FMO DATABASE

FMODB ID: K9QJ3

Calculation Name: 3DMM-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMM

Chain ID: D

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1014787.645657
FMO2-HF: Nuclear repulsion	966092.826695
FMO2-HF: Total energy	-48694.818962
FMO2-MP2: Total energy	-48836.047276

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(D:1:LEU)

Summations of interaction energy for fragment #1(D:1:LEU)

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.
-14.403	-14.058	24.173	-5.91	-18.606	-0.05

Interaction energy analysis for fragmet #1(D:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.064 / q_NPA : -0.038

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	D	3	GLN	0	0.032	0.011	3.792	-1.191	0.102	-0.016	-0.385	-0.891	0.002
4	D	4	THR	0	-0.051	0.010	5.322	0.570	0.603	-0.001	-0.004	-0.028	0.000
5	D	5	PRO	0	0.027	0.003	9.036	0.000	0.000	0.000	0.000	0.000	0.000
6	D	6	SER	0	0.072	0.031	10.300	-0.081	-0.081	0.000	0.000	0.000	0.000
7	D	7	SER	0	-0.023	-0.008	11.247	0.006	0.006	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.021	-0.008	14.415	0.033	0.033	0.000	0.000	0.000	0.000
9	D	9	LEU	0	0.035	0.028	16.336	-0.012	-0.012	0.000	0.000	0.000	0.000
10	D	10	VAL	0	-0.026	-0.021	18.653	0.016	0.016	0.000	0.000	0.000	0.000
11	D	11	GLN	0	0.034	0.011	21.486	0.006	0.006	0.000	0.000	0.000	0.000
12	D	12	THR	0	0.039	-0.027	24.566	-0.017	-0.017	0.000	0.000	0.000	0.000
13	D	13	ASN	0	-0.081	-0.050	25.290	0.016	0.016	0.000	0.000	0.000	0.000
14	D	14	HIS	0	-0.054	0.000	23.506	0.022	0.022	0.000	0.000	0.000	0.000
15	D	15	THR	0	-0.015	-0.032	18.526	-0.006	-0.006	0.000	0.000	0.000	0.000
16	D	16	ALA	0	-0.005	0.020	16.459	0.004	0.004	0.000	0.000	0.000	0.000
17	D	17	LYS	1	0.933	0.971	13.983	0.301	0.301	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.020	0.013	9.100	0.012	0.012	0.000	0.000	0.000	0.000
19	D	19	SER	0	-0.040	-0.015	8.452	0.089	0.089	0.000	0.000	0.000	0.000
20	D	20	CYS	0	0.005	0.013	2.673	-2.388	-2.363	4.106	-1.097	-3.035	0.000
21	D	21	GLU	-1	-0.935	-0.945	4.364	1.195	1.449	-0.001	-0.033	-0.220	0.000
22	D	22	VAL	0	-0.011	-0.022	2.889	-0.722	1.479	0.242	-0.873	-1.570	-0.006
23	D	23	LYS	1	1.003	0.988	3.655	-6.890	-6.530	0.001	-0.058	-0.303	0.000
24	D	24	SER	0	-0.024	0.008	5.153	-0.719	-0.719	0.000	0.000	0.000	0.000
25	D	25	ILE	0	0.043	-0.005	7.166	0.252	0.252	0.000	0.000	0.000	0.000
26	D	26	SER	0	0.003	0.024	10.207	-0.137	-0.137	0.000	0.000	0.000	0.000
27	D	27	LYS	1	0.956	0.966	11.014	-0.105	-0.105	0.000	0.000	0.000	0.000
28	D	28	LEU	0	-0.011	0.035	10.968	0.018	0.018	0.000	0.000	0.000	0.000
29	D	29	THR	0	-0.054	-0.045	10.241	0.025	0.025	0.000	0.000	0.000	0.000
30	D	30	SER	0	-0.046	-0.038	9.065	-0.042	-0.042	0.000	0.000	0.000	0.000
31	D	31	ILE	0	0.005	0.035	3.926	-0.212	0.000	0.003	-0.031	-0.183	0.000
32	D	32	TYR	0	0.023	0.000	5.746	0.201	0.201	0.000	0.000	0.000	0.000
33	D	33	TRP	0	0.026	0.011	6.102	-0.515	-0.515	0.000	0.000	0.000	0.000
34	D	34	LEU	0	-0.012	-0.016	7.457	0.194	0.194	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.824	0.899	10.087	0.394	0.394	0.000	0.000	0.000	0.000
36	D	36	GLU	-1	-0.890	-0.948	12.677	-0.736	-0.736	0.000	0.000	0.000	0.000
37	D	37	ARG	1	0.844	0.917	14.232	0.432	0.432	0.000	0.000	0.000	0.000
38	D	38	GLN	0	-0.002	-0.017	17.902	0.057	0.057	0.000	0.000	0.000	0.000
39	D	39	ASP	-1	-0.898	-0.967	19.794	-0.315	-0.315	0.000	0.000	0.000	0.000
40	D	40	PRO	0	-0.025	0.017	23.461	0.015	0.015	0.000	0.000	0.000	0.000
41	D	41	LYS	1	0.842	0.921	26.179	0.240	0.240	0.000	0.000	0.000	0.000
42	D	42	ASP	-1	-0.910	-0.954	23.798	-0.284	-0.284	0.000	0.000	0.000	0.000
43	D	43	LYS	1	0.935	0.981	15.585	0.561	0.561	0.000	0.000	0.000	0.000
44	D	44	TYR	0	-0.055	-0.039	17.541	0.003	0.003	0.000	0.000	0.000	0.000
45	D	45	PHE	0	-0.011	-0.007	10.496	-0.029	-0.029	0.000	0.000	0.000	0.000
46	D	46	GLU	-1	-0.826	-0.899	14.113	-0.370	-0.370	0.000	0.000	0.000	0.000
47	D	47	PHE	0	-0.033	-0.012	11.611	-0.101	-0.101	0.000	0.000	0.000	0.000
48	D	48	LEU	0	-0.006	0.010	12.088	0.055	0.055	0.000	0.000	0.000	0.000
49	D	49	ALA	0	0.059	0.002	11.841	0.085	0.085	0.000	0.000	0.000	0.000
50	D	50	SER	0	-0.018	0.004	10.495	-0.112	-0.112	0.000	0.000	0.000	0.000
51	D	51	TRP	0	0.047	0.019	10.560	0.068	0.068	0.000	0.000	0.000	0.000
52	D	52	SER	0	-0.043	-0.021	11.269	0.000	0.000	0.000	0.000	0.000	0.000
53	D	53	SER	0	0.011	-0.008	13.894	0.003	0.003	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.033	-0.018	15.649	0.000	0.000	0.000	0.000	0.000	0.000
55	D	55	LYS	1	0.997	0.995	17.554	0.177	0.177	0.000	0.000	0.000	0.000
56	D	56	GLY	0	0.052	0.047	16.683	0.004	0.004	0.000	0.000	0.000	0.000
57	D	57	VAL	0	-0.020	-0.020	14.803	-0.030	-0.030	0.000	0.000	0.000	0.000
58	D	58	LEU	0	-0.031	-0.007	15.163	0.040	0.040	0.000	0.000	0.000	0.000
59	D	59	TYR	0	-0.029	-0.039	15.417	-0.046	-0.046	0.000	0.000	0.000	0.000
60	D	60	GLY	0	0.013	0.009	16.696	0.018	0.018	0.000	0.000	0.000	0.000
61	D	61	GLU	-1	-0.911	-0.976	17.502	-0.236	-0.236	0.000	0.000	0.000	0.000
62	D	62	SER	0	0.000	0.007	18.155	0.011	0.011	0.000	0.000	0.000	0.000
63	D	63	VAL	0	-0.056	-0.020	16.300	0.013	0.013	0.000	0.000	0.000	0.000
64	D	64	ASP	-1	-0.819	-0.915	19.616	-0.228	-0.228	0.000	0.000	0.000	0.000
65	D	65	LYS	1	0.947	0.980	22.298	0.205	0.205	0.000	0.000	0.000	0.000
66	D	66	LYS	1	0.865	0.943	20.918	0.348	0.348	0.000	0.000	0.000	0.000
67	D	67	ARG	1	0.938	0.962	21.617	0.223	0.223	0.000	0.000	0.000	0.000
68	D	68	ASN	0	-0.004	0.005	20.134	0.009	0.009	0.000	0.000	0.000	0.000
69	D	69	ILE	0	0.014	0.017	14.752	-0.033	-0.033	0.000	0.000	0.000	0.000
70	D	70	ILE	0	0.019	0.022	16.580	0.033	0.033	0.000	0.000	0.000	0.000
71	D	71	LEU	0	-0.024	-0.020	11.458	-0.048	-0.048	0.000	0.000	0.000	0.000
72	D	72	GLU	-1	-0.912	-0.958	13.238	-0.224	-0.224	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.033	0.017	12.404	-0.036	-0.036	0.000	0.000	0.000	0.000
74	D	74	SER	0	-0.025	-0.006	10.490	-0.004	-0.004	0.000	0.000	0.000	0.000
75	D	75	ASP	-1	-0.896	-0.948	10.419	-0.069	-0.069	0.000	0.000	0.000	0.000
76	D	76	SER	0	0.001	-0.013	11.319	0.108	0.108	0.000	0.000	0.000	0.000
77	D	77	ARG	1	0.886	0.906	8.186	-0.920	-0.920	0.000	0.000	0.000	0.000
78	D	78	ARG	1	0.938	0.999	6.901	0.053	0.053	0.000	0.000	0.000	0.000
79	D	79	PRO	0	-0.014	0.008	5.970	-0.018	-0.018	0.000	0.000	0.000	0.000
80	D	80	PHE	0	0.039	-0.012	8.570	-0.200	-0.200	0.000	0.000	0.000	0.000
81	D	81	LEU	0	0.002	0.015	10.369	0.049	0.049	0.000	0.000	0.000	0.000
82	D	82	SER	0	0.009	-0.015	11.992	0.003	0.003	0.000	0.000	0.000	0.000
83	D	83	ILE	0	-0.002	-0.002	14.517	0.021	0.021	0.000	0.000	0.000	0.000
84	D	84	MET	0	-0.005	-0.007	17.709	0.025	0.025	0.000	0.000	0.000	0.000
85	D	85	ASN	0	-0.030	-0.014	21.399	0.005	0.005	0.000	0.000	0.000	0.000
86	D	86	VAL	0	0.019	0.037	19.913	0.004	0.004	0.000	0.000	0.000	0.000
87	D	87	LYS	1	0.936	0.962	22.532	0.248	0.248	0.000	0.000	0.000	0.000
88	D	88	PRO	0	0.094	0.047	22.852	-0.032	-0.032	0.000	0.000	0.000	0.000
89	D	89	GLU	-1	-0.851	-0.909	23.305	-0.282	-0.282	0.000	0.000	0.000	0.000
90	D	90	ASP	-1	-0.906	-0.944	19.194	-0.384	-0.384	0.000	0.000	0.000	0.000
91	D	91	SER	0	-0.055	-0.048	18.325	-0.061	-0.061	0.000	0.000	0.000	0.000
92	D	92	ASP	-1	-0.737	-0.863	16.063	-0.482	-0.482	0.000	0.000	0.000	0.000
93	D	93	PHE	0	-0.014	-0.003	11.751	-0.004	-0.004	0.000	0.000	0.000	0.000
94	D	94	TYR	0	-0.030	-0.015	10.576	-0.011	-0.011	0.000	0.000	0.000	0.000
95	D	95	PHE	0	0.020	0.011	6.162	-0.194	-0.194	0.000	0.000	0.000	0.000
96	D	97	ALA	0	-0.009	-0.022	2.870	-1.772	-0.876	0.385	-0.474	-0.808	-0.003
97	D	98	THR	0	0.023	0.003	2.438	-2.018	-0.240	1.162	-0.856	-2.084	-0.002
98	D	99	VAL	0	-0.001	-0.005	3.748	0.000	0.067	0.007	0.021	-0.095	0.000
99	D	100	GLY	0	0.016	0.015	7.409	0.119	0.119	0.000	0.000	0.000	0.000
100	D	101	SER	0	-0.029	-0.004	9.155	-0.076	-0.076	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.053	0.015	12.537	0.064	0.064	0.000	0.000	0.000	0.000
102	D	103	LYS	1	0.930	0.968	6.502	-1.080	-1.080	0.000	0.000	0.000	0.000
103	D	104	MET	0	0.030	0.019	6.901	0.044	0.044	0.000	0.000	0.000	0.000
104	D	105	VAL	0	-0.065	-0.039	2.060	1.591	-1.629	8.195	-1.425	-3.550	-0.001
105	D	106	PHE	0	0.058	0.025	2.655	-2.143	-0.636	1.131	-0.842	-1.795	-0.012
106	D	107	GLY	0	0.028	-0.011	2.007	-3.754	-4.168	8.788	-4.987	-3.387	-0.024
107	D	108	THR	0	-0.033	-0.024	2.877	5.445	0.798	0.171	5.134	-0.657	-0.004
108	D	109	GLY	0	-0.003	0.010	5.574	0.738	0.738	0.000	0.000	0.000	0.000
109	D	110	THR	0	-0.060	-0.054	7.612	0.028	0.028	0.000	0.000	0.000	0.000
110	D	111	LYS	1	0.917	0.962	10.305	0.578	0.578	0.000	0.000	0.000	0.000
111	D	112	LEU	0	-0.012	-0.002	13.895	0.050	0.050	0.000	0.000	0.000	0.000
112	D	113	THR	0	-0.041	-0.026	16.143	0.025	0.025	0.000	0.000	0.000	0.000
113	D	114	VAL	0	0.003	0.019	19.882	0.009	0.009	0.000	0.000	0.000	0.000
114	D	115	VAL	0	-0.002	0.007	22.458	0.009	0.009	0.000	0.000	0.000	0.000
115	D	116	ASP	-1	-0.814	-0.891	26.014	-0.201	-0.201	0.000	0.000	0.000	0.000
116	D	117	VAL	0	-0.037	-0.026	29.231	0.009	0.009	0.000	0.000	0.000	0.000
117	D	118	LEU	0	-0.004	-0.018	25.932	-0.014	-0.014	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.026	-0.002	28.972	0.008	0.008	0.000	0.000	0.000	0.000
119	D	120	THR	0	0.032	0.022	29.758	-0.005	-0.005	0.000	0.000	0.000	0.000
120	D	121	THR	0	-0.015	-0.029	31.281	0.002	0.002	0.000	0.000	0.000	0.000
121	D	122	ALA	0	0.013	0.030	34.012	0.000	0.000	0.000	0.000	0.000	0.000
122	D	123	PRO	0	-0.007	0.000	37.293	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1:LEU)