FMO DATABASE

FMODB ID: LZ1J9

Calculation Name: 3WMD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WMD

Chain ID: A

ChEMBL ID:

UniProt ID: Q846W7

Base Structure: X-ray

Registration Date: 2023-09-20

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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1289967.933047
FMO2-HF: Nuclear repulsion	1234967.016446
FMO2-HF: Total energy	-55000.916601
FMO2-MP2: Total energy	-55162.403463

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:1:MET)

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

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.
-16.433	-11.591	17.032	-4.341	-17.535	-0.031

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.028

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	3	GLU	-1	-0.862	-0.947	3.079	-1.968	1.001	0.122	-1.539	-1.553	0.001
4	A	4	PHE	0	0.049	0.014	5.709	0.604	0.604	0.000	0.000	0.000	0.000
5	A	5	ALA	0	-0.015	-0.016	2.180	-0.853	-0.885	2.490	-0.639	-1.819	0.002
6	A	6	ARG	1	0.866	0.912	2.006	0.676	1.875	4.206	-1.695	-3.710	-0.002
7	A	7	LYS	1	0.974	0.988	4.088	-1.656	-1.861	0.025	0.353	-0.174	0.000
8	A	8	LYS	1	0.901	0.959	5.597	-1.147	-1.147	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.879	0.942	2.596	-2.341	-1.441	0.763	-0.261	-1.403	-0.001
10	A	10	ALA	0	0.046	0.027	5.468	-0.428	-0.428	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.016	-0.002	8.750	-0.233	-0.233	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.900	-0.909	7.665	0.079	0.079	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.054	0.026	9.578	-0.153	-0.153	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.018	-0.017	11.203	-0.085	-0.085	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.904	0.943	9.964	-0.437	-0.437	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.809	0.879	9.305	-0.036	-0.036	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.015	0.021	14.639	-0.035	-0.035	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.071	-0.046	17.144	-0.036	-0.036	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.072	-0.034	17.383	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.025	0.019	19.078	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.891	-0.936	18.104	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.020	0.000	17.876	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.876	-0.942	17.617	-0.067	-0.067	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.011	-0.010	14.330	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.008	0.002	12.882	0.011	0.011	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.013	-0.011	12.968	0.018	0.018	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.903	-0.943	11.603	-0.289	-0.289	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.107	-0.040	7.565	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.055	-0.023	8.972	0.090	0.090	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.016	-0.006	9.871	-0.088	-0.088	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.003	-0.018	11.584	0.062	0.062	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.885	-0.931	13.578	-0.443	-0.443	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.050	-0.009	13.077	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.026	-0.016	14.344	0.025	0.025	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.009	0.002	15.558	0.021	0.021	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.871	-0.919	17.484	-0.092	-0.092	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.798	-0.855	19.433	0.087	0.087	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.035	0.006	21.363	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	39	VAL	0	0.006	-0.028	20.053	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.013	-0.002	22.800	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.061	-0.024	25.220	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.049	-0.029	24.992	-0.006	-0.006	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.015	0.011	21.302	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.020	0.022	20.603	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.044	-0.027	18.776	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.065	0.035	18.858	0.007	0.007	0.000	0.000	0.000	0.000
47	A	47	HIS	0	0.002	-0.019	17.747	0.019	0.019	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.872	-0.944	19.476	-0.093	-0.093	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.008	0.004	22.717	0.014	0.014	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.020	-0.009	16.143	0.016	0.016	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.968	0.986	20.225	0.080	0.080	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.030	0.017	21.745	0.012	0.012	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.085	-0.031	20.321	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.009	-0.042	16.041	0.021	0.021	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.926	-0.961	21.700	-0.020	-0.020	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.027	-0.011	24.607	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.000	-0.010	21.663	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.013	0.000	20.132	0.007	0.007	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.013	0.009	24.084	0.001	0.001	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.035	-0.008	26.944	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	HIS	0	-0.057	-0.022	25.585	0.003	0.003	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.061	-0.019	20.734	0.005	0.005	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.918	0.961	21.765	-0.106	-0.106	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.857	-0.962	16.807	0.209	0.209	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.955	-0.957	19.401	0.147	0.147	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.003	-0.011	15.247	0.002	0.002	0.000	0.000	0.000	0.000
67	A	67	ALA	0	-0.003	0.007	17.267	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.966	-0.995	15.317	0.371	0.371	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.016	-0.003	10.842	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.027	-0.012	11.918	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.016	-0.023	7.278	0.141	0.141	0.000	0.000	0.000	0.000
72	A	72	GLY	0	0.031	0.036	8.778	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	73	GLN	0	0.013	0.007	8.469	-0.175	-0.175	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.769	-0.880	8.202	-0.688	-0.688	0.000	0.000	0.000	0.000
75	A	75	ALA	0	-0.060	-0.029	3.665	-0.193	-0.016	0.000	-0.029	-0.148	0.000
76	A	76	THR	0	-0.030	-0.006	3.463	-3.293	-2.428	0.024	-0.470	-0.420	-0.003
77	A	77	HIS	0	-0.045	-0.049	5.226	0.665	0.772	-0.001	-0.001	-0.105	0.000
78	A	78	ALA	0	-0.015	-0.010	7.048	0.131	0.131	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.012	0.003	8.811	-0.087	-0.087	0.000	0.000	0.000	0.000
80	A	80	ILE	0	0.008	-0.001	12.257	0.075	0.075	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.009	0.003	14.357	-0.063	-0.063	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.011	-0.015	15.121	0.029	0.029	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.024	0.044	19.238	-0.031	-0.031	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.005	-0.012	21.564	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.014	-0.002	23.336	-0.011	-0.011	0.000	0.000	0.000	0.000
86	A	86	MET	0	-0.009	0.008	24.537	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.807	-0.898	27.642	0.039	0.039	0.000	0.000	0.000	0.000
88	A	88	TYR	0	0.006	-0.007	30.568	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.041	-0.005	32.795	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.057	0.021	29.690	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	VAL	0	0.040	0.006	27.420	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.054	0.013	30.807	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.055	-0.038	33.118	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.038	0.036	30.261	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	TYR	0	0.014	-0.015	26.448	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.013	-0.028	32.923	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.985	-0.972	36.394	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.886	0.953	28.855	0.004	0.004	0.000	0.000	0.000	0.000
99	A	99	GLY	0	-0.002	0.022	35.825	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.056	-0.044	28.252	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.004	0.009	32.307	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	LYS	1	0.911	0.948	35.883	-0.015	-0.015	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.012	0.002	38.755	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	PRO	0	0.011	0.023	37.820	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.909	-0.950	40.668	0.013	0.013	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.023	-0.003	40.026	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	PRO	0	-0.029	-0.022	37.891	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.022	-0.008	37.252	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	THR	0	0.020	0.013	37.222	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.019	0.010	36.477	0.003	0.003	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.869	0.919	28.918	-0.052	-0.052	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.032	-0.002	28.863	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	HIS	0	-0.038	-0.022	26.213	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.946	0.983	22.230	-0.085	-0.085	0.000	0.000	0.000	0.000
115	A	115	THR	0	0.001	0.014	23.654	0.016	0.016	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.036	0.013	20.334	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.048	-0.015	18.247	0.023	0.023	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.016	0.014	13.933	-0.028	-0.028	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.022	-0.018	12.720	0.040	0.040	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.013	0.005	8.339	-0.050	-0.050	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.948	0.984	8.031	0.465	0.465	0.000	0.000	0.000	0.000
122	A	122	MET	0	-0.042	-0.021	3.166	-0.357	0.382	0.678	-0.225	-1.191	0.001
123	A	123	ASP	-1	-0.730	-0.861	4.919	-3.369	-3.187	-0.001	-0.021	-0.160	0.000
124	A	124	ALA	0	-0.006	-0.021	2.473	-5.274	-2.355	0.863	-1.606	-2.175	-0.014
125	A	125	SER	0	-0.035	-0.014	3.070	-2.600	-0.680	0.355	-0.943	-1.332	-0.009
126	A	126	GLY	0	-0.047	-0.035	2.286	-0.717	-1.060	7.408	-4.294	-2.771	-0.001
127	A	127	LEU	0	0.024	0.027	2.958	6.451	-0.104	0.100	7.029	-0.574	-0.005
128	A	128	ILE	0	-0.016	-0.003	6.650	-0.025	-0.025	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.818	0.896	8.484	0.672	0.672	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.064	-0.061	10.704	-0.035	-0.035	0.000	0.000	0.000	0.000
131	A	131	LEU	0	-0.007	0.012	11.864	0.080	0.080	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.929	0.981	13.884	0.063	0.063	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.053	0.015	16.626	0.047	0.047	0.000	0.000	0.000	0.000
134	A	134	TYR	0	-0.022	-0.023	17.768	-0.034	-0.034	0.000	0.000	0.000	0.000
135	A	135	TRP	0	-0.043	-0.045	21.350	0.013	0.013	0.000	0.000	0.000	0.000
136	A	136	GLY	0	0.011	-0.001	24.339	-0.010	-0.010	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.007	-0.023	28.031	0.005	0.005	0.000	0.000	0.000	0.000
138	A	138	SER	0	0.000	-0.001	30.416	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.885	-0.900	26.476	0.059	0.059	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.033	-0.018	27.833	0.008	0.008	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.002	-0.009	29.990	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	142	VAL	0	-0.025	-0.009	32.101	0.002	0.002	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.002	-0.008	31.861	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.020	0.015	35.247	-0.003	-0.003	0.000	0.000	0.000	0.000

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