FMO DATABASE

FMODB ID: 4J81N

Calculation Name: 3RRU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RRU

Chain ID: A

ChEMBL ID:

UniProt ID: O75674

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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1352413.557703
FMO2-HF: Nuclear repulsion	1296343.937978
FMO2-HF: Total energy	-56069.619725
FMO2-MP2: Total energy	-56233.467752

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:9:ASP)

Summations of interaction energy for fragment #1(A:9:ASP)

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.
-227.899	-227.217	25.688	-13.64	-12.729	0.166

Interaction energy analysis for fragmet #1(A:9:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.784 / q_NPA : -0.908

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	11	TYR	0	-0.040	-0.025	1.935	-22.589	-21.576	7.771	-4.080	-4.704	0.045
4	A	12	ALA	0	0.004	0.011	2.299	-10.590	-9.416	0.837	-0.595	-1.415	0.002
5	A	13	THR	0	0.039	0.025	4.226	-8.813	-8.563	0.001	-0.063	-0.188	0.000
6	A	14	SER	0	0.039	0.016	7.191	1.073	1.073	0.000	0.000	0.000	0.000
7	A	15	VAL	0	0.055	0.021	10.592	0.207	0.207	0.000	0.000	0.000	0.000
8	A	16	GLY	0	0.024	0.016	6.861	-0.346	-0.346	0.000	0.000	0.000	0.000
9	A	17	HIS	0	0.024	0.014	6.787	-2.246	-2.246	0.000	0.000	0.000	0.000
10	A	18	LEU	0	0.004	0.002	8.110	-1.239	-1.239	0.000	0.000	0.000	0.000
11	A	19	ILE	0	0.028	0.019	9.359	-1.524	-1.524	0.000	0.000	0.000	0.000
12	A	20	GLU	-1	-0.933	-0.956	6.547	39.716	39.716	0.000	0.000	0.000	0.000
13	A	21	LYS	1	0.855	0.911	8.779	-30.570	-30.570	0.000	0.000	0.000	0.000
14	A	22	ALA	0	0.004	0.011	11.866	-1.679	-1.679	0.000	0.000	0.000	0.000
15	A	23	THR	0	-0.024	-0.010	11.748	-0.653	-0.653	0.000	0.000	0.000	0.000
16	A	24	PHE	0	-0.032	-0.016	10.616	0.333	0.333	0.000	0.000	0.000	0.000
17	A	25	ALA	0	0.016	0.003	13.382	-1.612	-1.612	0.000	0.000	0.000	0.000
18	A	26	GLY	0	-0.079	-0.023	15.602	-1.187	-1.187	0.000	0.000	0.000	0.000
19	A	27	VAL	0	0.020	0.016	16.524	-1.125	-1.125	0.000	0.000	0.000	0.000
20	A	28	GLN	0	0.006	0.004	19.241	0.132	0.132	0.000	0.000	0.000	0.000
21	A	29	THR	0	0.008	-0.022	21.740	-0.619	-0.619	0.000	0.000	0.000	0.000
22	A	30	GLU	-1	-0.823	-0.882	20.623	14.991	14.991	0.000	0.000	0.000	0.000
23	A	31	ASP	-1	-0.865	-0.919	19.508	14.160	14.160	0.000	0.000	0.000	0.000
24	A	32	TRP	0	0.036	-0.022	20.603	0.682	0.682	0.000	0.000	0.000	0.000
25	A	33	GLY	0	0.022	0.032	22.848	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	34	GLN	0	0.022	-0.003	15.537	-0.222	-0.222	0.000	0.000	0.000	0.000
27	A	35	PHE	0	-0.032	-0.030	17.301	0.761	0.761	0.000	0.000	0.000	0.000
28	A	36	MET	0	0.041	0.036	19.007	0.424	0.424	0.000	0.000	0.000	0.000
29	A	37	HIS	0	0.035	0.025	17.476	-0.334	-0.334	0.000	0.000	0.000	0.000
30	A	38	ILE	0	-0.053	-0.034	13.985	0.711	0.711	0.000	0.000	0.000	0.000
31	A	39	CYS	0	-0.034	-0.027	16.863	0.546	0.546	0.000	0.000	0.000	0.000
32	A	40	ASP	-1	-0.842	-0.917	19.181	13.488	13.488	0.000	0.000	0.000	0.000
33	A	41	ILE	0	-0.050	-0.027	14.898	0.057	0.057	0.000	0.000	0.000	0.000
34	A	42	ILE	0	-0.102	-0.051	14.485	0.530	0.530	0.000	0.000	0.000	0.000
35	A	43	ASN	0	-0.010	-0.028	17.297	0.073	0.073	0.000	0.000	0.000	0.000
36	A	44	THR	0	-0.044	-0.002	19.571	-0.381	-0.381	0.000	0.000	0.000	0.000
37	A	45	THR	0	-0.055	-0.023	13.840	-0.116	-0.116	0.000	0.000	0.000	0.000
38	A	46	GLN	0	0.029	0.002	16.637	0.199	0.199	0.000	0.000	0.000	0.000
39	A	47	ASP	-1	-0.802	-0.901	12.175	20.196	20.196	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.010	0.021	12.635	1.623	1.623	0.000	0.000	0.000	0.000
41	A	49	PRO	0	0.043	0.006	13.432	1.561	1.561	0.000	0.000	0.000	0.000
42	A	50	LYS	1	0.858	0.921	10.825	-20.370	-20.370	0.000	0.000	0.000	0.000
43	A	51	ASP	-1	-0.888	-0.961	8.688	30.526	30.526	0.000	0.000	0.000	0.000
44	A	52	ALA	0	0.014	0.021	8.993	3.525	3.525	0.000	0.000	0.000	0.000
45	A	53	VAL	0	0.000	-0.003	10.575	2.064	2.064	0.000	0.000	0.000	0.000
46	A	54	LYS	1	0.899	0.962	6.508	-30.272	-30.272	0.000	0.000	0.000	0.000
47	A	55	ALA	0	0.012	0.005	6.511	4.551	4.551	0.000	0.000	0.000	0.000
48	A	56	LEU	0	0.019	0.001	7.464	0.472	0.472	0.000	0.000	0.000	0.000
49	A	57	LYS	1	0.869	0.948	9.664	-25.275	-25.275	0.000	0.000	0.000	0.000
50	A	58	LYS	1	0.767	0.894	1.786	-139.555	-141.310	17.079	-8.902	-6.422	0.119
51	A	59	ARG	1	0.817	0.911	8.401	-31.259	-31.259	0.000	0.000	0.000	0.000
52	A	60	ILE	0	0.025	0.020	10.046	-2.351	-2.351	0.000	0.000	0.000	0.000
53	A	61	SER	0	0.005	-0.014	10.919	-2.453	-2.453	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.837	0.917	11.719	-24.913	-24.913	0.000	0.000	0.000	0.000
55	A	63	ASN	0	0.015	0.013	12.957	-1.283	-1.283	0.000	0.000	0.000	0.000
56	A	64	TYR	0	0.014	-0.013	14.966	-1.490	-1.490	0.000	0.000	0.000	0.000
57	A	65	ASN	0	-0.002	0.013	16.203	-1.887	-1.887	0.000	0.000	0.000	0.000
58	A	66	HIS	0	0.075	0.023	18.182	0.688	0.688	0.000	0.000	0.000	0.000
59	A	67	LYS	1	0.942	0.970	19.201	-13.584	-13.584	0.000	0.000	0.000	0.000
60	A	68	GLU	-1	-0.768	-0.853	12.913	26.237	26.237	0.000	0.000	0.000	0.000
61	A	69	ILE	0	-0.002	0.025	15.981	0.641	0.641	0.000	0.000	0.000	0.000
62	A	70	GLN	0	0.028	0.022	17.522	-0.197	-0.197	0.000	0.000	0.000	0.000
63	A	71	LEU	0	0.006	0.006	16.953	-0.345	-0.345	0.000	0.000	0.000	0.000
64	A	72	THR	0	0.010	-0.037	13.312	0.652	0.652	0.000	0.000	0.000	0.000
65	A	73	LEU	0	-0.057	-0.023	16.042	-0.193	-0.193	0.000	0.000	0.000	0.000
66	A	74	SER	0	-0.043	-0.052	19.106	-0.583	-0.583	0.000	0.000	0.000	0.000
67	A	75	LEU	0	0.014	0.029	13.928	-0.279	-0.279	0.000	0.000	0.000	0.000
68	A	76	ILE	0	-0.038	-0.028	15.475	0.018	0.018	0.000	0.000	0.000	0.000
69	A	77	ASP	-1	-0.932	-0.977	18.305	12.729	12.729	0.000	0.000	0.000	0.000
70	A	78	MET	0	0.015	0.028	20.302	-0.664	-0.664	0.000	0.000	0.000	0.000
71	A	79	CYS	0	0.019	0.005	17.510	-0.184	-0.184	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.077	-0.043	20.091	-0.336	-0.336	0.000	0.000	0.000	0.000
73	A	81	GLN	0	-0.062	-0.032	22.360	-0.892	-0.892	0.000	0.000	0.000	0.000
74	A	82	ASN	0	-0.006	0.005	22.723	-0.814	-0.814	0.000	0.000	0.000	0.000
75	A	83	CYS	0	-0.035	0.005	20.420	0.248	0.248	0.000	0.000	0.000	0.000
76	A	84	GLY	0	0.037	0.025	22.754	-0.273	-0.273	0.000	0.000	0.000	0.000
77	A	85	PRO	0	0.110	0.036	23.011	0.603	0.603	0.000	0.000	0.000	0.000
78	A	86	SER	0	-0.047	-0.001	19.933	0.368	0.368	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.044	0.020	15.399	1.013	1.013	0.000	0.000	0.000	0.000
80	A	88	GLN	0	0.018	-0.001	19.163	0.366	0.366	0.000	0.000	0.000	0.000
81	A	89	SER	0	0.004	-0.028	21.060	-0.276	-0.276	0.000	0.000	0.000	0.000
82	A	90	LEU	0	-0.093	-0.051	14.964	0.143	0.143	0.000	0.000	0.000	0.000
83	A	91	ILE	0	-0.017	0.006	16.147	0.813	0.813	0.000	0.000	0.000	0.000
84	A	92	VAL	0	0.007	0.003	18.422	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	93	LYS	1	0.970	1.017	17.467	-16.008	-16.008	0.000	0.000	0.000	0.000
86	A	94	LYS	1	0.900	0.920	19.145	-12.770	-12.770	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.959	-0.998	15.028	19.483	19.483	0.000	0.000	0.000	0.000
88	A	96	PHE	0	-0.028	-0.013	13.272	1.450	1.450	0.000	0.000	0.000	0.000
89	A	97	VAL	0	0.072	0.026	16.509	0.139	0.139	0.000	0.000	0.000	0.000
90	A	98	LYS	1	0.870	0.931	19.863	-14.236	-14.236	0.000	0.000	0.000	0.000
91	A	99	GLU	-1	-0.873	-0.939	16.462	15.494	15.494	0.000	0.000	0.000	0.000
92	A	100	ASN	0	-0.037	-0.037	13.122	1.457	1.457	0.000	0.000	0.000	0.000
93	A	101	LEU	0	0.039	0.037	16.730	-0.254	-0.254	0.000	0.000	0.000	0.000
94	A	102	VAL	0	0.038	0.010	19.351	-0.368	-0.368	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.881	0.965	18.599	-16.707	-16.707	0.000	0.000	0.000	0.000
96	A	104	LEU	0	0.010	0.001	16.892	-0.505	-0.505	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.011	0.006	20.769	-0.383	-0.383	0.000	0.000	0.000	0.000
98	A	106	ASN	0	-0.068	-0.027	22.949	-0.612	-0.612	0.000	0.000	0.000	0.000
99	A	107	PRO	0	0.107	0.029	24.566	0.313	0.313	0.000	0.000	0.000	0.000
100	A	108	ARG	1	0.924	0.987	20.801	-14.860	-14.860	0.000	0.000	0.000	0.000
101	A	109	TYR	0	-0.025	-0.015	18.023	0.193	0.193	0.000	0.000	0.000	0.000
102	A	110	ASN	0	-0.067	-0.042	22.364	-0.165	-0.165	0.000	0.000	0.000	0.000
103	A	111	LEU	0	0.030	0.041	21.151	-0.179	-0.179	0.000	0.000	0.000	0.000
104	A	112	PRO	0	0.029	0.011	24.786	-0.415	-0.415	0.000	0.000	0.000	0.000
105	A	113	LEU	0	0.079	0.023	27.275	0.291	0.291	0.000	0.000	0.000	0.000
106	A	114	ASP	-1	-0.905	-0.925	27.818	11.033	11.033	0.000	0.000	0.000	0.000
107	A	115	ILE	0	0.017	-0.016	21.970	0.141	0.141	0.000	0.000	0.000	0.000
108	A	116	GLN	0	-0.043	-0.018	24.825	0.152	0.152	0.000	0.000	0.000	0.000
109	A	117	ASN	0	0.013	-0.020	26.669	-0.038	-0.038	0.000	0.000	0.000	0.000
110	A	118	ARG	1	0.876	0.947	22.421	-14.124	-14.124	0.000	0.000	0.000	0.000
111	A	119	ILE	0	0.007	0.009	20.753	0.214	0.214	0.000	0.000	0.000	0.000
112	A	120	LEU	0	-0.008	-0.007	24.508	0.021	0.021	0.000	0.000	0.000	0.000
113	A	121	ASN	0	0.029	0.007	27.825	-0.392	-0.392	0.000	0.000	0.000	0.000
114	A	122	PHE	0	-0.008	0.027	20.663	-0.128	-0.128	0.000	0.000	0.000	0.000
115	A	123	ILE	0	-0.012	0.013	23.141	-0.152	-0.152	0.000	0.000	0.000	0.000
116	A	124	LYS	1	0.968	0.981	26.609	-9.758	-9.758	0.000	0.000	0.000	0.000
117	A	125	THR	0	-0.018	-0.031	27.905	-0.433	-0.433	0.000	0.000	0.000	0.000
118	A	126	TRP	0	0.011	-0.018	19.784	0.147	0.147	0.000	0.000	0.000	0.000
119	A	127	SER	0	-0.042	-0.024	27.216	-0.178	-0.178	0.000	0.000	0.000	0.000
120	A	128	GLN	0	-0.060	-0.021	29.555	-0.328	-0.328	0.000	0.000	0.000	0.000
121	A	129	GLY	0	-0.020	0.010	29.710	-0.292	-0.292	0.000	0.000	0.000	0.000
122	A	130	PHE	0	-0.007	-0.012	25.290	0.105	0.105	0.000	0.000	0.000	0.000
123	A	131	PRO	0	0.011	0.011	29.676	-0.194	-0.194	0.000	0.000	0.000	0.000
124	A	132	GLY	0	0.012	0.000	29.903	0.286	0.286	0.000	0.000	0.000	0.000
125	A	133	GLY	0	-0.033	-0.031	28.216	-0.056	-0.056	0.000	0.000	0.000	0.000
126	A	134	VAL	0	-0.012	-0.010	24.752	-0.052	-0.052	0.000	0.000	0.000	0.000
127	A	135	ASP	-1	-0.794	-0.847	25.756	10.855	10.855	0.000	0.000	0.000	0.000
128	A	136	VAL	0	-0.009	-0.017	25.633	0.538	0.538	0.000	0.000	0.000	0.000
129	A	137	SER	0	0.008	-0.028	27.336	-0.203	-0.203	0.000	0.000	0.000	0.000
130	A	138	GLU	-1	-0.849	-0.909	22.430	13.902	13.902	0.000	0.000	0.000	0.000
131	A	139	VAL	0	0.013	0.004	23.989	-0.078	-0.078	0.000	0.000	0.000	0.000
132	A	140	LYS	1	0.960	0.992	25.647	-9.923	-9.923	0.000	0.000	0.000	0.000
133	A	141	GLU	-1	-0.827	-0.917	28.744	9.731	9.731	0.000	0.000	0.000	0.000
134	A	142	VAL	0	-0.082	-0.045	23.908	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	143	TYR	0	0.016	-0.002	27.166	-0.074	-0.074	0.000	0.000	0.000	0.000
136	A	144	LEU	0	0.042	0.017	29.490	-0.237	-0.237	0.000	0.000	0.000	0.000
137	A	145	ASP	-1	-0.852	-0.903	29.599	10.288	10.288	0.000	0.000	0.000	0.000
138	A	146	LEU	0	-0.068	-0.038	26.401	-0.085	-0.085	0.000	0.000	0.000	0.000
139	A	147	VAL	0	-0.047	-0.007	30.880	-0.164	-0.164	0.000	0.000	0.000	0.000
140	A	148	LYS	1	0.794	0.899	33.254	-9.988	-9.988	0.000	0.000	0.000	0.000
141	A	149	LYS	1	0.861	0.926	28.975	-11.154	-11.154	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:9:ASP)