FMO DATABASE

FMODB ID: ZV7VN

Calculation Name: 1ALY-A-Xray372

Preferred Name: CD40 ligand

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1ALY

Chain ID: A

ChEMBL ID: CHEMBL3580491

UniProt ID: P29965

Base Structure: X-ray

Registration Date: 2023-09-22

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1272749.228887
FMO2-HF: Nuclear repulsion	1217407.645549
FMO2-HF: Total energy	-55341.583337
FMO2-MP2: Total energy	-55503.6565

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:116:GLY)

Summations of interaction energy for fragment #1(A:116:GLY)

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.
9.045	-11.51	27.832	-0.090000000000001	-7.188	-0.038

Interaction energy analysis for fragmet #1(A:116:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : 0.022

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	118	GLN	0	0.032	0.002	1.897	7.303	-5.167	9.456	6.262	-3.248	-0.040
4	A	119	ASN	0	-0.006	-0.032	1.643	2.970	-5.209	18.377	-6.338	-3.861	0.002
5	A	120	PRO	0	-0.038	-0.007	4.154	-0.491	-0.397	-0.001	-0.014	-0.079	0.000
6	A	121	GLN	0	0.068	0.046	7.384	-0.164	-0.164	0.000	0.000	0.000	0.000
7	A	122	ILE	0	-0.108	-0.037	10.111	0.301	0.301	0.000	0.000	0.000	0.000
8	A	123	ALA	0	0.006	-0.011	11.237	-0.199	-0.199	0.000	0.000	0.000	0.000
9	A	124	ALA	0	0.016	0.013	12.027	0.203	0.203	0.000	0.000	0.000	0.000
10	A	125	HIS	0	0.009	0.025	14.171	-0.110	-0.110	0.000	0.000	0.000	0.000
11	A	126	VAL	0	0.037	0.034	15.227	0.067	0.067	0.000	0.000	0.000	0.000
12	A	127	ILE	0	-0.008	-0.012	17.305	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	128	SER	0	-0.005	-0.010	20.488	0.009	0.009	0.000	0.000	0.000	0.000
14	A	129	GLU	-1	-0.932	-0.970	24.006	0.308	0.308	0.000	0.000	0.000	0.000
15	A	130	ALA	0	0.040	0.032	26.136	0.003	0.003	0.000	0.000	0.000	0.000
16	A	131	SER	0	-0.010	-0.008	29.526	0.016	0.016	0.000	0.000	0.000	0.000
17	A	132	SER	0	0.021	0.011	31.211	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	133	LYS	1	0.937	0.978	33.416	-0.167	-0.167	0.000	0.000	0.000	0.000
19	A	134	THR	0	0.065	0.015	35.087	0.003	0.003	0.000	0.000	0.000	0.000
20	A	135	THR	0	-0.055	-0.009	32.386	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	136	SER	0	0.007	0.007	34.017	0.007	0.007	0.000	0.000	0.000	0.000
22	A	137	VAL	0	-0.027	-0.014	29.867	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	138	LEU	0	-0.006	-0.014	27.362	0.001	0.001	0.000	0.000	0.000	0.000
24	A	139	GLN	0	-0.004	0.001	26.114	0.034	0.034	0.000	0.000	0.000	0.000
25	A	140	TRP	0	0.053	0.009	21.217	-0.011	-0.011	0.000	0.000	0.000	0.000
26	A	141	ALA	0	0.029	0.006	20.155	0.009	0.009	0.000	0.000	0.000	0.000
27	A	142	GLU	-1	-0.866	-0.941	13.906	0.969	0.969	0.000	0.000	0.000	0.000
28	A	143	LYS	1	0.888	0.941	16.161	-0.282	-0.282	0.000	0.000	0.000	0.000
29	A	144	GLY	0	0.014	-0.003	17.076	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	145	TYR	0	-0.016	-0.011	14.869	0.050	0.050	0.000	0.000	0.000	0.000
31	A	146	TYR	0	-0.012	0.008	11.598	-0.045	-0.045	0.000	0.000	0.000	0.000
32	A	147	THR	0	-0.048	-0.032	9.431	0.053	0.053	0.000	0.000	0.000	0.000
33	A	148	MET	0	0.039	0.015	9.909	-0.253	-0.253	0.000	0.000	0.000	0.000
34	A	149	SER	0	-0.060	-0.039	7.676	0.324	0.324	0.000	0.000	0.000	0.000
35	A	150	ASN	0	0.072	0.028	7.020	0.659	0.659	0.000	0.000	0.000	0.000
36	A	151	ASN	0	0.079	0.030	9.099	-0.296	-0.296	0.000	0.000	0.000	0.000
37	A	152	LEU	0	-0.032	-0.007	12.031	-0.273	-0.273	0.000	0.000	0.000	0.000
38	A	153	VAL	0	-0.040	-0.012	12.699	-0.211	-0.211	0.000	0.000	0.000	0.000
39	A	154	THR	0	0.020	-0.029	14.045	0.158	0.158	0.000	0.000	0.000	0.000
40	A	155	LEU	0	0.017	0.022	16.486	-0.113	-0.113	0.000	0.000	0.000	0.000
41	A	156	GLU	-1	-0.859	-0.881	18.724	0.587	0.587	0.000	0.000	0.000	0.000
42	A	157	ASN	0	0.031	0.008	21.803	-0.044	-0.044	0.000	0.000	0.000	0.000
43	A	158	GLY	0	-0.028	0.010	24.644	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	159	LYS	1	0.757	0.890	22.744	-0.367	-0.367	0.000	0.000	0.000	0.000
45	A	160	GLN	0	0.019	0.015	23.298	-0.041	-0.041	0.000	0.000	0.000	0.000
46	A	161	LEU	0	0.023	0.028	17.454	0.050	0.050	0.000	0.000	0.000	0.000
47	A	162	THR	0	-0.016	-0.030	19.795	-0.071	-0.071	0.000	0.000	0.000	0.000
48	A	163	VAL	0	0.031	0.023	17.906	0.081	0.081	0.000	0.000	0.000	0.000
49	A	164	LYS	1	0.843	0.900	15.911	-0.863	-0.863	0.000	0.000	0.000	0.000
50	A	165	ARG	1	0.948	0.971	15.779	-0.419	-0.419	0.000	0.000	0.000	0.000
51	A	166	GLN	0	-0.060	-0.023	19.265	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	167	GLY	0	0.011	0.005	21.152	0.006	0.006	0.000	0.000	0.000	0.000
53	A	168	LEU	0	0.028	0.023	22.677	0.007	0.007	0.000	0.000	0.000	0.000
54	A	169	TYR	0	-0.022	-0.032	17.249	0.039	0.039	0.000	0.000	0.000	0.000
55	A	170	TYR	0	0.040	0.024	20.115	-0.026	-0.026	0.000	0.000	0.000	0.000
56	A	171	ILE	0	-0.038	-0.011	20.172	0.041	0.041	0.000	0.000	0.000	0.000
57	A	172	TYR	0	-0.022	-0.032	17.425	-0.035	-0.035	0.000	0.000	0.000	0.000
58	A	173	ALA	0	0.013	0.000	22.513	0.033	0.033	0.000	0.000	0.000	0.000
59	A	174	GLN	0	-0.063	-0.018	24.699	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	175	VAL	0	0.052	0.009	26.270	0.014	0.014	0.000	0.000	0.000	0.000
61	A	176	THR	0	-0.010	0.000	28.917	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	177	PHE	0	0.024	0.016	31.065	0.008	0.008	0.000	0.000	0.000	0.000
63	A	178	CYS	0	-0.063	-0.053	34.238	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	179	SER	0	0.022	-0.030	37.235	0.002	0.002	0.000	0.000	0.000	0.000
65	A	180	ASN	0	-0.048	-0.028	40.450	-0.006	-0.006	0.000	0.000	0.000	0.000
66	A	181	ARG	1	0.839	0.947	42.895	-0.045	-0.045	0.000	0.000	0.000	0.000
67	A	182	GLU	-1	-0.801	-0.912	46.278	0.046	0.046	0.000	0.000	0.000	0.000
68	A	183	ALA	0	-0.057	-0.009	45.624	0.001	0.001	0.000	0.000	0.000	0.000
69	A	184	SER	0	-0.009	-0.010	42.193	0.001	0.001	0.000	0.000	0.000	0.000
70	A	185	SER	0	-0.023	-0.015	45.201	0.001	0.001	0.000	0.000	0.000	0.000
71	A	186	GLN	0	-0.014	-0.009	42.002	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	187	ALA	0	-0.002	0.013	45.875	0.001	0.001	0.000	0.000	0.000	0.000
73	A	188	PRO	0	-0.084	-0.041	41.406	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	189	PHE	0	0.027	0.026	33.529	0.005	0.005	0.000	0.000	0.000	0.000
75	A	190	ILE	0	-0.006	-0.025	36.173	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	191	ALA	0	0.017	0.025	31.219	0.007	0.007	0.000	0.000	0.000	0.000
77	A	192	SER	0	-0.031	-0.027	32.356	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	193	LEU	0	-0.012	0.013	25.861	0.012	0.012	0.000	0.000	0.000	0.000
79	A	194	CYS	0	-0.012	-0.022	28.770	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	195	LEU	0	-0.004	-0.005	26.745	0.019	0.019	0.000	0.000	0.000	0.000
81	A	196	LYS	1	0.969	0.996	26.018	-0.330	-0.330	0.000	0.000	0.000	0.000
82	A	197	SER	0	0.000	0.013	27.863	0.014	0.014	0.000	0.000	0.000	0.000
83	A	198	PRO	0	-0.006	-0.027	26.808	-0.015	-0.015	0.000	0.000	0.000	0.000
84	A	199	GLY	0	0.027	0.016	29.784	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	200	ARG	1	0.860	0.925	30.631	-0.200	-0.200	0.000	0.000	0.000	0.000
86	A	201	PHE	0	0.030	-0.011	33.971	0.008	0.008	0.000	0.000	0.000	0.000
87	A	202	GLU	-1	-0.896	-0.904	32.238	0.190	0.190	0.000	0.000	0.000	0.000
88	A	203	ARG	1	0.921	0.952	31.088	-0.176	-0.176	0.000	0.000	0.000	0.000
89	A	204	ILE	0	0.018	0.014	32.374	0.011	0.011	0.000	0.000	0.000	0.000
90	A	205	LEU	0	-0.064	-0.022	27.359	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	206	LEU	0	0.026	0.006	28.348	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	207	ARG	1	0.919	0.960	31.964	-0.096	-0.096	0.000	0.000	0.000	0.000
93	A	208	ALA	0	0.000	0.016	33.098	-0.007	-0.007	0.000	0.000	0.000	0.000
94	A	209	ALA	0	0.003	-0.002	34.867	0.005	0.005	0.000	0.000	0.000	0.000
95	A	210	ASN	0	0.000	0.004	35.834	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	211	THR	0	0.026	0.008	38.874	0.003	0.003	0.000	0.000	0.000	0.000
97	A	212	HIS	0	0.095	0.093	39.875	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	213	SER	0	-0.032	-0.030	43.169	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	214	SER	0	-0.014	0.016	46.776	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	215	ALA	0	0.108	0.038	49.627	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	216	LYS	1	0.896	0.934	46.145	-0.029	-0.029	0.000	0.000	0.000	0.000
102	A	217	PRO	0	0.065	0.019	45.456	0.003	0.003	0.000	0.000	0.000	0.000
103	A	219	GLY	0	0.036	0.035	40.534	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	220	GLN	0	-0.024	0.007	32.663	0.010	0.010	0.000	0.000	0.000	0.000
105	A	221	GLN	0	-0.028	-0.006	35.628	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	222	SER	0	0.044	0.006	30.443	0.008	0.008	0.000	0.000	0.000	0.000
107	A	223	ILE	0	-0.010	0.009	30.387	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	224	HIS	0	0.029	0.026	23.736	0.008	0.008	0.000	0.000	0.000	0.000
109	A	225	LEU	0	-0.007	-0.004	27.529	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	226	GLY	0	0.016	-0.014	25.835	0.014	0.014	0.000	0.000	0.000	0.000
111	A	227	GLY	0	-0.009	0.004	25.568	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	228	VAL	0	-0.009	-0.003	23.970	0.020	0.020	0.000	0.000	0.000	0.000
113	A	229	PHE	0	0.036	0.014	24.905	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	230	GLU	-1	-0.856	-0.925	24.742	0.225	0.225	0.000	0.000	0.000	0.000
115	A	231	LEU	0	-0.058	-0.012	21.533	0.006	0.006	0.000	0.000	0.000	0.000
116	A	232	GLN	0	0.084	0.034	24.205	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	233	PRO	0	0.008	0.004	22.136	0.027	0.027	0.000	0.000	0.000	0.000
118	A	234	GLY	0	0.007	-0.009	21.741	-0.023	-0.023	0.000	0.000	0.000	0.000
119	A	235	ALA	0	-0.063	-0.027	21.987	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	236	SER	0	-0.042	-0.034	23.560	-0.027	-0.027	0.000	0.000	0.000	0.000
121	A	237	VAL	0	0.027	0.013	22.450	-0.035	-0.035	0.000	0.000	0.000	0.000
122	A	238	PHE	0	0.023	0.005	24.215	0.031	0.031	0.000	0.000	0.000	0.000
123	A	239	VAL	0	0.023	0.018	25.673	-0.019	-0.019	0.000	0.000	0.000	0.000
124	A	240	ASN	0	0.056	0.034	28.344	0.006	0.006	0.000	0.000	0.000	0.000
125	A	241	VAL	0	-0.012	-0.014	31.495	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	242	THR	0	0.026	-0.014	34.158	0.003	0.003	0.000	0.000	0.000	0.000
127	A	243	ASP	-1	-0.845	-0.898	36.743	0.090	0.090	0.000	0.000	0.000	0.000
128	A	244	PRO	0	0.054	0.014	33.701	0.000	0.000	0.000	0.000	0.000	0.000
129	A	245	SER	0	-0.004	0.001	34.411	0.005	0.005	0.000	0.000	0.000	0.000
130	A	246	GLN	0	0.019	0.020	36.362	0.003	0.003	0.000	0.000	0.000	0.000
131	A	247	VAL	0	-0.060	-0.020	30.627	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	248	SER	0	0.009	-0.028	31.122	0.002	0.002	0.000	0.000	0.000	0.000
133	A	249	HIS	0	0.004	0.008	27.807	0.018	0.018	0.000	0.000	0.000	0.000
134	A	250	GLY	0	-0.072	0.002	25.686	0.007	0.007	0.000	0.000	0.000	0.000
135	A	251	THR	0	0.026	-0.022	22.851	0.003	0.003	0.000	0.000	0.000	0.000
136	A	252	GLY	0	0.035	0.006	22.576	-0.014	-0.014	0.000	0.000	0.000	0.000
137	A	253	PHE	0	-0.036	-0.005	23.620	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	254	THR	0	0.046	0.016	25.343	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	255	SER	0	-0.051	-0.030	20.553	0.020	0.020	0.000	0.000	0.000	0.000
140	A	256	PHE	0	-0.010	-0.009	20.554	-0.021	-0.021	0.000	0.000	0.000	0.000
141	A	257	GLY	0	0.045	0.016	18.058	0.052	0.052	0.000	0.000	0.000	0.000
142	A	258	LEU	0	-0.019	-0.013	16.085	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	259	LEU	0	0.014	0.008	15.317	0.062	0.062	0.000	0.000	0.000	0.000
144	A	260	LYS	1	0.915	0.963	15.545	-0.339	-0.339	0.000	0.000	0.000	0.000
145	A	261	LEU	0	0.007	0.012	16.835	-0.012	-0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:116:GLY)