Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: NN7QQ

Calculation Name: 2D7J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7J

Chain ID: A

ChEMBL ID:

UniProt ID: O59071

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2215622.517549
FMO2-HF: Nuclear repulsion 2140169.800037
FMO2-HF: Total energy -75452.717512
FMO2-MP2: Total energy -75671.181409


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:2:MET)


Summations of interaction energy for fragment #1(A:2: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.
-28.644-14.66921.075-11.337-23.712-0.075
Interaction energy analysis for fragmet #1(A:2:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.004
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   
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].
3A4VAL00.0540.0252.3831.2633.8821.860-1.166-3.313-0.004
4A5ILE0-0.028-0.0094.622-1.409-1.2920.007-0.009-0.1140.000
5A6MET00.000-0.0027.8950.0330.0330.0000.0000.0000.000
6A7ASP-1-0.860-0.94110.5570.4650.4650.0000.0000.0000.000
7A8ASN0-0.022-0.02613.183-0.083-0.0830.0000.0000.0000.000
8A9GLY00.0520.01916.385-0.062-0.0620.0000.0000.0000.000
9A10GLY0-0.040-0.01017.711-0.041-0.0410.0000.0000.0000.000
10A11GLN00.017-0.00418.3580.0210.0210.0000.0000.0000.000
11A12TYR0-0.036-0.02418.239-0.008-0.0080.0000.0000.0000.000
12A13VAL00.0670.04112.2670.0230.0230.0000.0000.0000.000
13A14HIS00.0560.01612.9440.0970.0970.0000.0000.0000.000
14A15ARG10.9060.96013.598-0.257-0.2570.0000.0000.0000.000
15A16ILE00.0630.05010.764-0.030-0.0300.0000.0000.0000.000
16A17TRP0-0.008-0.0145.957-0.334-0.3340.0000.0000.0000.000
17A18ARG10.9310.94910.240-0.397-0.3970.0000.0000.0000.000
18A19THR00.0150.00212.773-0.090-0.0900.0000.0000.0000.000
19A20LEU00.0280.0206.879-0.076-0.0760.0000.0000.0000.000
20A21ARG10.8790.9297.135-0.334-0.3340.0000.0000.0000.000
21A22TYR0-0.091-0.0299.940-0.139-0.1390.0000.0000.0000.000
22A23LEU0-0.012-0.01110.347-0.057-0.0570.0000.0000.0000.000
23A24GLY0-0.0320.0049.608-0.045-0.0450.0000.0000.0000.000
24A25VAL0-0.004-0.0044.343-0.334-0.236-0.001-0.009-0.0870.000
25A26GLU-1-0.857-0.9242.345-12.686-9.5736.217-3.648-5.683-0.044
26A27THR0-0.016-0.0242.524-1.5290.3442.674-2.190-2.357-0.015
27A28LYS10.8990.9532.046-1.579-2.3336.490-1.111-4.6250.008
28A29ILE0-0.0050.0184.5370.2550.385-0.0010.008-0.1370.000
29A30ILE0-0.014-0.0046.473-0.094-0.0940.0000.0000.0000.000
30A31PRO00.0570.0189.246-0.058-0.0580.0000.0000.0000.000
31A32ASN00.0310.02512.1210.0170.0170.0000.0000.0000.000
32A33THR00.0190.01313.949-0.025-0.0250.0000.0000.0000.000
33A34THR0-0.049-0.0229.665-0.048-0.0480.0000.0000.0000.000
34A35PRO00.0460.02413.0420.0030.0030.0000.0000.0000.000
35A36LEU00.0970.04711.948-0.007-0.0070.0000.0000.0000.000
36A37GLU-1-0.836-0.89811.141-0.342-0.3420.0000.0000.0000.000
37A38GLU-1-0.929-0.97010.145-0.128-0.1280.0000.0000.0000.000
38A39ILE0-0.004-0.0126.950-0.114-0.1140.0000.0000.0000.000
39A40LYS10.8300.9016.3440.0300.0300.0000.0000.0000.000
40A41ALA0-0.035-0.0237.471-0.277-0.2770.0000.0000.0000.000
41A42MET0-0.054-0.0182.836-1.314-0.0980.583-0.273-1.5270.000
42A43ASN0-0.065-0.0192.621-5.495-3.5980.691-1.082-1.506-0.015
43A44PRO00.0340.0202.088-2.418-0.7212.221-1.840-2.077-0.009
44A45LYS10.8770.9132.919-1.1530.5450.3360.032-2.0660.004
45A46GLY00.0710.0314.414-0.538-0.271-0.001-0.036-0.2300.000
46A47ILE0-0.056-0.0214.853-0.289-0.285-0.001-0.0130.0100.000
47A48ILE00.0060.0077.361-0.081-0.0810.0000.0000.0000.000
48A49PHE00.0340.02710.0320.1260.1260.0000.0000.0000.000
49A50SER00.0440.00912.901-0.050-0.0500.0000.0000.0000.000
50A51GLY00.0080.00414.459-0.058-0.0580.0000.0000.0000.000
51A52GLY00.009-0.01617.5370.0420.0420.0000.0000.0000.000
52A53PRO0-0.030-0.00820.218-0.016-0.0160.0000.0000.0000.000
53A54SER00.0560.02322.703-0.019-0.0190.0000.0000.0000.000
54A55LEU00.0290.00622.3280.0160.0160.0000.0000.0000.000
55A56GLU-1-0.970-0.96823.3090.1280.1280.0000.0000.0000.000
56A57ASN0-0.064-0.03519.413-0.013-0.0130.0000.0000.0000.000
57A58THR00.002-0.01518.3040.0270.0270.0000.0000.0000.000
58A59GLY0-0.0110.00916.9430.0320.0320.0000.0000.0000.000
59A60ASN0-0.034-0.04014.291-0.051-0.0510.0000.0000.0000.000
60A61CYS0-0.035-0.00813.8320.0230.0230.0000.0000.0000.000
61A62GLU-1-0.797-0.91014.9030.2030.2030.0000.0000.0000.000
62A63LYS10.8090.90515.929-0.082-0.0820.0000.0000.0000.000
63A64VAL00.000-0.01110.768-0.025-0.0250.0000.0000.0000.000
64A65LEU0-0.062-0.02113.688-0.018-0.0180.0000.0000.0000.000
65A66GLU-1-0.924-0.95816.1260.0550.0550.0000.0000.0000.000
66A67HIS00.0170.01315.2330.0040.0040.0000.0000.0000.000
67A68TYR0-0.011-0.01612.591-0.028-0.0280.0000.0000.0000.000
68A69ASP-1-0.889-0.94913.8680.0130.0130.0000.0000.0000.000
69A70GLU-1-0.887-0.91413.280-0.090-0.0900.0000.0000.0000.000
70A71PHE0-0.129-0.0768.191-0.069-0.0690.0000.0000.0000.000
71A72ASN0-0.083-0.05610.4690.0350.0350.0000.0000.0000.000
72A73VAL00.0050.0157.0190.0680.0680.0000.0000.0000.000
73A74PRO00.0240.0178.827-0.064-0.0640.0000.0000.0000.000
74A75ILE0-0.014-0.0029.4230.0320.0320.0000.0000.0000.000
75A76LEU0-0.0020.00511.428-0.040-0.0400.0000.0000.0000.000
76A77GLY00.0090.00312.8470.0730.0730.0000.0000.0000.000
77A78ILE0-0.005-0.01314.322-0.033-0.0330.0000.0000.0000.000
78A79CYS0-0.070-0.03517.4360.0060.0060.0000.0000.0000.000
79A80LEU00.0560.03619.532-0.008-0.0080.0000.0000.0000.000
80A81GLY00.0400.01716.601-0.012-0.0120.0000.0000.0000.000
81A82HIS0-0.0030.00417.511-0.003-0.0030.0000.0000.0000.000
82A83GLN0-0.029-0.03219.732-0.019-0.0190.0000.0000.0000.000
83A84LEU0-0.033-0.00716.556-0.016-0.0160.0000.0000.0000.000
84A85ILE00.0110.00615.353-0.018-0.0180.0000.0000.0000.000
85A86ALA0-0.008-0.00419.582-0.019-0.0190.0000.0000.0000.000
86A87LYS10.9670.97923.192-0.146-0.1460.0000.0000.0000.000
87A88PHE0-0.0080.00420.379-0.011-0.0110.0000.0000.0000.000
88A89PHE00.009-0.01318.121-0.012-0.0120.0000.0000.0000.000
89A90GLY00.0140.01623.575-0.009-0.0090.0000.0000.0000.000
90A91GLY00.0170.02126.209-0.008-0.0080.0000.0000.0000.000
91A92LYS10.7420.84827.859-0.092-0.0920.0000.0000.0000.000
92A93VAL00.0250.01525.3040.0050.0050.0000.0000.0000.000
93A94GLY0-0.056-0.02528.716-0.009-0.0090.0000.0000.0000.000
94A95ARG11.0241.00730.770-0.092-0.0920.0000.0000.0000.000
95A96GLY0-0.009-0.00632.140-0.006-0.0060.0000.0000.0000.000
96A97GLU-1-0.971-0.96533.2690.0850.0850.0000.0000.0000.000
97A98LYS10.9360.93533.373-0.107-0.1070.0000.0000.0000.000
98A99ALA00.0030.00131.8210.0080.0080.0000.0000.0000.000
99A100GLU-1-0.878-0.89730.7920.1120.1120.0000.0000.0000.000
100A101TYR0-0.007-0.01224.0870.0110.0110.0000.0000.0000.000
101A102SER0-0.060-0.03429.440-0.012-0.0120.0000.0000.0000.000
102A103LEU0-0.011-0.00427.3490.0100.0100.0000.0000.0000.000
103A104VAL0-0.036-0.01429.187-0.009-0.0090.0000.0000.0000.000
104A105GLU-1-0.828-0.90429.3970.1090.1090.0000.0000.0000.000
105A106ILE0-0.013-0.00324.541-0.002-0.0020.0000.0000.0000.000
106A107GLU-1-0.792-0.87629.2420.0830.0830.0000.0000.0000.000
107A108ILE0-0.023-0.02023.8980.0040.0040.0000.0000.0000.000
108A109ILE0-0.068-0.04827.159-0.008-0.0080.0000.0000.0000.000
109A110ASP-1-0.814-0.88825.1770.1150.1150.0000.0000.0000.000
110A111GLU-1-0.901-0.95923.0670.1190.1190.0000.0000.0000.000
111A112ASP-1-0.800-0.91719.5330.2020.2020.0000.0000.0000.000
112A113GLU-1-0.813-0.88515.8940.1830.1830.0000.0000.0000.000
113A114ILE0-0.004-0.01514.5970.0040.0040.0000.0000.0000.000
114A115PHE00.002-0.00616.8590.0050.0050.0000.0000.0000.000
115A116LYS10.9420.99018.226-0.133-0.1330.0000.0000.0000.000
116A117GLY0-0.030-0.02019.9320.0030.0030.0000.0000.0000.000
117A118LEU0-0.047-0.00319.514-0.007-0.0070.0000.0000.0000.000
118A119PRO00.002-0.02023.433-0.007-0.0070.0000.0000.0000.000
119A120LYS10.9180.96226.186-0.096-0.0960.0000.0000.0000.000
120A121ARG10.8470.92728.817-0.085-0.0850.0000.0000.0000.000
121A122LEU00.0200.02323.287-0.001-0.0010.0000.0000.0000.000
122A123LYS10.8280.90027.477-0.104-0.1040.0000.0000.0000.000
123A124VAL0-0.022-0.01224.1500.0090.0090.0000.0000.0000.000
124A125TRP00.0220.00023.620-0.015-0.0150.0000.0000.0000.000
125A126GLH0-0.033-0.08024.2360.0180.0180.0000.0000.0000.000
126A127SER0-0.010-0.02026.188-0.011-0.0110.0000.0000.0000.000
127A128HIS10.8630.93727.547-0.128-0.1280.0000.0000.0000.000
128A129MET0-0.0050.01328.736-0.007-0.0070.0000.0000.0000.000
129A130ASP-1-0.884-0.94727.4640.1280.1280.0000.0000.0000.000
130A131GLU-1-0.769-0.87827.0260.1320.1320.0000.0000.0000.000
131A132VAL00.0390.01724.520-0.006-0.0060.0000.0000.0000.000
132A133LYS10.7380.85227.701-0.113-0.1130.0000.0000.0000.000
133A134GLU-1-0.857-0.89929.9110.0810.0810.0000.0000.0000.000
134A135LEU00.0200.00325.9950.0090.0090.0000.0000.0000.000
135A136PRO0-0.021-0.00723.768-0.008-0.0080.0000.0000.0000.000
136A137PRO0-0.001-0.00726.932-0.001-0.0010.0000.0000.0000.000
137A138LYS10.8700.93125.181-0.076-0.0760.0000.0000.0000.000
138A139PHE00.0000.01619.9250.0110.0110.0000.0000.0000.000
139A140LYS10.8630.92622.739-0.144-0.1440.0000.0000.0000.000
140A141ILE0-0.018-0.01424.8890.0120.0120.0000.0000.0000.000
141A142LEU0-0.027-0.00820.507-0.005-0.0050.0000.0000.0000.000
142A143ALA0-0.020-0.02024.936-0.005-0.0050.0000.0000.0000.000
143A144ARG10.8670.93426.618-0.087-0.0870.0000.0000.0000.000
144A145SER0-0.001-0.04929.674-0.002-0.0020.0000.0000.0000.000
145A146GLU-1-0.933-0.96531.9050.0790.0790.0000.0000.0000.000
146A147THR0-0.020-0.00433.470-0.003-0.0030.0000.0000.0000.000
147A148CYS0-0.082-0.04029.7600.0020.0020.0000.0000.0000.000
148A149PRO00.0280.00931.0650.0040.0040.0000.0000.0000.000
149A150ILE00.004-0.00525.7100.0010.0010.0000.0000.0000.000
150A151GLU-1-0.706-0.77925.9600.1610.1610.0000.0000.0000.000
151A152ALA0-0.030-0.02621.6810.0190.0190.0000.0000.0000.000
152A153MET0-0.060-0.01220.818-0.025-0.0250.0000.0000.0000.000
153A154LYS10.8650.93417.965-0.160-0.1600.0000.0000.0000.000
154A155HIS00.0530.04619.587-0.016-0.0160.0000.0000.0000.000
155A156GLU-1-0.925-0.99621.3290.1030.1030.0000.0000.0000.000
156A157GLU-1-0.866-0.92422.2880.0860.0860.0000.0000.0000.000
157A158LEU0-0.0020.01617.2170.0000.0000.0000.0000.0000.000
158A159PRO0-0.0250.01013.726-0.001-0.0010.0000.0000.0000.000
159A160ILE00.0200.00514.1670.0390.0390.0000.0000.0000.000
160A161TYR0-0.061-0.06914.263-0.015-0.0150.0000.0000.0000.000
161A162GLY00.0050.00916.4370.0290.0290.0000.0000.0000.000
162A163VAL0-0.018-0.00517.939-0.021-0.0210.0000.0000.0000.000
163A164GLN00.024-0.00220.4610.0250.0250.0000.0000.0000.000
164A165PHE0-0.005-0.00720.2500.0030.0030.0000.0000.0000.000
165A166HIS10.8130.87918.812-0.279-0.2790.0000.0000.0000.000
166A167PRO00.0270.02816.220-0.020-0.0200.0000.0000.0000.000
167A168GLU-1-0.730-0.86115.3830.3760.3760.0000.0000.0000.000
168A169VAL0-0.127-0.06116.965-0.010-0.0100.0000.0000.0000.000
169A170ALA00.0510.02220.575-0.012-0.0120.0000.0000.0000.000
170A171HIS0-0.061-0.03621.958-0.014-0.0140.0000.0000.0000.000
171A172THR0-0.0090.00321.591-0.019-0.0190.0000.0000.0000.000
172A173GLU-1-0.789-0.87022.7750.1190.1190.0000.0000.0000.000
173A174LYS10.8710.91721.045-0.115-0.1150.0000.0000.0000.000
174A175GLY00.0230.01919.2880.0100.0100.0000.0000.0000.000
175A176GLU-1-0.897-0.95915.5450.2010.2010.0000.0000.0000.000
176A177GLU-1-0.876-0.93514.9320.1470.1470.0000.0000.0000.000
177A178ILE00.0400.03315.6630.0050.0050.0000.0000.0000.000
178A179LEU0-0.008-0.00511.7740.0280.0280.0000.0000.0000.000
179A180ARG10.9280.96611.120-0.082-0.0820.0000.0000.0000.000
180A181ASN0-0.063-0.03911.294-0.012-0.0120.0000.0000.0000.000
181A182PHE00.0450.0279.0250.0130.0130.0000.0000.0000.000
182A183ALA00.008-0.0117.0310.0420.0420.0000.0000.0000.000
183A184LYS10.8420.9177.356-0.118-0.1180.0000.0000.0000.000
184A185LEU0-0.0040.0069.9140.0090.0090.0000.0000.0000.000
185A186CYS0-0.064-0.0175.622-0.063-0.0630.0000.0000.0000.000
186A187GLY0-0.054-0.0196.7160.3700.3700.0000.0000.0000.000
187A188GLU-1-0.961-0.9617.4020.0870.0870.0000.0000.0000.000
188A189LEU0-0.027-0.01211.0670.0210.0210.0000.0000.0000.000