FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: YVV22

Calculation Name: 3MDK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MDK

Chain ID: A

ChEMBL ID:

UniProt ID: Q88N92

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2353793.358243
FMO2-HF: Nuclear repulsion 2272571.814721
FMO2-HF: Total energy -81221.543522
FMO2-MP2: Total energy -81454.760263


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:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-121.418-116.8618.177-6.372-16.365-0.068
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.901 / q_NPA : 0.942
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].
3A8ALA0-0.028-0.0202.497-13.006-10.8251.533-1.645-2.069-0.015
4A9CYS0-0.009-0.0085.1185.5545.650-0.001-0.006-0.0890.000
5A10TYR00.0010.0158.120-1.239-1.2390.0000.0000.0000.000
6A11SER00.0920.02511.3871.7391.7390.0000.0000.0000.000
7A12ASP-1-0.806-0.90813.339-17.556-17.5560.0000.0000.0000.000
8A13PRO00.014-0.00213.6640.2510.2510.0000.0000.0000.000
9A14ALA00.0450.03815.2370.4420.4420.0000.0000.0000.000
10A15ASP-1-0.797-0.88718.420-15.375-15.3750.0000.0000.0000.000
11A16HIS0-0.059-0.04618.617-1.347-1.3470.0000.0000.0000.000
12A17TYR0-0.045-0.05719.553-0.377-0.3770.0000.0000.0000.000
13A18SER00.004-0.00914.989-1.159-1.1590.0000.0000.0000.000
14A19HIS00.0070.01314.679-0.761-0.7610.0000.0000.0000.000
15A20ARG10.8980.93515.55513.69613.6960.0000.0000.0000.000
16A21VAL0-0.011-0.00511.288-0.349-0.3490.0000.0000.0000.000
17A22ARG10.7830.86210.63921.12321.1230.0000.0000.0000.000
18A23LEU00.0040.01411.444-1.291-1.2910.0000.0000.0000.000
19A24VAL00.0370.00813.210-0.119-0.1190.0000.0000.0000.000
20A25LEU0-0.034-0.0247.496-0.490-0.4900.0000.0000.0000.000
21A26ALA0-0.012-0.0039.667-1.314-1.3140.0000.0000.0000.000
22A27GLU-1-0.814-0.88811.110-16.991-16.9910.0000.0000.0000.000
23A28LYS10.7200.84810.94418.76918.7690.0000.0000.0000.000
24A29GLY00.0150.0269.7320.0940.0940.0000.0000.0000.000
25A30VAL0-0.044-0.0095.902-1.818-1.8180.0000.0000.0000.000
26A31SER0-0.025-0.0182.153-13.254-16.72510.116-2.458-4.187-0.024
27A32VAL00.0390.0012.515-8.323-5.5813.137-2.072-3.808-0.022
28A33GLN0-0.102-0.0522.302-6.762-3.6743.244-0.710-5.623-0.008
29A34LEU00.0230.0113.6588.2798.2010.1480.519-0.5890.001
30A35ILE0-0.041-0.0176.459-0.910-0.9100.0000.0000.0000.000
31A36ASP-1-0.871-0.9428.694-24.703-24.7030.0000.0000.0000.000
32A37VAL0-0.097-0.05211.6940.5630.5630.0000.0000.0000.000
33A38ASP-1-0.795-0.90115.008-14.594-14.5940.0000.0000.0000.000
34A39PRO0-0.003-0.00518.4110.1870.1870.0000.0000.0000.000
35A40ALA0-0.068-0.02621.0800.5520.5520.0000.0000.0000.000
36A41HIS0-0.077-0.04120.0520.4530.4530.0000.0000.0000.000
37A42LEU00.0370.02018.770-0.953-0.9530.0000.0000.0000.000
38A43PRO00.0350.01914.5340.4120.4120.0000.0000.0000.000
39A44ARG10.9280.95816.79514.85214.8520.0000.0000.0000.000
40A45LYS11.0070.99111.39524.35824.3580.0000.0000.0000.000
41A46LEU0-0.0160.01814.116-0.579-0.5790.0000.0000.0000.000
42A47ALA00.004-0.01315.3360.5200.5200.0000.0000.0000.000
43A48GLU-1-0.999-1.00315.843-16.660-16.6600.0000.0000.0000.000
44A49VAL0-0.0140.00012.8160.3600.3600.0000.0000.0000.000
45A50ASN0-0.016-0.01216.0941.1411.1410.0000.0000.0000.000
46A51PRO0-0.0120.00818.4170.0820.0820.0000.0000.0000.000
47A52TYR0-0.038-0.02921.3220.8250.8250.0000.0000.0000.000
48A53GLY0-0.0300.00019.5900.1830.1830.0000.0000.0000.000
49A54SER0-0.0030.00719.340-0.316-0.3160.0000.0000.0000.000
50A55VAL00.0040.02014.975-1.212-1.2120.0000.0000.0000.000
51A56PRO00.0160.00313.2860.8950.8950.0000.0000.0000.000
52A57THR0-0.050-0.04312.5101.6271.6270.0000.0000.0000.000
53A58LEU0-0.057-0.0197.593-2.280-2.2800.0000.0000.0000.000
54A59VAL0-0.004-0.0148.1762.2982.2980.0000.0000.0000.000
55A60ASP-1-0.849-0.9185.601-35.644-35.6440.0000.0000.0000.000
56A61ARG10.8990.9406.55522.88622.8860.0000.0000.0000.000
57A62ASP-1-0.955-0.9768.195-17.094-17.0940.0000.0000.0000.000
58A63LEU0-0.0290.00010.1431.1711.1710.0000.0000.0000.000
59A64ALA00.0310.00410.734-1.761-1.7610.0000.0000.0000.000
60A65LEU0-0.040-0.00412.8321.4301.4300.0000.0000.0000.000
61A66TYR00.0640.01313.855-0.954-0.9540.0000.0000.0000.000
62A67GLU-1-0.713-0.78316.483-13.377-13.3770.0000.0000.0000.000
63A68SER00.0220.00617.020-0.372-0.3720.0000.0000.0000.000
64A69THR0-0.101-0.12617.542-0.468-0.4680.0000.0000.0000.000
65A70VAL00.0400.02317.222-0.136-0.1360.0000.0000.0000.000
66A71VAL0-0.027-0.00612.450-0.528-0.5280.0000.0000.0000.000
67A72MET0-0.032-0.02114.332-0.794-0.7940.0000.0000.0000.000
68A73GLU-1-0.785-0.87316.200-13.355-13.3550.0000.0000.0000.000
69A74TYR00.0530.0379.4420.4050.4050.0000.0000.0000.000
70A75LEU0-0.050-0.0399.596-0.577-0.5770.0000.0000.0000.000
71A76GLU-1-0.796-0.90213.217-15.779-15.7790.0000.0000.0000.000
72A77GLU-1-0.984-0.98416.391-13.845-13.8450.0000.0000.0000.000
73A78ARG10.8440.93510.31820.63920.6390.0000.0000.0000.000
74A79TYR0-0.039-0.0206.830-0.934-0.9340.0000.0000.0000.000
75A80PRO00.0540.02912.7450.0320.0320.0000.0000.0000.000
76A81HIS0-0.076-0.01315.3430.8400.8400.0000.0000.0000.000
77A82PRO00.0440.01914.971-1.034-1.0340.0000.0000.0000.000
78A83PRO00.0340.02117.654-0.767-0.7670.0000.0000.0000.000
79A84LEU00.0210.01416.0780.0930.0930.0000.0000.0000.000
80A85MET0-0.042-0.02420.4070.4960.4960.0000.0000.0000.000
81A86PRO00.0530.04323.3510.1330.1330.0000.0000.0000.000
82A87VAL00.0770.02324.868-0.093-0.0930.0000.0000.0000.000
83A88TYR0-0.019-0.00926.8690.1570.1570.0000.0000.0000.000
84A89PRO00.024-0.00430.052-0.126-0.1260.0000.0000.0000.000
85A90VAL00.0350.02131.196-0.110-0.1100.0000.0000.0000.000
86A91ALA00.0370.01930.838-0.031-0.0310.0000.0000.0000.000
87A92ARG10.9290.96722.63611.98411.9840.0000.0000.0000.000
88A93GLY00.0240.01628.245-0.263-0.2630.0000.0000.0000.000
89A94ASN00.012-0.00730.7500.0450.0450.0000.0000.0000.000
90A95SER00.0180.01226.395-0.103-0.1030.0000.0000.0000.000
91A96ARG10.8380.89623.59411.71611.7160.0000.0000.0000.000
92A97LEU0-0.026-0.00127.535-0.061-0.0610.0000.0000.0000.000
93A98LEU0-0.0030.00629.1890.0930.0930.0000.0000.0000.000
94A99MET00.0330.01521.796-0.034-0.0340.0000.0000.0000.000
95A100HIS0-0.020-0.00826.9000.2250.2250.0000.0000.0000.000
96A101ARG10.9140.94529.1149.0179.0170.0000.0000.0000.000
97A102ILE00.0360.03426.3350.1530.1530.0000.0000.0000.000
98A103GLN00.006-0.00925.500-0.371-0.3710.0000.0000.0000.000
99A104ARG10.8930.93828.3419.0089.0080.0000.0000.0000.000
100A105ASP-1-0.884-0.93931.877-8.948-8.9480.0000.0000.0000.000
101A106TRP0-0.029-0.02829.2800.0360.0360.0000.0000.0000.000
102A107CYS0-0.0120.00825.908-0.133-0.1330.0000.0000.0000.000
103A108ALA00.0390.04128.351-0.060-0.0600.0000.0000.0000.000
104A109LEU0-0.010-0.00430.7440.1340.1340.0000.0000.0000.000
105A110ALA00.008-0.00428.1240.0920.0920.0000.0000.0000.000
106A111ASP-1-0.744-0.83726.814-12.255-12.2550.0000.0000.0000.000
107A112THR0-0.077-0.04629.3220.1860.1860.0000.0000.0000.000
108A113VAL0-0.038-0.02531.2350.1670.1670.0000.0000.0000.000
109A114LEU00.006-0.00325.7820.1040.1040.0000.0000.0000.000
110A115ASP-1-0.825-0.87929.146-10.643-10.6430.0000.0000.0000.000
111A116PRO0-0.010-0.01228.8200.4510.4510.0000.0000.0000.000
112A117ARG10.8950.93931.8909.8069.8060.0000.0000.0000.000
113A118SER0-0.0110.01534.0690.3760.3760.0000.0000.0000.000
114A119SER0-0.010-0.00336.0530.0530.0530.0000.0000.0000.000
115A120GLU-1-0.770-0.90037.953-8.775-8.7750.0000.0000.0000.000
116A121ALA0-0.048-0.00940.156-0.010-0.0100.0000.0000.0000.000
117A122ALA00.0490.02138.6040.0120.0120.0000.0000.0000.000
118A123ARG10.8120.89633.4699.2559.2550.0000.0000.0000.000
119A124THR0-0.065-0.04937.187-0.105-0.1050.0000.0000.0000.000
120A125GLU-1-0.968-0.97439.830-7.839-7.8390.0000.0000.0000.000
121A126ALA00.0450.03035.254-0.003-0.0030.0000.0000.0000.000
122A127ARG10.8880.93934.3089.0109.0100.0000.0000.0000.000
123A128LYS10.9150.95436.3287.3457.3450.0000.0000.0000.000
124A129ALA00.0460.02338.0770.0590.0590.0000.0000.0000.000
125A130LEU00.0330.02630.819-0.002-0.0020.0000.0000.0000.000
126A131ARG10.9570.97935.4608.0558.0550.0000.0000.0000.000
127A132GLU-1-0.976-0.98936.636-7.544-7.5440.0000.0000.0000.000
128A133SER0-0.0080.00235.7440.1110.1110.0000.0000.0000.000
129A134LEU00.0040.00131.116-0.004-0.0040.0000.0000.0000.000
130A135THR0-0.067-0.05335.0240.0130.0130.0000.0000.0000.000
131A136GLY0-0.027-0.00637.8940.1350.1350.0000.0000.0000.000
132A137VAL00.017-0.00133.7420.1250.1250.0000.0000.0000.000
133A138SER00.0380.02435.453-0.187-0.1870.0000.0000.0000.000
134A139PRO0-0.040-0.03236.383-0.120-0.1200.0000.0000.0000.000
135A140LEU00.0560.02434.8740.0220.0220.0000.0000.0000.000
136A141PHE0-0.047-0.02729.243-0.127-0.1270.0000.0000.0000.000
137A142SER0-0.061-0.03533.824-0.079-0.0790.0000.0000.0000.000
138A143GLU-1-1.000-0.98636.252-8.042-8.0420.0000.0000.0000.000
139A144PHE0-0.0120.01031.6390.0710.0710.0000.0000.0000.000
140A145ALA0-0.0190.00928.955-0.070-0.0700.0000.0000.0000.000
141A146CYS0-0.069-0.02025.015-0.400-0.4000.0000.0000.0000.000
142A147PHE00.039-0.00127.0960.4910.4910.0000.0000.0000.000
143A148MET0-0.053-0.02028.852-0.072-0.0720.0000.0000.0000.000
144A149SER0-0.009-0.00326.9750.1340.1340.0000.0000.0000.000
145A150ASP-1-0.843-0.93029.459-9.795-9.7950.0000.0000.0000.000
146A151GLU-1-0.967-0.98023.862-12.436-12.4360.0000.0000.0000.000
147A152GLN0-0.027-0.02419.8470.4630.4630.0000.0000.0000.000
148A153SER00.0390.00521.811-0.128-0.1280.0000.0000.0000.000
149A154LEU00.051-0.00617.736-0.315-0.3150.0000.0000.0000.000
150A155VAL00.0280.01521.020-0.076-0.0760.0000.0000.0000.000
151A156ASP-1-0.744-0.84522.144-12.524-12.5240.0000.0000.0000.000
152A157CYS0-0.041-0.01118.291-0.446-0.4460.0000.0000.0000.000
153A158CYS0-0.047-0.00920.104-0.405-0.4050.0000.0000.0000.000
154A159LEU00.0000.00622.4590.1610.1610.0000.0000.0000.000
155A160LEU0-0.005-0.01221.1040.1790.1790.0000.0000.0000.000
156A161PRO00.0160.02019.3180.1940.1940.0000.0000.0000.000
157A162ILE00.0080.00521.6220.2370.2370.0000.0000.0000.000
158A163LEU00.0240.00425.3270.3250.3250.0000.0000.0000.000
159A164TRP0-0.018-0.02020.7440.4860.4860.0000.0000.0000.000
160A165ARG10.7910.86519.00115.64815.6480.0000.0000.0000.000
161A166LEU0-0.022-0.00125.3800.3990.3990.0000.0000.0000.000
162A167PRO00.0240.01326.8430.3630.3630.0000.0000.0000.000
163A168VAL00.0200.00825.2670.2910.2910.0000.0000.0000.000
164A169LEU0-0.0180.00628.0310.2570.2570.0000.0000.0000.000
165A170GLY00.0020.02130.6080.3980.3980.0000.0000.0000.000
166A171ILE0-0.063-0.03932.2490.4130.4130.0000.0000.0000.000
167A172GLU-1-0.919-0.96032.721-8.971-8.9710.0000.0000.0000.000
168A173LEU0-0.027-0.01632.1630.2310.2310.0000.0000.0000.000
169A174PRO00.0130.02035.8730.1050.1050.0000.0000.0000.000
170A175ARG11.0010.98135.5818.4178.4170.0000.0000.0000.000
171A176GLN0-0.009-0.01639.764-0.028-0.0280.0000.0000.0000.000
172A177ALA0-0.0100.01236.0510.0460.0460.0000.0000.0000.000
173A178LYS10.8900.94735.5568.3778.3770.0000.0000.0000.000
174A179PRO00.0340.02734.792-0.226-0.2260.0000.0000.0000.000
175A180LEU00.0340.02830.322-0.299-0.2990.0000.0000.0000.000
176A181LEU0-0.014-0.02630.816-0.380-0.3800.0000.0000.0000.000
177A182ASP-1-0.800-0.90330.367-9.503-9.5030.0000.0000.0000.000
178A183TYR0-0.093-0.08125.435-0.439-0.4390.0000.0000.0000.000
179A184MET0-0.036-0.02226.343-0.358-0.3580.0000.0000.0000.000
180A185GLU-1-0.974-0.96525.631-10.755-10.7550.0000.0000.0000.000
181A186ARG10.8770.92125.81510.40810.4080.0000.0000.0000.000
182A187GLN0-0.013-0.00822.501-1.150-1.1500.0000.0000.0000.000
183A188PHE0-0.006-0.01621.210-0.674-0.6740.0000.0000.0000.000
184A189ALA00.0030.01220.295-0.711-0.7110.0000.0000.0000.000
185A190ARG10.7690.87118.59515.32215.3220.0000.0000.0000.000
186A191GLU-1-0.907-0.95915.134-18.144-18.1440.0000.0000.0000.000
187A192PRO00.0080.01313.514-1.017-1.0170.0000.0000.0000.000
188A193PHE00.0500.01214.018-1.006-1.0060.0000.0000.0000.000
189A194GLN00.002-0.01115.595-0.960-0.9600.0000.0000.0000.000
190A195ALA0-0.046-0.01810.206-0.587-0.5870.0000.0000.0000.000
191A196SER0-0.064-0.02810.584-1.724-1.7240.0000.0000.0000.000
192A197LEU0-0.057-0.00812.709-0.294-0.2940.0000.0000.0000.000
193A198SER0-0.002-0.02112.695-1.202-1.2020.0000.0000.0000.000
194A199SER00.019-0.01913.7430.7450.7450.0000.0000.0000.000
195A200VAL00.0820.03815.5870.9920.9920.0000.0000.0000.000
196A201GLU-1-0.720-0.83215.959-18.286-18.2860.0000.0000.0000.000
197A202ARG10.8560.93414.41119.43119.4310.0000.0000.0000.000
198A203GLU-1-0.961-0.97419.170-14.230-14.2300.0000.0000.0000.000
199A204MET0-0.077-0.01220.5990.7340.7340.0000.0000.0000.000
200A205ARG10.7930.90223.36112.77512.7750.0000.0000.0000.000