FMO DATABASE

FMODB ID: YV8J2

Calculation Name: 3UID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UID

Chain ID: A

ChEMBL ID:

UniProt ID: A0R731

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	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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1576484.336395
FMO2-HF: Nuclear repulsion	1514341.391402
FMO2-HF: Total energy	-62142.944993
FMO2-MP2: Total energy	-62327.156933

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:2:PRO)

Summations of interaction energy for fragment #1(A:2: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.
-18.921	-12.225	15.027	-9.741	-11.985	-0.071

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.004

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	4	THR	0	-0.086	-0.057	3.326	-2.187	0.711	0.036	-1.414	-1.520	0.004
4	A	5	ASP	-1	-0.944	-0.976	5.711	0.201	0.201	0.000	0.000	0.000	0.000
5	A	6	VAL	0	-0.024	-0.005	8.921	-0.093	-0.093	0.000	0.000	0.000	0.000
6	A	7	LYS	1	0.876	0.931	11.250	-0.043	-0.043	0.000	0.000	0.000	0.000
7	A	8	HIS	0	0.028	0.014	14.936	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.834	-0.880	18.129	0.053	0.053	0.000	0.000	0.000	0.000
9	A	10	LEU	0	0.019	-0.015	20.843	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.948	-0.969	24.107	0.026	0.026	0.000	0.000	0.000	0.000
11	A	12	THR	0	-0.081	-0.058	22.674	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	13	LEU	0	-0.027	0.007	23.796	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	14	THR	0	-0.002	-0.013	19.255	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.006	0.002	14.676	0.008	0.008	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.012	-0.009	13.161	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.011	-0.002	8.082	0.008	0.008	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.002	-0.006	8.538	-0.023	-0.023	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.023	0.013	4.175	-0.539	-0.344	0.000	-0.064	-0.131	0.000
19	A	20	GLU	-1	-0.780	-0.869	3.528	-1.058	-0.188	0.014	-0.320	-0.564	0.002
20	A	21	PHE	0	0.024	0.016	2.838	3.698	4.097	2.828	-1.058	-2.169	-0.007
21	A	22	ALA	0	-0.013	-0.010	4.752	0.043	0.126	-0.001	-0.006	-0.077	0.000
22	A	23	ALA	0	-0.009	-0.015	6.368	-0.132	-0.132	0.000	0.000	0.000	0.000
23	A	24	PRO	0	0.022	0.017	9.624	0.081	0.081	0.000	0.000	0.000	0.000
24	A	25	VAL	0	0.107	0.063	11.961	-0.061	-0.061	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.012	-0.015	13.210	-0.042	-0.042	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.838	0.913	11.367	0.339	0.339	0.000	0.000	0.000	0.000
27	A	28	ILE	0	0.042	0.020	7.718	-0.070	-0.070	0.000	0.000	0.000	0.000
28	A	29	TRP	0	0.011	0.016	11.103	-0.035	-0.035	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.012	-0.023	14.494	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	31	ILE	0	-0.060	-0.014	9.865	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	32	TYR	0	0.052	0.021	9.338	0.015	0.015	0.000	0.000	0.000	0.000
32	A	33	ALA	0	0.003	0.013	15.392	0.023	0.023	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.811	-0.883	17.415	-0.189	-0.189	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.032	0.014	17.701	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.806	0.860	19.032	0.171	0.171	0.000	0.000	0.000	0.000
36	A	37	GLN	0	-0.045	-0.029	14.230	-0.068	-0.068	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.028	0.035	13.908	-0.065	-0.065	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.775	-0.850	14.863	-0.232	-0.232	0.000	0.000	0.000	0.000
39	A	40	LYS	1	0.848	0.931	13.308	0.453	0.453	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.059	-0.037	9.956	-0.033	-0.033	0.000	0.000	0.000	0.000
41	A	42	TRP	0	0.049	0.007	11.151	-0.047	-0.047	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.025	0.032	13.586	0.032	0.032	0.000	0.000	0.000	0.000
43	A	44	PRO	0	-0.058	-0.020	12.311	0.005	0.005	0.000	0.000	0.000	0.000
44	A	45	PRO	0	-0.026	-0.034	14.387	0.038	0.038	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.071	-0.050	15.958	0.017	0.017	0.000	0.000	0.000	0.000
46	A	47	HIS	0	-0.026	0.013	15.438	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	48	PRO	0	0.000	0.009	16.834	-0.027	-0.027	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.046	0.040	17.238	0.008	0.008	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.082	-0.042	19.160	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.006	-0.006	18.794	0.001	0.001	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.066	-0.033	21.726	0.005	0.005	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.891	-0.915	25.449	-0.094	-0.094	0.000	0.000	0.000	0.000
53	A	54	HIS	0	-0.044	-0.057	19.174	0.002	0.002	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.910	-0.943	24.224	-0.076	-0.076	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.003	0.013	18.972	0.005	0.005	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.922	0.939	23.157	0.067	0.067	0.000	0.000	0.000	0.000
57	A	58	PRO	0	-0.017	-0.010	25.968	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	GLY	0	-0.033	-0.015	27.679	0.003	0.003	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.019	0.033	27.161	0.001	0.001	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.815	0.877	26.036	0.073	0.073	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.019	-0.005	20.270	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	63	THR	0	-0.006	-0.008	23.607	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.031	-0.025	19.607	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.033	0.004	21.978	0.011	0.011	0.000	0.000	0.000	0.000
65	A	66	MET	0	0.001	0.002	14.572	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	67	THR	0	-0.046	-0.016	18.351	0.029	0.029	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.052	0.018	17.694	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	69	PRO	0	0.052	0.025	16.284	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	70	ASH	0	-0.104	-0.104	18.066	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	71	GLY	0	-0.019	-0.015	20.752	0.009	0.009	0.000	0.000	0.000	0.000
71	A	72	GLU	-1	-0.908	-0.905	22.328	-0.086	-0.086	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.799	0.892	22.367	0.104	0.104	0.000	0.000	0.000	0.000
73	A	74	TYR	0	-0.011	-0.004	17.563	0.007	0.007	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.023	0.003	22.923	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.046	0.031	22.372	0.006	0.006	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.041	-0.026	23.369	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.015	-0.007	15.703	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.841	-0.916	23.205	-0.061	-0.061	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.008	-0.003	21.678	0.003	0.003	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.014	-0.016	24.474	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.012	-0.008	23.926	0.008	0.008	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.047	-0.029	21.516	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.970	-0.974	21.346	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.898	-0.916	19.666	-0.084	-0.084	0.000	0.000	0.000	0.000
85	A	86	PRO	0	-0.075	-0.050	16.692	0.007	0.007	0.000	0.000	0.000	0.000
86	A	87	HIS	0	0.028	-0.022	16.171	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.022	-0.030	16.490	0.012	0.012	0.000	0.000	0.000	0.000
88	A	89	PHE	0	-0.019	-0.006	15.240	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	90	SER	0	0.006	0.004	18.821	0.004	0.004	0.000	0.000	0.000	0.000
90	A	91	PHE	0	-0.019	-0.008	16.884	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	LEU	0	0.008	0.007	22.298	0.004	0.004	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.841	-0.921	20.444	-0.143	-0.143	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.023	0.020	22.760	0.010	0.010	0.000	0.000	0.000	0.000
94	A	95	PHE	0	0.033	0.018	20.588	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.027	-0.024	25.184	0.009	0.009	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.825	-0.919	27.199	-0.075	-0.075	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.866	-0.923	28.581	-0.107	-0.107	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.989	-0.991	29.914	-0.071	-0.071	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.069	-0.040	25.165	0.001	0.001	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.042	-0.015	29.687	0.005	0.005	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.004	-0.010	29.851	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.003	0.003	28.335	0.003	0.003	0.000	0.000	0.000	0.000
103	A	104	THR	0	-0.031	-0.013	27.248	0.001	0.001	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.939	-0.969	30.453	-0.044	-0.044	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.014	0.002	25.140	0.004	0.004	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.051	-0.019	28.077	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.000	-0.008	25.708	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.009	0.022	21.367	0.004	0.004	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.051	-0.039	23.113	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	111	ASN	0	0.004	0.000	18.039	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	112	VAL	0	-0.026	-0.010	18.308	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	TYR	0	0.015	0.020	13.782	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	114	THR	0	0.006	0.016	14.081	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.034	-0.016	10.481	0.023	0.023	0.000	0.000	0.000	0.000
115	A	116	THR	0	0.007	-0.006	12.324	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.861	-0.929	12.249	0.150	0.150	0.000	0.000	0.000	0.000
117	A	118	HIS	0	-0.034	-0.024	9.753	-0.034	-0.034	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.890	-0.938	9.989	0.558	0.558	0.000	0.000	0.000	0.000
119	A	120	GLY	0	-0.092	-0.038	11.658	-0.014	-0.014	0.000	0.000	0.000	0.000
120	A	121	GLY	0	-0.019	-0.004	8.708	-0.074	-0.074	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.018	-0.031	7.965	-0.101	-0.101	0.000	0.000	0.000	0.000
122	A	123	ARG	1	0.816	0.903	7.465	-0.362	-0.362	0.000	0.000	0.000	0.000
123	A	124	ALA	0	-0.030	-0.017	7.729	-0.200	-0.200	0.000	0.000	0.000	0.000
124	A	125	THR	0	0.001	-0.001	9.211	0.062	0.062	0.000	0.000	0.000	0.000
125	A	126	TYR	0	-0.022	-0.028	7.711	-0.044	-0.044	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.021	0.011	13.130	0.002	0.002	0.000	0.000	0.000	0.000
127	A	128	GLY	0	0.066	0.044	16.415	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	129	THR	0	-0.030	-0.024	18.448	0.015	0.015	0.000	0.000	0.000	0.000
129	A	130	TYR	0	0.008	-0.008	18.632	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.004	0.000	24.174	0.006	0.006	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.055	-0.072	27.065	0.003	0.003	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.050	0.030	26.209	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.855	-0.906	26.149	-0.022	-0.022	0.000	0.000	0.000	0.000
134	A	135	ALA	0	0.014	0.010	26.271	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	136	LEU	0	-0.030	-0.011	19.606	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	137	GLN	0	-0.079	-0.050	21.917	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	138	GLN	0	0.031	0.020	23.128	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	VAL	0	0.025	-0.002	19.037	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.056	-0.041	17.205	-0.015	-0.015	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.899	-0.936	19.003	-0.053	-0.053	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.094	-0.031	20.680	0.001	0.001	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.048	0.036	17.031	-0.011	-0.011	0.000	0.000	0.000	0.000
143	A	144	VAL	0	-0.030	-0.013	15.014	-0.033	-0.033	0.000	0.000	0.000	0.000
144	A	145	ILE	0	0.030	0.008	11.115	-0.042	-0.042	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.916	-0.947	10.602	-0.218	-0.218	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.035	0.021	10.646	-0.072	-0.072	0.000	0.000	0.000	0.000
147	A	148	ALA	0	0.000	-0.003	10.088	-0.081	-0.081	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.021	-0.035	6.406	-0.173	-0.173	0.000	0.000	0.000	0.000
149	A	150	SER	0	-0.044	-0.013	5.895	-0.320	-0.320	0.000	0.000	0.000	0.000
150	A	151	ALA	0	0.047	0.029	7.679	-0.160	-0.160	0.000	0.000	0.000	0.000
151	A	152	ILE	0	-0.008	0.000	2.455	-0.558	-0.171	0.711	-0.402	-0.697	0.001
152	A	153	ASN	0	0.017	0.004	3.601	-1.948	-1.164	0.012	-0.197	-0.599	-0.001
153	A	154	GLN	0	-0.050	-0.016	4.598	0.143	0.176	-0.001	-0.005	-0.028	0.000
154	A	155	ILE	0	0.001	-0.005	5.679	0.232	0.232	0.000	0.000	0.000	0.000
155	A	156	ASP	-1	-0.804	-0.911	1.940	-16.665	-15.684	11.429	-6.259	-6.151	-0.070
156	A	157	ALA	0	-0.074	-0.037	4.761	0.741	0.807	-0.001	-0.016	-0.049	0.000
157	A	158	LEU	0	-0.049	-0.021	8.038	0.271	0.271	0.000	0.000	0.000	0.000
158	A	159	LEU	0	-0.059	-0.017	5.718	0.246	0.246	0.000	0.000	0.000	0.000
159	A	160	THR	0	-0.010	0.004	8.235	0.195	0.195	0.000	0.000	0.000	0.000
160	A	161	ALA	0	-0.015	-0.008	10.511	-0.011	-0.011	0.000	0.000	0.000	0.000
161	A	162	THR	0	-0.084	-0.036	12.110	0.051	0.051	0.000	0.000	0.000	0.000
162	A	163	HIS	0	0.049	0.028	11.604	-0.060	-0.060	0.000	0.000	0.000	0.000
163	A	164	HIS	0	-0.032	-0.017	8.512	0.114	0.114	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)