FMO DATABASE

FMODB ID: 49G5N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1014977.431369
FMO2-HF: Nuclear repulsion	966281.440335
FMO2-HF: Total energy	-48695.991035
FMO2-MP2: Total energy	-48837.064658

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.
-19.155	-10.09	13.94	-6.276	-16.731	-0.047

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 : -0.056 / q_NPA : -0.035

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

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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	0.021	-0.023	3.792	-1.680	-0.223	-0.018	-0.476	-0.963	0.003
4	D	4	THR	0	-0.053	0.006	5.445	0.586	0.586	0.000	0.000	0.000	0.000
5	D	5	PRO	0	0.046	0.015	9.156	-0.021	-0.021	0.000	0.000	0.000	0.000
6	D	6	SER	0	0.079	0.033	10.425	-0.086	-0.086	0.000	0.000	0.000	0.000
7	D	7	SER	0	-0.045	-0.021	11.370	0.000	0.000	0.000	0.000	0.000	0.000
8	D	8	LEU	0	-0.021	-0.003	14.442	0.027	0.027	0.000	0.000	0.000	0.000
9	D	9	LEU	0	0.029	0.027	16.450	-0.013	-0.013	0.000	0.000	0.000	0.000
10	D	10	VAL	0	-0.018	-0.022	18.956	0.014	0.014	0.000	0.000	0.000	0.000
11	D	11	GLN	0	0.032	0.014	21.588	0.004	0.004	0.000	0.000	0.000	0.000
12	D	12	THR	0	0.020	-0.035	24.657	-0.015	-0.015	0.000	0.000	0.000	0.000
13	D	13	ASN	0	-0.082	-0.056	25.421	0.014	0.014	0.000	0.000	0.000	0.000
14	D	14	HIS	0	-0.039	0.006	23.674	0.018	0.018	0.000	0.000	0.000	0.000
15	D	15	THR	0	-0.015	-0.030	18.638	-0.006	-0.006	0.000	0.000	0.000	0.000
16	D	16	ALA	0	-0.002	0.019	16.620	0.006	0.006	0.000	0.000	0.000	0.000
17	D	17	LYS	1	0.838	0.918	14.190	0.283	0.283	0.000	0.000	0.000	0.000
18	D	18	MET	0	-0.010	0.005	8.877	0.024	0.024	0.000	0.000	0.000	0.000
19	D	19	SER	0	-0.031	-0.012	8.526	0.068	0.068	0.000	0.000	0.000	0.000
20	D	20	CYS	0	0.002	0.014	2.762	-2.607	-1.987	3.272	-0.940	-2.953	-0.002
21	D	21	GLU	-1	-0.848	-0.878	4.374	1.033	1.334	-0.001	-0.040	-0.261	0.000
22	D	22	VAL	0	-0.010	-0.012	2.687	-1.446	1.145	0.467	-1.002	-2.056	-0.006
23	D	23	LYS	1	0.992	0.986	3.509	-6.326	-5.869	0.006	-0.066	-0.397	0.000
24	D	24	SER	0	0.036	0.024	4.854	-0.469	-0.469	0.000	0.000	0.000	0.000
25	D	25	ILE	0	-0.004	-0.024	6.673	0.230	0.230	0.000	0.000	0.000	0.000
26	D	26	SER	0	0.019	0.026	9.609	-0.072	-0.072	0.000	0.000	0.000	0.000
27	D	27	LYS	1	0.950	0.966	10.373	-0.002	-0.002	0.000	0.000	0.000	0.000
28	D	28	LEU	0	0.012	0.035	10.380	-0.005	-0.005	0.000	0.000	0.000	0.000
29	D	29	THR	0	-0.048	-0.038	9.830	0.023	0.023	0.000	0.000	0.000	0.000
30	D	30	SER	0	-0.029	-0.043	8.726	-0.018	-0.018	0.000	0.000	0.000	0.000
31	D	31	ILE	0	-0.010	0.024	3.833	-0.284	-0.025	0.006	-0.050	-0.215	0.000
32	D	32	TYR	0	0.029	0.001	5.867	0.150	0.150	0.000	0.000	0.000	0.000
33	D	33	TRP	0	0.035	0.015	6.227	-0.425	-0.425	0.000	0.000	0.000	0.000
34	D	34	LEU	0	-0.011	-0.009	7.409	0.166	0.166	0.000	0.000	0.000	0.000
35	D	35	ARG	1	0.800	0.869	10.364	0.335	0.335	0.000	0.000	0.000	0.000
36	D	36	GLU	-1	-0.865	-0.938	13.001	-0.597	-0.597	0.000	0.000	0.000	0.000
37	D	37	ARG	1	0.831	0.900	14.588	0.378	0.378	0.000	0.000	0.000	0.000
38	D	38	GLN	0	-0.029	-0.022	18.252	0.045	0.045	0.000	0.000	0.000	0.000
39	D	39	ASP	-1	-0.843	-0.933	20.160	-0.266	-0.266	0.000	0.000	0.000	0.000
40	D	40	PRO	0	-0.020	0.022	23.824	0.010	0.010	0.000	0.000	0.000	0.000
41	D	41	LYS	1	0.803	0.891	26.379	0.222	0.222	0.000	0.000	0.000	0.000
42	D	42	ASP	-1	-0.889	-0.946	23.590	-0.242	-0.242	0.000	0.000	0.000	0.000
43	D	43	LYS	1	0.856	0.934	15.476	0.497	0.497	0.000	0.000	0.000	0.000
44	D	44	TYR	0	-0.036	-0.034	18.042	0.006	0.006	0.000	0.000	0.000	0.000
45	D	45	PHE	0	-0.017	-0.011	10.491	-0.032	-0.032	0.000	0.000	0.000	0.000
46	D	46	GLU	-1	-0.771	-0.835	14.413	-0.324	-0.324	0.000	0.000	0.000	0.000
47	D	47	PHE	0	-0.036	-0.015	11.799	-0.084	-0.084	0.000	0.000	0.000	0.000
48	D	48	LEU	0	0.006	0.011	12.422	0.050	0.050	0.000	0.000	0.000	0.000
49	D	49	ALA	0	0.055	0.007	12.000	0.075	0.075	0.000	0.000	0.000	0.000
50	D	50	SER	0	-0.015	0.002	10.574	-0.095	-0.095	0.000	0.000	0.000	0.000
51	D	51	TRP	0	0.048	0.021	10.504	0.063	0.063	0.000	0.000	0.000	0.000
52	D	52	SER	0	-0.044	-0.009	11.102	-0.010	-0.010	0.000	0.000	0.000	0.000
53	D	53	SER	0	0.008	-0.008	13.723	0.019	0.019	0.000	0.000	0.000	0.000
54	D	54	SER	0	-0.034	-0.016	15.339	0.004	0.004	0.000	0.000	0.000	0.000
55	D	55	LYS	1	0.990	0.989	17.368	0.195	0.195	0.000	0.000	0.000	0.000
56	D	56	GLY	0	0.061	0.051	16.460	0.007	0.007	0.000	0.000	0.000	0.000
57	D	57	VAL	0	-0.020	-0.021	14.840	-0.028	-0.028	0.000	0.000	0.000	0.000
58	D	58	LEU	0	-0.039	-0.009	15.181	0.037	0.037	0.000	0.000	0.000	0.000
59	D	59	TYR	0	-0.017	-0.030	15.483	-0.038	-0.038	0.000	0.000	0.000	0.000
60	D	60	GLY	0	0.028	0.021	16.821	0.016	0.016	0.000	0.000	0.000	0.000
61	D	61	GLU	-1	-0.851	-0.937	17.661	-0.210	-0.210	0.000	0.000	0.000	0.000
62	D	62	SER	0	-0.049	-0.040	18.577	0.015	0.015	0.000	0.000	0.000	0.000
63	D	63	VAL	0	-0.030	-0.017	16.738	0.015	0.015	0.000	0.000	0.000	0.000
64	D	64	ASP	-1	-0.829	-0.911	19.803	-0.199	-0.199	0.000	0.000	0.000	0.000
65	D	65	LYS	1	0.807	0.893	22.447	0.223	0.223	0.000	0.000	0.000	0.000
66	D	66	LYS	1	0.910	0.972	21.230	0.299	0.299	0.000	0.000	0.000	0.000
67	D	67	ARG	1	0.920	0.963	21.730	0.207	0.207	0.000	0.000	0.000	0.000
68	D	68	ASN	0	-0.016	-0.007	20.603	-0.003	-0.003	0.000	0.000	0.000	0.000
69	D	69	ILE	0	0.027	0.023	15.055	-0.027	-0.027	0.000	0.000	0.000	0.000
70	D	70	ILE	0	0.007	0.007	16.670	0.028	0.028	0.000	0.000	0.000	0.000
71	D	71	LEU	0	-0.007	-0.004	11.397	-0.039	-0.039	0.000	0.000	0.000	0.000
72	D	72	GLU	-1	-0.817	-0.903	13.230	-0.238	-0.238	0.000	0.000	0.000	0.000
73	D	73	SER	0	0.038	0.015	12.352	-0.052	-0.052	0.000	0.000	0.000	0.000
74	D	74	SER	0	-0.023	-0.011	10.177	-0.021	-0.021	0.000	0.000	0.000	0.000
75	D	75	ASP	-1	-0.909	-0.945	9.968	-0.125	-0.125	0.000	0.000	0.000	0.000
76	D	76	SER	0	-0.018	-0.024	11.194	0.091	0.091	0.000	0.000	0.000	0.000
77	D	77	ARG	1	0.876	0.920	7.975	-0.675	-0.675	0.000	0.000	0.000	0.000
78	D	78	ARG	1	0.845	0.922	6.651	-0.035	-0.035	0.000	0.000	0.000	0.000
79	D	79	PRO	0	-0.032	0.006	5.900	-0.010	-0.010	0.000	0.000	0.000	0.000
80	D	80	PHE	0	0.032	-0.013	8.498	-0.165	-0.165	0.000	0.000	0.000	0.000
81	D	81	LEU	0	-0.005	0.018	10.338	0.039	0.039	0.000	0.000	0.000	0.000
82	D	82	SER	0	-0.014	-0.034	12.074	0.005	0.005	0.000	0.000	0.000	0.000
83	D	83	ILE	0	0.002	0.001	14.787	0.015	0.015	0.000	0.000	0.000	0.000
84	D	84	MET	0	0.005	-0.003	17.881	0.022	0.022	0.000	0.000	0.000	0.000
85	D	85	ASN	0	-0.035	-0.002	21.554	0.003	0.003	0.000	0.000	0.000	0.000
86	D	86	VAL	0	0.006	0.027	19.774	0.001	0.001	0.000	0.000	0.000	0.000
87	D	87	LYS	1	0.994	0.993	22.764	0.206	0.206	0.000	0.000	0.000	0.000
88	D	88	PRO	0	0.090	0.045	23.090	-0.027	-0.027	0.000	0.000	0.000	0.000
89	D	89	GLU	-1	-0.860	-0.923	23.480	-0.237	-0.237	0.000	0.000	0.000	0.000
90	D	90	ASP	-1	-0.931	-0.962	19.396	-0.336	-0.336	0.000	0.000	0.000	0.000
91	D	91	SER	0	-0.024	-0.006	18.633	-0.051	-0.051	0.000	0.000	0.000	0.000
92	D	92	ASP	-1	-0.709	-0.836	16.346	-0.414	-0.414	0.000	0.000	0.000	0.000
93	D	93	PHE	0	-0.016	-0.012	12.126	-0.004	-0.004	0.000	0.000	0.000	0.000
94	D	94	TYR	0	-0.013	-0.014	10.901	-0.022	-0.022	0.000	0.000	0.000	0.000
95	D	95	PHE	0	0.023	0.025	6.593	-0.147	-0.147	0.000	0.000	0.000	0.000
96	D	97	ALA	0	-0.004	-0.016	3.056	-1.413	-0.761	0.129	-0.256	-0.525	-0.001
97	D	98	THR	0	0.006	-0.007	2.098	-1.532	0.039	2.309	-1.392	-2.488	-0.011
98	D	99	VAL	0	0.005	-0.006	3.988	-0.256	-0.115	0.006	-0.054	-0.092	0.000
99	D	100	GLY	0	0.018	0.019	7.641	0.108	0.108	0.000	0.000	0.000	0.000
100	D	101	SER	0	-0.029	-0.002	9.536	-0.043	-0.043	0.000	0.000	0.000	0.000
101	D	102	PRO	0	0.041	0.003	12.541	0.057	0.057	0.000	0.000	0.000	0.000
102	D	103	LYS	1	0.943	0.979	6.828	-0.525	-0.525	0.000	0.000	0.000	0.000
103	D	104	MET	0	0.035	0.021	6.827	0.012	0.012	0.000	0.000	0.000	0.000
104	D	105	VAL	0	-0.071	-0.040	2.319	-1.097	-0.153	1.958	-0.630	-2.273	0.001
105	D	106	PHE	0	0.063	0.027	2.950	-1.865	-0.271	0.320	-0.738	-1.176	-0.008
106	D	107	GLY	0	0.031	-0.002	2.206	-4.620	-3.542	5.344	-3.653	-2.769	-0.021
107	D	108	THR	0	-0.015	-0.014	2.962	3.433	0.833	0.142	3.021	-0.563	-0.002
108	D	109	GLY	0	-0.005	0.006	5.664	0.621	0.621	0.000	0.000	0.000	0.000
109	D	110	THR	0	-0.062	-0.042	7.704	0.045	0.045	0.000	0.000	0.000	0.000
110	D	111	LYS	1	0.886	0.949	10.410	0.457	0.457	0.000	0.000	0.000	0.000
111	D	112	LEU	0	-0.020	-0.005	13.996	0.047	0.047	0.000	0.000	0.000	0.000
112	D	113	THR	0	-0.025	-0.022	16.240	0.018	0.018	0.000	0.000	0.000	0.000
113	D	114	VAL	0	-0.007	0.010	19.980	0.009	0.009	0.000	0.000	0.000	0.000
114	D	115	VAL	0	0.006	0.011	22.551	0.008	0.008	0.000	0.000	0.000	0.000
115	D	116	ASP	-1	-0.812	-0.891	26.111	-0.167	-0.167	0.000	0.000	0.000	0.000
116	D	117	VAL	0	-0.040	-0.028	29.327	0.008	0.008	0.000	0.000	0.000	0.000
117	D	118	LEU	0	-0.006	-0.013	25.799	-0.011	-0.011	0.000	0.000	0.000	0.000
118	D	119	PRO	0	-0.005	0.001	29.086	0.007	0.007	0.000	0.000	0.000	0.000
119	D	120	THR	0	0.024	0.019	29.878	-0.003	-0.003	0.000	0.000	0.000	0.000
120	D	121	THR	0	-0.023	-0.031	31.404	0.003	0.003	0.000	0.000	0.000	0.000
121	D	122	ALA	0	-0.007	0.022	34.135	0.000	0.000	0.000	0.000	0.000	0.000
122	D	123	PRO	0	0.021	0.012	37.416	-0.002	-0.002	0.000	0.000	0.000	0.000

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