FMO DATABASE

FMODB ID: KG4Q3

Calculation Name: 1DVO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DVO

Chain ID: A

ChEMBL ID:

UniProt ID: P29367

Base Structure: X-ray

Registration Date: 2023-09-24

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1292488.731337
FMO2-HF: Nuclear repulsion	1231830.337859
FMO2-HF: Total energy	-60658.393479
FMO2-MP2: Total energy	-60835.720205

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:33:PRO)

Summations of interaction energy for fragment #1(A:33:PRO)

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.
-0.519	1.695	4.482	-2.702	-3.995	0.012

Interaction energy analysis for fragmet #1(A:33:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.018

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	35	LYS	1	1.066	1.022	3.635	-1.313	0.704	-0.007	-1.204	-0.807	0.004
4	A	36	TRP	0	0.038	0.021	6.436	0.160	0.160	0.000	0.000	0.000	0.000
5	A	37	LYS	1	0.933	0.971	1.874	-1.361	-2.127	4.431	-1.276	-2.389	0.008
6	A	38	VAL	0	0.055	0.031	3.210	-0.358	0.301	0.057	-0.155	-0.562	0.000
7	A	39	LYS	1	0.955	0.978	5.431	0.797	0.797	0.000	0.000	0.000	0.000
8	A	40	LYS	1	0.976	0.986	8.164	0.259	0.259	0.000	0.000	0.000	0.000
9	A	41	GLN	0	0.034	0.009	3.942	0.136	0.440	0.001	-0.067	-0.237	0.000
10	A	42	LYS	1	1.016	0.997	8.252	0.919	0.919	0.000	0.000	0.000	0.000
11	A	43	LEU	0	-0.029	-0.006	10.243	0.074	0.074	0.000	0.000	0.000	0.000
12	A	44	ALA	0	0.013	0.011	11.651	0.054	0.054	0.000	0.000	0.000	0.000
13	A	45	GLU	-1	-0.920	-0.963	9.702	-0.483	-0.483	0.000	0.000	0.000	0.000
14	A	46	LYS	1	0.849	0.926	13.600	0.265	0.265	0.000	0.000	0.000	0.000
15	A	47	ALA	0	0.035	0.014	16.093	0.026	0.026	0.000	0.000	0.000	0.000
16	A	48	ALA	0	0.007	0.009	16.361	0.024	0.024	0.000	0.000	0.000	0.000
17	A	49	ARG	1	0.995	0.997	13.862	0.319	0.319	0.000	0.000	0.000	0.000
18	A	50	GLU	-1	-0.881	-0.941	19.763	-0.173	-0.173	0.000	0.000	0.000	0.000
19	A	51	ALA	0	-0.007	0.014	21.309	0.014	0.014	0.000	0.000	0.000	0.000
20	A	52	GLU	-1	-0.936	-0.971	21.547	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	53	LEU	0	-0.013	-0.007	23.631	0.012	0.012	0.000	0.000	0.000	0.000
22	A	54	THR	0	-0.026	-0.038	25.711	0.010	0.010	0.000	0.000	0.000	0.000
23	A	55	ALA	0	-0.001	0.007	26.335	0.008	0.008	0.000	0.000	0.000	0.000
24	A	56	LYS	1	0.996	0.996	27.394	0.092	0.092	0.000	0.000	0.000	0.000
25	A	57	LYS	1	0.917	0.974	29.789	0.091	0.091	0.000	0.000	0.000	0.000
26	A	58	ALA	0	0.007	0.006	31.415	0.005	0.005	0.000	0.000	0.000	0.000
27	A	59	GLN	0	-0.022	-0.009	31.677	0.003	0.003	0.000	0.000	0.000	0.000
28	A	60	ALA	0	0.031	0.004	33.819	0.004	0.004	0.000	0.000	0.000	0.000
29	A	61	ARG	1	0.958	0.973	34.813	0.062	0.062	0.000	0.000	0.000	0.000
30	A	62	GLN	0	-0.033	-0.009	35.269	0.002	0.002	0.000	0.000	0.000	0.000
31	A	63	ALA	0	-0.014	-0.001	38.195	0.003	0.003	0.000	0.000	0.000	0.000
32	A	64	LEU	0	0.024	0.010	39.874	0.003	0.003	0.000	0.000	0.000	0.000
33	A	65	SER	0	0.008	0.014	41.758	0.002	0.002	0.000	0.000	0.000	0.000
34	A	66	ILE	0	0.018	0.008	43.815	0.001	0.001	0.000	0.000	0.000	0.000
35	A	67	TYR	0	-0.042	-0.024	43.355	0.002	0.002	0.000	0.000	0.000	0.000
36	A	68	LEU	0	-0.036	-0.024	43.727	0.000	0.000	0.000	0.000	0.000	0.000
37	A	69	ASN	0	0.048	0.028	47.757	0.000	0.000	0.000	0.000	0.000	0.000
38	A	70	LEU	0	-0.076	-0.029	50.683	0.002	0.002	0.000	0.000	0.000	0.000
39	A	71	PRO	0	-0.007	0.019	51.746	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	72	THR	0	0.046	0.021	49.915	0.001	0.001	0.000	0.000	0.000	0.000
41	A	73	LEU	0	0.023	-0.001	52.583	0.001	0.001	0.000	0.000	0.000	0.000
42	A	74	ASP	-1	-0.850	-0.926	53.757	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	75	GLU	-1	-0.860	-0.936	51.686	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	76	ALA	0	-0.060	-0.029	55.977	0.001	0.001	0.000	0.000	0.000	0.000
45	A	77	VAL	0	0.044	0.010	58.575	0.001	0.001	0.000	0.000	0.000	0.000
46	A	78	ASN	0	-0.009	-0.002	57.161	0.002	0.002	0.000	0.000	0.000	0.000
47	A	79	THR	0	-0.139	-0.064	59.316	0.000	0.000	0.000	0.000	0.000	0.000
48	A	80	LEU	0	-0.054	-0.046	61.841	0.001	0.001	0.000	0.000	0.000	0.000
49	A	81	LYS	1	0.936	0.979	63.901	0.023	0.023	0.000	0.000	0.000	0.000
50	A	82	PRO	0	-0.013	-0.010	64.136	0.001	0.001	0.000	0.000	0.000	0.000
51	A	83	TRP	0	-0.004	-0.001	65.720	0.001	0.001	0.000	0.000	0.000	0.000
52	A	84	TRP	0	-0.004	-0.009	67.111	0.000	0.000	0.000	0.000	0.000	0.000
53	A	85	PRO	0	0.041	0.019	68.778	0.000	0.000	0.000	0.000	0.000	0.000
54	A	86	GLY	0	0.057	0.041	69.829	0.000	0.000	0.000	0.000	0.000	0.000
55	A	87	LEU	0	-0.044	-0.027	68.148	0.000	0.000	0.000	0.000	0.000	0.000
56	A	88	PHE	0	-0.069	-0.047	62.990	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	89	ASP	-1	-0.909	-0.930	66.306	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	90	GLY	0	0.037	0.011	64.936	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	91	ASP	-1	-0.928	-0.982	59.571	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	92	THR	0	-0.044	-0.016	61.218	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	93	PRO	0	-0.048	-0.026	60.977	0.001	0.001	0.000	0.000	0.000	0.000
62	A	94	ARG	1	0.950	1.000	64.062	0.017	0.017	0.000	0.000	0.000	0.000
63	A	95	LEU	0	-0.032	-0.020	65.628	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	LEU	0	-0.006	-0.027	65.402	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	ALA	0	0.061	0.053	69.276	0.000	0.000	0.000	0.000	0.000	0.000
66	A	98	CYS	0	-0.044	-0.026	71.626	0.000	0.000	0.000	0.000	0.000	0.000
67	A	99	GLY	0	-0.007	-0.011	71.813	0.000	0.000	0.000	0.000	0.000	0.000
68	A	100	ILE	0	0.051	0.030	69.733	0.000	0.000	0.000	0.000	0.000	0.000
69	A	101	ARG	1	0.909	0.943	65.206	0.015	0.015	0.000	0.000	0.000	0.000
70	A	102	ASP	-1	-0.913	-0.954	70.251	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	103	VAL	0	0.075	0.049	73.466	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	LEU	0	-0.042	-0.030	68.563	0.000	0.000	0.000	0.000	0.000	0.000
73	A	105	LEU	0	-0.052	-0.054	69.025	0.000	0.000	0.000	0.000	0.000	0.000
74	A	106	GLU	-1	-0.925	-0.944	72.148	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	107	ASP	-1	-0.766	-0.883	73.693	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.066	-0.038	69.256	0.000	0.000	0.000	0.000	0.000	0.000
77	A	109	ALA	0	-0.013	0.000	72.377	0.000	0.000	0.000	0.000	0.000	0.000
78	A	110	GLN	0	-0.013	0.001	74.808	0.000	0.000	0.000	0.000	0.000	0.000
79	A	111	ARG	1	0.809	0.898	72.712	0.017	0.017	0.000	0.000	0.000	0.000
80	A	112	ASN	0	-0.031	-0.005	73.025	0.000	0.000	0.000	0.000	0.000	0.000
81	A	113	ILE	0	-0.011	0.007	68.137	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	114	PRO	0	0.007	0.010	65.660	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	LEU	0	-0.042	-0.030	63.459	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	116	SER	0	0.038	0.030	62.459	0.001	0.001	0.000	0.000	0.000	0.000
85	A	117	HIS	0	0.135	0.053	64.951	0.000	0.000	0.000	0.000	0.000	0.000
86	A	118	LYS	1	0.925	0.957	58.165	0.019	0.019	0.000	0.000	0.000	0.000
87	A	119	LYS	1	0.991	0.988	58.761	0.023	0.023	0.000	0.000	0.000	0.000
88	A	120	LEU	0	0.099	0.073	61.193	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	121	ARG	1	0.899	0.940	62.403	0.017	0.017	0.000	0.000	0.000	0.000
90	A	122	ARG	1	0.787	0.879	53.292	0.025	0.025	0.000	0.000	0.000	0.000
91	A	123	ALA	0	0.067	0.048	58.526	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	124	MET	0	0.062	0.034	59.951	0.000	0.000	0.000	0.000	0.000	0.000
93	A	125	LYS	1	0.901	0.950	58.326	0.019	0.019	0.000	0.000	0.000	0.000
94	A	126	ALA	0	0.023	0.013	56.015	0.000	0.000	0.000	0.000	0.000	0.000
95	A	127	ILE	0	0.047	0.033	57.173	0.000	0.000	0.000	0.000	0.000	0.000
96	A	128	THR	0	-0.038	-0.008	59.808	0.000	0.000	0.000	0.000	0.000	0.000
97	A	129	ARG	1	0.867	0.919	55.947	0.019	0.019	0.000	0.000	0.000	0.000
98	A	130	SER	0	-0.004	0.012	55.530	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	131	GLU	-1	-0.786	-0.917	51.574	-0.026	-0.026	0.000	0.000	0.000	0.000
100	A	132	SER	0	0.008	0.009	56.292	0.001	0.001	0.000	0.000	0.000	0.000
101	A	133	TYR	0	0.073	0.060	58.931	0.001	0.001	0.000	0.000	0.000	0.000
102	A	134	LEU	0	0.001	-0.016	57.244	0.001	0.001	0.000	0.000	0.000	0.000
103	A	135	CYS	0	-0.081	-0.039	58.312	0.001	0.001	0.000	0.000	0.000	0.000
104	A	136	ALA	0	-0.002	0.004	61.265	0.001	0.001	0.000	0.000	0.000	0.000
105	A	137	MET	0	-0.080	-0.030	64.086	0.000	0.000	0.000	0.000	0.000	0.000
106	A	138	LYS	1	0.960	0.988	64.514	0.017	0.017	0.000	0.000	0.000	0.000
107	A	139	ALA	0	0.019	0.004	68.023	0.000	0.000	0.000	0.000	0.000	0.000
108	A	140	GLY	0	-0.020	-0.010	71.475	0.000	0.000	0.000	0.000	0.000	0.000
109	A	141	ALA	0	-0.046	-0.003	69.958	0.000	0.000	0.000	0.000	0.000	0.000
110	A	142	CYS	0	-0.005	-0.005	71.909	0.000	0.000	0.000	0.000	0.000	0.000
111	A	143	ARG	1	0.811	0.898	68.258	0.014	0.014	0.000	0.000	0.000	0.000
112	A	144	TYR	0	0.006	-0.003	71.436	0.000	0.000	0.000	0.000	0.000	0.000
113	A	145	ASP	-1	-0.769	-0.886	72.518	-0.014	-0.014	0.000	0.000	0.000	0.000
114	A	146	THR	0	-0.059	-0.061	72.201	0.000	0.000	0.000	0.000	0.000	0.000
115	A	147	GLU	-1	-0.952	-0.964	74.267	-0.013	-0.013	0.000	0.000	0.000	0.000
116	A	148	GLY	0	-0.046	-0.016	75.372	0.000	0.000	0.000	0.000	0.000	0.000
117	A	149	TYR	0	-0.023	0.001	76.404	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	VAL	0	-0.057	-0.037	76.114	0.000	0.000	0.000	0.000	0.000	0.000
119	A	151	THR	0	-0.010	-0.043	75.314	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	GLU	-1	-0.818	-0.899	74.687	-0.013	-0.013	0.000	0.000	0.000	0.000
121	A	153	HIS	0	-0.010	-0.009	74.730	0.000	0.000	0.000	0.000	0.000	0.000
122	A	154	ILE	0	-0.055	-0.017	68.805	0.000	0.000	0.000	0.000	0.000	0.000
123	A	155	SER	0	0.043	0.018	72.055	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	GLN	0	0.059	0.008	70.782	0.000	0.000	0.000	0.000	0.000	0.000
125	A	157	GLU	-1	-0.873	-0.941	69.490	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	158	GLU	-1	-0.853	-0.919	67.810	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	159	GLU	-1	-0.832	-0.908	66.197	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	160	VAL	0	-0.013	-0.005	64.788	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	161	TYR	0	-0.037	-0.023	61.808	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	162	ALA	0	0.000	-0.007	61.839	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	163	ALA	0	0.029	0.024	60.269	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	164	GLU	-1	-0.798	-0.897	57.360	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	165	ARG	1	0.856	0.926	55.330	0.017	0.017	0.000	0.000	0.000	0.000
134	A	166	LEU	0	-0.001	0.007	55.578	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	167	ASP	-1	-0.814	-0.885	54.076	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	168	LYS	1	0.765	0.856	52.128	0.017	0.017	0.000	0.000	0.000	0.000
137	A	169	ILE	0	-0.009	0.004	51.119	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	170	ARG	1	0.966	0.985	50.517	0.022	0.022	0.000	0.000	0.000	0.000
139	A	171	ARG	1	0.817	0.913	47.608	0.019	0.019	0.000	0.000	0.000	0.000
140	A	172	GLN	0	-0.005	-0.004	46.336	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	173	ASN	0	-0.058	-0.050	46.183	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	174	ARG	1	0.949	0.968	44.054	0.027	0.027	0.000	0.000	0.000	0.000
143	A	175	ILE	0	0.033	0.035	41.476	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	176	LYS	1	0.944	0.963	41.240	0.030	0.030	0.000	0.000	0.000	0.000
145	A	177	ALA	0	-0.006	0.010	41.759	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	178	GLU	-1	-0.934	-0.959	36.500	-0.048	-0.048	0.000	0.000	0.000	0.000
147	A	179	LEU	0	-0.021	-0.026	37.114	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	180	GLN	0	-0.052	-0.025	37.070	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	181	ALA	0	0.050	0.019	36.293	-0.003	-0.003	0.000	0.000	0.000	0.000
150	A	182	VAL	0	-0.091	-0.027	31.767	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	183	LEU	0	-0.082	-0.064	32.727	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	184	ASP	-1	-0.941	-0.941	33.528	-0.063	-0.063	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:PRO)