.137	0.137	0.000	0.000	0.000	0.000
127	A	225	ARG	1	0.909	0.946	23.773	-0.264	-0.264	0.000	0.000	0.000	0.000
128	A	226	THR	0	-0.029	-0.048	25.250	0.007	0.007	0.000	0.000	0.000	0.000
129	A	227	ARG	1	0.951	0.984	26.958	-0.115	-0.115	0.000	0.000	0.000	0.000
130	A	228	LEU	0	0.018	0.026	29.327	-0.008	-0.008	0.000	0.000	0.000	0.000
131	A	229	TRP	0	0.042	0.018	23.802	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	230	ILE	0	0.032	0.014	28.313	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	231	THR	0	-0.035	-0.010	30.228	-0.014	-0.014	0.000	0.000	0.000	0.000
134	A	232	SER	0	-0.031	-0.036	30.509	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	233	ILE	0	0.022	0.017	26.225	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	234	LYS	1	0.984	0.993	30.394	-0.089	-0.089	0.000	0.000	0.000	0.000
137	A	235	ARG	1	0.863	0.950	33.564	-0.125	-0.125	0.000	0.000	0.000	0.000
138	A	236	LEU	0	0.044	0.025	27.880	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	237	ILE	0	0.002	0.015	32.162	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	238	THR	0	-0.016	-0.011	34.030	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	239	PHE	0	-0.002	0.017	32.530	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	240	GLU	-1	-0.702	-0.819	30.920	0.054	0.054	0.000	0.000	0.000	0.000
143	A	241	GLU	-1	-0.950	-0.958	34.496	0.038	0.038	0.000	0.000	0.000	0.000
144	A	242	TRP	0	0.003	0.016	37.547	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	243	TYR	0	-0.020	-0.031	34.340	-0.003	-0.003	0.000	0.000	0.000	0.000
146	A	244	THR	0	-0.075	-0.068	35.308	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	245	SER	0	-0.039	-0.013	37.942	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	246	ASN	0	-0.083	-0.033	40.676	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	247	HIS	0	0.016	0.023	37.511	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:79:MET)